The magazine of the Society for Applied Microbiology ■ June 2009 ■ Vol 10 No 2 ISSN 1479-2699

BACTERIOPHAGE THERAPY old treatment, new focus?

■ Antimicrobial resistance in bacterial enteric pathogens ■ Mediawatch: university press office ■ Summer conference 2009 ■ Engaging the public in infectious disease ■ Charles Darwin and microbes ■ Art, cybernetics and normal flora microbiology ■ An unwanted guest for dinner ■ Careers: sales manager ■ ■

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Technical sales: +44 (0)1274 595728 www.dwscientific.co.uk June 2009 ■ Vol 10 No 2 ■ ISSN 1479-2699 contentsthe magazine of the Society for Applied Microbiology members 04 Editorial: the effective communication of science

05 Contact point: full contact information for the Society

06 Benefits: what SfAM can do for you and how to join us

07 President’s and CEO’s columns

09 Membership Matters

38 Careers: sales manager

40 An unwanted guest for dinner 42 In the loop: news from PECS — virtual networking 20 43 Research Development Grant report

45 Students into Work grant reports

49 President’s Fund articles news 12 MediaWatch: the university press office 14 Med-Vet-Net: workpackage 34 28 32 publications The beauty of bacteria Charles Darwin and microbes 11 JournalWatch features information Microbiologist is published quarterly by the Society for Bacteriophage therapy: old treatment, new focus Applied Microbiology. ISSN 1479-2699. Registered in the 20 UK as a charity and Company limited by guarantee. Registered in England and Wales: 6462427. Registered 24 Antimicrobial resistance in bacterial enteric pathogens Charity: 1123044 © Society for Applied Microbiology 2007-2009. Material 28 Art, cybernetics and normal flora microbiology published in Microbiologist may not be reproduced, stored in a retrieval system, or transmitted in any form 31 Outbreak! Engaging the public in infectious disease without the prior permission of the Society. Editor: Lucy Harper. [email protected] 32 Historical Perspectives: Charles Darwin and microbes Contributions: These are always welcome and should be addressed to the Editor at: [email protected] 36 Statnote 16: regression line for prediction and calibration Advertising: Lucy Harper Tel: +44 (0)1234 326709. email: [email protected] meetings Design and print: Pollard Creativity. [email protected] 16 Summer conference 2009 Cover image: bacteriophage therapy — Stephen Pollard Society for Applied Microbiology, 19 Winter meeting 2010: biocides and tuberculosis Bedford Heights, Brickhill Drive, Bedford MK41 7PH, UK commercial Tel: +44 (0)1234 326661. Fax: +44 (0)1234 326678 53 Advertisements and news from our Corporate members www.sfam.org.uk

03 members

o you think the media have used hype in their Dcoverage of the recent Microbiologist is spread of the H1N1 virus? published quarterly by This is one of the questions the Society for Applied the Department of Health are Microbiology, a registered charity. asking the general public in ISSN 1479-2699 an attempt to assess how effectively the government’s Copy Dates: messages about this situation Vol 10 No.3 Sept 2009 are being communicated and Friday 26 June 2009 whether they are being understood. Other Vol 10 No.4 Dec 2009 questions include ‘Have Friday 25 Sept 2009 you visited your GP?’ and ‘Do you believe Vol 11 No.1 March 2010 Friday 18 Dec 2009 thousands have died from it?’* The Vol 11 No. 2 June 2010 effective Friday 26 March 2010 communication of science is important in a world where scientific Disclaimer: developments impact on the day-to-day lives of The Society assumes no responsibility for the the individual. This importance has been opinions expressed by recognised for some time, with the formation of contributors. The views editorial an entire discipline, incorporating qualifications, expressed by Society Lucy Harper discusses the media coverage conferences, organisations and committees officers and staff do not dedicated to the subject. But this subject necessarily represent the of the H1N1 virus and the importance of wouldn’t be able to thrive were it not for official position of the Society. Readers should scientists themselves getting involved and the effective communication of science note that scientific acknowledging the importance of the material is not refereed communication of their work. and represents only the SfAM supports the communication of science in many ways, from views of the authors. funding public engagement activities, through our Public The claims of advertisers contribute Engagement/Innovative Project grant, to recognising leading science cannot be guaranteed. communicators through the Communications Award. We’re always on the We are always looking Subscriptions: look-out for scientists who are keen to talk about their work to a wide and A subscription to for enthusiastic writers varied audience, from the news media to school children and the general who wish to contribute Microbiologist is articles to the magazine public. After all, when a news story breaks, it’s imperative that the public included in the annual on their chosen are armed with the correct information so that they can make informed SfAM membership fee. microbiological subject. (often important) decisions. Ultimately, the correct information can often For further information only be obtained from scientists — the experts at the bench-top. about the many benefits For further information of membership please please email the editor, One way in which you as members can get involved in communicating see page 6. Lucy Harper at: science is through publicising your work via the news media. On page 12 [email protected] you’ll find some invaluable advice about communicating your science Advertising: through your university press office. Information about SfAM has recently been involved in communicating applied advertising in microbiology to the general public through public engagement. We, in Microbiologist and how to submit advertise ments collaboration with the Beacons of Public Engagement, held an event in are can be found on the Manchester based around the public’s perception of microbiology, and you Society website. can read all about the event on page 31. In this issue of Microbiologist we also have a report from the first of Website: our website our Public Engagement/Innovative Project grants. SfAM’s ex-Honorary (www.sfam.org.uk) is General Secretary, Dr Anthony Hilton gave a series of Christmas lectures a timely source of up-to- to school children in the North East of England and he reports on the date information on all Society matters and success of these lectures on page 40. maintains a Finally, if you are interested in communicating your work to a wider comprehensive archive audience, then get in touch to find out how we can help you publicise your of articles and reports on work and ensure that you get the right message across. After all, SfAM is a variety of “the voice of applied microbiology”. microbiological topics.

* all information on the spread of the H1N1 virus from Mexico was correct at the time Lucy Harper of going to press

04 contact point

executive committee

COMMITTEE MEMBERS

HON PRESIDENT: Professor Geoff Hanlon, School of Pharmacy and Biomolecular Sciences, University of Brighton, Moulsecoomb, Brighton BN2 4GJ email: [email protected]

HON GENERAL SECRETARY: Dr Mark Fielder, School of Life Sciences, Kingston University, Penrhyn Road, Kingston upon Thames, Surrey KT1 2EE email: [email protected]

HON MEETINGS SECRETARY: Professor Martin Adams, School of Biomedical & Molecular Sciences, University of Surrey, Guildford,Surrey GU2 7XH Society for Applied Microbiology, email: [email protected] Bedford Heights, Brickhill Drive, Bedford MK41 7PH, UK HON TREASURER: Professor Valerie Edwards-Jones, Research Development Unit, tel: +44 (0)1234 326661 Manchester Metropolitan University, fax: +44 (0)1234 326678 Lower Chatham St, Manchester M15 5HA email: [email protected] email: [email protected] www.sfam.org.uk ORDINARY COMMITTEE MEMBERS UNTIL JULY 2009

Professor Carol Phillips, School of Health, The University of Northampton, Boughton Green Road, Northampton NN2 7AL email: [email protected] society office staff Professor Joanna Verran, Manchester Metropolitan University, Dept Biological Sciences, Chester Street, Manchester M1 5GD CHIEF EXECUTIVE OFFICER: Philip Wheat email: [email protected] email: [email protected] tel: +44 (0)1234 326661 Mr Mark Reed, Pro-Lab Diagnostics, 7 Westwood Court, Neston Cheshire CH64 3UJ COMMUNICATIONS MANAGER: Lucy Harper email: [email protected] email: [email protected] tel: +44 (0)1234 326709 MEMBERSHIP CO-ORDINATOR: Julie Wright ORDINARY COMMITTEE MEMBERS UNTIL JULY 2010 email: [email protected] tel: +44 (0)1234 326846 Mr Steve Davies MA CSci FIBMS, Microbiology Department, Northern General Hospital, Herries Road, Sheffield S7 5AU EVENTS ORGANISER: Sally Cryer email: [email protected] email: [email protected] tel: +44 (0)1234 761752 Dr Louise Fielding, Food Research and Consultancy Unit, Cardiff School of Health Sciences, University of Wales Institute Cardiff, Llandaff Campus, Western Avenue, OFFICE ADMINISTRATOR: Kate Coggins Cardiff CF5 2YB email: [email protected] email: [email protected] tel: +44 (0)1234 326661 Professor Andrew Fox, Health Protection Agency North West, PO Box 209, Clinical Sciences Building, Manchester Royal Infirmary, Manchester M13 9WZ email:[email protected] Dr Andrew McBain, School of Pharmacy & Pharmaceutical Sciences, Stopford Building, University of Manchester, Manchester M13 9PT publications subcommittee email: [email protected]

FEATURES EDITOR: Claire Cassar email: [email protected] ORDINARY COMMITTEE MEMBERS UNTIL JULY 2011

FEATURES EDITOR: Louise Fielding Professor Christine Dodd, Division of Food Sciences, School of Biosciences, University email: [email protected] of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD REGULAR CONTENT EDITOR: Andrew Fox email: [email protected] email: [email protected] Dr Leon Gorris, Unilever, SEAC Risk Analysis Group, Colworth House, Sharnbrook, GRANTS EDITOR: Louise Hill-King Bedfordshire MK44 1LQ email: [email protected] email: [email protected]

05 members

benefits membership options

The Society for Applied Microbiology is the voice of applied microbiology within the UK and was founded in 1931. Society members ■ Full ordinary membership gives access to our play a leading role in shaping the future of applied microbiology, and enjoy many grants and awards, online access to the many benefits, including: Journal of Applied Microbiology, Letters in Applied ■ The opportunity to apply for one of our many grants or funds Microbiology, Environmental Microbiology, ■ Eligibility to win any of our awards or nominate a candidate for the Environmental Microbiology Reports and Microbial SfAM Communications Award Biotechnology, copies of Microbiologist, preferential registration rates at Society meetings and access to ■ Access to our five peer-reviewed Journals: Journal of Applied the members areas of the website. Microbiology, Letters in Applied Microbiology, Environmental Microbiology, Environmental Microbiology Reports and Microbial ■ Full student membership confers the same Biotechnology benefits as Full membership at a specially reduced ■ Free access to the entire collection of digitised back files for JAM and rate for full time students not in receipt of a taxable LAM dating back to 1938 salary. ■ A topical quarterly magazine, Microbiologist ■ Substantially reduced rates for attendance at SfAM meetings and ■ Associate membership is only open to those conferences with an interest in applied microbiology without it ■ Networking with worldwide professionals in over 80 countries being a prime aspect of their job. For example, school teachers and those taking a career break; on ■ Access to private members area of the SfAM website maternity leave, or working temporarily in other ■ Monthly email bulletins with the latest news from SfAM areas. It does not provide access to any journals or ■ Invitation to the annual Environmental Microbiology lecture Society grants and awards. ■ Fostering cross disciplinary research ■ A 25% discount on the extensive Wiley-Blackwell collection of titles ■ Honorary membership of the Society is by Detailed information about all these benefits and more can be found on election only and this honour is conferred on the Society website at: www.sfam.org.uk persons of distinction in the field of applied microbiology. Honorary members have access to our GRANTS & AWARDS: Many grants, awards and prizes are available to online journals. members including the W H Pierce Memorial Prize and prizes for student oral presentations and posters at the Summer conference. In addition to ■ Retirement membership is available to Full these substantial awards, the Society has funds to assist members in their members once they have retired from their careers as microbiologists. These include the President’s Fund, Conference employment. Retired members are entitled to all the Studentships, Sponsored Lecture Grants and the popular Students into benefits of Full membership except grants and Work Scheme. access to the Society’s journals. Full details of all the Society’s grants and awards can be found on the ■ website together with PDF downloadable application forms. Corporate membership is open to all companies with an interest in microbiology. JOURNALS: The Society publishes two monthly journals: Journal of Corporate members benefits include: Applied Microbiology and Letters in Applied Microbiology. We also ● Quarter page advertisement in each issue of produce this quarterly colour magazine, Microbiologist, which contains Microbiologist (which can be upgraded to a larger features, topical news stories and full details of our meetings. The Society size at discounted rates) ● the opportunity to publish press releases, is also a partner with Wiley-Blackwell in the monthly journals company news, etc., in each issue of Environmental Microbiology, Environmental Microbiology Reports Microbiologist and Microbial Biotechnology. ● FREE banner advert on the Society Website with a All Full and Student members receive free access to the online versions direct link to your company site. of the Society’s journals, and can also submit papers to our journals via an ● Up to three members of company staff attending online submission service. Society meetings at members' rate (this means a 50% discount on non member registration rate). MEETINGS: We hold three annual meetings; the winter meeting is a one- day meeting with parallel sessions on topical subjects. The spring meeting JOIN US! is a one-day meeting tailored for personnel in clinical microbiology. The summer conference is held every July and comprises a main symposium, a You can apply for membership on, or offline. To apply offline, please contact the Membership Co- poster session, the AGM and a lively social programme. All members are ordinator, Julie Wright on +44 (0)1234 326846, or invited to our prestigious annual lecture held to commemorate the success email [email protected]. Alternatively, write to her of our Environmental Microbiology journal. We also hold joint ventures at: with other organisations on topics of mutual interest. The Society for Applied Microbiology, Bedford WEBSITE: The website is the best source of detailed information on the Heights, Brickhill Drive, Bedford MK41 7PH, UK Society and its many activities. It has fully interactive membership areas where you can find archive issues of Microbiologist, exclusive SfAM documentation and much more. www.sfam.org.uk

06 n these difficult economic times it’s good to Prize was instituted in 1984 by Oxoid and is have a reason to celebrate. That celebration awarded each year to a young scientist (under Ineed not necessarily involve cracking open the 40 years of age) who has made an important champagne and dancing until dawn, but may contribution in the field of applied microbiology. simply be a celebration of achievement, either This award is a dual celebration since it acts as a past or present. vehicle for highlighting young talent whilst at Every year since 1977 the American Society the same time celebrating the achievements of a for Microbiology has presented the Procter and distinguished microbiologist of the past. Bill Gamble Award, the aim of which is to recognise Pierce joined Oxoid Ltd shortly after it was distinguished achievement in research and formed at around the time of World War I and development in applied (non-clinical) and was a lifelong member of SfAM. He rose to environmental microbiology. The award carries a become Chief Bacteriologist and led the cash prize of $2,000 and the recipient is invited development of dehydrated culture media used to present a lecture at the ASM General Meeting by all microbiologists in their everyday work. where they are also an honoured guest at the In a similar vein the Lewis B Perry Memorial ASM awards banquet. A lecture is given annually by a distinguished glance down the list of microbiologist in memory of another. Lew Perry previous laureates spent his entire career with the National president’s reveals an array of names Collection of Industrial, Marine and Food representing the glitterati Bacteria (NCIMB) where he became a senior of the world of scientist. He was a shy, modest man who was microbiology. extremely generous with his time, willingly column Since Procter and teaching younger colleagues the essential skills Geoff Hanlon reviews the Society’s long Gamble is a global of microbiology with his trademark attention to association with awards and prizes company they were detail. Lew Perry, again a lifelong SfAM member, conscious that this award died in 2003 and his family have generously tended to recognise offered to fund an award in his memory for a American scientists and hence they were very period of 10 years. keen to instigate an equivalent award in Europe. Both the W. H. Pierce prize and the Lew Perry I was therefore delighted when last year a lecture are given at the annual summer meeting. colleague at P&G asked if SfAM would At that time also we present the SfAM administer the award in Europe in the same way communications award for an individual who has that ASM does in the USA. The company had communicated their work most effectively in looked at different microbiology societies and applied microbiology to the general public. It is decided that SfAM was the most appropriate. also an occasion to recognise young scientists The value of the prize is to be the same ($2,000) with the student conference prizes for best oral and the recipient will be invited to give a lecture presentation and best poster. at our Spring Meeting in April. The name of the The Denver Russell Memorial lecture was award is the SfAM/Procter & Gamble Applied established in 2006 to commemorate the Health Care Microbiology award and will be achievements of a microbiologist whom many of awarded to distinguished individuals who have us knew personally and had the privilege of used microbiology research to gain a better calling a colleague. Denver was one of my PhD understanding of human health. By the time you supervisors and I am proud to have been co- read this article the first award will have been author on just a few of his 450 publications. He made. was a world authority on biocide usage and its The first, and highly deserved recipient of the possible association with antibiotic resistance. award is Professor Sally Bloomfield who His knowledge of microbiology was qualified initially as a pharmacist, but then went encyclopaedic and he was author or editor of 16 on to develop a career in microbiology, with a books including the standard undergraduate text specific interest in the prevention of infectious “Pharmaceutical Microbiology” with his old diseases and in microbial quality assurance. For friend Barry Hugo. The impetus for an award in 25 years, Professor Bloomfield was an academic his name came from the healthcare industry with in the Department of Pharmacy, Kings College, which he had close working relationship. London but from 1997 to 2003 joined Unilever Not all of our awards are in memory of Research to develop a programme involved with individuals. The recently introduced raising awareness of the importance of hygiene Environmental Microbiology lecture is a in the domestic setting. During this time she was celebration of the achievements of the journal of instrumental in setting up the International that name published by Wiley Blackwell in Scientific Forum on Home Hygiene. association with SfAM. The inaugural lecture was SfAM has, of course, been associated with held in September 2008 and was given by Rita other awards for outstanding achievement over a Colwell who is a true thoroughbred in the field number of years. The W. H. Pierce Memorial of microbiology with a quite astonishing CV.

07 members

Her lecture entitled “Climates, oceans, global and he is a pioneer in the development and use warming and Cholera” was, as you might of metagenomics to address environmental expect, excellent and a recording placed on the microbiological questions. website has been downloaded over 2,000 times. I started by saying that the P&G Award The success of this lecture encouraged us to presented by the ASM has recognized some truly make this an annual event. distinguished microbiologists. It will not The second Environmental Microbiology therefore surprise you to learn that Rita Colwell lecture is to be held this year on 12th October at and Ed DeLong were both former recipients of the Royal Society of Medicine, London and in the this award. I hope you will join me this year in last edition of Microbiologist you will all have celebrating all these achievements. received an invitation to attend. I hope that as many of you as possible will be able to come and listen to what will be another inspiring lecture this time by Professor Edward DeLong of the Professor Geoff Hanlon Massachusetts Institute of Technology. Professor President of the Society DeLong is recognised for his remarkable achievements in the field of marine microbiology

n these troubled financial times it is very journals (Journal and Letters in Applied pleasing to report that membership of SfAM is Microbiology, Environmental Microbiology, Istill on the increase. I estimate that our peak Reports in Environmental Microbiology and membership number for 2009 will be just over Microbial Biotechnology). In addition, all 1,500, a large increase compared with this time members also receive quarterly copies of the in 2006 when membership numbers stood at Microbiologist. This policy of including the approximately 1,300. It is also pleasing to report society’s publications within the membership that the increase is not only due to new compares extremely favourably with the policy members from the United of other membership societies, where additional Kingdom but we now charges are made to access scientific have members from over publications. 80 countries of the Finally, the society offers a whole plethora of ceo’s world: the Society can grants for members who are eligible. Once again truly claim to be an in recent years more members are successfully international membership applying for the variety of grants on offer (full Society. terms and conditions for all grants can be found column The increase in at ). I must emphasise that grants are available Philip Wheat reports on the latest membership is due to to all eligible members irrespective of whether developments within the Society many different reasons. they are based in the United Kingdom or Firstly, the Society has elsewhere. been a lot more active in During the summer SfAM will be exhibiting at the last few years, in a number of conferences. We always appreciate terms of promotion and seeing our members and listening to what they making people aware of all our activities and have to say about the Society, so don’t forget to those with which we are involved. If you would come visit the SfAM stand if you’re attending the like to help to further promote the Society to following meetings: International Food colleagues/students in your institution please Technology (Anaheim, US, 7th - 9th June) and contact me ([email protected]) and I will be International Association of Food Protection happy to send you our advertising material. (Gaylord Resort, US, 12th – 15th July). Secondly, in the current challenging financial climate, membership does provide excellent value for money. There are so many benefits — almost too many to discuss in this brief column. Philp Wheat We feel we offer terrific value, for instance, Chief Executive Officer standard full and student membership entitles an individual to online access to five peer reviewed

08 Membership Changes

NEW MEMBERS Nigeria

G. Adewumi; O. Okpalanozie We would like to warmly welcome the following new members and hope that you Pakistan will participate fully in the activities of the Society. A. Tahir

Australia Singapore

R. Al Jassim; M. Benghezal; C. Kurekci; H. Rahman B. Chua

Austria South Africa

L. Boddrossy J. Lues

Columbia Thailand

A. Trespalacios S. Fuangfong

France UAE

D. Meyer S. Singh

Greece UK

I. Ntaikou; M. Rissakis S. Ahmed; A. Alnimr; T. Bailey; M. Bell; A. Benson; J. Caddick; E. Campion; H. Ciesielczuk; S. Costello; India R. Daniel; M. Dempsey; H. Esom; S. Foley; M. Fowler; N. Gibbins; C. Goswell; N. Green; A. Guha Roy; R. Kumar G. Hayburn; C. Hobday; G. Kane; S. Kava; J. Ma; K. Mallard; L. Marsh; D. McEwan; K. Miller; C. Milne; Iran D. Morrow; E. Nya; G. O’Neill; L. Ouoba; C. Parry; D. Perera; J. Ramsay; A. Salman; V. Shanmuganathan; M. Didari Khamseh Motlagh; A. Makhdoumi-Kakhki; L. Snyder; H. Tan; E. Theophilou; M. Walker; S. White B. Samareh-Abolhasani

Ireland USA

B. Boots; F. Brennan; J. Brown; S. Cooney; F. Fang H. Barton; Y. Hasegawa; K. Richardson

Italy West Indies V. Prajapat F Grieco

Mexico UK NEW CORPORATE

E. Ortiz-Vazquez E & O Laboratories Ltd; NCIMB Ltd

New Zealand LOSSES

P. Andrew Dr P W Jones, Full Ordinary Member since 1991, Institute of Animal Health, Berks. UK.

Erratum The Editors of Microbiologist would like to apologise for the following errors which appeared in the article entitled: Zoonoses: past, present and future in the March 2009 issue of Microbiologist. In table 1. the causative agents Borrelia afzelii and Borrelia garninii should not have been represented as: B- afzelii and B-garinii, they should have been written: B. afzelii and B. garinii. Furthermore, the agents Tinea corporis, Tinea cruris and Tinea pedis should have been written as follows: T. corporis, T. cruris and T. pedis. In addition, the legend to one image on page 27 should have read: E. Coli 0157 (SEM).

09 members

Lost members: do you know where these members are? We currently have some members on our records who have moved away or to another job and have not informed us of their new address. Do you know of the whereabouts of any of the following members?

Name Last known address Mr T W G Downey MedImmune UK Ltd., Liverpool Dr R A Collett University College Worcester, UK Dr Emma Best Leeds General Infirmary, UK Professor E Senior Centre for Advanced Water Technology, Singapore Professor M H Brown Unilever Research, Bedfordshire, UK Mr Kevin Shade Bio-Products Laboratory, Hertfordshire, UK Mrs Christine Moody Norpath Laboratories Ltd., County Durham, UK Mr Yui Cheung University of Glasgow, UK Mr Andrew Lamb University of Bolton, UK Miss Nicola Petty University of Cambridge, UK Dr P N Hobson Grampian, UK Mr R T Parry Spain Mr Vicente Gomez-Alvarez Morrill Science Centre, Amherst, USA Miss Azra Khan City Hospital, Birmingham, UK Dr Joseph Kleinhenz Cabot Creamery, Vermont, USA Miss Cassie Pope Royal Free Hospital, London Dr Guy Derdelinckx Kuleuven Malting and Brewing, Belgium

If you can help, then please contact Julie Wright, Membership & Finance Co-ordinator. Email: [email protected] or telephone: +44 (0) 1234 326661. membership matters

Congratulations!

Some of our members may be aware that at the end of April, past President of SfAM, Professor Peter Silley, embarked on his 2009 challenge of riding a push bike from Lands End to John O'Groats. Having successfully completed his challenge, Professor Silley raised a considerable amount of money for two well- deserving charities which are close to his heart. SfAM would like to extend our congratulations to Peter for this worthwhile accomplishment.

10 publications

Journal of Applied Microbiology Reverse dissimilatory sulfite reductase as phylogenetic The following articles published in 2009 were marker for a subgroup of sulfur-oxidizing the most downloaded articles from Journal of prokaryotes. Alexander Loy, Stephan Duller, Christian Applied Microbiology between January – March Baranyi, Marc Mußmann, Jörg Ott, Itai Sharon, Oded 2009: Béjà, Denis Le Paslier, Christiane Dahl & Michael Wagner, Vol. 11, No. 2, February 2009. Applications of cyanobacteria in biotechnology R.M.M. Abed, S. Dobretsov & K. Sudesh. Vol. 106, Metagenomic and stable isotopic analyses of modern No. 1, January 2009. freshwater microbialites in Cuatro Ciénegas, Mexico. Mya Breitbart, Ana Hoare, Anthony Nitti, Janet Microbial nitrilases: versatile, spiral forming, industrial Siefert, Matthew Haynes, Elizabeth Dinsdale, Robert enzymes. R.N. Thuku, D. Brady, M.J. Benedik & B.T. Edwards, Valeria Souza, Forest Rohwer & David Sewell, Vol. 106, No. 3, March 2009. Hollander, Vol. 11, No. 1, January 2009. Fermented pig liquid feed: nutritional, safety and Swarming motility: a multicellular behaviour regulatory aspects. C. Plumed-Ferrer & A. von conferring antimicrobial resistance. Sandra Lai, Julien Wright, Vol. 106, No. 2, February 2009. Tremblay & Eric Déziel, Vol. 11, No. 1, January 2009. Is the replication of somatic coliphages in water Microbial Biotechnology environments The following articles published in 2009 were significant? J. Jofre, Vol. the most downloaded articles from Microbial 106, No. 4, April 2009. Biotechnology between January – March 2009: Cloning, expression and Microbial biotechnology for producing high volume characterisation of the chemicals. Lawrence P. Wackett, Vol. 2, No. 1, serine protease gene journalWatch January 2009. from Chaetomium thermophilum. A.-N. Li A broad range of themes in Microbial Biotechnology. News about the Society’s journals & D.-C. Li, Vol. 106, No Craig Daniels & Juan-Luis Ramos, Vol. 2, No. 1, 2, February 2009. January 2009. Uracil influences quorum sensing and biofilm Letters in Applied Microbiology formation in Pseudomonas aeruginosa and The following articles published in 2009 were fluorouracil is an antagonist. Akihiro Ueda, Can the most downloaded articles from Letters in Attila, Marvin Whiteley & Thomas K. Wood, Vol. 2, Applied Microbiology between January – March No. 1, January 2009. 2009: Positively regulated bacterial expression systems Bacterial spoilage of wine and approaches to Trygve Brautaset, Rahmi Lale & Svein Valla, Vol. 2, minimize it. E.J. Bartowsky, Vol. 48, No. 2, February No. 1, January 2009. 2009. Editorial. The Editors, Vol. 2, No. 1, January 2009. Comparison of T-RFLP and DGGE techniques to Environmental Microbiology Reports assess denitrifier community composition in soil. K. Highlights of the second issue of Environmental Enwall & S. Hallin, Vol. 48, No. 1, January 2009. Microbiology Reports: Improved treatment of vulvovaginal candidiasis with Oestrogenicity of prenylflavonoids from hops: fluconazole plus probiotic Lactobacillus rhamnosus activation of pro-oestrogens by intestinal bacteria GR-1 and Lactobacillus reuteri RC-14. R.C.R. Sam Possemiers & Willy Verstraete, Vol. 1, No. 2, Martinez, S.A. Franceschini, M.C. Patta, S.M. April 2009. Quintana, R.C. Candido, J.C. Ferreira, E.C.P. De Martinis & G. Reid, Vol. 48, No. 3, March 2009. Honeybee colony collapse due to Nosema ceranae in professional apiaries. Mariano Higes, Raquel Martín- Isolation and characterization of alginate-degrading Hernández, Encarna Garrido-Bailón, Amelia V. bacteria for disposal of seaweed wastes. J.-C. Tang, González-Porto, Pilar García-Palencia, Aranzazu H. Taniguchi, H. Chu, Q. Zhou & S. Nagata, Vol. 48, Meana, María J. del Nozal, R. Mayo & José L. Bernal, No. 1, January 2009. Vol. 1, No. 2, April 2009. Bifidobacterium and Lactobacillus DNA in the human South American native bumblebees (Hymenoptera: placenta. R. Satokari, T. Grönroos, K. Laitinen, S. Apidae) infected by Nosema ceranae (Microsporidia), Salminen & E. Isolauri, Vol. 48, No. 1, January 2009. an emerging pathogen of honeybees (Apis mellifera). Environmental Microbiology Santiago Plischuk, Raquel Martín-Hernández, Lourdes The following articles published in 2009 were Prieto, Mariano Lucía, Cristina Botías, Aránzazu the most downloaded articles from Meana, Alberto H. Abrahamovich, Carlos Lange & Environmental Microbiology between January – Mariano Higes, Vol. 1, No. 2, April 2009. March 2009: Quorum sensing in Pseudomonas aeruginosa biofilms T. R. de Kievit, Vol. 11, No. 2, February 2009. Lucy Collister Insights on Escherichia coli biofilm formation and Wiley-Blackwell inhibition from whole-transcriptome profiling Thomas K. Wood, Vol. 11, No. 1, January 2009.

11 news

The University Press Office

hen I walk into the press office at 8.45am I never know what to expect. I Wcould be met with a tirade of enquiries from the media about that day’s superbug story in the first half an hour. What makes this go without a hitch is the able and willing scientist who answers the phone with a positive response. Your press officers use two different techniques to try to help you get the best media coverage for your research: proactive and reactive response to media enquiries. Proactive work means we’re trying to interest the public in the research our scientists are doing at that university, or being funded by that research council, or being presented at that society’s conference, for example.

Your research As a university press officer, typically a researcher or journal will contact me about a forthcoming paper. I will go and meet the researcher to find out more about what they are doing and to decide whether the research is suitable to publicise. If the new findings are newsworthy, if they have an impact on people’s lives or if they are intrinsically fascinating, I may decide to issue a press release. If the research is of interest to the university community, I could choose to publicise the new study internally, in a magazine or on the website. There are also lots of new media options, including podcasting, video interviews and even Twitter. A press officer has to make a judgement call about each story. The research might be our policy on wonderful scientifically, with flawless methods mediawatch that change the way proteins are purified the media forever, but that does not necessarily make a microbiology in the news story newsworthy. A great story has drama, a human aspect and is almost tangible; can you We will: If you have any views on science in the show us images or tell us stories? ■ always do our best media which you think should feature in this to provide facts, Danielle Reeves, Senior Press Officer at information and column, please send them to the Editor at: Imperial College London, says time is of the explanation. [email protected] essence when it comes to press releases. “If you ■ if speculation is have some research that is interesting and required, explain the newsworthy, that the world needs to know rationale behind that about, the easiest way for us to publicise it is speculation. if you have a paper being published. Usually, ■ desist from hyping a journalists will only write about something story—whether it is the the day it appears in the public domain, so journalist or the we need to know in advance if we are going scientist doing the to tell them about it. Let your press officer hyping. know at an early stage, when your paper has been accepted or even when you submit it for publication.”

12 Lucy Goodchild provides us with an insight into the way your University Press Office can help you publicise your work

Writing and issuing a press release can be a happy to talk to many journalists and producers lengthy process. After the initial meeting with the about a news story are vital in situations like scientist, I will review my notes and draft a press this. We also receive several different calls and release, using all the information I can get my emails about different subjects from different hands on. Accuracy is vital – the reputation of media outlets on any given day. Having access to the scientist and the university is important to a large number of scientists who are happy to protect – but detail comes down to yet another talk to the media and comment on stories is judgement call. essential for a press officer to deal with the The purpose of a press release is to sell a enquiries effectively. story to journalists. We must explain the main The first thing you can do as a scientist to findings of your research and say why they are help with media enquiries is to sign up to important to the general public in 500 words. databases. Get in touch with press officers at Just as there is a certain style to adopt when you your university, funding body, professional write an abstract or a scientific paper, press society and charity to get onto their expert lists releases also have their own style. Myc and media guides. If we don’t know you want to Riggulsford, Managing Director of The Walnut deal with the media, we can’t help you! Bureau and science journalist, broadcaster and There are a few main things to remember if media training consultant, puts it simply: “Tell you want to be a successful media contact. them the most important things first — tell According to Myc, the first thing is simple: them what you’ve done. Imagine a sentence “Don’t use jargon!” It’s all about making your that starts ‘scientists from the Society for science accessible and interesting. “Make Applied Microbiology announced today that...’ mental pictures for people. Describe things in — What would you say in the next 25 words? a way that lets them see what you’re talking Can you sum up what it is you are trying to about, instead of using theoretical language,” say? Work out what the important news is.” said Myc. But how can you tell if you’re getting it This can be difficult for some scientists, right? “Imagine yourself bursting through the especially if they have been working on a study doors of a primary school and saying ‘hey for years; the details a scientist considers kids, guess what?’ You should be important can be very different to those a understandable.” journalist might be looking for. Talking to the media can be daunting but The answer? Trust us! “If you are working don’t forget, you are not alone. You are with me on a press release and I send it to surrounded by press officers. In fact, you will be you for revisions, it would be helpful if you hard pushed to avoid us. We’re not just here to could bear in mind that we are professional help journalists, we can also support you and experts in this field, just as you are in your offer advice. I never give out a scientist’s number field,” said Danielle. “If the first draft I send without permission each time a journalist calls. I you is somewhat different to the way you always make sure I know who I’m talking to characterise your research, bear with me. We before I put a producer in touch with a will always work together to come to a mutual researcher. I love science (especially agreement on a press release, but it would be microbiology) and I could listen to hours of very helpful if you could keep an open mind lectures but I also know what the media will want and trust us.” to hear – the two are not always the same. I love to meet scientists and find out about them. And Their research there are lots of press officers just like me Press offices can serve as little black books waiting to hear from you. for journalists. Most universities, research Oh, and last but not least…if you’re being councils, societies and charities that have press interviewed, make sure you mention the name of officers will have a database of experts, which your university or Society! they can search through if a journalist calls asking to speak to an expert. This is where reactive work comes in. It is common for a press office to be Lucy Goodchild contacted by several media outlets about the Imperial College London same thing, especially if a big story has broken, and it can be a surprise. Scientists who are

13 news

Workpackage 34 — ampylobacter is known to be the world’s most common cause of food-borne the prevention and Cbacterial infections. Recent studies suggest control of that up to 60 per cent of campylobacteriosis Campylobacter in cases are attributable to the handling and consumption of contaminated poultry meat. broilers The colonisation of poultry, particularly broilers, by Campylobacter is also widely recognised, and poultry meat frequently becomes contaminated with these organisms during processing. Indeed, an EU baseline survey of broilers, completed in January this year, is anticipated to demonstrate that for most EU countries the majority of broiler flocks produced are colonised. Nevertheless, little is known about the sources of Campylobacter on poultry farms or the mechanisms of ■ Critically evaluate the indirect poultry- colonisation. Such information, however, is derived routes of Campylobacter essential for targeted interventions and effective infections in humans colonisation prevention strategies on farms. Aiming to breach that information gap by ■ Investigate and develop understanding of developing and expanding our knowledge of the effective methods of control and prevention animal host aspects of Campylobacter As with all of Med-Vet-Net’s projects, WP34 is transmission is Med-Vet-Net’s newest research taking a highly collaborative approach, using an initiative, Workpackage 34 — Sources, integrated research network of experts from control and prevention of Campylobacter in within the network partnership as well as poultry. external collaborators who are invited to contribute information and attend meetings. Consolidate, evaluate, disseminate That exchange of information has been The Workpackage (WP), which began in particularly important with colleagues from September 2008 under the leadership of WP30, who are aiming to develop a combined Professor Diane Newell on behalf of the microbiological and epidemiological approach Veterinary Laboratories Agency, is undertaking a for investigating host-microbe interactions of series of tasks designed to consolidate what is med-vet-net Campylobacter jejuni — an objective closely presently a highly fragmented information base. related to WP34. Joint meetings between the two At its conclusion in August this year, the WP will WPs are ensuring that any novel information Med-Vet-Net is a also have examined the role of poultry in European Network of obtained by either project is shared. Excellence that aims to environmental contamination and developed an understanding of how to best control and improve research on Stimulating outcomes prevent the colonisation of the agent in broiler the prevention and A range of outcomes are anticipated from control of zoonoses by flocks. WP34’s activities which are expected to not only integrating veterinary, The specific objectives of the project are to: enhance Europe’s collective knowledge but also medical and food ■ Collate, manage and archive the European science research. generate greater interest, from farmers and vets information base on Campylobacter in Comprising 15 to researchers and policymakers, in an often poultry European partners and overlooked aspect of a global problem. over 300 scientists, ■ Develop and collate knowledge of the Med-Vet-Net will These outcomes include: molecular basis of colonisation of the avian enable these scientists ■ An integrated European network of gut to share and enhance expertise on the prevention and control of their knowledge and ■ Disseminate knowledge on the Campylobacter in poultry, with common skills, and develop interests and aims, and a contact list to collaborative research epidemiology of poultry colonisation and projects. the survival of campylobacters in the improve communications and enable poultry environment collaboration outside of Med-Vet-Net

14 Med-Vet-Net’s final conference Med-Vet-Net is hosting its fifth and final Annual Scientific Meeting this month. With the theme ‘Microbial Communities’, this year’s conference (3–6 June) will be held in the historically significant and culturally rich Spanish region of San Lorenzo de El Escorial, 45km north-east of Madrid. Organised by Med- Vet-Net’s Spanish partners, Complutense University Madrid (UCM) and the Instituto de Salud Carlos III (ISCIII), the meeting at the UNESCO World Heritage Site will attract more than 200 delegates from within and outside the Network. Headlining the three-day conference are seven keynote speakers from Canada, the UK, Spain, France and the Netherlands who will give presentations on topics ranging from the union of epidemiology and risk assessment to the genomic view of the biodiversity of Listeria. The specific keynote topics and their ■ An Endnote-based database of publications presenters are: on Campylobacter in poultry from 1980 to ■ Brett Finlay, University of British Columbia, date Canada: Pathogenic E. coli: contribution ■ A list of genes described to affect of the pathogen, host, and microbiota colonisation (positively or negatively) and ■ Fernando Baquero, Hospital ´Ramon y their properties Cajal´, Spain: Ecogenetical Dynamics of ■ Bioinfomatics studies comparing these Bacterial Pathogens genes with the core genome (the fraction of ■ Peter Teunis, National Institute for Public genes present in every Campylobacter Health and the Environment (RIVM), The genome) as opposed to the variable Netherlands: Epidemiology and risk genome fraction, identifying gene assessment: an unsettled union? combinations of non-essential or redundant colonisation factors, identifying, if possible, ■ Peter Mertens, Biotechnology and regulatory networks in which colonisation Biological Sciences Research Council genes participate, and the protein-protein (BBSRC), UK: The emergence and interactions for colonisation factors that are spread of Bluetongue virus across active in protein complexes Europe: The impact of climate change, information insect vectors and vaccination ■ A report recommending the genes to be investigated in future colonisation studies ■ Carmen Buchrieser, Institut Pasteur, France: A full review of Med- Biodiversity and evolution of pathogenic Vet-Net’s final Annual ■ A collation and annotation of Listeria: a genomics view Meeting will be in the Campylobacter genes and mechanisms next issue of associated with environmental survival as ■ Patrice Courvalin, Institut Pasteur, France: Microbiologist. More defined using in vitro models. Evolution and dissemination of information about the glycopeptide resistance operons conference can also be ■ An international workshop on “Immunity to found on Med-Vet- and vaccination against Campylobacter ■ JM Sánchez-Vizcaino, Complutense Net’s website at: jejuni in chickens” — the first time this University Madrid (UCM), Spain: New tools www.medvetnet.org/ mvnconf09. topic has been explored in an open forum. in the prevention and control of The meeting, held in April 2009, attracted a emerging diseases For more information broad audience of scientists and industry about Met-Vet-Net, representatives. visit: Tania Cutting www.medvetnet.org or contact Teresa Communications Adviser To learn more about WP 34 and its progress, Belcher on: Med-Vet-Net visit the Med-Vet-Net website at: www.medvetnet. +44 (0)1908 698810 org/wp34.

15 meetings

Summer conference 2009 CPD ACCREDITATION ■ Including the Lewis B Perry Memorial Lecture — Prion zoonoses: past, present and future given by John Collinge 22 points awarded

Fur, feather and fever — zoonotic challenges of the 21st century Manchester Metropolitan University, Manchester Monday 6 to Thursday 9 July 2009

Including sessions on: ■ Arthropod borne zoonoses

■ Wildlife and companion animals

■ Livestock and foodborne zoonoses

■ Emerging and re-emerging zoonoses

There will be a packed social programme including:

■ Drinks reception and lecture on Monday 6 July followed by Quiz Night

■ Trade exhibition on Tuesday 7 July with wine and prizes

■ Conference dinner at the URBIS Centre on Wednesday 8 July, including the presentation of the SfAM Communications Award

For the latest information please visit us online at www.sfam.org.uk

16 Programme

Monday 6th July Wildlife and companion 14.00-14.35 Farm to fork — emerging animals trends in foodborne zoonoses 14.00 onwards Arrive and Register 14.00-14.35 Bats, bites and fury — can Tom Humphrey, University of Bristol, UK 11.00–17.00 Basic statistics for applied we control rabies? Tiziana Lembo, University of microbiology 14.35-15.00 Tea/posters Basil Jarvis (A short course Glasgow, UK. primarily for PECS 15.00-16.00 Student presentations members and student 14.35-15.10 Controlling wildlife members) reservoirs for bovine TB Glyn Hewinsonn, Veterinary 16.00-16.30 W H Pierce memorial prize Laboratories Agency, UK 18.00-18.50 Lewis B Perry memorial 16.30-17.00 AGM lecture: prion zoonoses: 15.10-15.45 Zoonoses in UK wildlife past, present and future 19.30-20.00 Drinks reception, dinner John Collinge and their detection through sentinels URBIS Centre, Manchester. 19.00-20.00 Drinks reception Anna Meridith, Edinburgh Thursday 9th July 15.45-16.15 Tea/posters 20.00 Evening at leisure 09.00-09.35 New trends in 16.15-16.50 Exotic pets — what are the toxoplasmosis 21.30 Quiz night — Jury’s Inn Delfien Verhelst, University of Hotel zoonotic risks? F. Meslin, World Health Ghent, Belgium Tuesday 7th July Organisation, Switzerland Emerging and re-emerging Arthropod-borne zoonoses 16.50-18.00 Student Session zoonoses 16.50-19.00 Trade Show 09.35-10.10 Modelling zoonotic 09.00-09.35 What is a zoonosis? disease — challenges & Malcolm Bennett, University Wednesday 8th July successes of Liverpool, UK Nigel French Massey Uni, NZ 09.00-09.35 Controlling wildlife 09.35-10.00 Plague — historical zoonoses without 10.10-10.45 Drivers of zoonotic disease perspectives to modern eliminating wildlife emergence in general, infection trends Marc Artois, Ecole Nationale using Nipah virus as a case Nils Chr Stenseth, University Veterinaire de, Lyon, France study of Oslo, Norway Jonathan Epstein, The 09.35-10.10 Nature bites back! Consortium for Conservation 10.10-10.45 Lyme borreliosis — facts & Marina Morgan Medicine, New York and fantasy University of Kingston, UK Sue O’Connell, Health Protection Agency, Livestock and foodborne 10.45-11.15 Coffee/posters Southampton zoonoses 11.15-11.50 Predicting pandemics or 10.45-11.15 Coffee/posters 10.10-10.45 Anthrax — wool-sorters disease in Belgium! scare mongering? Dilys Morgan, HPA, UK 11.15-11.50 Bartonellosis an Pierre Wattiau, VAR-CODA- increasingly recognised CERVA, Brussels, Belgium 11.50-12.25 Emerging/re-emerging zoonosis viral zoonoses Bruno Chomel, School of 10.45-11.15 Coffee/posters Ernie Gould, France Veterinary Medicine, University of California, USA 11.15-11.50 New challenges and perspectives on brucellosis 12.25-13.00 Leishmaniasis and pet travel 11.50-12.25 Rickettsiosis — the Phil Elzer, LSU, USA David Hill, National Travel unwanted holiday Health Network and Centre souvenir 11.50-12.25 Cryptosporiosis — Speaker to be challenges for control 13.00-14.00 Lunch & Close confirmed Rachel Chalmers

12.25-13.00 Relapsing fever — 12.25-13.25 Lunch forgotten but not gone This programme was correct at the Sally Cutler, University of East 13.25-14.00 Unravelling the mysteries time of going to press. For the latest London, UK of Q Fever programme please visit us online at Didier Raoult, Marseilles, www.sfam.org.uk 13.00-14.00 Lunch France

17 meetings BOOKING FORM and INVOICE S f AM SUMMER CONFERENCE 6 — 9 July 2009 CLOSING DATE FOR REGISTRATIONS: Friday 26 June 2009 EARLY BIRD DISCOUNT of £30.00 is applied to all bookings made before Friday 5 June 2009 Cancellation policy: Up to 30 days prior to the event all cancellations will be subject to a 10% cancellation fee, up to 14 days prior to the event there will be a 50% cancellation fee, and no refunds will be given on cancellations made within 7 days of the event. *Non members please note: You can add 1 year’s membership to your event booking using this form, then register at the member rate and spend the same amount of money or less! Student, Honorary, Associate Full Member Student Non -Member Non - Member FEES BEFORE 5 JUNE 2009 & Retired Member

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18 SfAM Environmental Microbiology Lecture Deciphering microbial community dynamics, from genomes to biomes presented by Professor Edward de Long of Massachusetts Institute of Technology (MIT), USA Royal Society of Medicine, London, UK ● Monday 12 October 2009

The Environmental Microbiology lecture will be presented by Professor Edward de Long of Massachusetts Institute of Technology (MIT), USA. He will present a lecture entitled ‘Deciphering microbial community dynamics, from genomes to biomes’. Invitations were sent to members in the last issue of the Microbiologist giving a deadline for responses of 30th April. Those members who responded to the invitation will be sent further information nearer the date. If you have any queries about attending the lecture please contact Sally Cryer on 01234 761752. For members unable to attend, the lecture will be available online immediately after the event.

Winter meeting 2010 ■ Including the Denver Russell Memorial Lecture

A one day meeting on biocides and tuberculosis

Royal Society, London Monday 11 January 2010

■ For further information please visit the Society website or contact Sally Cryer. Email: [email protected]. Telephone: 01234 761752

19 features BACTERIOPHAGE THERAPY

he control and management of old treatment, new focus? infections and infectious diseases Tusing antibiotics faces ever- increasing challenges from the development and spread of resistance to such compounds. This has become a major problem worldwide, and there are fears that the clinical management of many infectious diseases will become severely constrained. As a consequence a number of alternative antimicrobial strategies are currently being investigated. One approach to antibacterial therapy which has been used since the beginning of the twentieth century is the application of bacteria-specific lytic viruses or bacteriophages. The history, biology and early therapeutic use of bacteriophages can be found in a number of reviews and textbooks (Kutter & Sulakvelidze, 2005; Hanlon, 2007; Abedon, 2008) and this article will examine some of the recent developments and obstacles in the field of bacteriophage therapy.

Early development of bacteriophage therapy Much of the pioneering work with bacteriophages and bacteriophage therapy was inconclusive and the therapeutic outcome was sometimes worse than the presenting infection, leading to mistrust and scepticism. The ‘Bacteriophage Inquiry’ in India in 1927 and an American Medical Association review in 1931 failed to produce conclusive evidence as to the efficacy of the therapy. The development of antibiotics and antimicrobial chemotherapy at around the same time halted further serious investigation, and by the end of the Second World War, bacteriophage therapy was seen as a marginal curiosity. Research on bacteriophages did not stop with the advent of antibiotics but continued in countries in the former Soviet Republics, where antibiotics were inaccessible. Advances in knowledge, techniques and application increased so that a substantial body of evidence accumulated, and active programmes were initiated to develop and distribute bacteriophage therapeutics throughout the Soviet bloc. The Eliava Institute in Georgia became the premier bacteriophage research establishment, Jonathan Caplin examines the recent developments and producing a wide range of preparations obstacles in the field of bacteriophage therapy containing bacteriophage and ‘cocktails’ of specific bacteriophages. Incidentally, Félix d’Hérelle (who announced his

20 discovery of bacteriophages in 1917, aeruginosa using a cocktail of six and localised applications, for example independently of Frederick Twort who bacteriophages produced by the UK ‘PhageBioderm’ a biodegradable first described their lytic behaviour in start-up company Biocontrol. Very material impregnated with 1915) introduced bacteriophages to positive results have been reported from bacteriophage, designed for the George Eliava in 1926 on a visit to the the trial in terms of clinical and treatment of skin infections, and then Tbilisi Institute of Bacteriology. bacteriological efficiency and safety ‘PhageBiodent’ for periodontal and concerns. The therapeutic cocktail is gingival applications. Resurgence of interest in the West currently being examined in Phase 3 After the collapse of the Soviet Union trials. Administration of the Safety concerns in 1989, bacteriophage therapy came to bacteriophage cocktail was via an A number of companies focussing on the attention of the West once again, aerosol delivery system which was the development of bacteriophage this time with supporting evidence of granted a patent by the European Patent therapy were formed during the 1990s therapeutic efficacy observed in Eastern Office in 2008. A similar concept to exploit the niche for intravenous Europe. Unfortunately, language involving the nebulisation of antibacterial therapeutics. However, the difficulties and the lack of detailed bacteriophages of Burkholderia combination of clinical trial documentation and double-blind cepacia Complex to treat cystic fibrosis requirements, problems with unwanted controls in many of the trials, meant has recently been described (Golshahi et immunological reactions, and that the body of work as a whole was al., 2008). intellectual property rights issues led not regarded seriously, and there was As well as clinical trials, basic many of these companies to turn to insufficient evidence for its acceptance research has been ongoing. At the 17th veterinary and agricultural applications, and approval for use as a therapeutic Biennial International Evergreen Phage which were perceived as less option. Biology Meeting held in Olympia USA in regulatorily tricky areas. Such a change However, the spectre of increasing August 2007, bacteriophage therapy in direction resulted in the US Food and levels of multi-antibiotic resistance sessions covered a range of infections Drug Administration (FDA) approving a focused minds once again on and bacteria such as Otitis Media (ear product developed by Intralytix in 2006. bacteriophages as therapeutic tools. infection) and Pseudomonas The product contained bacteriophages Basic research into the biology and aeruginosa, urinary tract infections active against Listeria monocytogenes ecology of bacteriophages, together with (UTIs) and Klebsiella species, and was designed as a disinfectant spray advances in molecular biological Burkholderia species, Group A for packaged meats. Subsequently, other techniques and purification methods, Streptococcus, and Bacillus anthracis products from companies such as enabled the development of well infections (http://academic.evergreen. Omnilytics and EBI Food Safety have characterised, specifically targeted and edu/ projects/phage/). been approved by the US FDA and given highly purified bacteriophage mixtures Despite all the interest and debate, approval under the ‘generally regarded for therapeutic use, and scientists and few clinical evaluations of bacteriophage as safe’ (GRAS) system. The approval of clinicians in Europe and America began therapy have been published to date in these products shows recognition that the first clinical trials. the West. A possible reason for this lack bacteriophages are considered safe for For example, a cocktail of eight of advance may be that the data use on food destined for human bacteriophages (five against available are at a very early stage with consumption. This is a step towards Pseudomonas aeruginosa, two against few meaningful and significant results, acceptance of bacteriophage therapy in Staphylococcus aureus and one against thus making it difficult to attract general. The ubiquitous nature of Escherichia coli) was used to treat funding. Secondly, bacteriophage bacteriophages, estimated to be the infected leg ulcers in Texas, USA (Marza therapy is somewhat of a grey area to most numerous organisms on the planet et al., 2006). The bacteriophages were most regulatory agencies and (Abedon, 2008) means that humans are supplied by Intralytix, a US company consequently questions of medical ethics exposed to them from birth, and have founded by a former Georgian and procedural pathways abound. been in symbiotic relationship with them microbiologist. Following the trial, the Within existing frameworks it is virtually for thousands of years. In fact it is Southwest Regional Wound Care Centre impossible to start clinical investigations impossible not to ingest bacteriophages in Texas used bacteriophages in to generate the data required to since they form part of the natural flora conjunction with other methods, to treat demonstrate the safety and efficacy of of the human oral cavity and antibiotic-resistant infections bacteriophage-based therapeutics. It gastrointestinal tract, and are present in (www.woundcarecenter.net). The use of should also be noted that in the former municipal drinking water and various bacteriophage T4 against E. coli in Soviet Republics, the vast majority of food items. cases of diarrhoea is being assessed in bacteriophage preparations were There were also concerns regarding Bangladesh by Nestlé, the Swiss designed for use as non-systemic the safety of intravenous bacteriophage multinational food corporation. This medications i.e. lavage, sprays, preparations, a problem not readily follows safety testing on human ointments and dressings. Several encountered in Eastern Europe since volunteers (Bruttin & Brüssow, 2005). preparations were for oral or rectal there was a preference for topical Phase 2a clinical trials were conducted (suppository) delivery, and the few applications in those countries. in 2007 at the Royal National Throat, injectable preparations were for Bacteriophages have the potential to Nose and Ear Hospital in London, on intramuscular or intraperitoneal elicit strong immune responses mainly the treatment of chronic inner ear administration. Thus nearly all the work due to their protein content, and as a infections caused by Pseudomonas from Eastern Europe involved topical consequence the system can clear the

21 features

bacteriophages from the body rapidly. bacteriophages for intra-nasal The phenomenon of bacteriophage The interaction between bacteriophages decolonisation of MRSA and for oral mutation leading to resistance has also and antibodies is of concern because if therapy against C. difficile associated been cited as a concern, and resistance the bacteriophage elicits an antibody disease (http://www.phicotherapeutics. to the therapeutic bacteriophage has mediated response, further treatment co.uk/). been noted in some animal studies. with that particular bacteriophage would The major problem with these However the use of bacteriophage be negated. Another concern over the approaches is the approval of genetically cocktails has the potential to minimise use of intravenous bacteriophage engineered agents, added to the fact that or prevent the development of preparations is the chance of the patient the bacteriophages themselves are not resistance. developing the Jarisch-Herxheimer categorised as therapeutic modalities, The conversion of a lytic reaction - systemic shock resulting from thus proving a real challenge to bacteriophage into a lysogenic lifecycle the sudden release of polysaccharide pharmaceutical companies wishing to could be a major problem if the endotoxins into the bloodstream during pursue this route. Two of the major bacteriophage genome integrates with the lysis of susceptible bacteria. The bacteriophage companies, Intralytix and that of its host. Subsequent reactivation problem of lytic toxicity has been Biocontrol, are only working with could result in the transfer of bacterial investigated specifically in a veterinary ‘natural’ or unmodified bacteriophages virulence factors and the bacteriophage trial of active bacteriophage therapy, for these very reasons. mediated transfer of virulent bacterial and no significant adverse reactions or genes into other bacteria. In order to effects were noted (Soothill, 2004). avoid this, care must be taken to ensure The wealth of data from Eastern that the potential therapeutic Europe suggests that bacteriophage bacteriophage is predominantly or therapy is safe (Sulakvelidze, 2005), and wholly lytic, and does not carry any experience at clinics where toxic genes or housekeeping genes for bacteriophage therapy is provided initiating lysogeny. There are little data indicates that the treatment is effective on the genomes and proteomes of lytic and without negative side-effects. One of bacteriophages, so questions of the largest bodies of published work in lysogenic, toxic or virulent genes remain English on bacteriophage therapy comes unanswered at present. from the Hirszfeld Institute of From a regulatory point of view, Immunology and Experimental Therapy bacteriophages are rather ambiguous, in Wroclaw, Poland. Their experience and the fact that they are self-replicating over the past 30 years in treating nearly biological entities is another 2000 patients suffering from a variety of complication. To meet current often life-threatening infections was very regulatory approval, such a product positive, with an overall rate of success must comprise of a highly purified, of 60% to 90% and no reports of serious characterised, and validated adverse reactions (Stone, 2002). bacteriophage or mixture of bacteriophages, together with optimised Novel approaches to PHP innoculation administration protocols, supported by bacteriophage therapy properly controlled efficacy and safety Until recently, bacteriophage Obstacles to the acceptance of studies. There are no specific therapies have been based on complete bacteriophage therapy frameworks for bacteriophage therapy virus particle preparations or purified Despite the accumulating biological, in the current Medicinal Product bacteriophage lytic enzymes such as molecular and clinical evidence Regulation (EC, 2001), so short-term lysins and holins (Fischetti, 2005). supporting the use of bacteriophage borderline solutions under the Novel developments include phage therapy, there are a number of hurdles responsibility of a medical ethics display, where an antibacterial peptide to be overcome before it is accepted and committee or under the umbrella of the or protein is displayed on the surface of considered a therapeutic option. These Declaration of Helsinki are possible a genetically modified bacteriophage. problems can be regarded as biological, options. It has been proposed (Verbeken The bacteriophage is designed not to proteomic and regulatory. For example, et al. 2007) that a long-term solution lyse but rather to deliver the attached little is known about bacteriophage would be the creation of a specific antibacterial to the target bacteria interactions in the gut and other section for bacteriophage therapy under (Westwater et al. 2003). anaerobic environments, and some work the Advanced Therapy Medicinal Bacteriophages have also been used has shown that T-even bacteriophage Product Regulation (EC, 2003). as potential vehicles for the delivery of display oxygen-dependent growth on The development of bacteriophage vaccines. The bacteriophages can carry their host strain and inhibition of lysis therapeutics is also hindered by issues antigens on their surface or deliver a under anaerobiosis. It is also thought of intellectual property rights. DNA extension cassette that has been that bile salts and gut carbohydrates Bacteriophages have been used as engineered into the bacteriophage may sequester the bivalent metal ions therapeutic agents for almost a century genome (Clark & March, 2004). The UK needed by bacteriophages for adsorption and are thus unpatentable. As a company Phico Therapeutics Ltd. are and replication (Chibani-Chennoufi et consequence, few pharmaceutical developing engineered ‘improved’ al. 2004). companies would be willing to invest the

22 sums of money required to develop a product for bacteriophage therapy unless their results are ‘protected’ by an international patent. Another potential obstacle for the clinical application of bacteriophages is the perceived ‘fear’ of viruses. Viruses are seen by many members of the public as ‘like bacteria but more dangerous’ or as ‘enemies of life’, and the idea of injecting them into patients or spraying them onto food raises real if unwarranted concerns.

Is there a future for bacteriophage therapy? If the necessary regulatory and ethical hurdles are overcome and bacteriophages become accepted as therapeutic agents, this could stimulate the development of new approaches and methodologies. It is possible that initially agricultural, veterinary, food hygiene and food safety applications will MAIN PHOTO: Bacteroides ovatus B124 Bacteriophage (Siphoviridae) © D.Diston, predominate until sufficient data from University of Brighton, 2009. INSET: Petri plates clinical and safety trials are available. New pharmacokinetic data, advances in biocompatibility studies and a greater understanding of bacteriophage-bacteria references interactions will enable novel targets to ■ Abedon, S.T. (2008) In: Bacteriophage Ecology: Population Growth, Evolution, and Impact of Bacterial be identified and the efficacy of Viruses. Cambridge University Press, Cambridge, UK. bacteriophage-based therapies to be ■ Bruttin, A. & Brussow, H. (2005) Human volunteers receiving E. coli phage T4 orally: a safety test of improved. It is also possible that phage therapy. Antimicro. Agents Chemotherapy. 49, pp2874–2878. bacteriophage therapy will be ■ Chibani-Chennoufi ,S. Bruttin, A. Dillmann, M.L. Brussow, H. (2004) Phage-host interaction: An approached like other biological control ecological perspective. J Bacteriol. 186, 3677-86. methods used in agriculture, with the ■ aim to reduce bacterial infections and Clark, J.R. & March, J.B. (2004) Bacterial viruses as human vaccines? Expert Rev. Vaccines 3, pp463–476. spread of diseases using a range of ■ EC (2001) Commission Directive 2001/83/EC of the European Parliament and of the Council of 6 modalities and therapeutic agents, as November 2001 on the Community code relating to medicinal products for human use. Official Journal of the European Communities. part of an ‘integrated pathogen management’ plan. ■ EC (2003) Commission Directive 2003/63/EC of 25 June 2003 amending Directive 2001/83/EC of the At the start of the twentieth century European Parliament and of the Council of 6 November 2001 on the Community code relating to medicinal products for human use. Official Journal of the European Union. bacteriophage therapy was seen as the ■ answer to bacterial infections but initial Fischetti, V.A. (2005) Bacteriophage lytic enzymes: novel antiinfectives. Trends Microbiol. 13, pp491–496. therapeutic problems and the advent of ■ Golshahi, L. Seed, K. Dennis, J. Finlay, W. (2008) Toward Modern Inhalational Bacteriophage Therapy: antibiotics pushed it into the Nebulization of Bacteriophages of Burkholderia cepacia Complex. J. Aerosol Med. Pulm. Drug Delivery. 21, background. pp351-360. Now at the start of the twenty-first ■ Hanlon, G. (2007) Bacteriophage Therapy. Microbiologist. 8 (1), pp30-32. Society for Applied century with the ever increasing Microbiology, March 2007. problem of antibiotic resistance, we ■ Kutter, E. & Sulakvelidze, A. (Eds) 2005. Bacteriophages Biology and Applications. CRC Press Boca Raton, have the wealth of clinical experience FL, USA. from colleagues from the former Soviet ■ Marza, J.A. Soothill, J.S. Boydell, P. & Collyns, T.A. (2006) Multiplication of therapeutically administered Republics and the necessary biological bacteriophages in Pseudomonas aeruginosa infected patients. Burns 32, 644–646. knowledge and tools to re-evaluate the ■ Soothill, J.S. Hawkins, C. Anggard, E.A. & Harper, D.R. (2004) Therapeutic use of bacteriophages. Lancet therapeutic potential of these ‘bacteria Inf. Dis. 4, pp544–545. eaters’. ■ Stone, R. (2002) Stalin’s forgotten cure. Science 298, pp728-31. ■ Verbeken, G. De Vos, D. Vaneechoutte, M. Merabishvili, M. Zizi, M. Pirnay, J-P. (2007) European regulatory conundrum of phage therapy. Future Microbiol. 2, pp485-491. Jonathan Caplin ■ Westwater, C. Kasman, L.M. Schofield, D.A. Werner, P.A. Dolan, J.W. Schmidt, M.G. & Norris, J.S. (2003) University of Brighton Use of genetically engineered phage to deliver antimicrobial agents to bacteria: an alternative therapy for treatment of bacterial infections. Antimicrob. Agents Chemother. 47, pp1301–1307.

23 features

ntimicrobial resistance was Antimicrobial recognised as a potential Aproblem for the treatment of diseases caused by enteric bacteria in both humans and food production resistance in animals as long ago as the 1960s. Following the identification of linked transmissible resistance to several bacterial enteric unrelated classes of antimicrobial drugs in Shigella from cases of human infection in Japan in 1963, such pathogens resistance rapidly became widespread, culminating in the appearance and John Threlfall provides an overview of resistance in Salmonella and spread of epidemic clones of Campylobacter and discusses the problems associated with the emergence of Salmonella Typhimurium in the United Kingdom (UK) particularly, from 1965. resistance in such organisms Concern about the origins of resistance in such strains, and the possible role of antibiotics in food animals, particularly calves, contributed significantly to the formation in 1968 of the ‘Swann Committee’. This group were tasked with investigating the contribution of antibiotics in food animals to the

Typhimurium development of resistance in zoonotic enteric pathogens. The recommendations of the Swann Committee were far reaching and

Salmonella culminated in the withdrawal of

24 antibiotics as growth promoters in the co-trimoxazole in the late 1970s/early ubiquitous in drug-resistant strains of S. UK and in due course in the European 1980s. The efficacy of these Typhi, evolutionary diversity within this Union. Nevertheless, resistant strains antimicrobials was undermined in the ‘Typhi-specific’ compatibility group has have continued to proliferate, and at late 1980s following the emergence of recently been observed among HI1 present there are increasing problems epidemic strains of S. Typhi, not only plasmids from multi-resistant strains of not only with a global increase in the with resistance to chloramphenicol, S.Typhi isolated in Vietnam over a ten- occurrence of strains with multiple streptomycin, sulphonamides and year time period in the 1990s (Wain et resistance, but also with the emergence tetracyclines, but also with additional al., 2003) and more recently worldwide of resistance to antibiotics regarded as resistance to ampicillin and (Phan et al., 2009). In strains with ‘first-line’, or ‘critical’ by the World trimethoprim/sulphamethoxazole (= co- decreased susceptibility to ciprofloxacin, Health Organisation (WHO). This article trimoxazole) (=ACSSuTTm). Outbreaks such resistance has been chromosomally provides an overview of resistance in with such strains were initially encoded resulting from a single two key enteric pathogens, namely recognised in Pakistan, but the strains mutation within the gyrA gene. In Salmonella, and Campylobacter and rapidly became widely disseminated. In contrast, in strains with high level discusses problems and recent events the 1990s, fluoroquinolones became the resistance, two mutations in gyrA and a associated with the emergence of drug of choice for the first-line further mutation in the parC region has resistance in such organisms. treatment of typhoid fever, initially in been identified. adults but subsequently in children. In Infections caused by S. Paratyphi A, Salmonella turn, incidents and outbreaks of although not as severe as typhoid fever, Salmonella enterica has been infection with strains of S. Typhi may also require antimicrobial regarded as the ‘definitive’ enteric resistant to quinolone antibiotics, intervention before the results of pathogen in respect of antimicrobial particularly nalidixic acid, coupled with susceptibility tests are available. As with resistance, particularly in relation to its decreased susceptibility to ciprofloxacin typhoid fever, the first-line drugs are the ability to acquire a variety of resistance (MIC: 0.25 – 1.0 mg/L) became fluoroquinolones. A substantive increase genes by plasmid acquisition, to develop increasingly reported. Of particular note in strains of S. Paratyphi A with resistance to certain key antimicrobials were substantive outbreaks with such decreased susceptibility to ciprofloxacin by mutation, and also because of the strains in Tajikistan and Vietnam in the has been reported in both India and zoonotic reservoirs of many serovars. late 1990s and early 2000s. Clinical Vietnam since the late 1990s and in the From a clinical perspective, failures with infections caused by strains UK, over 70% of isolates from cases of salmonellosis in humans falls into three of S. Typhi with decreased susceptibility infection in 2006 exhibited decreased broad categories: enteric fever; invasive to ciprofloxacin were first reported in susceptibility to ciprofloxacin, an disease (non-typhoidal); gastroenteritis. the UK in the early 1990s, and have increase of 300% since 2001 (Threlfall subsequently become increasingly et al., 2008). Enteric fever common. In 2006, 68% of typhoid cases In developing countries the primary in the UK involved strains that exhibited Invasive disease (non-typhoidal) disease presentation is that of enteric reduced susceptibility to ciprofloxacin Certain other serovars — e.g., fever, caused for the most part by and concomitant resistance to nalidixic Cholerae-suis, Dublin, and Virchow – are organisms such as Salmonella Typhi or acid (Threlfall et al., 2008). Since 2005, also invasive. In general such organisms S. Paratyphi A. Although vaccines are strains of S. Typhi with high level do not exhibit resistance to available to combat S. Typhi, these are fluoroquinolone resistance (‘clinical’ antimicrobials, although multiple not widely used and there are no resistance) have been identified in resistance, including clinical resistance vaccines approved for Paratyphi A. sporadic cases in India but do not to fluoroquinolones, has been reported Treatment with an appropriate appear to have become widely in fatal cases of infection with S. antimicrobial may therefore be essential, disseminated. As yet, no strains of Cholerae-suis in Taiwan. In developing and can be life-saving. Chloramphenicol typhoid with ‘clinical’ resistance to countries a different picture has was the undisputed first-line drug used ciprofloxacin have been identified in emerged, with serovars normally until the 1970s, when its efficacy was cases of infection in the UK. In cases of regarded as non-invasive. For example, seriously undermined by a series of treatment failures with fluoroquinolone Typhimurium, Wien, Senftenberg, are outbreaks in countries as far apart as antibiotics, third generation associated with highly virulent infections Mexico, India, and Vietnam. cephalosporins such as ceftriaxone have with a high degree of morbidity and Chloramphenicol-resistant strains which been recommended, but in developing mortality. In developing countries, were also resistant to streptomycin, countries the cost of such antimicrobials particularly in the Indian sub-continent sulphonamides and tetracyclines can be prohibitive. Azithromycin, a and South-east Asia, serotypes such as (CSSuT) became endemic throughout macrolide antibiotic, has also been Typhimurium, Wien, Johannesburg and the Indian sub-continent and common in evaluated for the treatment of infections Oranienburg have undergone changes developed countries in travellers caused by multi-resistant typhoid, with both in their epidemiology and their returning from such regions. As a result encouraging results (Parry, 2004). clinical disease. An additional feature of of the emergence and spread of In strains of S. Typhi with resistance these strains has been the possession of chloramphenicol-resistant strains on an to chloramphenicol, trimethoprim and plasmid-mediated multidrug resistance, almost global scale, ampicillin was ampicillin, such resistances have almost often exhibiting resistance to seven or introduced for the first-line treatment of invariably been encoded by plasmids of more antimicrobials. With the exception typhoid in the early 1970s, followed by the HI1 incompatibility group. Although of resistance to furazolidone and, since

25 features

1990, to nalidixic acid, resistances in nontyphoidal salmonella bacteremia the late 1980s (Threlfall, 2000) and is these strains have invariably been were due to S. Typhimurium, with most still on-going, albeit with decreasing plasmid-encoded. The most common strains exhibiting multidrug resistance numbers of isolations (Figure 1). In presentation has been that of severe to ampicillin, cotrimoxazole, and 1996 infections with MR DT 104 were gastroenteritis often accompanied by chloramphenicol (Gordon et al,. 2008). recognised in cattle and humans in septicaemia (up to 40% in some Such strains have now replaced S. Typhi North America, and particularly in the outbreaks) with up to 30% mortality. as the predominant cause of invasive USA the organism has been responsible The main method of transmission is by salmonellosis in tropical Africa. for many outbreaks in both cattle and person-to-person spread either in humans. In MR DT 104 of R-type hospitals or in the community, and Gastroenteritis ACSSuT resistances are contained in a antibiotic resistance appears to have In developed countries salmonella 16kilobase (kb) region of the 43kb developed as a result of the use of infections are primarily zoonotic in Salmonella Genomic Island SGI-1 antibiotics in human medicine, origin and the most common comprised of integrons containing particularly in those countries where presentation is that of gastroenteritis. respectively the ASu (blaCARB-2 and sul1) there is little control over the use of When resistance is present, it has often and SSp (aadA2) genes (Sp, antibiotics. A particular property of the been acquired prior to transmission of spectinomycin), with intervening majority of these multiresistant strains is the organism through the food chain to plasmid-derived genes coding for the possession of a plasmid of the FI humans. The most important serovars in resistance to chloramphenicol / incompatibility group coding not only the UK and Europe are Enteritidis and florphenicol (florR) and tetracyclines for multiple resistance, but also for Typhimurium. For all these serovars the (tetG). Although chromosomally- production of the hydroxamate main method of spread is through the encoded, in recent years SGI-1 has been siderophore aerobactin. This is a known food chain. In most cases the clinical identified in several different salmonella virulence factor for some enteric and presentation is that of mild to moderate serovars, including S. Agona, S. Albany urinary tract pathogens. A 30-year enteritis. The disease is usually self- and S. Paratyphi B variant Java, which is indicative of horizontal transfer of SGI- Figure 1 1. Such strains have caused infections in humans and cattle and there is speculation of a connection with ornamental fish originating in the Far East. Both resistance and multiple resistance in salmonellas in European countries are becoming increasingly prevalent and increasingly diverse. A five-year study of antimicrobial resistance in over 130,00 isolates of Salmonella from patients in ten European countries from 2000-2004 showed that resistance to nalidixic acid had increased from 14 to 20% over this period, and in S. Enteritidis, from 10 to 26% (Meakins et al., 2008). In Spain, the UK and Denmark emergent multi- resistant strains of S. enterica serotype [4,5,12:i:-] have been associated with a number of human infections since the mid-1990s (Guerra et al., 2000). In retrospective molecular study of this limiting and antimicrobial therapy is these strains resistance has been group of plasmids, from strains of S. seldom required. mediated by an unusual plasmid Typhimurium from several countries, For the last four decades the history containing resistance genes located has demonstrated that such plasmids of multiple resistance in Salmonella within a class 1 integron and also the have evolved through sequential enterica in the UK has been dominated spvA, spvB and spvC S. Typhimurium acquisition of integrons carrying by three major clones of S. plasmid virulence genes. CTX-M-9, -15 different arrays of antibiotic resistance Typhimurium, namely definitive phage and -17 to-18 enzymes have recently genes (Carattoli et al., 2001). types (DTs) 29, 204/204c/193 and 104 been identified in different serovars Nontyphoidal salmonellae with multiple (Figure 1). The most recent epidemic, of from humans in the UK (Batchelor et drug resistance have also become the multiresistant (MR) S. Typhimurium DT al., 2005) and plasmid-mediated CTX-M- most common cause of bacteremia in 104 (= MR DT 104) with resistance to like enzymes have been increasingly tropical Africa, particularly among ampicillin, chloramphenicol, reported in a range of serovars in food susceptible children and HIV-infected streptomycin/spectinomycin (SSp), production animals in several European adults. In a study in Malawi from 1999- sulphonamides and tetracyclines (= countries, notably S. Virchow in Spain, 2004 a total of 75% of the cases of ACSSpSuT), started in cattle in the UK Belgium and France (Carattoli 2009).

26 The use of third-generation cephalosporins in poultry has been suggested as major contributory factor references in this respect. A further recent development in the UK has been the ■ Batchelor, M., K. Hopkins, E. J. Threlfall, F. A. Clifton-Hadley, A. D. Stallwood, R. H. Davies, & Liebana, E. emergence of plasmid-mediated (20005). bla(CTX-M) genes in clinical Salmonella isolates recovered from humans in England and Wales from 1992 resistance to quinolone antimicrobials in to 2003. Antimicrobial Agents and Chemotherapy 49, pp1319-1322 several salmonella serovars, mediated by ■ Carattoli, A (2009). Resistance families in Enterobacteriaceae. Antimicrobial Agents and Chemotherapy, in press different qnr genes (Hopkins et al., ■ Carattoli, A., Villa, L., Pezzella, C., Bordi, E. & Visca P. (2001) Expanding drug resistance through integron acquisition by IncFI plasmids of Salmonella enterica Typhimurium. Emerging Infectious Diseases 7, pp444 - 447 2008). Of concern is the frequent ■ Chief Medical Officer (2009). Annual Report 2009: On the state of public health. Department of Health. association of plasmid-mediated Available at: www.dh.gov.uk/publications quinolone resistance with resistance to ■ Engberg, J., Aarestrup, F.M., Taylor, D.E., Gerner-Smidt, P. & Nachamkin I. (2001) Quinolone and macrolide third-generation cephalosporins in such resistance in Campylobacter jejuni and C. coli: resistance mechanisms and trends in human isolates. Emerging strains. To date plasmid-mediated Infectious Diseases 7, pp24-34 resistance to quinolone antibiotics in UK ■ Gordon, M.A., Graham, S.M., Walsh, A.L., Wilson, L, Phiri, A., Molyneux, E., Zijlstra, E.E., Heyderman, R.S., Hart, salmonella isolates has not been C.A., & Molyneux, M.E. (2008) Epidemics of invasive Salmonella enterica serovar enteritidis and S. enterica Serovar typhimurium infection associated with multidrug resistance among adults and children in Malawi. Clinical Infectious reported in isolates from food- Disease 46, pp963-969 production animals. ■ Guerra, B., Laconcha, I., Soto, S.M., Gonzalez-Hevia, M.A.,& Mendoza, M.C. (2000). Molecular characterisation Campylobacter is the most of emergent multiresistant Salmonella enterica serotype [4,5,12:i:-] organisms causing human salmonellosis. FEMS commonly isolated pathogen from cases Microbiology Letters 190, pp341-347 of food-poisoning, not only in the UK ■ Hopkins, K.L., Day, M. & Threlfall, E.J. (2008) Plasmid-mediated quinolone resistance in Salmonella enterica in the UK. Emerging Infectious Diseases 14, pp340-342 but also in many European countries. As ■ Meakins, S., Fisher, I.S.T., Berghold, C, Gerner-Smidt, P., Tschäpe, H., Cormican, M., Luzzi, I., Schneider, F., with salmonellosis, antibiotics are not Wannett, W., Coia, J., Echeita, A. & Threlfall E.J. (on behalf of Enter-net participants) (2008) Antimicrobial drug recommended for treatment of resistance in human non-typhoidal Salmonella isolates in Europe 2000-04: a report from the Enter-net international uncomplicated campylobacteriosis. surveillance network. Microbial Drug Resistance 14, pp31-35 Nevertheless, should treatment be ■ Parry, C. M. (2004). The treatment of multidrug-resistant and nalidixic acid-resistant typhoid fever in Vietnam. required, macrolide antibiotics such as Transactions of the Royal Society of Tropical Medicine and Hygiene 8, pp413-422. erythromycin, and fluoroquinolones are ■ Phan, M.D., Kidgell, C., Nair, S., Holt, K.E., Turner, A.K., Hinds, J., Butcher, P., Cooke, F.J., Thomson, N.R., Titball, R., Bhutta, Z. A., Hasan, R., Dougan, G. & Wain, J. (2009) Variation in Salmonella enterica serovar Typhi IncHI1 the drugs of choice. In this respect data plasmids during the global spread of resistant typhoid fever. Antimicrobial Agents and Chemo. 53, pp716-727 for human isolates of C. jejuni and C. ■ Threlfall, E.J.. (2000) Epidemic Salmonella typhimurium DT 104 – a truly international epidemic clone. Journal of coli from Denmark, the UK, the USA, Antimicrobial Chemotherapy 46, pp7-10 Italy, Finland, the Netherlands, France ■ Threlfall E,J., de Pinna, E., Day, M., Lawrence, J. & Jones J. (2008) Alternatives to ciprofloxacin use for enteric and Spain have demonstrated increases fever, United Kingdom. Emerging Infectious Diseases 14, pp860-861 in the incidence of resistance to ■ Wain, J., L. T. Diem Nga, C. Kidgell, K. James, S. Fortune, D. T. Song, T. Ali, O. Gaora, C. Parry, J. Parkhill, J., Farrar, N. J. White, & Dougan, G. (2003). Molecular analysis of incHI1 antimicrobial resistance plasmids from fluoroquinolones from <1% to between Salmonella serovar Typhi strains associated with typhoid fever. Antimicrobial Agents and Chemo. 47, pp2732-2739. 10% (UK) and 80% (Spain) in the 1990s and early 2000s (Enberg et al., 2001). More recent data from the UK generation cephalosporins and salmonella- or campylobacter-induced demonstrated an increase in the quinolones to the development of enteritis in humans, it may be argued incidence of fluoroquinolone-resistant resistance in a range of organisms, that drug resistance in such organisms isolates of C. jejuni from cases of including Salmonella. This has is of little consequence for public health. human infection from 10% in 1993-96 culminated in the recent report from the Nevertheless, antibiotics are used for the to 21% in 2003. As poultry is generally Chief Medical Officer (Chief Medical treatment of gastroenteritis in regarded as a primary reservoir for Officer, 2009), who has stated that in immunocompromised patients and Campylobacter, the use of addition to the substantive use of sometimes for treating particularly fluoroquinolones in this food animal was antibiotics in human medicine, vulnerable patients; in such cases considered an important contributory antibiotics are also used in large treatment with an appropriate antibiotic factor. quantities on animals, thereby adding to is often essential and may be life-saving. Over the last forty years many the threat of resistance. Following on In this respect the increased occurrence, outbreaks of infection in developed from this observation, he recommended both nationally and internationally, of countries, particularly those caused by that there should be a ban on the use of strains of S. enterica and such drug-resistant non-typhoidal certain types of antibiotics (quinolones Campylobacter with decreased salmonella strains, have been linked to and cephalosporins) in animals, in order susceptibility to fluoroquinolones and/or foods of animal origin. In turn this has to protect their activity in humans. resistance to third-generation led to speculation about the role of Whether such a ban can be implemented cephalosporins is an unwelcome antimicrobials in animals bred for food unilaterally for the UK is debatable, but development. in contributing to the development and the comments in the report do highlight spread of such strains. In recent years increasing concern about the use of there has been considerable speculation certain key therapeutic antimicrobials in John Threlfall about the contribution of the livestock. Health Protection Agency prophylactic use in food production As antibiotics are not recommended Colindale animals of antimicrobials such as third- for the treatment of mild to moderate

27 features

Art, Cybernetics and Normal Flora Microbiology

“Soil Flora” — Anna Dumitriu and Dr Simon Park All images © copyright Anna Dumitriu

acteria are dialogue between beautiful, I know myself, other artists, Bthat and you know philosophers, scientists, that, but the majority medics and workshop simply do not. People are participants or exhibition exposed to a daily barrage of visitors. adverts and newspaper warnings that In 2007 I undertook a project recommend no less than the total with cleaning staff and microbiologists at genocide of all bacteria (with the exception of the Eastbourne District General Hospital who so called ‘friendly’ ones of course). The term bacteria is collected samples of microbes from their own homes. They synonymous with dirt and the ‘normal’ reaction to the worked together with me in the hospital microbiology labs suggestion that something is covered with bacteria is one of (the microbiologists aiding the cleaning staff), and engaged in disgust or fear, rather than a matter-of-fact acceptance or the creation of new artworks, including a major sound work amazement. Through my work I am attempting to look at the for performance. Initially, people are clearly ashamed at any deeper importance of bacteria aesthetically, philosophically suggestion that their worlds are teeming with microscopic life. and scientifically. I am interested in the normal environmental Asking someone to reveal their normal flora is an intimate flora and I believe that the wider public need to be given the process of negotiation and education. But participation in the tools to appreciate the microbiological world. The public project usually leads to a paradigm shift for both participants would then be capable of making reasoned judgments about and audience from that of shame to one of understanding. what they read in the press. Perhaps this is where art can An important outcome of the project at Eastbourne hospital help. was a performance which involved one to one conversations The normal flora project is an ongoing art project through with people waiting in the hospital foyer and café. I invited which I am attempting to engage the public in developing a these people to crochet the microbes found on my own bed greater understanding of the microbial world. Many of the with me, whilst we chatted about their perceptions of normal artworks I have produced for this are developed flora microbiology. This crocheted piece has since been collaboratively and project participants take on the role of exhibited in a number of locations and is now larger than a artist, researcher and scientist in a hands-on way investigating double bed. The piece is being created collaboratively through their own eco-systems. The final outcomes emerge (taking the conversations with participants who are shown images of the form of digital works, sound works and installations) in a actual bacteria on my bed. These discussions lead to their

28 “School Flora – Swabbing for Normal Flora” — Anna Dumitriu interpretations being incorporated into the work, which grows microbes, plating them up, growing them and getting to know larger every time it is exhibited. them (my constant companions) is a performance, I am taking In 2008 I completed ‘School Flora’, which involved working on a role and attempting to embody that knowledge. closely with the science students at Varndean School in As well as collaborating with microbiologists Dr John Paul Brighton over a period of one year. Working with me (and (Royal Sussex County Hospital/University of Brighton) and Dr aided by the medical students I teach) the Varndean students Simon Park (University of Surrey), I am also artist in took swabs of microbes from around the school: from the residence/visiting research fellow in the Centre for drinking fountain to the books in the library. These samples Computational Neuroscience and Robotics at The University were then cultured and used as the basis for a series of new of Sussex. This is the heart of one of the largest Artificial Life artworks inspired by the microbes we found. This was research groups in the world. The primary concern of the developed collaboratively, between myself, the students and group is to understand what constitutes life so they can the science teaching staff in the school. The project went far attempt to model it or even recreate it through artificial life beyond a traditional school art project and stood as a major processes (these are generally computational but can include artwork in its own right. The art installations set out to reveal wet processes too). A central question for the group is: can the unobserved wonders of the microbial eco-system that life be considered as an abstract concept not linked to comprised the school, as well as dispelling myths and biological processes? Through my ongoing residency, I am misunderstandings. able to further research complex living systems, in particular I have strong views on the structure of art/science evolutionary and adaptive systems to which bacteria (as the collaborative practice and how I believe this should operate. ‘simplest’ living organisms) are strongly relevant. For me it is very important to undertake the practical work Modern Artificial Life research takes the ‘bottom up’ myself as much as possible, to understand the techniques and approach, to try and understand the simplest forms of life methodologies and for my collaborators to try to do the same before trying to understand more complex organisms. But of from an artistic point of view. I am aiming to assimilate as course even the simplest organism is highly complex, a much practical expertise as I can. I do not believe that it is complex system of intertwining feedback loops associated really possible to engage fully with scientific research without with an environment. These ideas stem from the field of coming from an informed position, so I need to experience Cybernetics, the interdisciplinary study of the structure of processes myself and I constantly strive to increase my complex systems, especially communication processes, knowledge and skills. For me, the process of swabbing for control mechanisms and feedback principles.

29 features

“Cybernetic Bacteria 1” — Anna Dumitriu and Dr Simon Park “Chair and Bed Flora” — Anna Dumitriu Behaviour of bacteria is clearly complex especially in terms reach out to wide, non-specialist audiences and communicate of their ability to act co-operatively and communicate. As ideas in news ways. Through this work thousands of people microbiologists, you recognise that bacteria are constantly have re-evaluated their understanding of the word bacteria sending messages to each other. This research has inspired and this looks set to continue as the project broadens to an ‘Cybernetic Bacteria’, an ongoing transdisciplinary international scale. investigation bringing together art, philosophy, computing and microbiology to investigate the relationship of bacterial communication with our own digital communications information networks. The project is looking specifically at ‘packet data’ and bacterial quorum sensing, to reflect the far greater level ■ If you would like to view Anna’s work she is currently exhibiting of complexity in communication taking place at a microscopic her newly commissioned work on bacterial communication at The level in comparison with human communication technologies Science Gallery in Dublin until Friday 17th July 2009 such as the Internet. The first artwork in the series involves a clear plastic tube of liquid agar jelly planted into the earth - allowing the soil bacteria below to grow upwards and become visible to the audience. 100 µL of Homoserine Lactone is added and the bacteria below pass this ‘message’ on to their neighbours. My performance was in many ways incredibly insignificant, I dropped a small quantity of hormone into a large tube of jelly, and it was all over in a few seconds. But for those few seconds I instigated an action with tiny but incredibly far-reaching effects. I interacted with the bacterial communications network of our planet, and I was connected. The next stage of the project involves a multiple screen artwork showing network traffic taking place in real time (web traffic, mobile technology and Bluetooth), a film of bacterial communication occurring (using Chromobacterium violaceum CV026) and an interactive visualisation of the data from both sources generated using artificial life technology (Cellular Automata). The next exciting chapter for my work will involve working alongside Dr Minna Mannisto (based at The Finnish Forestry Institute METLA), an Arctic Microbiologist investigating the complex ecosystems of the soil dwelling psychrophiles she works with and how they relate to our changing climate. These kinds of artworks can create a far greater understanding of the complexity and beauty of the “Bed Flora – TEM image” — Anna Dumitriu and Dr John Paul microbiological world and enable the wider public to have a much more balanced view when confronted with shocking reports in the news or when observing advertisements that are specifically designed to scare them. In fact the public have a Anna Dumitriu strong distrust of the media messages they are being given and relish the opportunity to investigate further. Art is able to

30 Outbreak! Engaging the public in infectious disease

hy were an unexpected life, describing the different ways in type virus from Africa to a small village collection of members of the which it is relevant to everybody’s lives in California. How would the Wgeneral public, scientists, every day: from infectious disease to governments deal with this deadly artists, musicians and families gathered food, brewing and the environment. We disease? Would they identify it, and in the Mammals Gallery of Manchester then heard some ideas from the more importantly, was there a cure? I Museum on a cold and wet Monday audience which were as diverse as the won’t tell you what happens in the end evening in March? Surrounded by audience’s backgrounds, ranging from, in case you’ve not seen the film yourself, mammals of all shapes, sizes and ‘making microbiology sexy’ to but rest assured there wasn’t a single species (of particular relevance was a ‘demonstrations of how microbes can be person who wasn’t gripped until the display of our primate ancestors) and used in the home’ — e.g. in home- end. under the watchful eye (well, eye brewing and baking. After a quick stretch, Jo continued a socket) of the skeleton of a whale These were all great ideas, but would stimulating and informed discussion, suspended from the ceiling, we were their thoughts about microbiology (and drawing ideas from the audience who gathered together to watch the film therefore their ideas) be stimulated by had definitely been inspired through ‘Outbreak’ and to find out what non- watching the film? Well, after a few watching the film. Everyone was full of scientist members of the public want to more munchies, we sat and watched ideas and questions about how know about microbiology. We were attentively for the entire duration, microbiology does or could impact on taking steps to finding out the answers through the spread of a novel Ebola- their lives and how SfAM can continue to the following questions: Why does to engage the public in applied microbiology matter? Why would any microbiology — so much so that we non-scientist want to know about almost stayed beyond our welcome. microbiology? But most importantly, After a thought provoking evening, what can SfAM do to educate, inform the ideas continue to flood in to the and entertain the masses on this Manchester Beacon of Public fascinating subject? Engagement who were instrumental in The evening began with some light organising the event. I would like to refreshment to stop tummies rumbling thank Sam and Erinma in particular. If during the film and to provide some you have spoken to your non-scientist ‘brain food’ for the participants who had aunt or uncle, mum or dad, brother or previously been armed with postcards sister about microbiology, then you may and pens so they could jot down any have some ideas about ways in which ideas that sprang to mind. After a bite, SfAM can help to make microbiology we sat beneath the elegant arches of the more accessible, and engage the public Gallery and listened to Professor Joanna in applied microbiology. If so, let us Verran of Manchester Metropolitan know — and watch this space to find University expertly facilitate a out how you can get involved. discussion about what microbiology is and how it affects us. We listened Lucy Harper intently as Jo brought microbiology to

31 features

Historical Perspectives: Charles Darwin and microbes

The fact that Charles Darwin took an interest in the developing science of microbiology is hardly ever mentioned in biographies about his life and work. Here, Milton Wainwright explains how Darwin’s letters show that he was interested in microbes, even to the point of wondering if his long-suffering stomach problem was caused by a microbial infection

LEFT: Charles Darwin’s study at Down House, near London

ince the biographies, and other but also sought a microbial explanation the recent controversy over so-called accounts of Charles Darwin’s work, for the unpleasant stomach disease red rain. Red rains have long been Smake few, if any, reference to which plagued him throughout most his observed falling all over the world. They microbes, I have always assumed that life. can of course be made up of dust, like Darwin took no interest in microbiology. those which occasionally reach the UK However, this always seemed unlikely, Darwin and algae from the Sahara. However, of interest to especially since the publication of On The first interaction between Darwin us is the fact that they are often the Origin of Species in 1859 coincided and microorganisms comes about while, microbial in nature. The recent red rain with a period which saw major as a young naturalist, he voyaged on the event of Kerala in Southern India developments in our understanding of Beagle. While on board, he became provides a good example. Wrongly the nature and role of ‘germs’. Darwin interested in some red “dust” which attributed by many to dust, or even was interested in all aspects of natural occasionally coated the ship. In his more exotically, bat blood, these rains history so it would have been strange book, Voyages of the Beagle he notes are full of single cell organisms, having had he totally ignored this growing that he sent the German microscopist an algae-like morphology. It has been science. When I came to do a search of and microbial taxonomist, Professor suggested that these recent red rain Darwin’s letters I soon found that Christian Ehrenberg five packets of cells have highly unusual properties and Darwin did, in fact, take a keen interest “dust”. Ehrenberg, an unjustly neglected may be of extraterrestrial origin; but a in the burgeoning science of pioneer of microbiology, did much to more prosaic explanation is that they microbiology, including the more applied establish a framework for classifying were picked up from the oceans in some aspects of the subject such as the animalcules. On examining Darwin’s kind of vortex and then deposited over control of potato blight. This interest samples, he found that that “the dust southern India. While on the Beagle, lead him to interact with some of the consists in great part of infusoria with Darwin also observed more common lesser known (pre-Pasteur) originators siliceous shields”. Ehrenberg went on to algae which he collected near Keeling of the germ theory and their work in identify sixty seven different species Atoll, in the Indian Ocean. These he addition to some of the better known which; with the exception of two marine described as little masses of confervae, pioneers such as Robert Koch and species, these proved to be fresh water a few inches square, which consisted of Eduard Klein. As we shall see, Darwin species. small algae. His interest in algae is also not only took an interest in the Darwin’s observations on red “dust” illustrated by a letter he wrote to Joseph possibility that microbes cause disease have a modern resonance in relation to Hooker on the 28th April, 1845 when he

32 ▲ John Tyndall the physicist and mathematician who took an interest in spontaneous generation ▲

Sir John Goodsir, early pioneer of microbiology who examined Darwin’s samples for infectious microbes

33 features

mentioned that he was returning some a Swedish anti-vivisection activist. In his a dilapidated mansion in the Quantock specimens and drawings of Confervae. letter, Darwin explained that he had Hills in Somerset, was referred to as always been against experiments which “the thunder and lightning man” and Darwin’s interest in potato caused suffering to animals, but he was locally reviled as an atheist; he also disease nevertheless emphasised that probably acted as the model for Mary Darwin’s interest in research on the improvements in medicine could only be Shelley’s, Frankenstein. cause of potato disease provides an achieved by the use of regulated As early as 1866, Darwin entered the example of his keen interest in the vivisection. argument over the continued occurrence practical application of biology to of spontaneous generation by stating (in human affairs. Between February 1876 Darwin and Joseph Lister a letter to J.V. Carus, 21st Nov, 1866) and March 1882, Darwin exchanged Joseph Lister is well known as the that “As for myself I cannot believe in some 93 letters with a certain James surgeon usually credited with having spontaneous generation.” During the Torbitt concerning support for one of introduced antiseptic surgery into 1870s, Darwin also corresponded with Torbitt’s commercial projects, namely medicine. Lister mainly used carbolic John Tyndall who was working on the the development and distribution of acid to disinfect wounds, but he was spontaneous generation controversy. In potato plants resistant to the light blight always on the look out for better, less his experiments, Tyndall set up a large caused by the fungus Phytopthora caustic, alternatives. It is interesting to number of open tubes containing infestans. This was the cause of the note then that in a letter dated 7th Oct, extracts of vegetables and somewhat repeated crop failures in the UK, 1878, Darwin suggests that “benzoic exotic meats, like venison and pheasant. Europe, and of course Ireland, during acid would be a deadly poison to These, he showed, soon became the nineteenth century. Torbitt was an bacteria and their allies.” He also contaminated with airborne bacteria and enterprising grocer and wine merchant expresses surprise to Lister that he is fungi. In this way, Tyndall demonstrated from Belfast. His project required considering the use of borax as a what was referred to by Victorian selecting the small number of plants that disinfectant, as Darwin claims that scientists as “panspermia”, that is the survived in a field infested with the borax has no effect on the growth of ability of microbes to live in the air from blight fungus and using these to produce Drosera (i.e. the Sundew), although it where they contaminate organic-rich new seed which would hopefully apparently was readily killed by extracts and also, by extension, infect produce blight-resistant plants. Darwin phosphoric acid. Presumably Darwin’s humans and animals (the word also lobbied civil servants on Torbitt’s claim that benzoic acid would kill panspermia is used today to refer to the behalf in order to secure funding for this bacteria was similarly based on transfer of life between planets). Tyndall important work and also provided some experiments using Drosera, rather than also observed numerous examples of funds of his own. bacteria themselves. Indeed I can find microbial antagonism, and in particular, no evidence that Darwin ever actually the ability of fungi to kill bacteria; Darwin’s interest in the worked on the isolation and growth of unfortunately however, he missed the development of microbiology bacteria. opportunity to translate these Darwin obviously took an interest in observations into the discovery of the major developments which were Darwin and spontaneous antibiotics. taking place in microbiology from the generation Tyndall sent Darwin one of his 1860s onwards. In April of 1862, Henry Unlike that other British Victorian unopened tubes which Darwin left Holland wrote to Darwin to recommend champion of transmutation (or exposed to the air. In a letter dated 20th Pasteur’s memoir on the subject. evolution), Robert Chambers, Darwin October 1875, Darwin related the news Holland was one of Queen Victoria’s did not speculate on the origin of life, to Tyndall that “the tube of boiled doctors and a leading expert on fresh other than to suggest it might have infusion, dated October the 16th, was water, microscopic algae. In later life, he formed in a “warm little pond”, an idea clear on the 19th, but on the 20th it claimed that he had beaten Robert Koch he probably got from his grandfather, was muddy and contained bacteria to the recognition that cholera is caused Erasmus Darwin. Chambers, the author in living movement”. Tyndall sent by bacteria. In a letter, dated 24th July, of the much reviled, but influential book tubes of broth to various people asking 1874, Eduard Klein provided Darwin on transmutation, The Vestiges of the them to expose them to the air in their with details of the smallest micrococci Natural History of Creation claimed locale; the recipients included, amongst which can be distinctly seen under the that life could arise spontaneously at others, Darwin, Mr Francis Darwin microscope. Three years later (1st any time. He based this belief on what (Darwin’s son) at High Elms, Sir John January,1877), Darwin’s interest in seemed like good science at the time Lubbock and Joseph Hooker. Every one bacteria was shown to continue when he based on the findings of Andrew Crosse of these tubes were reported to be received, from Ferdinand Cohn, details and W. H. Weekes. Crosse claimed that contaminated, no matter where in the of Koch’s work on bacteria including he could create life (so-called acari) by country they were exposed, thus giving some of the first microscope passing a low current of electricity Tyndall the proof of his idea that photographs of these organisms. through solutions containing silica; airborne microbes were to be found Finally, as late as April 14th 1881, Weeks verified this experiment and everywhere. Darwin wrote to Frithiof Holmgren Chambers used their work in his theory On the 1st of February, 1871, Darwin expressing interest in Pasteur’s work on of evolution with the idea that life wrote a letter to Hooker again the modification of “the germs of the originally arose spontaneously and expressing his interest in the most malignant disease”. Holmgren was continues to do so. Crosse, who lived in experiments that were then ongoing on

34 spontaneous generation, when he found nothing. The full letter, from Charlton Bastian who, even as late as mentioned B.T Lownes’ observations Goodsir to Darwin, dated August 21st, the early years of the twentieth century, that boiling does not kill certain moulds. 1863 reads as follows: claimed he could generate microbes de This he thought was curious because it “I will most certainly examine a novo in the test tube. flew in the face of Pasteur’s slide or a small quantity of fluid with experiments. Pasteur claimed that his flocculent and tenacious matter sent Conclusions boiled broth remained sterile and would in a tube or small phial. The As we have seen, Darwin took a keen do so indefinitely, yet Lownes could not spherical bodies are probably the eels interest in many aspects of microbiology repeat this. Five years later, Darwin of Torula and spores of Penicillium. If including a personal interest in the again took an interest in the Sarcina be present it will be at once possible role of Sarcina as a cause of spontaneous generation controversy detected by its square form and his stomach problems. Despite this (4th Feb, 1876) when he informed John peculiar segmentation. Sarcina and however, there is no evidence that Tyndall that he was happy that he was Torula often occur together. Mr Darwin ever used the new techniques not giving up his research into the (William) Jenner prescribes that were being developed to isolate and problem. He suggested that the issue hydrosulphite of soda. Your medical grow bacteria and moulds. As a would never be resolved until someone advisor may try creosote. One drop naturalist he had a keen interest in explained how John Burdon Sanderson taken at bedtime and afterwards, two algae, and doubtless used his simple and others “succeed in getting drops in the forenoon and two at microscope to observe protozoa. bacteria in infusions boiled for a long bedtime.” Perhaps he felt that the development of time”. Burdon Sanderson, by the way, We a can infer from this that Darwin the new science of microbiology, which was one of Britain’s leading exponents used his own microscope to examine the needed practice in the use of some of the new science of microbiology and sample before he sent it to Goodsir. unusual techniques, was best left to although he was totally convinced of the younger scientists. As we have seen merits of spontaneous generation, his Darwin’s interest in however, this did not prevent him from experiments for a while at least tended extremophiles taking a keen interest in the to give credence to the possibility that During the late Victorian period the development of the new science of life can arise de novo. Reverend William Henry Dallinger (often microbiology, especially of course where collaborating with John Drysdale) did it impinged on anything to do with Did Darwin suffer from a bacterial some studies on the ability of bacteria to selection and evolution. infection? withstand extremes of heat and cold. It is a well known that after voyaging Like many naturalists of the period, on the Beagle, Darwin suffered Dallinger was a man of the cloth, in this further reading throughout his life from a debilitating case a Wesleyan. His work involved stomach complaint and many theories showing how bacterial resistance to ■ Charles Darwin’s letters can be accessed have been suggested to provide a post extremes of temperature could be by searching Google for “Darwin hoc diagnose of his illness, most of achieved by “training” them to grow at Correspondence”; unfortunately, most of which centre around the possibility that high and low temperatures. Darwin the letters used here are not yet available Darwin suffered from Chagas’ disease. would obviously have taken an interest in full. In the early 1860s, Darwin sought the in this work because it showed that ■ Torbitt’s work on potato blight: Dearce, advice of one of the leading medical organisms are able to adapt to their M. (2008). Correspondence of Charles practitioners of the day, Sir John environment. Dallinger concluded that Darwin on James Torbitt’s project to breed Goodsir. As early as 1842, Goodsir had his experiments demonstrated the blight-resistant potatoes. Archives of shown that animalcules could be inheritance of acquired characteristics Natural History 35, pp208-222. obtained from the vomit of people and argued with Weismann on this point ■ William Dallinger’s work: Haas, J.W. suffering from gastric illness. He named (letter, July 2nd, 1878). In his letter, (2000). The Reverend Dr William Henry the organism Sarcina goodsir and went Darwin states that he has no doubt that Dallinger, Notes and Records of the Royal on to suggest that it causes stomach Dallinger’s experiments on mutation of Society of London, 54, pp53-65. disease. He also claimed that that the lower organism under changed ■ John Tyndall’s work on microbial organism be eradicated, and the patient conditions of life will be curious and antagonism: Wainwright, M. (1985). Re- cured using hyposulphites. He therefore valuable. He goes on to say that “the examination of John Tyndall’s studies on was arguably the first to demonstrate fact of their being accustomed to microbial antagonism. Transactions of the the presence of a microbe in an internal higher temperatures than to those British Mycological Society 85, pp562-569. infection, suggest it caused the disease which they are adapted is very ■ Sir John Goodsir’s work on Sarcina: in question and then provide a cure, this remarkable and explains existence of Wainwright, M. (2003). An alternative some thirty years before Pasteur took an algae in hot springs”. A year earlier history of microbiology. Advances in interest in microorganisms. A great deal Darwin wrote to Hooker (Jan 25th Applied Microbiology 52, pp333-356. was known about Sarcina ventriculi, 1877) expressing an interest in the as it became known, by the 1860s when ability of bacteria to resist the cold. Like Milton Wainwright Darwin sent Goodsir a sample of his most other scientists of his day, Department of Molecular vomit for analysis. Goodsir tested Dallinger conducted experiments on Biology and Biotechnology, Darwin’s sample for Sarcina, but no spontaneous generation and became, University of Sheffield, UK doubt to Darwin’s disappointment, not surprisingly, an opponent of Henry

35 features

In the seventeenth of a series of articles about statistics for biologists, Anthony Hilton & Richard Armstrong discuss: Using a regression line for prediction and calibration Stat Note 17 n Statnote 16 (Hilton & Armstrong, 2009), the use of based colony counting technique. In these circumstances a regression methods to analyse the relationship between two researcher may employ direct counting techniques using Ivariables X and Y was described. How to fit a regression microscopy and a haemocytometer slide, for example, or line to data by the method of least squares was discussed, as more frequently use measurements of OD of the culture broth well as the methods of testing the goodness of fit of the line as a prediction of cell number. In this latter situation, a to the points. Another use of a regression analysis is to use calibration graph must first be derived to reveal the the line to predict a value of Y from a reading of X, e.g., to relationship between the cfu per ml of culture broth for a predict bacterial cell number from optical density (OD) given bacterium and the corresponding OD usually measured readings. This aspect of regression studies is also called at 600nm. When correlation data is used in this way to make ‘calibration’, i.e., estimating a quantity that may be difficult to predictions of one parameter from measurements of another, measure from a variable that may be much easier to measure. it is important to be aware of the limitations in accuracy of This Statnote describes the various predictions that can be such predictions. made using a regression line and discusses their limitations. Scenario Theory A 10ml volume of sterile nutrient broth was inoculated There are two types of prediction problems that can be with a culture of Staphylococcus aureus and incubated at solved using a regression line and it is important to 37°C for 24 hours. Following incubation the culture was understand the difference between them. First, there is the serially diluted down to 10-9 by mixing 1ml of culture with prediction of the population regression line µ at the point x. 9ml of fresh nutrient broth in a sterile Universal tube. From Hence, we may wish to make inferences about the height of each of the tubes within the prepared dilution series, 1ml of the population regression line at the point X, i.e., the culture media was transferred into a disposable plastic average value of Y associated with a value of x. Second, cuvette and the OD measured at 600nm using a standard there is prediction of an individual new member of the spectrophotometer which had been previously blanked

population y1 for which x1 has been measured. The second against a cuvette containing uninoculated nutrient broth. In a problem is probably the most commonly encountered and is similar manner, from each of the tubes within the first most relevant to calibration studies. In both of these dilution series, further serial dilutions in sterile nutrient broth prediction problems, however, the predicted value of Y is were prepared as required and 0.1ml of this second dilution actually the same but the standard errors (SE) of the two series inoculated onto the surface of a nutrient agar plate. estimates will be different because in the first instance, a The inoculum was spread across the surface of the agar using population value or mean is being estimated while in the a sterile spreader and the plates incubated at 37°C for 24 second, an individual value is being estimated. Formulae for hours. Following incubation the cfu ml-1 in each of the tubes the calculation of the different SE corresponding to these two within the first dilution series was calculated by counting the prediction problems are given by Snedecor & Cochran colonies at an appropriate dilution. The data were collated (1980). In most cases, significantly greater errors will result and are presented graphically in Figure 1 by plotting the cfu -1 when estimating an individual rather than a population value. ml on the x-axis against the corresponding OD600 measurement on the y-axis. Background In some experimental protocols it is necessary to estimate Fitting the regression line the number of bacterial cells present in a culture broth where The first stage in a calibration study is to fit a regression time limitations may prevent the use of a standard culture- line to the data using the method of least squares as

36 where Y* is the mean of the Y values and b the slope of the Figure 1. Regression of bacterial cell numbers (Y) on OD (X) line. Hence, if OD = 1.1 then estimated Y is 3.28885 x 109 (r2 = 98%, F = 398.04 (P < 0.001),‘t’ = 19.95 (P < 0.001). The (+95% confidence limits = 3.59498 x 109; -95% confidence two sets of confidence bands represent confidence intervals limits = 2.982719 x 109). for the population regression line (red) and for making individual predictions of y for a new value x (blue). Interpretation There are a number of problems that need to be considered when using a regression line for calibration. First, the confidence bands are parabolic in shape and have curved borders that may widen significantly at the limits of the data especially if the line is a relatively poor fit. Hence, estimates of y can have large errors at the limits of the data. As discussed in statnote 16, there is no established ‘cut-off’ in r2 below which the line would be regarded as a poor fit for calibration purposes. As the value of r2 decreases, however, the confidence bands widen and predictions of y become increasingly inaccurate. A regression line is likely to be most useful for calibration if the range of values of the X variable is large, if there is a good representation of the x,y values across the range of X, and if several estimates of y are made at each x. Second, a regression line is sometimes used several times in the course of an investigation to predict a number of new values. In this circumstance, the probability that all of the confidence intervals include the correct value of Y will be described in Statnote 16 (Hilton & Armstrong, 2009). To less than P = 0.95 and a correction of the P values may be estimate bacterial cell numbers from OD requires the fitting necessary using Bonferroni’s inequalities (Snedecor & of the regression of bacterial numbers (Y) on OD (X) and this Cochran, 1980). Third, y may have been measured at several line (Figure 1) has the equation: fixed values of x but the intention may be to predict x from y and this prediction must be made from the regression of Y on Y = -1.333 x 109 + 3.111 x 109X (1) X. This is a significantly more complex calculation and the All the usual ‘goodness of fit’ tests (see Statnote 16, Hilton method together with the appropriate SE is described in & Armstrong, 2009) suggest that the line is a good fit to the Snedecor & Cochran (1980). data. Hence, r2 = 0.98, i.e., 98% of the variance in bacterial The relationship between two variables may have been numbers is accounted for by OD, the value of F = 398.0, studied at various times or in different laboratories giving rise suggests a highly significant line is present (P < 0.001) and to two or more estimates of the relationship between Y and X. the ‘t’ test of the slope of the line gave a value of t = 19.95, In these circumstances, it may be of interest to discover which suggests the line has a highly significant slope (P < whether the various regression lines are the same. If they are, 0.001). All of these tests provide confidence that the an investigator may wish to combine the data from different regression line is a good fit to the data and therefore is studies and fit a single regression line to the whole of the suitable for calibration. data. This application of regression studies involves comparing two or more regression lines and will be discussed Confidence intervals for a regression line in the next Statnote. Two sets of 95% confidence intervals have been fitted to the regression line in Figure 1. The inner confidence bands (in red) are the confidence limits for predictions of the population regression line and hence, we would be 95% references confident that the average value of Y for any x would lie ■ Hilton A & Armstrong RA (2009) Statnote 16: Fitting a regression line to within these boundaries. The outer confidence intervals (in data. Microbiologist Vol. 10 No. 1, pp40-42. blue) are those for predicting an individual y corresponding ■ Snedecor GW & Cochran WG (1980) Statistical methods, 7th Ed. Iowa to a value of x. It is important not to confuse the two types of State University Press, Ames Iowa. prediction problem. If, for example, the regression of weight on height was plotted for a sample of 20 year-old men (Snedecor & Cochran, 1980), the purpose might be to predict the average weight of such men at a specific height (inner confidence bands) or the individual weight of a new male Anthony Hilton whose height was known (outer confidence bands). As mentioned earlier, the two estimates are the same, but the SE Dr Anthony1 Hilton and Dr Richard and therefore the confidence bands are different. Armstrong2 Using Figure 1 for prediction and calibration, the predicted 1Biology & Biomedical Sciences and 2Vision value of y for a new value x is: Sciences, Aston University, Birmingham, UK

y = Y* + bx (2) Armstrong Richard

37 members

careers

Sales Manager David Warering explains how he has used his life experience to help him on the road to his current career

here do you see yourself in team who serve our customers with the oocysts in swimming pool water as well five years time? This is a latest technology to suit their needs. as working in a global business that has Wtypical interview question and How did I get here? Well, to answer a significant interest in detection must appear in numerous guides to this question I must start at the methods for Cryptosporidium and interview technique. My answer to this beginning of a strange and winding Giardia in drinking water. question is that in fact I have no idea, road. My family has been associated During the summer break between but I don’t necessarily think this is a bad with farming for as long as I can school and college I worked on a thing. It gives me the opportunity to be remember. Many of my father’s family chicken farm collecting eggs and anywhere and allows me the freedom to are farmers and almost all of my assisting with general farm duties. This accept or reject opportunities that come siblings have, at one time or another, was quite a disgusting job for many my way in the coming months and delivered unpasteurised milk from door reasons but good preparation for my years. Something I’ve learned about to door for a businessman that was a later career as Head of the Enteric career decisions is that one has to be close friend of the family. Many years Microbiology Laboratory at the Public able to recognise opportunities for later I found myself incorporating a Health Laboratory in Preston analysing learning and value and draw upon all life hypothesis on population genetics of 15,000 human faecal samples per year. experiences. I am out of my comfort host association between Chickens defecate a lot and in such zone most of the time, and that is a Campylobacter jejuni Sequence type cramped conditions it is easy to great place from which to learn. 61 and cattle, with a major vector being understand the rapid spread of One year ago I would not have seen the consumption of unpasteurised milk. Salmonella enteritidis phage type 4, myself in my current role as European I have no doubt that my knowledge of which was the scourge of the poultry Sales Manager specialising in milking parlour practice and doorstep industry in the 1980s and 90s (for Transplantation Diagnostics for the delivery had some influence in my younger readers look up “Edwina Curry biotechnology giant, Life technologies. confidence to propose such a and eggs” for the start of a national Way back then, which seems like a hypothesis, not to mention the scandal and listen to Professor Tom lifetime ago, I was Business confirmed hypothesis that birds pecking Humphrey for more details). Later, as a Development manager for Europe and at foil capped milk bottles could also be Clinical Scientist I was developing rapid Asia Pacific Regions working for a vector for transmission of screening methods for Salmonella Invitrogen’s Environmental Diagnostics Campylobacter jejuni. outbreak investigations. Division, a rather grand title for my Whilst at school I had a job of Three of my family were in the team of one, but nonetheless an assisting with the cleaning of the school armed forces and there was a critical important role with a large revenue swimming pool. This offered me free point at the age of 17 when, after a target and a complex multi-cultural swimming at lunchtimes but also long process I was offered a place in responsibility. Now I am back working provided the opportunity to learn about the RAF as an engineering apprentice. I in the business of Clinical Diagnostics, chlorination and filtration in swimming decided not to accept this offer as I was which is where I started my science pool hygiene. Later in life I found no good at Maths so I am sure this career and I’m loving every minute of myself in an R&D role developing a would have been a bad move, but my the challenge. I am a Sales Manager by protocol to use immunomagnetic main reason for this choice was that title, but really I am a mentor to my separation to detect Cryptosporidium back at college I was in the first XI at

38 football and had half the number of by MAST diagnostics. This was my first President Arthur Gilmour if I would lessons that were timetabled at school. attempt at product development, an consider the opportunity of becoming Several months later, bored by college, I experience and skill set which I was editor of SfAM News (the forerunner of answered an advert for a Junior grateful for when I moved out of the Microbiologist). With no idea what it Laboratory Technician at the local public science arena and into a entailed but with an interest to learn hospital and my career in science began commercial biotechnology company as more, I said confidently — “Yes, why in earnest. Research and Product Development not”. I immediately had a deadline to I had a broad education in pathology manager. produce the next issue. I signed up for sciences — haematology, blood At the pinnacle of my public science a distance learning course in editing transfusion, biochemistry, career I was most fortunate to work manuscripts and with virtual carte histopathology and microbiology, and at with Professor Andrew Fox. Our work blanche to create a new feel for the the next decision point I decided to together during my PhD studies on magazine, I set about learning the specialise in microbiology. On my first epidemiology of zoonotic transmission process of soliciting content, writing day (and, also, by coincidence, my last of Campylobacter led to collaborative editorials, agreeing layouts with the day) in the microbiology department at research with Professor Martin Maiden designer and editing final copy. I learnt Preston, I worked on the fæces bench in and colleagues at Oxford University so much about the publication process the Preston Public Health Laboratory — (the only chance I would ever get to go that I can now interact with marketing part of the PHLS network of 53 labs at to Oxford!), on the first large scale colleagues to produce a captivating that time. On the first day I was a junior multi-locus sequence analysis studies of marketing flyer, technical note or and on the last day I was Team Leader. well defined sets of isolates. This brochure for a new product. I played soccer for the lab team and provided fascinating insights into the In your career, you have to recognise after three successive years of likely ecology and host associations your strengths and play to them. I don’t comprehensive defeats and relegation, with this enigmatic pathogen. We wrote consider myself a good scientist, writer the team resigned from the competitive a grant application to the Food or salesperson but I do think I am a league and moved to play friendly Standards Agency for funding to good mentor. I have also learnt matches only. At this time I was quite elaborate on these hypotheses and sufficient technical skills in many areas handy at football and I assumed the role investigate seasonal trends in strain of science and business to be able to of player manager for the team. I specific ecology and epidemiology. This apply my teaching and mentoring skills carefully selected the opposition and application was one of the first major to best effect. My good friend and months later we were winning matches. business case proposals that I had colleague Dr Andrew Sails is a great The point of this anecdote is to worked on and allowed me to develop scientist and is far better than I could illustrate that in a different context I skills in value proposition, budgeting, ever be, because he is a scholar. I learnt was able to shout orders at more senior setting goals and milestones which are from him how a real science scholar members of laboratory staff and crucial in any successful business works with a real passion for scientific demonstrate my leadership skills in an enterprise. understanding, but I think I taught him environment outside the laboratory. I do My name appears on over 40 a thing or two about how to manage in believe that this was influential in publications but I won’t claim credit for science and to manage people. showing some of those who later more than two first author papers. My My work is very varied now. I spend became my mentors that I had forte is not technical writing but prose time coaching sales people, researching leadership qualities that they may not and I have an eye for detail that is for new market opportunities, writing have had the opportunity to see quite so better suited to editing. I learnt a lot business cases, planning strategy and clearly in the workplace. from a single publication working with negotiating. I have found that in life you In my first senior and management the eminent Professor Martin Skirrow. I always have the opportunity to learn, position and I was fortunate to have the could not believe my luck to be invited you just have to recognise what you are opportunity to setup the to attend an SfAM workshop in Reading learning and use that knowledge for self Campylobacter Reference Unit at in 1992 with Eric Bolton, David improvement. I have been fortunate Preston. On the back of Dr Sameeh Hutchinson and Martin Skirrow. The enough to work with many very talented Salama’s PhD studies with Professor proceedings were published in The people, some of them scientists, some Eric Bolton, we had the opportunity to Technical Series Manual No 29. managers and some just interesting use a new Phage typing scheme for Working on this manuscript with Martin people who can teach you a thing or Campylobacter jejuni in conjunction Skirrow was painstaking. His perfect two. with the exisiting biotyping scheme use of the English language was What will I be doing in five years developed by Eric Bolton. During this enlightening and his eye for the finest time? I have no idea but I am training tenure we attempted to put together a grammatical detail and his patience and for my next job right now and every day. resistotyping scheme based on filter mentoring through the multitude of paper discs impregnated with various draft versions was a valuable learning antimicrobials and a trio of experience for me and a formative discriminatory pre-formed enzymes experience. At my second SfAM tests which were dehydrated for committee meeting and as a newly David Wareing stability. We performed a six lab ring elected member I happened to look up trial with reasonable success and the at the opportune moment of the product was eventually manufactured proceedings and was asked by

39 members

he Science Learning Centre North East has been engaging teachers Tand their pupils with their An unwanted Christmas lecture series for four years. These are demonstration-packed, fun- filled science events for young people targeted at Year 6/7 pupils from local guest for schools. They take place in industry venues spread across the North East region to provide an opportunity for school dinner children to visit an industrial environment, sometimes for the first time, whilst participating in some Public engagement / innovative project grant report exciting science demonstrations. The theme of the lectures changes every year and previous events have involved TV personalities such as Jonathan Hare from BBC TV’s Rough Science and Ian Dunne, the science presenter. This year I was approached to deliver a lecture series in microbiology entitled An unwanted guest for dinner which focused on food hygiene and safety. The lecture was loosely structured around the ‘4 Cs’ principles of food safety (Cooking, Cleaning, Chilling and Cross-contamination) adopted by the Food Standards Agency and linked in with the ‘Germwatch’ media campaign. The one-hour lecture session was filled with opportunities for the students to undertake mini-experiments and get involved with demonstrations. The session began by introducing bacteria, particularly their small size, and using a Smartie placed in the palm of the children’s hand as a reference they were asked how big their hand would need to grow in order to make a bacterium as big as the Smartie: answers ranged in size from a big as a cat to planet earth. This was followed by the classic demonstration of bacteria isolated from the mouth of a willing volunteer as pioneered by Anton van Leuwenhoek and revealed by a microscope eyepiece video camera attached to an AV projector. If you ever forget why you became a microbiologist you just need look at the wonderment on a child’s face when they see for the first time bacteria scurrying over a microscope slide. The importance of storing chilled food correctly was presented to the students followed by an interactive session using a laser thermometer to probe the temperature of a fridge and a selection of chilled foods. In addition, there was an activity loading a fridge with different food groups to demonstrate the importance of

40 Teachers from the schools whose children saw the lectures had some great things to say:

“It was a very enjoyable afternoon for all of our children and adults as well! I am sure that both schools got a lot out of the hour — our Head was very impressed! We did not expect the goodie-bags but they were much appreciated by all. The pictures that I took will be placed on the web-site that I am developing for preventing raw to ready-to-eat food an experience they would not forget in a school. contamination using that essential hurry. Over the eight lecture sessions Thank you once more for an excellent comedy prop, a rubber chicken! The approximately 800 pupils attended. afternoon” lecture continued with more information I’d like to thank SfAM for their on cooking and with an interactive quiz support of this lecture series through for students to decide on whether the innovative project / public Robin Carr certain meat they were shown was engagement grant, without which it cooked properly. would not have been possible to provide Cleaning, particularly hand hygiene, all the hands-on interactive sessions “Today I took my class to… listen to was demonstrated using the ‘Glitterbug’ which are so important in maintaining the Christmas Lecture by Dr Anthony disclosing cream and UV illumination engagement with younger students. This and a chopping board was sampled type of activity is invaluable, not only Hilton ‘Grime Investigation’ — just using ATP bioluminescence to determine because it increases the visibility of the thought I’d let you know they found if it had been cleaned properly after use. Society with industry, the public, For each activity a student volunteer was students and their teachers; it inspires it very interesting, loved the venue requested (for which there was no our future generation of microbiologists, and the goody bag! They were very shortage) and the reward of a giant inspires achievement and provides enthusiastic — great to see children microbe to take home made sure it was aspirational role models for children. enjoying science. The talk was really pitched at the right level for Year 6 to 7 children and Dr Hilton did a graeat job. Many Thanks”

Pauline Taylor

Dr Anthony C Hilton University of Aston

41 members

Virtual networking

and a research blog. To find other researchers who share common interests you simply search by keywords and then get connected by either sending a message or creating a research link. You can also create and join groups to share ideas and discuss particular methods/subjects etc. These groups are also another great way to find researchers with similar interests. General News from the SfAM Post-Graduate forums are available covering a variety of and Early-Career Scientist Committee topics including supervisor relations, surviving your viva, writing your thesis and postgraduate jobs. These are excellent sources of advice and support Networking with fellow researchers and cover all aspects of a research outside your department and institution degree. The conference diary facility PECS NEWS is an integral part of the research allows you to add and search upcoming process. From an academic perspective it conferences, save them into your diary PECS recently held committee can promote collaboration, generate new and see who else within the community elections and we would like to ideas and prevent duplication of effort is also planning to attend. welcome our newly appointed (Graduate Junction, 2008). On a personal In addition to networking facilities, committee members, Katie Fisher level it develops communication skills Graduate Junction also provides listings (events officer), Andrew Hall and confidence and gets you talking of graduate journals. These are online (webmaster), Jo Heaton and James about your own research. Generally we open access journals which are ideal Collins (events team). network face to face, at conferences, publications for postgraduates to The summer conference is fast meetings, training workshops and disseminate their research to the wider approaching; join us at the PECS seminars. However, since the conception scientific community. One graduate student session which this year of chat rooms and social networking journal listed is Kaleidoscope, the focuses on practical networking skills. sites such as Facebook, MySpace and interdisciplinary postgraduate journal of Remember conference studentships Twitter, the internet has become an the institute of advanced study are available for student members environment in which to network (www.dur.ac.uk/kaleidoscope), which who wish to attend the summer virtually. This has lead to the accepts articles and reviews from conference. development of several social / postgraduates in any discipline. We hope to see you all there! professional networking websites such as Online resources like Graduate LinkedIn (www.linkedin.com), and now Junction are invaluable tools which there are sites designed specifically for enable early career scientist to build scientists such as nature network research networks, collaborate nationally (www.network.nature.com), labroots and internationally and begin to break (www.labroots.com), labmeeting the barriers between disciplines, allowing (www.labmeeting.com) and Graduate research projects to be considered from a Junction (www.graduatejunction.com). multi-disciplinary perspective. The ability Congratulations! Graduate Junction is a scientific to network is essential to the success of networking website for graduate a career in research. Congratulations go to Andrew Hall researchers worldwide, which aims to With the number of scientific who was awarded his PhD in February promote discussion and collaboration networking websites increasing I have no at the University of Wales Institute across disciplines and countries. It has a doubt that virtual networking will Cardiff. PECS wish Andrew all the best similar format to social networking sites, become a routine means for scientists to in his future career. once registered you create a profile from ‘get connected’ in the future. If you know a SfAM student or early which you can share your research career scientist who you would like to interests with the global research see congratulated in this section please community. Your profile can contain a Vicki McCune get in touch and we will publish their summary of your work, keywords to describe your research interests, a list of PECS Communications achievements on this page. Email: Officer, Newcastle University [email protected] publications, a description of your research skills and can include a photo

42 Research development fund report Intestinal bacteria and ulcerative colitis

he human colonic microbiota (Figure 1). The peak age of incidence is mucosal biofilms are involved in the comprises several hundred between 20 and 40 years, and one of the disease. These bacteria could be Tbacterial species, sub-species and main symptoms is bloody diarrhoea, pathogens that colonise the epithelial biotypes, and a close metabolic which is often associated with mucus, surface and invade underlying tissues, or relationship exists between these urgency, tenesmus and abdominal pain. non-pathogenic commensal species organisms and the host. Many factors The disease begins distally in the occupying adhesion sites on the mucosa control microbial colonisation of the rectum, progressing up the bowel over and preventing pathogen adhesion large intestine, the most significant time, towards the right colon. It is (Macfarlane et al., 2009). being diet, environment, digestive thought that 60,000 to 120,000 people Our work on gut biofilms has shown function, and the anatomical structure that mucosal surfaces in the large bowel of the digestive tract. Colonic bacteria are heavily colonised by complex interact with host physiological microbiotas that are structurally distinct processes in a multiplicity of ways, from microbial communities found in including the metabolism of xenobiotics, the gut lumen (Macfarlane et al., 2004). mineral absorption and immune system Microscopic analyses demonstrated that development, as well as the activation many of the bacteria in mucosal biofilms and destruction of toxins, genotoxins were present in microcolonies (Figure and mutagens (McBain & Macfarlane, 2). Using culturing techniques, few 1998; Macfarlane & Macfarlane, 2004). consistent differences were seen in The fundamental composition of the microbiota composition in rectal colonic microbiota is basically similar in biopsies obtained from healthy people different people, but marked inter- and UC patients, which might be individual variations can be seen at explained, in part, by natural inter- species level (Finegold et al., 1983). individual variation, and the relatively The ecological, physiological low patient numbers involved in the significance of this is unclear at present, Figure. 1. Light micrograph taken studies. However, marked variations largely because little is really known during endoscopy of the distal colon in were recorded in some bacterial groups, about the multicellular organisation of a patient with ulcerative colitis, but it was difficult to assign a role for the microbiota, or of the metabolic showing the boundary between normal specific bacterial species in UC relationships and interactions that exist and inflamed mucosae aetiology. Seventy-two bacterial taxa between various bacterial communities, belonging to 18 genera were detected and how this relates to host health and on the rectal mucosa, with 20 species wellbeing. The normal gut microbiota is are affected by UC in the UK, with 6,000 being common to the UC and healthy a partner in a symbiotic association with to 12,000 new cases being diagnosed cohorts, although only differences in the host, particularly those species annually (Shivananda et al., 1996; bifidobacteria, numbers of which were involved in the final stages of the Loftus, 2004). Studies with animals 30-fold higher in healthy tissues, were digestive process, but some organisms, show that intestinal bacteria are statistically significant. Bacteria including certain clostridia, enterococci, associated with UC initiation and/or belonging to the genus eubacteria and peptostreptococci have maintenance, but there is no firm Peptostreptococcus were only isolated the potential to promote dysbiosis in the evidence for a specific transmissible from the UC patients, who also had large bowel, particularly when the agent in this disease, and Koch’s proportionally more enterobacteria. equilibrium of the ecosystem has been postulates have not been demonstrated. Previous work had similarly shown that disturbed. There is mounting evidence In the search for a singular causative peptostreptococci only occurred on UC that putatively commensal species in the organism, a number of investigators rectal mucosae (Matsuda et al., 2000). normal microbiota are linked to the have looked at Bacteroides spp. and Some species belonging to this genus aetiology of inflammatory bowel different subtypes of E. coli. However, are known pathogens (Ezaki et al., diseases such as ulcerative colitis (UC) the various organisms that have been 1991), and while they do not seem to be (Cummings et al., 2003). implicated in UC are not found in all able to colonise the healthy rectal UC is an acute and chronic relapsing patients, although there is some epithelium, these bacteria are commonly illness that only affects the large gut evidence that bacteria growing in found in faeces (Finegold et al., 1983).

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references

■ Cummings J H, Macfarlane G T, Macfarlane S. (2003) Intestinal bacteria and ulcerative colitis. Curr Iss Intest Microbiol; 4: pp9-20. ■ Ezaki T, Oyaizu H, & Yabuuchi E. (1991) The anaerobic gram-positive cocci. In: The Prokaryotes vol II 2nd edn. Balows A, Truper H G, Dworkin M, Harder W, Schleifer K H. pp1878-1892. New York: Springer-Verlag. ■ Famularo G, Moretti S, Marcellini S, De Simone C. (1997) Stimulation of immunity by probiotics. In: Probiotics: Therapeutic and other Beneficial Effects ed. Fuller R. pp133-161. London: Chapman & Hall. ■ Finegold S M, Sutter V L, Mathisen, G E. (1983) Normal indigenous intestinal flora. In: Human Intestinal Microflora in Health and Disease ed. Hentges DJ. pp3-31. London: Academic Press. ■ Furrie E, Macfarlane S, Cummings J H, Macfarlane G T. (2004) Systemic antibodies towards mucosal bacteria in ulcerative colitis and Crohn’s disease differentially activate the innate immune response. Gut; 53: pp91-98. ■ Furrie E, Macfarlane S, Kennedy A, Cummings J H, Walsh S V, O’Neil D A, Macfarlane G T. (2005) Synbiotic therapy (Bifidobacterium longum/Synergy 1) initiates resolution of inflammation in patients Figure. 2. Live/dead confocal light micrograph of a bacterial microcolony on the with active ulcerative colitis: a randomised controlled rectal mucosa stained with BaclightTM pilot trial. Gut; 54: pp242-249. ■ Gill H S, Rutherfurd K J, Cross M L, Gopal P K. (2001) Enhancement of immunity in the elderly by dietary supplementation with the probiotic Bifidobacterium lactis HN019. Am J Clin Nutr; 74: Low numbers of bifidobacteria, which blinded randomised controlled trial, pp833-839. are viewed as being beneficial lasting one month, which involved 18 ■ Loftus E Jr. (2004) Clinical epidemiology of organisms, or the absence of particular patients with active UC. Results showed inflammatory bowel disease: incidence, prevalence bifidobacterial taxa on the mucosa may that bifidobacterial numbers increased and environmental influences. Gastroenterology; 126: pp1504-1517. be of significance in UC, as a number of 40-fold on the rectal epithelium, and species have well documented that mucosal inflammation was reduced ■ Lu L, Walker A. (2001) Pathologic and physiologic interactions of bacteria with the gastrointestinal immunomodulatory properties in the synbiotic group compared to epithelium. Am J Clin Nutr; 73: pp1124S-1130S. (Famularo et al., 1997). These bacteria patients receiving the placebo. ■ Macfarlane G T, Blackett K L, Nakayama T, Steed are believed to contribute towards host Messenger RNA levels for inducible H, Macfarlane S. (2009) The gut microbiota in defences through interactions with the human beta defensins 2, 3 and 4, which inflammatory bowel disease. Curr Pharmaceut Design. In press. gut immune system and via colonisation are strongly up-regulated in active UC, ■ Macfarlane S, Furrie E, Cummings J H, Macfarlane resistance (Gill et al., 2001; Lu & were significantly reduced in patients G T. (2004) Chemotaxonomic analysis of bacterial Walker, 2001). Compared to other receiving the synbiotic. TNFα and IL-1a, populations colonizing the rectal mucosa in patients mucosal isolates, bifidobacteria and which are inflammatory cytokines that with ulcerative colitis. Clin Infect Dis; 38: pp1690- 1699. peptostreptococci were shown to be drive inflammation and induce defensin ■ Macfarlane G T, Macfarlane S. (2004) Human highly immunogenic in UC patients expression, were also significantly colonic microbiota: ecology, physiology and (Furrie et al., 2004), lending further reduced after treatment. Biopsies taken metabolic potential of intestinal bacteria. In: Allergic support to the notion that the presence from the synbiotic patients showed Diseases and the Environment Eds. Isolauri I, and Walker W A. pp179-198. Basel: Vevey/S Karger AG. or absence of these organisms could be regeneration of epithelial tissue. Overall, ■ Matsuda H, Fujiyama Y, Andoh A, Ushijima T, linked to the disease process. the study demonstrated that short-term Kajinami T, Bamba T. (2000) Characterization of Since the immune response against synbiotic treatment resulted in antibody responses against rectal mucosa-associated normal gut inhabitants is thought to improvements in the full clinical bacterial flora in patients with ulcerative colitis. J Gastroenterol Hepatol; 15: pp61-68. drive inflammatory processes in UC, appearance of chronic inflammation in ■ McBain A J, Macfarlane G T. (1996) Ecological and modulation of bacterial communities on patients receiving therapy, and indicated physiological studies on large intestinal bacteria in the gut mucosa through the use of that there is potential for developing relation to production of hydrolytic and reductive probiotics and prebiotics offers inexpensive new bifidobacterial-based enzymes involved in formation of genotoxic metabolites. J Med Microbiol; 47: pp407-416. prospects for modifying the disease therapies for use in the treatment of ■ Shivananda S, Lennard-Jones J, Logan R, Fear N, state. With this in mind, a synbiotic inflammatory bowel disease. Price A, Carpenter L, van Blankenstein M. (1996) combining a probiotic Bifidobacterium Incidence of inflammatory bowel disease across longum strain isolated from healthy Europe: is there a difference between the north and south? Results of the European collaborative study rectal epithelium, and an inulin-based Katie L. Blackett on inflammatory bowel disease. Gut; 39: pp690- prebiotic (Synergy 1) was used in a pilot and George T. Macfarlane 697. study to treat UC patients (Furrie et al., University of Dundee 2005). The investigation was a double-

44 Students into Work Grant reports The Sticky Problem of Biofilms formed by information Staphylococcus aureus

I am currently entering the fourth human infections, 65% are thought to am I eligible - year of my BSc with honours be associated with this form of growth. Microbiology degree course at Glasgow The ica operon is currently the best can I apply? Caledonian University and was excited investigated and most widely Yes — if you are FULL member when at the end of my third year the understood mechanism of biofilm who can offer an undergraduate opportunity arose to benefit from a 10- formation, but there is recent evidence microbiology student the chance week summer studentship in the that other genes may be involved in the to obtain work experience. If you University’s research microbiology lab. development of these structures. Mack would like to read about the My project aimed to study the sticky et al. (1994) proposed a two-step experiences of Students who problem of biofilm formation in model for biofilm formation in have benefited from this Grant, Staphylococcus aureus and support staphylococci. The two steps can be you can do so in each issue of the research currently underway in this genetically separated. The first step in Microbiologist. field. biofilm formation is the attachment of S. aureus is a Gram-positive cells to a solid surface. The surface can For Further information visit: bacterium which is a highly successful be within the host or it can be an www.sfam.org.uk/grants.php human pathogen. This organism can artificial medical device, for example a cause a range of infections from venous catheter. The second step is superficial skin and soft tissue secretion of the polysaccharide infections to deep-seated infections intracellular adhesin (PIA) causing the such as septicaemia and endocarditis. S. cells to stick together and in turn form aureus is one of the most frequently the biofilm. isolated Gram-positive bacteria from In this project, my aim was to see hospital associated infections and how different environmental factors approximately 45% of S. aureus affect the phenotype of S. aureus isolates are methicillin-resistant biofilms. These included supplementing (Biendenbach et al., 2004; Boyce et al., the growth media with different sugars, 2005). The number of death certificates adding salt and altering the pH of the mentioning methicillin resistant S. medium. Six clinical isolates of aureus (MRSA) stabilised at 1,652 in S.aureus were collected from the 2006. This followed a dramatic increase Scottish MRSA Reference Laboratory from 51 to 1,649 deaths between 1993 (Stobhill Hospital, Glasgow). These and 2005. There are two dominant consisted of three methicillin sensitive clones of MRSA that cause S. aureus (MSSA) isolates and three approximately 93% of infections in MRSA isolates. The MRSA isolates Scotland. Epidemic MRSA-15 (EMRSA- consisted of two of the most commonly 15) causes 70% of these infections, isolated genotypes in Scottish hospitals epidemic MRSA-16 (EMRSA-16) isolates (an EMRSA-15 and an EMRSA-16) and are responsible for approximately 23% a sporadic Scottish clone. of infections and 7% of MRSA infections After cultivation of each are caused by sporadically occurring staphylococcal isolate in brain heart clones (Morrison, 2003). Why the vast infusion (BHI) broth, the number of proportion of infections is caused by so cells in each culture was adjusted to few clones remains unknown. 1x106cfu/ml. Biofilms were grown in Although S. aureus is a common BHI broth in 96-well microtitre plates commensal organism of the skin and biofilm biomass was quantified by surface, inhabiting in particular the crystal violet staining. The absorbance epithelia of the nose, it is associated of crystal violet, eluted using 70% with many types of infection. One of the ethanol, was measured at 570nm using reasons that S. aureus is such a a microtitre plate reader (BMG successful pathogen may be due to its LUMIstar* plate reader, BMG, ability to form biofilms on almost any Germany). Characterisation of the abiotic or biotic surface. A biofilm is a strain phenotype was also undertaken structured community of micro- using the Congo red agar assay. Congo organisms encapsulated within a self- red agar can give some indication of developed polysaccharide matrix. Of all slime production, which is associated

45 members

References ■ Biedenbach, D.J., Moet, G.J. & Jones, R.N. (2004). Occurrence and antimicrobial resistance pattern comparisons among bloodstream infection isolates from the SENTRY Antimicrobial Surveillance Program (1997- 2002). Diagnostic Microbiology and Infectious Disease Vol 50, pp59-69. ■ Boyce, J.M., Cookson, B. Christiansen K, et al. (2005). Methicillin Resistant Staphylococcus aureus. The Lancet Infectious Diseases Vol 5, No 10, pp653-663. ■ Mack, D, Nedelmann, M, Krokotsch, A, et al. (1994). Characterization of transposon mutants of biofilm- producing Staphylococcus epidermidis impaired in the accumulative phase of biofilm production: genetic identification of a hexosamine-containing polysaccharide intercellular adhesin. Infection and Immunity, Vol 62, No 8, pp3244-3253. ■ Morrison, D. (2003). MRSA — changing epidemiology and new threats. SCIEH Weekly Report, Vol 37, pp1-12.

Figure 1. MRSA isolates grown on Congo red agar plates. The sporadic MRSA clone Isolation and (left) has black, dry crusty colonies, whereas the EMRSA-15 clone (right) is non- pigmented. Despite the differing phenotypes, both clones were able to form biofilms characterisation of the using the microtitre plate model. periplasmic sensory domain of Tlp7 chemoreceptor of with biofilm growth, by the appearance and the MRSA strains in their ability to of dark, crusty colonies (Figure 1). form biofilms under the different Campylobacter jejuni Using the two techniques, biofilm conditions tested. formation was evaluated in response to The addition of the various sugars to Campylobacter jejuni, which was each of the environmental stimuli under Congo red agar did alter the strain first identified as a human diarrhoeal assessment. phenotypes, but the effects noted were pathogen in 1973, is now the most Carriage of selected genes thought to strain dependent and did not correlate frequently diagnosed bacterial cause of be involved in biofilm formation was with the ability of the organisms to form human gastroenteritis worldwide, also investigated. Genomic DNA was biofilms under comparable growth surpassing Escherichia coli O157:H7, extracted from overnight cultures of conditions in the microtitre plate assay. Salmonella species and Shigella each strain using an alkaline lysis and Consistent with the findings of species as causes of enteric infections phenol chloroform DNA extraction previous studies, icaA was present in all (Allos, 2001; Altekruse et al., 1999). method. The presence of four biofilm- of the staphylococci screened. Similarly, Apart from gastroenteritis, associated genes (icaA, sasG, clpC and isaA and clpC were also present. The Campylobacter infections have been isaA) was then evaluated for the six remaining gene, sasG, was present in reported to be associated with other clinical isolates of S. aureus by PCR. some of the strains but not others, severe conditions, such as meningitis, After statistical analysis of the results indicating that it was not essential for nephritis, acute arthritis and urinary using GraphPad Prism software, it was biofilm formation. tract infections (Hu & Kopecko, 2000). concluded that adding salt to the I would like to take this opportunity The most recognised serious post- growth medium had no effect on any of to thank SfAM for their generous infection complication of the strains; neither did altering the pH funding which has allowed me to gain Campylobacter infection is Guillain- nor supplementing the medium with valuable work experience. The Barré syndrome (GBS), an autoimmune lactose. The three remaining sugars techniques I have learned in the lab will demyelinating disease of the peripheral produced strain-dependent results; undoubtedly help me in my final fourth nervous system (Allos, 2001). C. jejuni whereby biofilm formation was either year honours project. I would also like is zoonotic and is part of the commensal unaffected or enhanced. However, the to thank my supervisor, Dr. Sue Lang, intestinal flora in poultry and domestic Scottish sporadic isolate in particular who made it possible for me to animals, which are the main reservoirs produced a significantly enhanced undertake this studentship. for human disease. Human biofilm when mannitol or glucose was Finally, thanks to all of lab C122 for campylobacteriosis is considered to be added to the growth medium all their help, especially Dr. Karen Smith mainly a food-borne disease. The (supplementation of 0.5-5% and 0.5-1% and Cristina Teles. I would fully primary mode of transmission to humans respectively). recommend this scheme to students who is via consumption of contaminated and Of the MSSA investigated, one strain wish to gain firsthand experience within undercooked poultry. Less frequent also demonstrated the ability to form a a working lab environment and have a sources include unpasteurised milk, robust biofilm with mannitol at all passion for research. contaminated drinking water and contact concentrations, but no significant with pets and other animals (Blaser, enhancement was seen with the 1997; Ketley, 1997). addition of glucose. There was no Danielle McEwan Although C. jejuni has been apparent difference between the MSSA recognised as a significant pathogen,

46 not much is known about the vector (Promega) by standard molecular Figure 1b. Western blot showing the mechanisms of its pathogenesis. The cloning techniques. Competent E.coli expression of 16.7kDa Tlp7peri -His chemotactic behaviour of C. jejuni DH5α cells were transformed with the fusion protein towards the intestinal mucin plays an plasmid construct and grown on Luria important role in colonisation, adhesion Broth plates with antibiotic 1 2 3 4 5 and subsequent invasion of intestinal supplementation containing IPTG epithelial cells (Ketley, 1997; Szymanski (isopropyl β-D-thiogalactopyranoside) et al., 1995). Sequencing of the and X-Gal (5-bromo-4-chloro-3-indolyl- C. jejuni NCTC 11168 genome and β-D-galactoside). Recombinants were comparative genome sequence analysis selected by blue/white colony selection. revealed a number of genes involved in The plasmid was then isolated from the chemotaxis, including ten genes coding putative recombinants and the presence peri for ten putative chemoreceptors, named of the intact Tlp7 insert was 16.7kDa ➜ transducer-like proteins or Tlp confirmed by PCR, restriction enzyme receptors. Tlp receptors are classified cleavage and sequencing. into several groups according to their The Tlp7 periplasmic domain Lane 1: All Blue protein marker (BioRad) structural similarities (Parkhill et al., encoding DNA fragment was excised Lane 2: Induced Bl21 (DE3) clone 1 2000; Marchant et al., 2002). Group A from the recombinant pGEM-T Easy Lane 3: Uninduced Bl21 (DE3) clone 1 Lane 4: Induced Bl21 (DE3) clone 2 Tlp receptors have a similar structure to cloning vector and cloned into the pET- Lane 5: Uninduced Bl21 (DE3) clone 2 methyl-accepting chemotactic proteins 19b expression vector. The pET-19b (MCP) of Escherichia coli, where the expression vector contains a The purified Tlp7peri protein will be chemotactic signal transduction pathway polyhistidine tag, an ampicillin resistance used in a glycan and amino acid array to has been extensively studied. The highly gene selection marker and an IPTG- determine the binding ligand specific for variable periplasmic (chemosensory) inducible T7 RNA polymerase promoter, Tlp7peri. Identification of the specific domains of group A Tlp receptors are which enables the overexpression of ligand, which binds to the periplasmic responsible for sensing chemical target His-fusion protein. The plasmid domain, will allow us to elucidate the gradients in the external environment, construct was then transformed into the role of the Tlp7 chemoreceptor in which is followed by the initiation of a E.coli expression host strain BL21[DE3]. chemotaxis. This may potentially signal transduction cascade allowing the Expression of the 16.7kDa Tlp7peri provide an insight into the mechanisms bacteria to relocate to the more -His fusion protein was induced by IPTG of colonisation in animals and disease favourable environment. It has not yet which enabled detection of the protein production in humans allowing the been established which specific ligand by Western blot analysis using anti-His development of new targets for novel binds to a particular Tlp receptor. antibodies (Figure 1a and 1b). antimicrobials. This project aimed to isolate and A protein solubility test was characterise the C. jejuni NCTC 11168 performed and showed that large References chemosensory domain of the Tlp7 quantities of the target protein were ■ Allos, B.M. (2001). Campylobacter jejuni infections: chemoreceptor (Tlp7peri). present in the soluble fraction, which update on emerging issues and trends. Clinical Infectious The coding sequence of the Tlp7peri is will allow the purification of Tlp7peri -His Diseases, Vol 32, pp1201-1206. ■ Altekruse, S.F., Stern, N.J., Fields, P.I. & Swerdlow, D.L. conserved within C. jejuni strains. In fusion protein by nickel affinity gel (1999). Campylobacter jejuni — an emerging foodborne some of these strains there is a mutation chromatography. Due to time limitations pathogen. Emerging Infectious Diseases, Vol 5, pp28-35. creating the stop codon after the coding the project was paused at this stage. ■ Blaser, M.J. (1997). Epidemiological and clinical features of Campylobacter jejuni infection. Journal of Infectious sequence of the periplasmic sensory Diseases, Vol 176, pp103-105. domain, which means that the Tlp7 ■ Hu, L. & Kopecko, D.J. (2000). Interactions of receptor is likely to be a pseudogene. Figure 1a. SDS-PAGE gel depicting a campylobacter with eukaryotic cells: gut and luminal small scale protein expression of colonization and mucosal invasion mechanisms. In Interestingly, in one of C. jejuni strains Campylobacter. Nachamkin, I. and Blaser, M.J. (eds). peri (HB93-13) the Tlp7 receptor is a 16.7kDa Tlp7 -His fusion protein Washington: ASM Press, pp191-215. ■ functional gene as there is no such 1 2 3 4 5 Ketley, J.M. (1997). Pathogenesis of enteric infection by Campylobacter. Microbiology, Vol 143, p521. mutation. This allows us to speculate ■ Marchant, J., Wren, B. & Ketley, J. (2002) Exploiting that the Tlp7 receptor might be genome sequence: predictions for mechanisms of functional at least in some C. jejuni campylobacter chemotaxis. Trends in Microbiology, Vol 10, pp155-159. strains. Characterisation of Tlp7peri will ■ Parkhill, J., Wren, B., Mungall, K., Ketley, J.M., provide a deeper insight into the role of Churcher, C., Basham, D., Chillingworth, T.,Davies, R.M., Tlp7 receptor in the chemotactic Feltwell, T., Holroyd, S., Jagels, K., Karlyshev, A.V., Moule, S., Pallen, M.J.,Penn, C.W., Quail, M.A., Rajandream, behaviour of C. jejuni. A DNA sequence 16.7kDa ➜ M.A., Rutherford, K.M., van Vilet, A.H.M., Whitehead,S. of Tlp7peri was amplified by PCR from & Barrell, B.G. (2000). The genome sequence of the food-borne pathogen Campylobacter jejuni reveals the C. jejuni NCTC 11168 strain using hypervariable sequences. Nature Vol 403, pp665-668. specifically designed primers. The NdeI ■ Szymanski, C., King, M., Haardt, M. & Armstrong, G.D. and XhoI restriction sites were Lane 1: All Blue protein marker (BioRad) (1995). Campylobacter jejuni motility and invasion of caco-2 cells. Infection and Immunity Vol 63, pp4295- incorporated into the primer termini for Lane 2: Induced Bl21 (DE3) clone 1 4300. future cloning procedures. The 456bp Lane 3: Uninduced Bl21 (DE3) clone 1 Lane 4: Induced Bl21 (DE3) clone 2 Tlp7 PCR fragments were ligated into Lane 5: Uninduced Bl21 (DE3) clone 2 Dina Zarubina the intermediate pGEM-T Easy cloning

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Amplified Fragment including their sample ID, strain supervisor Dr Bob Madden for the number, source, original speciation, opportunity he has provided, and also Length Polymorphism concentration of DNA, country of origin Lynn Moran and Carmel Kelly for their of Campylobacter and date received had to be entered commitment, patience and friendliness manually into the database. This was an in welcoming me to the lab and teaching species extremely tedious and time consuming me the techniques and skills needed to task but was essential for future perform AFLP. During my study of the reference to these samples and for I believe that the SfAM Students into microbiology BSc at Queen’s University further analysis to compare these Work scheme provides an extremely Belfast, the class was informed by Dr samples with other samples within the worthwhile and rewarding opportunity Madden of the opportunity to apply for database. to students and I am grateful for the an SfAM project over the summer Analysis of the sample profiles was by experience that I have gained. vacation. I was excited when I was unweighted pair group with offered a 10 week summer placement at mathematical average (UPGMA) cluster the Agri-Food and Biosciences Institute analysis. This portrayed four distinct Carole Daly (AFBI) within the Food Microbiology clusters of Campylobacter species: branch. Dr Madden’s team has worked C. jejuni, C. coli, C. lari and C. fetus. with Campylobacter species for over C. coli showed the least diversity with 15 years. From the isolates obtained isolates clustering at ≥66.9% similarity President’s between 1994 and 2002, they have built and C. jejuni the greatest diversity with up a collection of extracted DNA. A isolates clustering at ≥19.4%. It was Fund reports variety of different genotyping evident that many samples had been techniques were applied to the isolates misidentified by the phenotyping before the method of amplified fragment techniques. Of the samples, 18 C. jejuni length polymorphism (AFLP) was seen isolates were observed to cluster with information to best suit the lab’s requirements, but C. coli and 14 C. coli isolates clustered this was only applied to isolates with C. jejuni. The majority of the obtained after 2002. My aim was to samples clustered within the four main am I eligible - can I determine whether the quality of the species clusters and some of the apply? archived DNA samples was adequate for outbreak strains showed ≥98% If you often find difficulty in funding AFLP, since the samples may have similarity: with the method used, ≥ attendance at meetings. It is not only our degraded during storage. Where the profiles showing 90% similarity were student members who require our help. quality was acceptable, DNA from as regarded as identical. Senior microbiologists often find difficulty many Campylobacter isolates as Another interesting observation was in funding attendance at meetings. If you possible would be subjected to AFLP that some of the veterinary samples are in this position you are eligible for this typing and all available information were labelled C. upsaliensis. However, fund. added to the existing large bioinfor- C. upsaliensis is resistant to restriction For Further information visit: matics database. digestion by BglII hence cannot www.sfam.org.uk/grants.php AFLP utilises two restriction enzymes generate an AFLP profile by the method to generate fragments of DNA which can used. These samples did, however, then undergo PCR amplification. Hence, produce an AFLP profile and clustered the methods I used encompassed many with C. coli, hence they were definitely techniques including DNA digestion, not C. upsaliensis. Of the isolates PCR, gel electrophoresis, use of the which were subject to AFLP, 32 did not DNA sequencer and bioinformatics. The cluster with the four major clusters or DNA sequencer sizes fragments with each other. Thus, the true identity providing AFLP profiles which can then of these samples is not known and be compared using BioNumerics to further analysis, such as 16S sequence provide the clustering of subspecies and analysis, will be necessary to identify the degree of relatedness between each these isolates. profile. For my project, DNA from 514 Overall the data of over 400 isolates isolates was available from organisms are now available within the department’s which had all originally been identified bioinformatics database and will benefit by phenotyping. The isolates were from further studies by AFBI staff. The project a variety of sources including clinical, has highlighted that phenotyping veterinary and food. All of the DNA techniques are not always reliable in isolates were initially subjected to correctly identifying Campylobacter spp. quality assessment using the “Thermo This opportunity has provided me NanoDrop 1000.” These samples were with the invaluable first hand experience then subjected to AFLP. Of the 514 of working within a lab and confirmed samples, 425 provided acceptable DNA my aspirations to continue with research profiles. The data of all of the isolates to a PhD. I would like to thank my

48 President’s Fund reports The relationship upon the hypothalamus and suppression Eradication of H. pylori leads to an of fat utilisation in adipose tissue (Wren increase in plasma ghrelin levels. As between H. pylori et al., 2001). Plasma concentrations of ghrelin stimulates the release of growth colonisation and levels ghrelin increase prior to a meal and are hormone, a deficiency or reduced level lowest post-prandially. Plasma ghrelin of ghrelin may provide an explanation of Leptin and Ghrelin levels are reduced in obesity. Acylated for the reduced height in children ghrelin is the active form although the colonised by H. pylori. The high My visit to Sri Lanka, courtesy of de-acylated form may also have incidence of H. pylori infection in the President’s Fund, was at the request biological relevance. children in some countries seems to of Dr Fernando of the Medical Faculty of The release of growth hormone is contribute to the decreased serum levels the University of Sri Jayawardenapura also regulated by growth hormone of ghrelin and to the decreased appetite (USJ) who invited me to give a lecture releasing hormone (GHRH), which is and dyspeptic symptoms in these at the 120th Sri Lanka Medical released from the hypothalamus, and children. On the other hand, some Association meeting. Whilst in Sri Lanka somatostatin (SS) which is an inhibitory studies have found no relationship I took the opportunity to set up a factor synthesised by many tissues between colonisation by H. pylori and research project on the relationship including D cells in the stomach. Growth ghrelin or leptin levels. between colonisation by Helicobacter hormone has a direct effect upon Little is known about the relationship pylori and the levels of the orexigenic adipose tissue, increasing triglyceride between H. pylori virulence factors hormones leptin and ghrelin. breakdown, and a direct effect upon the (e.g. CagA/ VacA) and appetite Increasingly, extra-gastric and extra- liver to secrete insulin-like growth hormones and there is little published intestinal diseases are being linked to factor-1 (IGF-1). It is this latter factor data on the effect of different gastric colonisation by H. pylori and special that is responsible, in part, for growth pathologies on these hormones, interest has been focussed on the enhancing effects by: stimulating the especially in children. The issue relationship between body weight proliferation of chondrocytes and regarding the differences in plasma regulation, stature and body mass index, myeloblasts; stimulating protein ghrelin/leptin between H. pylori positive after it was reported that the eradication synthesis in many tissues; increasing fat and negative patients is still under of H. pylori was associated with a utilisation and partly controlling blood debate. Also, whether colonisation by significant increase in body weight and glucose levels. Plasma levels of growth H. pylori affects ghrelin/leptin dynamics BMI (Furuta et al., 2002) and a report hormone are highest during deep sleep. over the long term and its relation to linked colonisation by H. pylori with Leptin is also an important factor in obesity and associated diseases are short stature (Demir et al., 2001). regulating body weight and metabolism. important questions that remain to be Indeed, it has been suggested that It is found predominantly in adipose answered. Thus, in developed countries, decreasing prevalence of H. pylori in tissue but also in the stomach and H. pylori negative children may have the population may be causally related placenta. As triglycerides accumulate in relatively high concentrations of ghrelin to increasing obesity and therefore the adipocytes the level of leptin also and may reach their full growth gastro-oesophageal reflux disease increases and there is a correlation potential then grow into overweight (GORD) and an increasing incidence of between body fat and blood leptin adults with obesity and associated oesophageal adenocarcinoma. Similarly, levels. Leptin acts upon the cardiovascular problems, whilst in attention has focused on H. pylori as a hypothalamus to decrease hunger and developing countries, where H. pylori risk factor for both insulin resistance food consumption and increase energy prevalence is high, they may not achieve and cardiovascular disease such as metabolism (Schneider et al., 2006). It full stature and some will develop peptic atheroma, stroke, ischaemic heart also has effects upon reproduction. ulcer disease (PUD) or adenocarcinoma disease and thrombo-embolic These two hormones are key of the stomach. phenomena. On the other hand, some regulators of the release of growth These few studies confirm that these studies have not found an association hormone and metabolic control, and hormones have not been thoroughly between colonisation by H. pylori and disturbances may represent a plausible investigated in H. pylori infection, growth retardation or cardiovascular biological explanation for short stature particularly in relation to the virulence disease. and the evolution of atherosclerosis. characteristics of H. pylori. This is the A complex hormonal interaction Both hormones are affected by H. rationale for our study which includes exists to control appetite, metabolism pylori colonisation. Serum ghrelin and Sri Lanka, Italy and Lithuania. We are and growth. Ghrelin, a recently leptin concentrations are significantly recruiting both adults and children who discovered hormone produced lower in H. pylori-infected than in non- are either complaining of dyspepsia or principally by epithelial cells in the infected children (Plonka et al., 2006). are healthy controls. Their H. pylori fundus of the stomach, has two major Histologically, ghrelin-immunoreactive status will be determined. Patients will biological activities: regulation of energy cells are significantly reduced in undergo gastroscopy, biopsy and PCR balance and stimulation of the secretion H. pylori positive individuals. The for H. pylori. All subjects will have of growth hormone from the anterior degree of gastric atrophy associated serology (HelicoBlot 2), leptin and pituitary. It regulates energy balance by with H. pylori colonisation also appears ghrelin levels determined, their BMI increasing hunger through its action to be linked to the plasma ghrelin levels. measured and insulin resistance

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determined. We shall then be able to ubiquitous soil-borne organisms. The correlate the strain type of H. pylori saprotrophic lifestyles of these fungi and Figure 1. Serodiagnosis of invasive with levels of orexigenic hormones, potentially infectious Aspergillus spp., aspergillosis using an Aspergillus- insulin resistance and their BMI. enable them to utilise a wide range of specific lateral flow device. Samples of substrates including decaying plant serum from a healthy individual (1) and References material thereby facilitating efficient from a patient with invasive ■ Demir, H.,Saltik, I.N., Kocak, N., Yuce, A., Ozen, H. & colonisation of their natural habitats, aspergillosis (2) were applied to LFDs Gurakan, F. (2001) Subnormal growth in children with and the results recorded after 15 Helicobacter pylori infection. Archives of Disease in soils and composts. As soil saprotrophs Childhood, 84, pp.89-90. they play an important role in the minutes. A single internal control line is ■ Furuta, T., Shirai, N., Xiao, F., Takashima, M. & Hanai, seen with serum from the healthy H. (2002) Effect of Helicobacter pylori infection and its recycling of organic matter in terrestrial eradication. Alimentary Pharmacology and Therapeutics, ecosystems and, while some species individual, while two lines are seen 16, pp.799-806. such as F. solani are plant pathogens with the invasive aspergillosis patient’s ■ Plonka, M., Bielanski, W., Konturek, S.J., Targosz, A., serum showing the presence of Sliwowski, Z., Dobrzanska, M., Kaminska, A., Sito, E., also, others such as Trichoderma spp Konturek, P.C. & Brzozowski, T. (2006) Helicobacter circulating Aspergillus antigen. infection and serum gastrin, ghrelin and leptin in children display mycoparasitic and plant-growth- of Polish shepherds. Digestive and Liver Disease, 38, promotional activities that have been pp.91-97. exploited in the biological control of ■ Schneider, J.E. (2006) Metabolic and hormonal control of the desire for food and sex: implications for obesity plant disease and in the enhancement of and eating disorders. Hormones and Behavior, 50, crop productivity. Despite these positive 1 2 pp.562-571. ■ Wren, A.M., Seal, L.J., Cohen, M.A., Brynes, A.E., attributes, soil-borne fungi can have Frost, G.S., Murphy, K.G., Dhillo, W.S., Ghatei, M.A. & significant negative impacts on human Bloom, S.R. (2001) Ghrelin enhances appetite and increases food intake in humans. Journal of Clinical health, causing frequently fatal Endocrinology & Metabolism, 86, p5992. disseminated infections in the immunocompromised host, with John Holton disproportionately high rates of mortality and morbidity. A. fumigatus, F. solani and S. apiospermum are agents of Use of monoclonal ‘hyalohyphomycosis’, a term used to antibody-based describe infections caused by hyaline, septate, fungi in infected tissues. diagnostic assays for A. fumigatus, second only to Candida the detection of spp. as the cause of nosocomial (hospital-acquired) invasive fungal invasive mycoses infections, is first and foremost a pulmonary pathogen causing The frequency of invasive mycoses aspergillomas (fungus balls) that by opportunistic fungal pathogens has occlude the lung cavities. However, the increased dramatically over the past two fungus can also invade the host via lung decades. This increase is directly related tissue resulting in a disease known as to increasing patient populations at risk invasive aspergillosis (IA). This disease for the development of infections, which is now a major direct or contributory include the elderly, premature babies, cause of death at leukaemia treatment particularly of immunocompromised solid-organ and bone marrow transplant centres and bone marrow and solid patients, and now account for ~25% of recipients, individuals with AIDS, organ transplantation centres. non-Aspergillus infections in organ neoplastic disease and those receiving Fusarium spp. have long been transplant patients. R. oryzae, an immunosuppressive therapies or associated with infections of the skin, aseptate fungus, is the most important cytotoxic drugs. In addition to well- nail and cornea, but are now becoming agent of mucormycosis in patients that known opportunistic pathogens such as increasingly recognised as a cause of have serious underlying conditions such Candida albicans, Cryptococcus invasive fungal infection (fusariosis) in as diabetes mellitus, starvation, burns, neoformans and Aspergillus neutropaenic patients and in those or other major trauma. fumigatus, other species of yeast-like undergoing transplantation. Indeed, Opportunistic mycoses represent fungi and filamentous fungi have some hospitals have reported Fusarium formidable diagnostic challenges. It is emerged as serious pathogens of spp. to be second only to Aspergillus imperative that diagnosis is made humans over recent years. Many of spp. as the cause of life-threatening without delay, since prognosis worsens these organisms such as the zygomycete filamentous fungal infections in their significantly in the absence of Rhizopus oryzae and members of the transplant patients. S. apiospermum is recognition and timely intervention with ascomycete phylum, for example a well known causative agent of antifungal agents. Identification of fungi Paecilomyces spp., Scedosporium mycetoma (tumour-like swellings with in histological sections is problematic apiospermum (the anamorphic, asexual draining sinuses), but this species and because of a common appearance state of the fungus Pseudallescheria the related species Scedosporium (colourless, septate hyphae with a wide boydii), Fusarium solani, and prolificans have also recently emerged range of branching angles). Definitive Trichoderma longibrachiatum, are as significant invasive pathogens, identification in hyalohyphomycosis

50 therefore requires isolation of fungi in serum or plasma samples from patients harbour diverse types of microflora. culture and identification using at risk from IA and avoids the need for Hence, the possibility of finding novel morphological characteristics such as invasive biopsy sampling. Similar microorganisms and novel products spore-bearing structures. This takes devices will be developed for the rapid from this environment is not remote. considerable time and requires serodiagnosis of fusariosis, Mangrove lignocellulose supports a vast taxonomic expertise. Consequently, mucormycosis and blood-borne range of microorganisms. About a rapid diagnostic tests that accurately C. glabrata infection and will provide thousand species from 585 genera have discriminate between the different diagnostic platforms for the routine been cited for fungi alone. pathogens are urgently needed. A testing and management of patients at It is distressing to note that much of characteristic of fungi such as risk from invasive mycoses. the mangrove forests in the country A. fumigatus, F. solani, R. oryzae and have been lost due to overexploitation Candida spp., in particular, is by coastal dwellers and conversion to angioinvasion and dissemination via the References settlements, aquaculture, salt beds and ■ Thornton, C.R., Pitt, D., Wakley, G.E. & Talbot, N.J. blood. This property presents an (2002). Production of a monoclonal antibody specific to industry (Primavera, 2000). From the opportunity to track the fungi the genus Trichoderma and closely related fungi, and its original estimate of 500,000 hectares, use to detect Trichoderma spp. in naturally infested immunologically using techniques that composts. Microbiology, Vol 148, pp1263-1279. our mangrove forests have decreased to detect characteristic signatures created ■ Thornton, C.R. (2004). An immunological approach to only 120,000 hectares. Hence, being by their circulating antigens. quantifying the saprotrophic growth dynamics of with the Philippine National Collection Trichoderma species during antagonistic interactions with One such technique is hybridoma Rhizoctonia solani in a soil-less mix. Environmental of Microorganisms, my staff and I took technology. It allows the production of Microbiology, Vol 6, pp323-334. on a major undertaking of bio- ■ Thornton, C.R., Groenhof, A.C., Forrest, R. & Lamotte, monoclonal antibodies (mAbs) that are R. (2004). A one-step, immunochromatographic lateral prospecting and preserving microbial specific to individual genera, species or flow device specific to Rhizoctonia solani and certain flora from various mangrove areas in the related species, and its use to detect and quantify even isolates of fungi and are capable of R.solani in soil. Phytopathology, Vol 94, pp280-288. country before more of this important discriminating between active growth ■ Thornton, C.R. & Talbot, N.J. (2006). natural resource is lost forever. With Immunofluorescence microscopy and immunogold EM for and quiescent spore production. investigating fungal infections of plants. Nature Protocols, additional funding from the University of Monoclonal antibodies have been used Vol 1, pp2506-2511. the Philippines Center for Integrative successfully to detect fungi in soil and ■ Thornton, C.R. (2008). Tracking fungi in soil with and Developmental Studies and the monoclonal antibodies. European Journal of Plant composts (Thornton, 2008, Thornton et Pathology, Vol 121, pp347-353. Commission on Higher Education, we al., 2002) and in plant material were able to conduct the study for two (Thornton & Talbot, 2006) and to years and to collect samples from 35 develop highly specific and sensitive Christopher R Thornton mangrove sites in six provinces in four immunological assays for the major islands (Luzon, Mindoro, Cebu quantification of interacting populations and Bohol) (Figure 1). of fungi in mixed species soil-based systems (Thornton, 2004). Monoclonal Exploring the microbial antibodies have also been used to flora of Philippine Figure 1. Collecting samples from develop user-friendly, diagnostic tests mangrove sites in the Philippines (lateral flow devices (LFDs)) for the mangroves for enzymes rapid detection of plant pathogens and and antimicrobials beneficial fungi in soils and in plant materials (Thornton, 2008, Thornton et The search for natural sources of al., 2004). One such device has been novel pharmaceutical products is still developed for tracking biocontrol strains very much ongoing worldwide. The of Trichoderma in the plant Philippines, an archipelago of 1700 rhizosphere (Thornton, 2008). Lateral islands, is one of the most diverse areas flow technology is now being used at in the world, so could be a potential Exeter University to develop highly source. Among the places in the country, specific LFDs for the rapid detection of its mangrove ecosystem is a good fungi of medical importance. candidate to search for novel Monoclonal antibodies specific to microorganisms. The Philippines are Scedosporium spp., Rhizopus spp., home to rich mangrove forests. They are Fusarium spp. and the drug-resistant still an untapped ecosystem in terms of yeast Candida glabrata are currently microbial diversity, especially those that being developed. An LFD specific to are under the protection of the Decaying leaves, wood (twigs) water Aspergillus spp., has already been Department of Environment and Natural and mud samples were collected away developed for the rapid serodiagnosis of Resources. from human settlements and bacteria, IA (see accompanying figure). The LFD Mangroves are a dynamic ecosystem. yeasts and moulds were isolated from incorporates a mAb that binds to a Being a natural sink, microbial them. This was done by serial dilution in protein epitope on an extracellular interactions in the mangroves are vital, 1.5% Sodium Chloride (NaCl) and antigen secreted constitutively during converting plant litter to nutritious food spread-plating on marine agar invasive growth of the pathogen. sources for marine organisms. supplemented with cycloheximide for Circulating antigen can be detected in Mangroves, therefore, would naturally bacteria, yeast mannitol agar with 1.5%

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NaCl supplemented with Rose Bengal common mould species. against the human pathogens S. aureus for yeasts and acidified potato dextrose Assays for degradative enzymes (including MRSA), C. albicans and agar with 1.5% NaCl for moulds. revealed a good number of strains E. coli. Some isolates also showed Representative colonies, differing in producing lipase (bacteria: 265 strains vibriostatic activity against the shrimp morphological and cultural of 429 assayed, yeasts: 71 of 100, pathogens V. harveyi and V. campbellii characteristics, were selected, purified moulds: 77 of 152), amylase (bacteria: (Figure 2b). and preserved by L-drying and by deep- 139 of 421, yeasts: 9 of 100, moulds: 64 freezing at -70oC with glycerol as back- of 141), proteinase (bacteria: 218 of up. Mould isolates were kept on agar 273, yeasts: 41 of 100, moulds: 91 of Figure 2b. Isolates showing vibriostatic slants with sterile mineral oil. A total of 144), cellulase (bacteria: 67 of 133, activity against the shrimp pathogens V. 1,234 isolates (929 bacteria, 168 yeasts moulds: 40 of 79, yeasts: none of 45) , harveyi and V. campbellii and 137 moulds) were preserved. and the LMEs, xylanase (bacteria: 3 of 133, moulds: 41 of 79, yeasts: none of Screening for Enzymes 45) and polyphenoloxidase (bacteria: 18 The isolates were assayed for lipase, of 293, yeasts: 3 of 100, moulds: 5 of amylase, proteinase, cellulase, the 133). Some strains even exhibited lignin-modifying enzymes (LMEs) — multiple enzymatic properties. Figure 2a laccase, xylanase, polyphenoloxidase — shows a bacterial isolate exhibiting and also the peroxidase types of LMEs. casein hydrolysis. These enzymes were selected for their various agricultural and industrial uses. Screening for antimicrobials Cellulase and amylase, which are Antimicrobial activity of the purified produced by species of Trichoderma mangrove bacterial isolates were tested and Aspergillus, for example, are used against the human pathogens as food additives in poultry. Cellulases Escherichia coli, Candida spp. and are used to hydrolyse wood. Some Staphylococcus aureus using the zone strains of marine bacteria have also of inhibition assay. Isolates that inhibited been reported to have cellulolytic S. aureus were further assayed against activities and have been useful in feed five strains of methicillin-resistant Some of the isolates with promising formulations (Inagaki, 1998). Rhizopus S. aureus (MRSA) obtained from the enzyme and/or antimicrobial properties spp., on the other hand, produce lipase Philippine General Hospital have been identified. Characterisation that can potentially substitute triclosan Microbiology Laboratory. The isolates and identification of the other isolates is in the soap industry. Xylans, the major were also tested against important still ongoing. components of the hemicellulosic shrimp pathogens in aquaculture, Vibrio My sincere gratitude goes to SfAM for fractions of terrestrial plants are tough harveyi and Vibrio campbellii. the financial support from the President’s materials to degrade. A variety of Microorganisms are a prolific source Fund and to the organisers of the 11th microorganisms have been reported to of structurally diverse bioactive International Culture Collection Congress degrade wood xylans including yeasts metabolites and have yielded some of (ICCC-11) which enabled me, from the e.g. Cryptococcus albidus, the most important products of the other side of the globe, to present part of Aureobasidium pullulan and pharmaceutical industry. Of the 12,000 my work in two poster papers at this Trichosporon spp and bacteria e.g. antibiotics known in 1995, 55% were event in Goslar, Germany and to Bacillus subtilis as well as the more produced by filamentous bacteria, 11% participate in the pre-congress training from other actinomycetes, 12% from on culture collection quality management non filamentous bacteria and 22% from Figure 2a. Bacterial isolate exhibiting in DSMZ in Braunschweig from October filamentous fungi. New antibiotics are casein hydrolysis 6th-11th, 2007. needed because of the development of resistant pathogens, the evolution of new diseases, the existence of naturally References resistant bacteria (e.g. Pseudomonas ■ Demain, A.L. (1999). Pharmaceutically active secondary aeruginosa in cystic fibrosis patients), metabolites of microorganisms. Applied Microbioliology and Biotechnology, Vol 52, pp455-463. and the toxicity of some of the current ■ Inagaki, K., Nakahira, K., Musai, K., Tamura, T. & compounds (Strohl, 1997). New Tanaka, H. (1999). Gene cloning and characterisation of an acidic xylanase from Acidobacterium capsulatum. bioactive products from microbes are Bioscience, Biotechnology and Biochemistry, Vol 62 No 6, being discovered at an amazing pace: pp1061-1067. 200-300 per year in the late 1970s, ■ Primavera, J.H. (2000). Development and conservation of Philippine mangroves: Institutional issues. Ecological increasing to 500 per year by 1997 Economics, Vol 35, pp91-106. (Demain, 1999). Thus, we hope that ■ Strohl, W.R. (1997) Industrial antibiotics: today and the future. In Strohl, W.R. (ed). Biotechnology of Antibiotics, isolates with promising antimicrobial 2nd ed. Marcel Dekker, New York. pp1-47. properties will also be discovered from our diverse mangrove ecosystem. Indeed, a number of the isolates Rosario Gionson-Monsalud exhibited antimicrobial properties

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ROOM TEMPERATURE STORAGE

ÊÊÊÊÊÊÊÊÊÊÊÊÊÊ “>ˆ\ʈ˜vœJÌiV ˜œ‡«>Ì °Vœ“ÊÊÊÊÊwww.techno-path.com 7 Westwood Court, Neston, Cheshire CH64 3UJ /  "*
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54 advertise in Microbiologist With a targeted circulation of 2,000 copies, Microbiologist is an effective way to reach decision makers in industry, academia and public services, both in the UK and worldwide. For more information about advertising your products or services in Microbiologist please contact the Manufacturer of premium dehydrated culture media since 1978 Society Office on 01234 326846 or visit the website s Manufactured in ISO approved facilities s Many ISO formulae available at www.sfam.org.uk s Custom packaging and manufacturing available s Chromogenic and pre-supplemented media available

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55 commercial

Microbiological Laboratory to 20%; control CO2 in 0.1% increments from 0.1% to 15%; control relative humidity up to Manuals from Campden BRI 90%; and provide precise temperature control. The data capture option allows information to be Campden BRI produces a number of manuals downloaded onto a memory stick for further of relevance to laboratory microbiologists. In analysis. addition to the well established Manual of The modern design of the Hypoxystation Microbiological Methods (Guideline 43), now in its includes a full colour touch screen panel that fifth edition, we have recently published the sixth displays a host of information about real time edition of the Catalogue of Rapid Microbiological environmental parameters in the workstation. A Methods (Review 1). Using simple tables for ease removable front option is also available. of cross-referencing, it lists over 400 kits from around 50 kit manufacturers. It covers pathogens further information of interest to the agri-food chain, spoilage organisms (e.g. yeasts) and hygiene testing. visit: www.dwscientific.co.uk In addition to the name Tel: +44 (0)1274 595728 and principle for each Email: [email protected] method, it gives the time corporate taken for the test, the name of the manufacturer along with contact details, NCIMB Microbial news comments on validation Identification Service status of the method, and The latest news, views and microbiological references for further The NCIMB Microbial Identification Service has developments from our corporate members reading. over 30 years´ experience of providing fast, As well as these confidential and accurate identification of bacteria methods publications, A and fungi, now to Good Manufacturing Practice code of practice for microbiology laboratories standards. handling food, drink and associated samples Over the years we have isolated and identified (Guideline No. 9), now in its third edition, will help organisms from some very unusual sources, would food microbiologists to run their laboratories safely you believe microchips and bedbugs! Our and efficiently and help ensure that they generate particular expertise however is in the results that are valid and meaningful. pharmaceutical, environmental and personal healthcare sectors where we provide a rapid and further information flexible service to suit our clients’ needs. visit: www.campden.co.uk We use the MicroSeq® methodology for Tel: +44 (0)1386 842048 genotypic identification which is one of the most Email: [email protected] accurate and reproducible solutions for bacterial and fungal identification available. MicroSeq® together with the UK’s National Collection of Industrial, Food and Marine Bacteria provides us Oxygen control for with a unique source of reference material to microbiology? ensure we give our clients the assurance they require in their identifications. Don Whitley Scientific’s H35 Hypoxystation was Genotypic identification is ideal for ● originally developed for cell culture research, Viable and non-viable material ● however it has emerged that this workstation has Organisms with complex growth applications within microbiology. It’s not only requirements ● cell/tissue culture scientists who might want to Gram variable isolates ● Slow-growers have tight control over O2 and CO2. ● According to Klaus Winzer at the Centre for Other fall-through organisms difficult to Biomolecular Sciences at Nottingham University, classify using other techniques there is a place for the Hypoxystation in his Other services available include secure storage laboratory. Dr Winzer has ordered a unit and preservation of bacterial cultures, chemical specifically for the accurate, precise control of analysis, ecotoxicological testing, and an extensive oxygen that the H35 will afford him in his work range of bacteria, bacteriophage and plasmids. with microaerophilic and capnophilic bacteria. He further information also intends to use the H35 to investigate how strictly anaerobic bacteria such as clostridia visit: www.ncimb.com respond to oxygen exposure. Tel: +44 (0) 1224 711100 The main features of the H35 include the ability Email: [email protected] to control oxygen in 0.1% increments from 0.1%

56 result, it is increasingly important to test food products and ingredients for allergens, as part of an allergen HACCP plan, to ensure that products have not been contaminated via raw materials, production lines or the environment in general. Raw materials, finished products and environmental swabs can all be tested using the ELISA Systems tests. Products in the range include tests for almond, buckwheat, crustaceans, egg, gliadin, hazelnut, milk (separate tests for casein and beta-lactoglobulin), mustard, peanut, sesame and soy. Bacterial resistance is futile One advantageous feature of these products is Lab M’s Captivate enhances the simple extraction process, which minimises the immunomagnetic searation sample preparation time and is common across the range. All critical test reagents are in a ready Lab M’s innovative Captivate™ to use liquid format, and presented in colour immunomagnetic separation (IMS) products coded bottles, making the tests quicker and easier accelerate bacterial isolation from food and to use. environmental samples. The antibody-coated further information microscopic paramagnetic beads enhance a range of microbiological processes, reducing the need for visit: www.oxoid.com traditional enrichment procedures. In addition to Tel: +44 (0) 1256 841144 its ready-made Captivate™ range for E. coli Email: [email protected] serotypes and Salmonella isolation, Lab M provides a custom coating service. Of particular importance in the isolation of Escherichia coli O157:H7 from meat and milk samples, Captivate can reduce the time required for total viable counts, delivering presumptive negative results for pathogens more rapidly. By combining the power of Captivate beads with Lab M’s chromogenic media, bacterial testing methods NRS II™ Transwabs® reach new levels of sensitivity and efficiency. Captivate beads consist of a magnetite core A new generation of environmental enveloped by a ceramic zirconium oxide coating sampling devices for the food and and have an average size of 2.5 µm. When mixed pharmaceutical industries. Medical Wire has with a sample suspension and incubated, the launched a new range of surface sampling devices, antibody-coated beads “capture” the target based on the best selling NRS™ Transwab®, and bacteria by forming an antibody-antigen complex. using a new swab and tube combination designed These complexes are separated from any for effectiveness and convenience. background organisms or interfering materials All NRS II™ devices feature Medical Wire’s new using a magnetic concentrator. The beads can leak proof labelled screw cap tube made from then be plated to the appropriate selective media shatter proof polypropylene, with a highly visible or used in other analyses following a blue shaft swab attached to the cap. The tubes are straightforward wash procedure. pre-filled with the specified volume of solution further information with a choice of NRS™ (Medical Wire’s classic neutralising solution), Buffered Peptone Water, visit: www.labm.com Butterfield Solution, DE Neutralising Broth, Tel: +44 (0)161 797 5729 Letheen Broth, or Peptone Saline. A dry swab Email: [email protected] version is also available for customers who need to use their own formulations. These devices conform to the requirements of Food allergen test kits ISO18593, and other national and international available from Oxoid standards. further information The world leading ELISA Systems range of quick and easy-to-use food allergen tests kits is now visit: www.mwe.co.uk or www.mwe-usa.com available from Oxoid. Foods with the potential to Tel: +44 (0)1225 810361 cause an allergic reaction are often those Email: [email protected] commonly used by food manufacturers, as a

57 commercial

Certificates of Analysis from information SGL Are you a corporate Now available from the SGL website, product member of the Society? Certificates of Analysis. With any laboratory quality If so, this section of Microbiologist is for system the manufacturers Certificate of Analysis is you. Here you can a key document showing that the product publish short press being used in the releases, acquisition laboratory is fit for notices, news of new Range Extension for purpose. Traditionally staff appointments, these documents are technical developments Microbiology Stains supplied in paper and much more. Microbiology Stains manufactured by Pro-Lab format at the request Each corporate member Diagnostics now includes a full range of staining of the laboratory. SGL of the society may are now able to provide publish up to 200 kits, including Gram kits with various words on a topic counterstains, Cryptosporidium Staining Kits, and electronic copies of these documents that can be related to their field of a full range of ZN Staining Kits, in 250ml and downloaded from our website at your activity in each issue of 500ml format, samples available on request. convenience, all you need is the product batch Microbiologist. For Immersion oil is also available, now supplied number. So, to download your Certificates of further information free of Dibutyl Phthalate (DBP) in convenient 50 ml Analysis please visit www. sglab. co.uk. please contact Lucy dropper bottles. Samples on request. Harper by email at: further information [email protected] visit: www.sglab.co.uk Both corporate members and ordinary Tel: +44 (0)1536 403815 members of the Society Email: [email protected] will find a wealth of useful information and resources in this section. Microbial Identification — can it get any simpler?

Technopath are pleased to announce the release of the new semi-automated version of the revolutionary Biolog Identification system. Building Ruskinn Success Story on the success of the automated version this brings Biolog to the labs that don't have a large Renowned Internationally for the design of high throughput of identifications. quality Anaerobic, Microaerophilic and Hypoxic With no gram stain, no pre-tests and no follow Work Stations, Ruskinn Technology Limited has on tests microbial identification is now simpler introduced more innovative features to the range than ever before. There is only 1 test panel for all of cabinets available. The Gas Mixer Q offers 0- aerobic bacteria which makes stock control much 20.9% O2 control with incremental steps of 0.1% simpler and with over 1,000 species covered in the (both gases) giving precise environments. Visual database the Biolog system is suitable for a wide alarms, a 0-30% CO2 gas analyzer for direct CO2 range of laboratories. control, Auto- Communication Port to download Biolog also offers the unique opportunity to data to PC/memory stick, event log for gas, build your own custom database from your own Hypoxic Cycling for maximum, Retrofit Interface to isolates and retrospectively analyse all your data all existing Invivo2 placements and a Touch screen and compare the history of your identifications. to facilitate user interface. The identification panel itself takes only 1 Pro-Lab Diagnostics are proud to represent minute to set-up and with additional bolt on Ruskinn Technology in the UK and have recently databases it is possible to also identify Anaerobes, been awarded the accolade of International Yeast and Moulds. Existing Biolog customers can Distributor of the Year, a clear indication of the simply upgrade their systems without the need of quality and reliability of the cabinets. purchasing new equipment.

further information further information visit: www.pro-lab.com. visit: www.techno-path.com Tel: +44 (0) 151 353 1613 Tel: +44 (0)283 0833 808 Email: [email protected] Email: [email protected]

58 BD Diagnostic Systems

Solutions for Industrial & Clinical Microbiology

BD Diagnostics 21 Between Towns Road Cowley Oxford OX4 3LY Tel: 01865 781677 Fax: 01865 781528 www.bd.com BD, BD Logo and all other trademarks are the property of Becton, Dickinson and Company. ©2005 BD. of Becton, Dickinson and Company. the property BD, BD Logo and all other trademarks are Complete Media Assurance

Culture Media for Harmonised Microbial Limit Tests (Ph. Eur, USP, JP)

Oxoid have the full range of culture media for the microbiological examination of non-sterile pharmaceutical products: s &ULLYVALIDATEDACCORDINGTOTHEHARMONISED-,4METHODSIN the Ph. Eur, USP and JP s 6ALIDATIONPACKAGEAVAILABLEONREQUEST s #OMPLETERANGEFORMICROBIALENUMERATIONANDTESTSFOR specified micro-organisms s 1UALITY#ONTROLTESTEDUSINGRECOMMENDEDSTRAINS

To find out more contact: Tel: +44 (0) 1256 841144 Fax: +44 (0) 1256 329728 Oxoid, Wade Road, Basingstoke, Email: oxoid.pharma@thermofisher.com DEDICATED TO MICROBIOLOGY Hants RG24 8PW www.oxoid.com