MICROBIOLOGY NEWSLETTER Showed That Antigens and Nucleic Acid from NEW SCHEMES and UPDATES These Parasites Can Be Detected in Lyophilised Faeces

July 2015

MICROBIOLOGY NEWSLETTER showed that antigens and nucleic acid from NEW SCHEMES AND UPDATES these parasites can be detected in lyophilised faeces. Microscopy based fluorescent conjugat- ed antibodies can also be detected in lyophilised Parasitology Goes Molecular! faeces. Molecular Diagnosis of Malaria UK NEQAS Parasitology intends to commence a After a successful pre-pilot Scheme for the molec- pre-pilot scheme for the non-microscopic detec- ular diagnosis of malaria in which a total of 28 par- tion of these parasites later in the year. If you ticipants from 19 countries participated, the would like to participate in this pre-pilot scheme, scheme is now entering its pilot stage. The pilot please contact Monika Manser at para- stage will consist of four lyophilised blood speci- [email protected]. mens in two distributions, one batch to be sent in August 2015 and the other to be sent in February 2016. The pre-pilot scheme was successful for the following reasons:  Lyophilised blood proved to be an effective matrix as it was straightforward to reconsti- tute and extract the DNA.  The majority of participants’ results were in good agreement with the intended results.  It fulfilled the criteria of EQA in that the specimens should help participants take individu- Oocysts of Cryptosporidium sp. stained al action to investigate and remedy any dis-

crepant results.  Lyophilised blood proved to be a stable matrix when shipped at ambient temperature, as shown by the pre and post distribution results. This obviates the need for a cold chain during distribution, significantly reduc- es associated costs and opens up the distribution of such samples to a much wider audience.

Non-microscopic detection of modified Ziehl-Neelsen Cryptosporidium species, Giardia intestinalis and Entamoeba histolytica

The use of tests other than microscopy for the ex- amination of faecal specimens for Cryptosporidi- um species, Giardia intestinalis and Entamoeba histolytica is becoming increasingly popular in clinical laboratories. UK NEQAS Parasitology has re- sponded to this observation and has examined different preservatives For Microbiology and alternative specimen forms in in order to be able to detect these parasites by non-microscopic methods. A small study

SCHEMES UPDATES WHAT’S IN A NAME?

Interpretative Comments Scheme Update A rose smells as sweet by any other name The Microbiology Interpretative Comments What names do has exercised philosophers and scheme was established in 2009 as a tool to authors for centuries. A rose does indeed smell support CPD for Medical Microbiologists and as sweet by any other name but that makes life Virologists through the provision of clinical very difficult if you are trying to buy that lovely scenarios. Participants were invited to provide pink rose you saw on holiday for a prime position free text answers to questions posed by the in your garden. You may recognise its smell and organising panel. Model answers, supported form but without a name you could be in for a lot by a commentary and references were then of nursery visiting. posted, together with all other participant’s We have some experience of this in microbiology, anonymised answers, to allow participants to and medical microbiology in particular. We have self-assess their knowledge and its application lived through a period of lumpers and splitters as to the scenario. Following consultation with biochemical profiling became more sophisticated. participants in 2014, the distributions were We may be about to enter another similar era as changed to include an MCQ format for the genomics and mass spectrometry give us more Q&As associated with the distributions. The data than we are used to. introduction of the MCQ format has been successful with an increasing level of What we call bacteria is important for us but also participation during the last year, averaging important for the clinicians who read our reports. over 100 participants for each distribution. We want the end result to be the best possible treatment for the patient and for the population in

which they find themselves. We have moved be- Although the original scheme covered mainly yond “bacteria present, susceptible to tetracy- Bacteriology, Parasitology and Mycology, a cline” to reporting Staphylococcus aureus sus- recent initiative has been to add bi-monthly ceptible to tetracycline. However we tend to re- Virology distributions. Now distributions are port MRSA rather than Staphylococcus aureus been posted monthly, with the focus of cases resistant to methicillin; the former has more alternating between Virology and Microbiology. meaning to our colleagues than the latter. From the virology perspective, cases will In sequencing terms a Streptococcus mitis and a reflect scenarios that would reasonably occur pneumococcus are indistinguishable yet we in a general hospital, to illustrate common would clearly report a pneumococcus as such if pitfalls, as well as some more unusual presen- we thought it was present. Indeed we would do tations. We hope the addition of regular the necessary tests to exclude or confirm its pres- virology distributions will attract Virologists to ence rather than leave an identification at Strep- register with the scheme. Although UK NEQAS tococcus mitis, whatever a sequencing identifica- has not yet implemented scoring for the inter- tion based scheme stated. In some ways we have pretative scheme, there is a potential to pro- a similar but less well thought through problem vide scores for individual participants, which with the MALDI-TOF. This sophisticated technol- might be useful to demonstrate competence ogy can readily identify organisms with more ap- e.g. for appraisal & revalidation. We would wel- parent certainty than biochemical testing. Howev- come feedback from Virology colleagues about er when being faced with a MALDI-TOF identifi- the scheme. cation we do need to remember some basic prin- Dr Paul Chadwick ciples; the underlying science (blow up an organ- ism and identify the unique bits) is potentially im- IC Scheme Organiser precise, the output is based on an (expanding) database of previous results and has a sensitivity and specificity which may or may not be taken into account. We then have to consider the impact and utlity of our report; a recent UK NEQAS wound swab distribution illustrates this point. WHAT’S IN A NAME?

The intended result was Aeromonas hydrophila Fortunately only a small number, counted in the and this result was obtained by traditional bio- hundreds rather than the thousands, are seen chemical results. The MALDI-ToF gave a result of causing human infection, although with advanc- Aeromonas blahblah, a little known sub-species of es in medical science the pool of patients sus- hydrophila. To report it as such is scientifically cor- ceptible to fungal infection is ever increasing rect but probably less useful to clinical colleagues and we regularly see opportunistic infections than including the term hydrophila in the report. As with previously unreported species. Medical my- always we should consider the output of our tests, cologists therefore have an easier time than what it means for the patient and how we can best plant or insect pathologists and much of the convey that to our clinical colleagues. more weighty literature on the intricacies of ge- That rose we saw may well have delicately col- netic relatedness are of more relevance to oured buds which open to form perfectly shaped, them. large rosette blooms of rich, deep pink, with a Of course one of the interesting things about wonderfully strong, sweet heady fragranced flow- fungi is that they have sexual (teleomorph) as ers. If we were told it was a Rosa Ausbord we well as asexual (anamorph) forms and over the might struggle to find it; if we were told it was a years this had added to the classification Gertrude Jeykll we would be able to get one from innumerous retailers. conundrums as each form had its own name. However, recent changes in the ‘International Dr Tony Elston Nomenclature for algae, fungi and plants’ has Chairman NQAAP for Microbiology resulted in the move to one name per species. This is an excellent initiative in the longer term but may lead to short-term confusion. There has always been a convention that the sexual or teleomorphic name takes precedence but over the years medical mycologist have pretty much One fungus – one name: keeping up with the ignored this as it was the asexual or anamor- taxonomists. phic state we were growing in the laboratory, so If I was to tell you that the second most common that was what we reported. This together with yeast causing invasive infection is only distantly the fact that many accepted fungal genera have related to Candida albicans and is actually in the proved to be polyphylogenetic and must there- Nakaseomyces clade, that Neosartorya is the fore be split and renamed means that we will most common invasive mould pathogen and that certainly have to introduce and get used to new Haematonectria haematococca is the mould most names for old familiar morphologies. What is frequently isolated from blood culture you might also clear is that phenotypic identification based wonder if I had been ingesting some of the more on colonial and microscopic morphology may hallucinogenic members of the 5th Kingdom. How- not be possible in several medically important ever, if the rules of taxonomy are followed then groups such as the old Fusarium (812 species Candida glabrata, Aspergillus fumigatus and at the last count) and Acremonium (209 spe- Fusarium solani species complex may well be cies) genera. more correctly referred to by these names. This In such cases it may be comforting to remem- however is a mere snap-shot of the upheaval cur- ber that it doesn’t much matter to the patient rently underway in the fungal world. what the fungus is actually called, it is which For many years fungal taxonomists had relied on antifungal drug(s) it responds to that is im- careful analysis of phenotypic traits such as mor- portant so timely susceptibility testing may take phological, physiological and biochemical charac- on an added importance if the identification is going to take a while. teristics to construct taxonomic trees, however recent advances in molecular technology have given them very powerful tools to probe the geno- typic relationships. Fungi are one of the largest and most fascinating groups of organisms on the planet and more species are being discovered on a daily basis WHAT’S IN A NAME? One lesson we learned was not to follow the In many cases a pragmatic approach has been taxonomists too quickly in the renaming game. adopted for rationalising the classifications. For A case in point was with the mucoraceous example the type species of the Aspergillus ge- mould Absidia corymbifera which for a couple nus is A. glaucus so this clade should have of years became Mycocladus corymbiferus until been the only one that retained the Aspergillus finally settling into the name by which it was genus name whilst the remainder reverted to first described (as is the usual nomenclature their teleomorph genera. However there were rule) of Lichtheimia corymbifera. I think that this other Aspergillus species with a compelling rea- is a great name for this species as licht-heim is son supporting a desire to retain the current ter- German for light-home which beautifully de- minology: A. fumigatus in the medical field, A. scribes the lamp-like appearance of the sporing flavus from a food science and mycotoxin per- head (Fig 2). spective and A. nidulans due to its widespread use as a genetic model. One of these could have been erected as the new type species but that would have meant the others would still re- vert to their teleomorph names. Instead a fix Fig. 2 proposed by the International Commission of Lichtheimia corymbifera Penicillium and Aspergillus (ICPA) supports the retention of Aspergillus for a majority of the species and use of the teleomorph name to indicate the presence of structures with biological signifi- cance e.g. Aspergillus nidulans with emericella- type fruiting bodies (Fig 1).

When introducing new names for old familiar species it is important to make clinicians aware of the change as in ‘formerly known as’ and it may be necessary to continue this for several

years. I know some labs still note that what is now Neoscytalidium dimidiatum used to be known as Hendersonula toruloidea although that name was replaced more than a quarter of a century ago and has been through several changes since! There are few people in the field now who will even remember the name

Monilia albicans but when I first started in medical mycology there were still some die-hard clinicians that insisted on this terminology for Fig 1. Aspergillus nidulans with emericella-type fruit- what is now widely accepted as Candida albi- ing body cans. So times move on and we should em- brace these nomenclature changes which will in the end lead to a much more stable bed-rock and a better understanding of the true genetic relationships in the fungal world. WHAT’S IN A NAME?

As a final word the following is a list of some of the more common names we have already adopted (this is by no means a definitive list):

Previous name Adopted name Absidia corymbifera Lichtheimia corymbifera

Bipolaris australiensis/hawaiiensis Curvularia australiensis/hawaiiensis

Chrysosporium keratinophylum Aphanoascus keratinophilus

Cylindrocarpon lichenicola Fusarium lichenicola

Geosmithia argillacea Rasamsonia argillacea

Ochroconis gallopava Verruconis gallopava

Paecilomyces lilacinus Purpureocillium lilacinum

Penicillium marneffei Talaromyces marneffei

Philophora richardsiae Pleurostomophora richardsiae

Ramichloridium mackenziei Rhinocladiella mackenziei

Scopulariopsis brevicaulis Microascus brevicaulis

Scytalidium dimidiatum Neoscytalidium dimidiatum (at one time Hendersonula toruloidea) Trichosporon capitatum Saprochaete capitata (via Blastoschizomy- ces capitatus) Scedosporium prolificans Lomentospora prolificans (will be next)

Acremonium spp. Sarocladium spp. (medically important species) (soon) Fusarium solani clade Haematonectria haematococca (one day!)

Dr Elizabeth Johnson Director, National Mycology Reference Laboratory, Bristol (UK)

RETIRING ORGANISER—DR VIVIENNE JAMES

Sixteen years working as part of UK NEQAS: To enable the continued developments many of our processes have been streamlined; not all of the reflections of a retiring Organiser these changes were seen by the participants as

beneficial at the time! In 1999 there were 17 sepa- The past sixteen years have witnessed a large rate dispatches that became a logistical nightmare number of changes affecting the operation and when we needed to introduce additional schemes delivery of UK NEQAS for Microbiology. and dispatches. So in 2002 the distributions were Although the management of the EQA schemes consolidated and the number of dispatches was is the responsibility of the Organisers, for the reduced to 13. We continue to have between 12 service to be useful to participants it is essential and 13 dispatches a year. The extent of the pack- that there is a wide range of advice and coming processes is truly phenomenal with around ment available to the Organisers. This is provid- 160,000 samples of nearly 600 different speci- ed by a Steering Committee and specialist Advi- mens sent a year, to participants in over 60 coun- sory Groups, consisting of experienced microbi- tries, with very few errors. The participation rate ologists representing the interests of the labora- when counted as participants registered in tory community. In 1999 the Chairman of the schemes about 11,000 and when estimated as Steering Committee was Dr Ian Farrell. He was distributions received by participants is nearly succeeded in 2004 by Dr Erwin Brown and then 40,000. To assist in the process and further re- in 2009 by the current Chairman Professor Pe- duce errors due to human factors we introduced a ter Hawkey. Virology advice was provided un- barcode system so that hopefully every participant der the Chairmanship of Professor Paul Griffiths receives the correct schemes and the right num- and more recently by Professor Goura Kudesia. ber of specimens. The Specialist Antimicrobial Susceptibility Test- Handling all the participants’ details and distribu- ing Group continues to be chaired by Dr Derek tion results necessitates the use of a database. Brown. I am truly indebted to them for their ad- The original EQA database was DOS (Disk Oper- vice, support, leadership and friendship. ating System) based and written by the Organiser The majority of the developments in relation to Jerry Snell. The database held the participant reg- the schemes available have been made to ad- istration information, results information and pro- dress the quality assurance needs for molecular duced summary statistics on performance. Those testing. There are now eleven schemes suitable of you who were participating at that time may re- for laboratories using molecular methods for the member that the individual results and perfor- qualitative and /or quantitative detection of over mance information for each distribution was post- 20 different microorganisms and where relevant ed as a single A4 sheet along with the summary these include genotyping. The range of serolo- report that was produced using a combination of gy schemes has increased by over 50% and we MS Word and Excel. In 2001, in anticipation of the have introduced schemes to address point of retirement of the Organiser, we moved to a care and rapid testing methods. The original MUMPS (Massachusetts General Hospital Utility provision of 18 schemes has increased to the Multi-Programming System) based system devel- current 43 and in the intervening years five ad- oped for EQA by colleagues at the Wolfson Insti- ditional schemes have been discontinued. tute and UK NEQAS for Clinical Chemistry. The Things have not remained static with the extant move to a new system necessitated extensive schemes. The schemes are reviewed on a reg- checking to ensure the transferred data was accu- ular basis and all schemes have been devel- rate. The benefits where that the statistical opera- oped so that the distribution reports include in- tions were automated and individualised reports formation of methods used which is really help- were generated directly from the database. As a ful in determining if there is an issue with a rea- follow on from this, in 2004, we were able to pub- gent, kit or particular methodology. lish the reports on the secure area of the website.

RETIRING ORGANISER This meant we could reduce the environmental This is just a snapshot of all the changes that impact and more importantly participants are able have taken place. It doesn’t include introduc- to retrieve their reports at any time. The improve- tion of new equipment, introduction of new as- ments to the database didn’t stop there. In 2005 says or the specifics of the development of new the operating system was upgraded to SQL schemes. As those of you involved in gaining (Structured Query Language) in line with the cur- accreditation to new standards will know these rent industry standard for databases. Our web- changes require intensive planning, procure- sites also continued to be improved with the se- ment, validation and verification to ensure the cure site accepting direct entry of results in 2007 changes are fit for purpose and such that you and a total revamp of the main website in 2013. retain your accreditation status. In addition to The website is a major information resource for this we moved laboratories and offices twice in both prospective new participants as well as for this time although we are now back where we our current participants. Of course if you can’t find first started in refurbished and open plan offices the information you want there you can always and laboratories. email us or give us a call. Of course none of the achievements of the past In the background to all these IT changes has sixteen years could have happened without the been the work to support them and our IT manag- hard work and professionalism of the staff. er has been kept very busy creating a virtualised Here the changes have been extensive with network, creating additional databases to record people coming and going. Of the original team all aspects of the design, characterisation and pro- in 1999 there are still six people remaining in- duction of the specimens from the raw materials to cluding Christine Walton the Organiser of the the final product. bacteriology EQA schemes. Back in 1999 there were four virologists, five bacteriologists, two Quality is at the core of our operation. In 1999 we parasitologists, three administrators and five had a very well developed quality management support staff. Many of these staff doubled up in system (QMS) in place. The EQA schemes were the roles needed to run an EQA service so in accredited by CPA to ISO Guide 43:1997 addition to their primary area of expertise they (Proficiency testing by interlaboratory compari- took on additional duties such as laboratory sons) and we had the honor of having the refer- manager, quality and IT; the Laboratory Direc- ence number CPA (EQA) 001. Our quality man- tor was the Organiser and an IT whiz. In 2015 ager at that time was also responsible for the la- there are eight virologists, eight bacteriologists, boratory aspects for the virology schemes. In three parasitologists, eight administrators, up to 2004 we were fortunate in recruiting Shân Lloyd nine support staff with a production supervisor, as our Quality Manager. Shân had been em- a laboratory/operations manager, a quality ployed by the WHO and she had the drive and de- team of two, an IT manager and a project team termination to convert the QMS to a fully electronic of three. system. We introduced Qpulse in a stepwise fash- ion and this was completed in 2006. Of course It is 44 years since the microbiology NEQAS nothing in this field stands still with new versions distributions started in 1971 so my story relates of software being introduced regularly. I was for- to just a fraction of the history of the service tunate to be a UK expert involved in the prepara- which continues to evolve to fulfil the needs of tion of the first international standard for EQA/PT its participants. In the next 16 years we are providers, Conformity assessment — General re- likely to witness major changes in the detec- quirements for proficiency testing, ISO/CASCO tion, characterisation and diagnosis of infec- 17043 that was published in 2010. In 2012 we tious diseases and I wish all concerned suc- were accredited to this standard by UKAS. cess for the future.

RETIRING ORGANISER NEQAS FOR MICROBIOLOGY OPERATIONS TEAM

Please contact our Operations team if you have any queries regarding requests for repeat

samples, website problems or any other customer issues:

UK NEQAS for Microbiology PO BOX 63003 London NW9 1GH Tel: 020 8905 9890 Email: [email protected] Website: www.ukneqasmicro.org.uk

The Operations team members are:

Mrs Rinu Bandopadhyay Mr Sukamal Das Mrs Nazma Kadri

Mrs Vay Mistry Mr Vipul Sharma 2005 Mr Joshim Uddin

UK NEQAS MICROBIOLOGY With thanks from the UK NEQAS Team… DIVISION 2015 SCIENTIFIC MEETING Vivienne has steered UK NEQAS microbiology through times of great change over the last 16 years, and would oversee many defining moments and major developments. So on behalf of the team, and from me personally, I wish Vivienne all the best in retirement. Christine Walton

Bacteriology Scheme Organiser

Registration is now open – early bird price available up to 30 September. For more information please contact email: [email protected]