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BD-CS-057, REV 0 | AUGUST 2017 | Page 1
EXPLIFY RESPIRATORY PATHOGENS BY NEXT GENERATION SEQUENCING Limitations Negative results do not rule out viral, bacterial, or fungal infections. Targeted, PCR-based tests are generally more sensitive and are preferred when specific pathogens are suspected, especially for DNA viruses (Adenovirus, CMV, HHV6, HSV, and VZV), mycobacteria, and fungi. The analytical sensitivity of this test depends on the cellularity of the sample and the concentration of all microbes present. Analytical sensitivity is assessed using Internal Controls that are added to each sample. Sequencing data for Internal Controls is quantified. Samples with Internal Control values below the validated minimum may have reduced analytical sensitivity or contain inhibitors and are reported as ‘Reduced Analytical Sensitivity’. Additional respiratory pathogens to those reported cannot be excluded in samples with ‘Reduced Analytical Sensitivity’. Due to the complexity of next generation sequencing methodologies, there may be a risk of false-positive results. Contamination with organisms from the upper respiratory tract during specimen collection can also occur. The detection of viral, bacterial, and fungal nucleic acid does not imply organisms causing invasive infection. Results from this test need to be interpreted in conjunction with the clinical history, results of other laboratory tests, epidemiologic information, and other available data. Confirmation of positive results by an alternate method may be indicated in select cases. Validated Organisms BACTERIA Achromobacter -
Lpr0050 and Lpr0024 in Legionella Pneumophila
Characterization of the role of the small regulatory RNA (sRNAs) lpr0050 and lpr0024 in Legionella pneumophila Malak Sadek Natural Resource Sciences Department McGill University Montreal, Canada Supervisor: Prof. Sébastien P. Faucher June , 2019 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master of Science © Malak Sadek 2019 1 Abstract Legionella pneumophila is a facultative intracellular pathogen, and it is the causative agent of Legionnaires’ disease, a life-threatening form of pneumonia. L. pneumophila is commonly found in most water systems including freshwater bodies, rivers, and lakes as well as in engineered water systems and man-made water distribution systems such as cooling towers. Free-living amoeba in aquatic environments are the primary reservoir of L. pneumophila. Following inhalation of contaminated water droplets by humans, L. pneumophila infects and replicates within lung alveolar macrophages and potentially causes Legionnaires’ disease (LD) in susceptible individuals. The bacterium establishes its intracellular niche by forming the Legionella-containing vacuoles (LCVs). L. pneumophila governs the formation of the LCV and intracellular growth through the Icm/Dot type IVB secretion system. Icm/Dot is able to translocate around 300 protein effectors in the host cell allowing L. pneumophila to modulate many signalling and metabolic pathways of the host to its benefit. It is believed that Small Regulatory RNAs (sRNAs) are major players of regulation of virulence-related genes in L. pneumophila. We investigated the regulatory role of the two sRNA Lpr0050 and Lpr0024. Lpr0050 is encoded on the complementary strand of the effector SdeA. Using northern blot we showed that the cis-encoded sRNALpr0050 is expressed in the Exponential (E) phase and Post-Exponential (PE) phase in the wild-type, ΔcpxR and ΔletS. -
NCTC) Bacterial Strain Equivalents to American Type Culture Collection (ATCC) Bacterial Strains
This list shows National Collection of Type Cultures (NCTC) bacterial strain equivalents to American Type Culture Collection (ATCC) bacterial strains. NCTC Number CurrentName ATCC Number NCTC 7212 Acetobacter pasteurianus ATCC 23761 NCTC 10138 Acholeplasma axanthum ATCC 25176 NCTC 10171 Acholeplasma equifetale ATCC 29724 NCTC 10128 Acholeplasma granularum ATCC 19168 NCTC 10172 Acholeplasma hippikon ATCC 29725 NCTC 10116 Acholeplasma laidlawii ATCC 23206 NCTC 10134 Acholeplasma modicum ATCC 29102 NCTC 10188 Acholeplasma morum ATCC 33211 NCTC 10150 Acholeplasma oculi ATCC 27350 NCTC 10198 Acholeplasma parvum ATCC 29892 NCTC 8582 Achromobacter denitrificans ATCC 15173 NCTC 10309 Achromobacter metalcaligenes ATCC 17910 NCTC 10807 Achromobacter xylosoxidans subsp. xylosoxidans ATCC 27061 NCTC 10808 Achromobacter xylosoxidans subsp. xylosoxidans ATCC 17062 NCTC 10809 Achromobacter xylosoxidans subsp. xylosoxidans ATCC 27063 NCTC 12156 Acinetobacter baumannii ATCC 19606 NCTC 10303 Acinetobacter baumannii ATCC 17904 NCTC 7844 Acinetobacter calcoaceticus ATCC 15308 NCTC 12983 Acinetobacter calcoaceticus ATCC 23055 NCTC 8102 acinetobacter dna group 13 ATCC 17903 NCTC 10304 Acinetobacter genospecies 13 ATCC 17905 NCTC 10306 Acinetobacter haemolyticus ATCC 17907 NCTC 10305 Acinetobacter haemolyticus subsp haemolyticus ATCC 17906 NCTC 10308 Acinetobacter johnsonii ATCC 17909 NCTC 10307 Acinetobacter junii ATCC 17908 NCTC 5866 Acinetobacter lwoffii ATCC 15309 NCTC 12870 Actinobacillus delphinicola ATCC 700179 NCTC 8529 Actinobacillus equuli ATCC 19392 -
Legionella Survey in the Plumbing System of a Sparse Academic Campus: a Case Study at the University of Perugia
Article Legionella Survey in the Plumbing System of a Sparse Academic Campus: A Case Study at the University of Perugia Ermanno Federici 1,*, Silvia Meniconi 2, Elisa Ceci 1, Elisa Mazzetti 2, Chiara Casagrande 1, Elena Montalbani 1, Stefania Businelli 3, Tatiana Mariani 3, Paolo Mugnaioli 3, Giovanni Cenci 1 and Bruno Brunone 2 1 Dipartimento di Chimica, Biologia e Biotecnologie, University of Perugia, 06123 Perugia, Italy; [email protected] (E.C.); [email protected] (C.C.); [email protected] (E.M.); [email protected] (G.C.) 2 Dipartimento di Ingegneria Civile ed Ambientale, University of Perugia, 06123 Perugia, Italy; [email protected] (S.M.); [email protected] (E.M.); [email protected] (B.B.) 3 Ripartizione Tecnica, University of Perugia, 06123 Perugia, Italy; [email protected] (S.B.); [email protected] (T.M.); [email protected] (P.M.) * Correspondence: [email protected]; Tel.: +39-075-5857330 Received: 30 June 2017; Accepted: 29 August 2017; Published: 1 September 2017 Abstract: We have monitored the presence of bacteria belonging to the genus Legionella in the plumbing of buildings at the University of Perugia (Italy). More than 300 water samples were collected from 156 control-point taps in 41 buildings comprised in the eight campuses of the University. Legionella was absent in most samples, while it was found in only 12 buildings (29% of the total). Molecular analysis indicated the presence of L. pneumophila (serogroups 1, 8 and 6–10), L. taurinensis and L. anisa. In only three cases contamination levels were above the limit at which remedial actions are required, according to international guidelines. -
Metatranscriptomic Analysis of Community Structure And
School of Environmental Sciences Metatranscriptomic analysis of community structure and metabolism of the rhizosphere microbiome by Thomas Richard Turner Submitted in partial fulfilment of the requirement for the degree of Doctor of Philosophy, September 2013 This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derived there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. i Declaration I declare that this is an account of my own research and has not been submitted for a degree at any other university. The use of material from other sources has been properly and fully acknowledged, where appropriate. Thomas Richard Turner ii Acknowledgements I would like to thank my supervisors, Phil Poole and Alastair Grant, for their continued support and guidance over the past four years. I’m grateful to all members of my lab, both past and present, for advice and friendship. Graham Hood, I don’t know how we put up with each other, but I don’t think I could have done this without you. Cheers Salt! KK, thank you for all your help in the lab, and for Uma’s biryanis! Andrzej Tkatcz, thanks for the useful discussions about our projects. Alison East, thank you for all your support, particularly ensuring Graham and I did not kill each other. I’m grateful to Allan Downie and Colin Murrell for advice. For sequencing support, I’d like to thank TGAC, particularly Darren Heavens, Sophie Janacek, Kirsten McKlay and Melanie Febrer, as well as John Walshaw, Mark Alston and David Swarbreck for bioinformatic support. -
The Risk to Human Health from Free-Living Amoebae Interaction with Legionella in Drinking and Recycled Water Systems
THE RISK TO HUMAN HEALTH FROM FREE-LIVING AMOEBAE INTERACTION WITH LEGIONELLA IN DRINKING AND RECYCLED WATER SYSTEMS Dissertation submitted by JACQUELINE MARIE THOMAS BACHELOR OF SCIENCE (HONOURS) AND BACHELOR OF ARTS, UNSW In partial fulfillment of the requirements for the award of DOCTOR OF PHILOSOPHY in ENVIRONMENTAL ENGINEERING SCHOOL OF CIVIL AND ENVIRONMENTAL ENGINEERING FACULTY OF ENGINEERING MAY 2012 SUPERVISORS Professor Nicholas Ashbolt Office of Research and Development United States Environmental Protection Agency Cincinnati, Ohio USA and School of Civil and Environmental Engineering Faculty of Engineering The University of New South Wales Sydney, Australia Professor Richard Stuetz School of Civil and Environmental Engineering Faculty of Engineering The University of New South Wales Sydney, Australia Doctor Torsten Thomas School of Biotechnology and Biomolecular Sciences Faculty of Science The University of New South Wales Sydney, Australia ORIGINALITY STATEMENT '1 hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom 1 have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.' Signed ~ ............................ -
List of the Pathogens Intended to Be Controlled Under Section 18 B.E
(Unofficial Translation) NOTIFICATION OF THE MINISTRY OF PUBLIC HEALTH RE: LIST OF THE PATHOGENS INTENDED TO BE CONTROLLED UNDER SECTION 18 B.E. 2561 (2018) By virtue of the provision pursuant to Section 5 paragraph one, Section 6 (1) and Section 18 of Pathogens and Animal Toxins Act, B.E. 2558 (2015), the Minister of Public Health, with the advice of the Pathogens and Animal Toxins Committee, has therefore issued this notification as follows: Clause 1 This notification is called “Notification of the Ministry of Public Health Re: list of the pathogens intended to be controlled under Section 18, B.E. 2561 (2018).” Clause 2 This Notification shall come into force as from the following date of its publication in the Government Gazette. Clause 3 The Notification of Ministry of Public Health Re: list of the pathogens intended to be controlled under Section 18, B.E. 2560 (2017) shall be cancelled. Clause 4 Define the pathogens codes and such codes shall have the following sequences: (1) English alphabets that used for indicating the type of pathogens are as follows: B stands for Bacteria F stands for fungus V stands for Virus P stands for Parasites T stands for Biological substances that are not Prion R stands for Prion (2) Pathogen risk group (3) Number indicating the sequence of each type of pathogens Clause 5 Pathogens intended to be controlled under Section 18, shall proceed as follows: (1) In the case of being the pathogens that are utilized and subjected to other law, such law shall be complied. (2) Apart from (1), the law on pathogens and animal toxin shall be complied. -
Genetic and Functional Studies of the Mip Protein of Legionella
t1.ì. Genetic and Functional Studies of the Mip Protein of Legionella Rodney Mark Ratcliff, BSc (Hons)' MASM Infectious Diseases Laboratories Institute of Medical and Veterinary Science and Department of Microbiology and Immunology UniversitY of Adelaide. Adelaide, South Australia A thesis submitted to the University of Adelaide for the degree of I)octor of Philosophy 15'h March 2000 amended 14th June 2000 Colonies of several Legionella strains on charcoal yeast extract agar (CYE) after 4 days incubation at 37"C in air. Various magnifications show typical ground-glass opalescent appearance. Some pure strains exhibit pleomorphic growth or colour. The top two photographs demonstrate typical red (LH) and blue-white (RH) fluorescence exhibited by some species when illuminated by a Woods (IJV) Lamp. * t Table of Contents .1 Chapter One: Introduction .1 Background .............'. .2 Morphology and TaxonomY J Legionellosis ............. 5 Mode of transmission "..'....'. 7 Environmental habitat 8 Interactions between Legionella and phagocytic hosts 9 Attachment 11 Engulfment and internalisation.'.. 13 Intracellular processing 13 Intracellular replication of legionellae .. " "' " "' 15 Host cell death and bacterial release 18 Virulence (the Genetic factors involved with intracellular multiplication and host cell killing .20 icm/dot system) Legiolysin .25 Msp (Znn* metaloprotease) ...'..... .25 .28 Lipopolysaccharide .29 The association of flagella with disease.. .30 Type IV fimbriae.... .31 Major outer membrane proteins....'.......'. JJ Heat shock proteins'.'. .34 Macrophage infectivity potentiator (Mip) protein Virulenceiraits of Legionella species other than L. pneumophila..........' .39 phylogeny .41 Chapter One (continued): Introduction to bacterial classification and .41 Identificati on of Legionella...'.,..'.. .46 Phylogeny .52 Methods of phylogenetic analysis' .53 Parsimony methods.'.. .55 Distance methods UPGMA cluster analYsis.'.'... -
Aquascreen® Legionella Species Qpcr Detection Kit
AquaScreen® Legionella species qPCR Detection Kit INSTRUCTIONS FOR USE FOR USE IN RESEARCH AND QUALITY CONTROL Symbols Lot No. Cat. No. Expiry date Storage temperature Number of reactions Manufacturer INDICATION The AquaScreen® Legionella species qPCR Detection kit is specifically designed for the quantitative detection of several Legionella species in water samples prepared with the AquaScreen® FastExt- ract kit. Its design complies with the requirements of AFNOR T90-471 and ISO/TS 12869:2012. Legionella are ubiquitous bacteria in surface water and moist soil, where they parasitize protozoa. The optimal growth temperature lies between +15 and +45 °C, whereas these gram-negative bacteria are dormant below 20 °C and do not survive above 60 °C. Importantly, Legionella are well-known as opportunistic intracellular human pathogens causing Legionnaires’ disease and Pontiac fever. The transmission occurs through inhalation of contami- nated aerosols generated by an infected source (e.g. human-made water systems like shower- heads, sink faucets, heaters, cooling towers, and many more). In order to efficiently prevent Legionella outbreaks, water safety control measures need syste- matic application but also reliable validation by fast Legionella testing. TEST PRINCIPLE The AquaScreen® Legionella species Kit uses qPCR for quantitative detection of legionella in wa- ter samples. In contrast to more time-consuming culture-based methods, AquaScreen® assays need less than six hours including sample preparation and qPCR to reliably detect Legionella. Moreover, the AquaScreen® qPCR assay has proven excellent performance in terms of specificity and sensitivity: other bacterial genera remain undetected whereas linear quantification is obtai- ned up to 1 x 106 particles per sample, therefore requiring no material dilution. -
Antigenic Heterogeneity Among Legionella, Fluoribacter, and Tatlockia Species Analyzed by Crossed Immunoelectrophoresis
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Oct. 1987, p. 351-356 Vol. 37, No. 4 0020-7713/87/040351-06$02.00/0 Copyright 0 1987, International Union of Microbiological Societies Antigenic Heterogeneity Among Legionella, Fluoribacter, and Tatlockia Species Analyzed by Crossed Immunoelectrophoresis MICHAEL T. COLLINS,l* JETTE M. BANGSBORG,2 AND NIELS H@IBY2 Department of Pathobiological Sciences, University of Wisconsin, Madison, Wisconsin 53706’ and State Serum Institute, Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark2 Crossed immunoelectrophoresis (XIE) reference systems were established for Fluoribacter (Legionella) (containing Fluoribacter bozemanae, Fluoribacter dumofii, and Fluoribacter gormanii) and for Tatlockia (Legionella) micdadei. The Fluoribacter and Tatlockia XIE reference systems contained 54 and 72 anode- migrating antigens, respectively. These two systems, together with the previously described polyvalent Legionella pneumophila (serogroups 1 through 6) XIE reference system, were used to study the cross- reactivities of antigens from organisms comprising the three proposed genera in the family Legionellaceae. Antigenic homology was expressed as the matching coefficient (MC), the ratio of the number of cross-reactive antigens to the total number of antigens. The MCs for individual L. pneumophila serogroups when the polyvalent L. pneumophila antibody was used were 0.98 f 0.05, which was significantly higher than the MCs determined by using Fluoribacter or Tatlockia antibodies (0.50 f 0.13) (P < 0.001). The MCs for the three species of Fluoribacter when polyvalent Fluoribacter antibody was used were 0.93 & 0.10, which was also significantly higher than the MCs when heterologous antibodies were used (0.40 f 0.04) (P< 0.001). The MCs for T. -
Bacterial Species Exclusively Identified in Male Subjects
Supplementary Table 1: Bacterial species exclusively identified in male subjects Acholeplasma ales Clostridium magnum Lactobacillus ruminis Pseudomonas collierea Acholeplasma cavigenitalium Clostridium malenominatum Lactobacillus salivarius Pseudomonas jinjuensis Acholeplasma equifetale Clostridium nitrophenolicum Lactobacillus versmoldensis Pseudomonas luteola Acholeplasma granularum Clostridium paraputrificum Lactococcus lactis Pseudomonas panipatensis Acholeplasma hippikon Clostridium perfringens Legionella fallonii Pseudomonas poae Acidaminobacter hydrogenoformans Clostridium proteolyticum Legionella taurinensis Pseudomonas tropicalis Acidaminococcus intestini Clostridium proteolyticus Legionella worsleiensis Pseudonocardia acaciae Clostridium Acidiphilium acidophilum saccharoperbutylacetonicum Lentzea californiensis Pseudonocardia asaccharolytica Pseudonocardia Acidiphilium organovorum Clostridium sulfidigenes Leptotrichia buccalis hydrocarbonoxydans Acidiphilium symbioticum Clostridium termitidis Leptotrichia shahii Pseudoxanthomonas mexicana Acidisoma tundrae Clostridium tetani Leptotrichia wadei Pullulanibacillus naganoensis Acidovorax facilis Clostridium thermoalcaliphilum Leucobacter albus Rhizobium mesoamericanum Acinetobacter indicus Clostridium tunisiense Lewinella marina Rhodanobacter thiooxydans Acinetobacter venetianus Cohnella fontinalis Luteimonas aquatica Rhodobacter blasticus Actinoallomurus luridus Cohnella laeviribosi Luteimonas mephitis Rhodobacter gluconicum Actinobacillus pleuropneumoniae Collinsella stercoris -
Pesnyakevich.Pdf
щ УДК 579.61(075.8)+579.63(075.8) ББК 52.64я73+51.201.7я73 П28 Рецензенты: кафедра биотехнологии и биоэкологии Белорусского государственного технологическго университета (заведующий кафедрой кандидат химических наук, доцент В. Н. Леонтьев); кандидат биологических наук, доцент Н. А. Белясова; кандидат биологических наук, доцент Л. Н. Валентович Песнякевич, А. Г. П28 Медицинская и санитарная микробиология : учеб. пособие / А. Г. Пес- някевич. – Минск, 2017. – 231 с. ISBN 978-985-566-452-0. Рассматриваются инфекционный процесс как взаимодействие патогена и ор- ганизма-хозяина, патогенность и вирулентность как общие свойства возбудите- лей инфекционных заболеваний, факторы патогенности и вирулентности болезне- творных бактерий и их действие на клеточно-молекулярном уровне. Описываются общие принципы борьбы с инфекционными заболеваниями, а также основы про- филактики и терапии инфекционных болезней. Приводятся современные сведения о систематическом положении возбудителей инфекционных заболеваний бактери- альной этиологии и вызываемых ими инфекционных процессах. Предназначено для студентов, обучающихся в учреждениях высшего образова- ния по специальностям «Биология (по направлениям)», «Микробиология». УДК 579.61(075.8)+579.63(075.8) ББК 52.64я73+51.201.7я73 ISBN 978-985-566-452-0 © Песнякевич А. Г., 2017 © БГУ, 2017 ВВЕДЕНИЕ Предлагаемое учебное пособие написано согласно программе, утверж- денной для студентов биологического факультета Белорусского государ- ственного университета. По этой причине в книге отсутствуют общие све дения о строении, физиологии и экологии микроорганизмов, а также о строении и функционировании иммунной системы млекопитающих, уже известные студентам пятого года обучения из общих курсов «Ми- кробиология» и «Основы иммунологии». Кроме того, в разделе «Частная медицинская микробиология» рассматриваются только бактериальные возбудители инфекционных заболеваний человека, поскольку о па тоген- ных грибах и вирусах студенты биофака БГУ узнают из других курсов, читаемых на факультете.