DOCSLIB.ORG

MALDI-TOF Mass Spectrometry in Microbiology

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

MALDI-TOF Mass Spectrometry in Microbiology Edited by Markus Kostrzewa and Caister Academic Press Sören Schubert MALDI-TOF Mass Spectrometry in Microbiology Edited by Markus Kostrzewa Bruker Daltonik GmbH Bremen Germany and Sören Schubert Max von Pettenkofer-Institut Munich Germany Caister Academic Press Copyright © 2016 Caister Academic Press Norfolk, UK www.caister.com British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN: 978-1-910190-41-8 (paperback) ISBN: 978-1-910190-42-5 (ebook) Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or publisher. The author and publisher do not assume responsibility for the validity of any products or procedures mentioned or described in this book or for the consequences of their use. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the publisher. No claim to original U.S. Government works. Cover design adapted from images courtesy of Bruker Daltonics Inc. Ebooks Ebooks supplied to individuals are single-user only and must not be reproduced, copied, stored in a retrieval system, or distributed by any means, electronic, mechanical, photocopying, email, internet or otherwise. Ebooks supplied to academic libraries, corporations, government organizations, public libraries, and school libraries are subject to the terms and conditions specified by the supplier. Contents Contributors v Preface ix Introduction 1 Haroun N. Shah 1 Matrix Assisted Laser Desorption Ionization Time-of-flight Mass Spectrometry for the Clinical Laboratory 9 Christopher D. Doern, Robert C. Jerris and Mark D. Gonzalez 2 Analysis of Anaerobes and Some Other Fastidious Bacteria 33 Elisabeth Nagy 3 Identification, Typing and Susceptibility Testing of Fungi (Including Yeasts) by MALDI-TOF MS 49 Anna Kolecka, Maurizio Sanguinetti, Teun Boekhout and Brunella Posteraro 4 Molecular Typing of Bacteria/Fungi Using MALDI-TOF MS 79 Silpak Biswas, Frédérique Gouriet and Jean-Marc Rolain 5 MALDI-TOF MS for Determination of Resistance to Antibiotics 93 Jaroslav Hrabák, Monika Dolejská and Costas C. Papagiannitsis 6 Application of MALDI-TOF MS in Veterinary and Food Microbiology 109 Claudia Hess, Merima Alispahic and Michael Hess 7 MALDI-TOF MS for Environmental Analysis, Microbiome Research and as a Tool for Biological Resource Centres 127 Markus Kostrzewa, Chantal Bizet and Dominique Clermont iv | Contents 8 The World of Nucleic Acid-based Mass Spectrometry for Microbial and Viral Detection 141 Christiane Honisch 9 Future Trends and Perspectives of MALDI-TOF MS in the Microbiology Laboratory 157 Sören Schubert and Markus Kostrzewa Index 161 Contributors Merima Alispahic Teun Boekhout Clinic for Poultry and Fish Medicine CBS Fungal Biodiversity Centre (CBS-KNAW) University of Veterinary Medicine Vienna Utrecht Vienna The Netherlands; and Austria Institute of Microbiology Chinese Academy of Sciences [email protected] Beijing; and Department of Dermatology Silpak Biswas Shanghai Key Laboratory of Molecular Medical Faculty of Medicine and Pharmacy Mycology IHU Méditerranée Infection Institute of Dermatology and Medical Aix-Marseille University Mycology Marseille Changzheng Hospital France Second Military Medical University [email protected] Shanghai China Chantal Bizet [email protected] Institute Pasteur Collection de l’Institut Pasteur; and Dominique Clermont Centre de Ressources Biologiques de l’Institut Institute Pasteur Pasteur Collection de l’Institut Pasteur Microbiology Department Microbiology Department Paris Paris France France [email protected] [email protected] vi | Contributors Christopher D. Doern Michael Hess Virginia Commonwealth University Medical Clinic for Poultry and Fish Medicine Center University of Veterinary Medicine Vienna Medical College of Virginia Campus Vienna Richmond, VA Austria USA [email protected] [email protected] Christiane Honisch Monika Dolejská Illumina, Inc. Biomedical Center San Diego, CA Faculty of Medicine and University Hospital USA in Plzen [email protected] Charles University in Prague Plzen; and Department of Wildlife Diseases Jaroslav Hrabák Faculty of Veterinary and Ecology Biomedical Center Central European Institute of Technology Faculty of Medicine in Plzen; and University of Veterinary and Pharmaceutical Department of Microbiology Sciences Brno Faculty of Medicine and University Hospital Brno in Plzen Czech Republic Charles University in Prague Plzen [email protected] Czech Republic [email protected] Mark D. Gonzalez Children’s Healthcare of Atlanta Emory University School of Medicine Robert C. Jerris Atlanta, GA Children’s Healthcare of Atlanta USA Emory University School of Medicine Atlanta, GA [email protected] USA [email protected] Frédérique Gouriet Faculty of Medicine and Pharmacy IHU Méditerranée Infection Anna Kolecka Aix-Marseille University CBS Fungal Biodiversity Centre (CBS-KNAW) Marseille Utrecht France The Netherlands [email protected] [email protected] Claudia Hess Markus Kostrzewa Clinic for Poultry and Fish Medicine Bruker Daltonik GmbH University of Veterinary Medicine Vienna Bremen Vienna Germany Austria [email protected] [email protected] Contributors | vii Elizabeth Nagy Jean-Marc Rolain Institue of Clinical Microbiology Faculty of Medicine and Pharmacy University of Szeged IHU Méditerranée Infection Szeged Aix-Marseille University Hungary Marseille France [email protected] [email protected] Costas C. Papagiannitsis Biomedical Center Maurizio Sanguinetti Faculty of Medicine in Plzen; and Institute of Microbiology Department of Microbiology Catholic University of Rome Faculty of Medicine and University Hospital Rome in Plzen Italy Charles University in Prague [email protected] Plzen Czech Republic Sören Schubert [email protected] Max von Pettenkofer-Institut Munich Brunella Posteraro Germany Institute of Public Health (Section of Hygiene) [email protected] Catholic University of Rome Rome Italy Haroun N. Shah Department of Natural Sciences [email protected] Middlesex University Middlesex [email protected] Current Books of Interest Brain-eating Amoebae: Biology and Pathogenesis of Naegleria fowleri 2016 Staphylococcus: Genetics and Physiology 2016 Chloroplasts: Current Research and Future Trends 2016 Microbial Biodegradation: From Omics to Function and Application 2016 Influenza: Current Research 2016 Aspergillus and Penicillium in the Post-genomic Era 2016 Omics in Plant Disease Resistance 2016 Acidophiles: Life in Extremely Acidic Environments 2016 Climate Change and Microbial Ecology: Current Research and Future Trends 2016 Biofilms in Bioremediation: Current Research and Emerging Technologies 2016 Microalgae: Current Research and Applications 2016 Gas Plasma Sterilization in Microbiology: Theory, Applications, Pitfalls and New Perspectives 2016 Virus Evolution: Current Research and Future Directions 2016 Arboviruses: Molecular Biology, Evolution and Control 2016 Shigella: Molecular and Cellular Biology 2016 Aquatic Biofilms: Ecology, Water Quality and Wastewater Treatment 2016 Alphaviruses: Current Biology 2016 Thermophilic Microorganisms 2015 Flow Cytometry in Microbiology: Technology and Applications 2015 Probiotics and Prebiotics: Current Research and Future Trends 2015 Epigenetics: Current Research and Emerging Trends 2015 Corynebacterium glutamicum: From Systems Biology to Biotechnological Applications 2015 Advanced Vaccine Research Methods for the Decade of Vaccines 2015 Antifungals: From Genomics to Resistance and the Development of Novel Agents 2015 Bacteria-Plant Interactions: Advanced Research and Future Trends 2015 Aeromonas 2015 Antibiotics: Current Innovations and Future Trends 2015 Leishmania: Current Biology and Control 2015 Acanthamoeba: Biology and Pathogenesis (2nd edition) 2015 Full details at www.caister.com Preface Microbiology is thought to be a very conservative area in science and medicine with clini- cal microbiology being its most conservative part. Still Gram-staining and microscopy are central tools in the microbiology laboratory like a century ago. But sometimes revolutions change the game. Such a revolution has taken place when MALDI-TOF mass spectrometry has entered microbiological practice. Less than a decade has passed since the first routine users started to express their excitement about the benefits they gained with the new technology, about increased accuracy for the broad spectrum of nearly all microorganisms appearing in daily practice, tremendously shortened time to get an identification result, and significantly lowered overall costs. While the technology started its success story in Europe, it quickly also entered the Americas as well as Asian countries and now is getting adapted there. Clinical diagnostic was the first area where MALDI-TOF MS was introduced for broad spectrum microorganism identification in routine practice. Both direct impact on healthcare and economic advantages were powerful drivers helping to overcome conservative reserva- tion. But other fields quickly followed, from scientific research in different areas to industrial quality control. The spectrum of organisms which were investigated using the
Recommended publications
  • Diagnosis of Gallibacterium Anatis in Layers: First Report in Turkey

    Diagnosis of Gallibacterium Anatis in Layers: First Report in Turkey

    Brazilian Journal of Poultry Science Revista Brasileira de Ciência Avícola ISSN 1516-635X 2019 / v.21 / n.3 / 001-008 Diagnosis of Gallibacterium Anatis in Layers: First Report in Turkey http://dx.doi.org/10.1590/1806-9061-2019-1019 Original Article Author(s) ABSTRACT Yaman SI https://orcid.org/0000-0002-9998-3806 Gallibacterium anatis, a member of the Pasteurellaceae family, leads Sahan Yapicier OII https://orcid.org/0000-0003-3579-9425 to decrease in egg-production, animal welfare and increase in mortality. I Burdur Mehmet Akif Ersoy University, The Health This study aimed to diagnose G. Anatis, which caused economic losses Sciences Institute, Department of Microbiology, in laying hens by using conventional and molecular techniques. In 15030, Burdur, Turkey. II BurdurMehmet Akif Ersoy University, Faculty of this study, G. anatis was examined from a total of 200 dead chicken Veterinary Medicine, Department of Microbiology, tissues (heart, liver, lung, spleen and trachea) in laying hen farms 15030, Burdur, Turkey. that observed a decrease in egg production with respiratory system infection. Conventional methods based on colony morphology, sugar fermentation tests and hemolytic properties and molecular conformation using 16S rRNA-23S rRNA specific primers were performed to identify G. anatis. G. anatis was isolated in 20 (10%) of the examined samples and isolates were confirmed by conventional PCR. A total of 11 (2.2%) positivity was obtained as isolates were the result of PCR performed on tissues and organs directly. As a result, the presence of G. anatis was detected for the first time in Turkey by this study. It was thought that G.
  • Peptoniphilus Stercorisuis Sp. Nov., Isolated from a Swine Manure Storage Tank and Description of Peptoniphilaceae Fam

    Peptoniphilus Stercorisuis Sp. Nov., Isolated from a Swine Manure Storage Tank and Description of Peptoniphilaceae Fam

    10848 International Journal of Systematic and Evolutionary Microbiology (2014), 64, 3538–3545 DOI 10.1099/ijs.0.058941-0 Peptoniphilus stercorisuis sp. nov., isolated from a swine manure storage tank and description of Peptoniphilaceae fam. nov. Crystal N. Johnson,1 Terence R. Whitehead,2 Michael A. Cotta,2 Robert E. Rhoades1 and Paul A. Lawson1,3 Correspondence 1Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Paul A. Lawson OK 73019 USA [email protected] 2Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University Street, Peoria, IL 61604, USA 3Ecology and Evolutionary Biology Program, University of Oklahoma, Norman, OK 73019 USA A species of a previously unknown Gram-positive-staining, anaerobic, coccus-shaped bacterium recovered from a swine manure storage tank was characterized using phenotypic, chemotaxonomic, and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies and biochemical characteristics demonstrated that this organism is genotypically and phenotypically distinct, and represents a previously unknown sub-line within the order Clostridiales, within the phylum Firmicutes. Pairwise sequence analysis demonstrated that the novel organism clustered within the genus Peptoniphilus, most closely related to Peptoniphilus methioninivorax sharing a 16S rRNA gene sequence similarity of 95.5 %. The major long-chain fatty acids were found to be C14 : 0 (22.4 %), C16 : 0 (15.6 %), C16 : 1v7c (11.3 %) and C16 : 0 ALDE (10.1 %) and the DNA G +C content was 31.8 mol%. Based upon the phenotypic and phylogenetic findings presented, a novel species Peptoniphilus stercorisuis sp. nov. is proposed. The type strain is SF-S1T (5DSM 27563T5NBRC 109839T).
  • Identification of Pasteurella Species and Morphologically Similar Organisms

    Identification of Pasteurella Species and Morphologically Similar Organisms

    UK Standards for Microbiology Investigations Identification of Pasteurella species and Morphologically Similar Organisms Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 1 of 28 © Crown copyright 2015 Identification of Pasteurella species and Morphologically Similar Organisms Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website https://www.gov.uk/uk- standards-for-microbiology-investigations-smi-quality-and-consistency-in-clinical- laboratories. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for-microbiology-investigations- steering-committee). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories UK Standards for Microbiology Investigations are produced in association with: Logos correct at time of publishing. Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 2 of 28 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Pasteurella species and Morphologically Similar Organisms Contents ACKNOWLEDGMENTS .........................................................................................................
  • Phenotypic and Molecular Characterization of the Capsular Serotypes of Pasteurella Multocida Isolates from Pneumonic Cases of Cattle in Ethiopia

    Phenotypic and Molecular Characterization of the Capsular Serotypes of Pasteurella Multocida Isolates from Pneumonic Cases of Cattle in Ethiopia

    Phenotypic and Molecular Characterization of the Capsular Serotypes of Pasteurella multocida Isolates from Pneumonic Cases of Cattle in Ethiopia Mirtneh Akalu Yilma ( [email protected] ) Koneru Lakshmaiah Education Foundation https://orcid.org/0000-0001-5936-6873 Murthy Bhadra Vemulapati Koneru Lakshmaiah Education Foundation Takele Abayneh Tefera Veterinaerinstituttet Martha Yami VeterinaryInstitute Teferi Degefa Negi VeterinaryInstitue Alebachew Belay VeterinaryInstitute Getaw Derese VeterinaryInstitute Esayas Gelaye Leykun Veterinaerinstituttet Research article Keywords: Biovar, Capsular type, Cattle, Ethiopia, Pasteurella multocida Posted Date: January 19th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-61749/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/13 Abstract Background: Pasteurella multocida is a heterogeneous species and opportunistic pathogen associated with pneumonia in cattle. Losses due to pneumonia and associated expenses are estimated to be higher in Ethiopia with limited information about the distribution of capsular serotypes. Hence, this study was designed to determine the phenotypic and capsular serotypes of P. multocida from pneumonic cases of cattle. Methods: A cross sectional study with purposive sampling method was employed in 400 cattle from April 2018 to January 2019. Nasopharyngeal swabs and lung tissue samples were collected from clinically suspected pneumonic cases of calves (n = 170) and adult cattle (n = 230). Samples were analyzed using bacteriological and molecular assay. Results: Bacteriological analysis revealed isolation of 61 (15.25%) P. multocida subspecies multocida. Incidence was higher in calves 35 (57.38%) compared to adult cattle 26 (42.62%) at P < 0.5. PCR assay targeting KMT1 gene (~460 bp) conrmed P.
  • Gallibacterium Anatis: an Emerging Pathogen of Poultry Birds And

    Gallibacterium Anatis: an Emerging Pathogen of Poultry Birds And

    ary Scien in ce r te & e T V e f c h o Journal of Veterinary Science & n n l o o a a l l n n o o r r g g u u Singh, et al., J Veterinar Sci Techno 2016, 7:3 y y o o J J Technology DOI: 10.4172/2157-7579.1000324 ISSN: 2157-7579 Review Article Open Access Gallibacterium anatis: An Emerging Pathogen of Poultry Birds and Domiciled Birds Shiv Varan Singh, Bhoj R Singh*, Dharmendra K Sinha, Vinodh Kumar OR, Prasanna Vadhana A, Monika Bhardwaj and Sakshi Dubey Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar-243 122, Uttar Pradesh, India *Corresponding author: Dr. Bhoj R Singh, Acting Head of Division of Epidemiology, ICAR-IVRI, Izatnagar-243122, Uttar Pradesh, India, Tel: +91-8449033222; E-mail: [email protected] Rec date: Feb 09, 2016; Acc date: Mar 16, 2016; Pub date: Mar 18, 2016 Copyright: © 2016 Singh SV, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract Gallibacterium anatis though known since long as opportunistic pathogen of intensively reared poultry birds has emerged in last few years as multiple drug resistance pathogen causing heavy mortality outbreaks not only in poultry birds but also in other domiciled or domestic birds. Due to its fastidious nature, commensal status and with no pathgnomonic lesions in diseased birds G. anatis infection often remains obscure for diagnosis.
  • Urinicoccus Massiliensis Gen. Nov., Sp. Nov., a New Bacterium Isolated from a Human Urine Sample from a 7-Year-Old Boy Hospitalized for Dental Care

    Urinicoccus Massiliensis Gen. Nov., Sp. Nov., a New Bacterium Isolated from a Human Urine Sample from a 7-Year-Old Boy Hospitalized for Dental Care

    NEW SPECIES Urinicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from a human urine sample from a 7-year-old boy hospitalized for dental care E. K. Yimagou1, H. Anani2, A. Yacouba1, I. Hasni1, J.-P. Baudoin1, D. Raoult3 and J. Y. Bou Khalil1 1) Aix Marseille University, IRD, AP-HM, MEPHI, 2) Aix Marseille Univ, IRD, AP-HM, VITROME, IHU-Méditerranée Infection, Marseille, France and 3) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia Abstract Urinicoccus massiliensis strain Marseille-P1992T (= CSURP1992 = DSM100581) is a species of a new genus isolated from human urine. © 2019 The Authors. Published by Elsevier Ltd. Keywords: Culturomics, new species, taxonogenomics, urine, Urinicoccus massiliensis Original Submission: 16 July 2019; Revised Submission: 10 October 2019; Accepted: 17 October 2019 Article published online: 30 October 2019 previously described [7]. The obtained spectra (Fig. 1) were Corresponding author. J. Y. Bou Khalil, MEPHI, Institut Hospitalo- imported into MALDI Biotyper 3.0 software (Bruker Daltonics) Universitaire Méditerranée Infection, 19–21 Boulevard Jean Moulin 13385 Marseille Cedex 05. France and analysed against the main spectra of the bacteria included in E-mail: [email protected] the database (Bruker database constantly updated http://www. mediterraneeinfection.com/article.php?larub=280&titre=urms- database). The initial growth was obtained 10 days after culture on a blood culture vial (Becton Dickinson, Le Pont-de-Claix, Introduction France) supplemented with 5 mL of 0.2-μm-filtered rumen fluid in anaerobic conditions at 37°C and pH 7.5. Culturomics is a concept involving the development of different Strain identification culture conditions in order to enlarge our knowledge of the The 16S rRNA gene was sequenced in order to classify this human microbiota through the discovery of previously uncul- bacterium.
  • Outline Release 7 7C

    Outline Release 7 7C

    Garrity, et. al., March 6, 2007 Taxonomic Outline of the Bacteria and Archaea, Release 7.7 March 6, 2007. Part 7 – The Bacteria: Phylum “Firmicutes”: Class “Clostridia” George M. Garrity, Timothy G. Lilburn, James R. Cole, Scott H. Harrison, Jean Euzéby, and Brian J. Tindall F Phylum Firmicutes AL N4Lid DOI: 10.1601/nm.3874 Class "Clostridia" N4Lid DOI: 10.1601/nm.3875 71 Order Clostridiales AL Prévot 1953. N4Lid DOI: 10.1601/nm.3876 Family Clostridiaceae AL Pribram 1933. N4Lid DOI: 10.1601/nm.3877 Genus Clostridium AL Prazmowski 1880. GOLD ID: Gi00163. GCAT ID: 000971_GCAT. Entrez genome id: 80. Sequenced strain: BC1 is from a non-type strain. Genome sequencing is incomplete. Number of genomes of this species sequenced 6 (GOLD) 6 (NCBI). N4Lid DOI: 10.1601/nm.3878 Clostridium butyricum AL Prazmowski 1880. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 19398. High-quality 16S rRNA sequence S000436450 (RDP), M59085 (Genbank). N4Lid DOI: 10.1601/nm.3879 Clostridium aceticum VP (ex Wieringa 1940) Gottschalk and Braun 1981. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 35044. High-quality 16S rRNA sequence S000016027 (RDP), Y18183 (Genbank). N4Lid DOI: 10.1601/nm.3881 Clostridium acetireducens VP Örlygsson et al. 1996. Source of type material recommended for DOE sponsored genome sequencing by the JGI: DSM 10703. High-quality 16S rRNA sequence S000004716 (RDP), X79862 (Genbank). N4Lid DOI: 10.1601/nm.3882 Clostridium acetobutylicum AL McCoy et al. 1926. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 824.
  • Urinicoccus Massiliensis Gen. Nov., Sp. Nov., a New Bacterium Isolated from a Human Urine Sample from a 7-Year-Old Boy Hospitalized for Dental Care

    Urinicoccus Massiliensis Gen. Nov., Sp. Nov., a New Bacterium Isolated from a Human Urine Sample from a 7-Year-Old Boy Hospitalized for Dental Care

    NEW SPECIES Urinicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from a human urine sample from a 7-year-old boy hospitalized for dental care E. K. Yimagou1, H. Anani2, A. Yacouba1, I. Hasni1, J.-P. Baudoin1, D. Raoult3 and J. Y. Bou Khalil1 1) Aix Marseille University, IRD, AP-HM, MEPHI, 2) Aix Marseille Univ, IRD, AP-HM, VITROME, IHU-Méditerranée Infection, Marseille, France and 3) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia Abstract Urinicoccus massiliensis strain Marseille-P1992T (= CSURP1992 = DSM100581) is a species of a new genus isolated from human urine. © 2019 The Authors. Published by Elsevier Ltd. Keywords: Culturomics, new species, taxonogenomics, urine, Urinicoccus massiliensis Original Submission: 16 July 2019; Revised Submission: 10 October 2019; Accepted: 17 October 2019 Article published online: 30 October 2019 previously described [7]. The obtained spectra (Fig. 1) were Corresponding author. J. Y. Bou Khalil, MEPHI, Institut Hospitalo- imported into MALDI Biotyper 3.0 software (Bruker Daltonics) Universitaire Méditerranée Infection, 19–21 Boulevard Jean Moulin 13385 Marseille Cedex 05. France and analysed against the main spectra of the bacteria included in E-mail: [email protected] the database (Bruker database constantly updated http://www. mediterraneeinfection.com/article.php?larub=280&titre=urms- database). The initial growth was obtained 10 days after culture on a blood culture vial (Becton Dickinson, Le Pont-de-Claix, Introduction France) supplemented with 5 mL of 0.2-μm-filtered rumen fluid in anaerobic conditions at 37°C and pH 7.5. Culturomics is a concept involving the development of different Strain identification culture conditions in order to enlarge our knowledge of the The 16S rRNA gene was sequenced in order to classify this human microbiota through the discovery of previously uncul- bacterium.
  • Phenotypic and Molecular Characterization of the Capsular Serotypes of Pasteurella Multocida Isolates from Bovine Respiratory Disease Cases in Ethiopia

    Phenotypic and Molecular Characterization of the Capsular Serotypes of Pasteurella Multocida Isolates from Bovine Respiratory Disease Cases in Ethiopia

    Phenotypic and Molecular Characterization of the Capsular Serotypes of Pasteurella Multocida Isolates From Bovine Respiratory Disease Cases in Ethiopia Mirtneh Akalu Yilma ( [email protected] ) Koneru Lakshmaiah Education Foundation https://orcid.org/0000-0001-5936-6873 Murthy Bhadra Vemulapati Koneru Lakshmaiah Education Foundation Takele Abayneh Tefera Veterinaerinstituttet Martha Yami VeterinaryInstitute Teferi Degefa Negi VeterinaryInstitue Alebachew Belay VeterinaryInstitute Getaw Derese VeterinaryInstitute Esayas Gelaye Leykun Veterinaerinstituttet Research article Keywords: Antibiogram, Biovar, Capsular type, Cattle, Ethiopia, Pasteurella multocida Posted Date: September 9th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-61749/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/15 Abstract Background: Pasteurella multocida is a heterogeneous species and opportunistic pathogen that causes bovine respiratory disease. This disease is one of an economically important disease in Ethiopia. Losses due to mortality and associated expenses are estimated to be higher in the country. Studies revealed that limited information is available regarding the capsular types, genotypes, and antimicrobial sensitivity of P. multocida isolates circulating in the country. This suggests, further molecular advances to understand the etiological diversity of the pathogens representing severe threats to the cattle population. Results: Bacteriological analysis of nasopharyngeal swab and pneumonic lung tissue samples collected from a total of 400 samples revealed isolation of 61 (15.25%) P. multocida subspecies multocida. 35 (20.59%) were isolated from calves and 26 (11.30%) from adult cattle. Molecular analysis using PCR assay targeting KMT1 gene (~460 bp) amplication was shown in all presumptive isolates. Capsular typing also conrmed the presence of serogroup A (hyaD-hyaC) gene (~1044 bp) and serogroup D (dcbF) gene (~657 bp) from 56 (91.80%) and 5 (8.20%) isolates, respectively.
  • Genome Analysis and Phylogenetic Relatedness of Gallibacterium Anatis Strains from Poultry Timothy J

    Genome Analysis and Phylogenetic Relatedness of Gallibacterium Anatis Strains from Poultry Timothy J

    Veterinary Microbiology and Preventive Medicine Veterinary Microbiology and Preventive Medicine Publications 1-24-2013 Genome Analysis and Phylogenetic Relatedness of Gallibacterium anatis Strains from Poultry Timothy J. Johnson University of Minnesota Jessica L. Danzeisen University of Minnesota Darrell W. Trampel Iowa State University, [email protected] Lisa K. Nolan Iowa State University, [email protected] Torsten Seemann FMoolnloaswh U thinivser asitndy additional works at: http://lib.dr.iastate.edu/vmpm_pubs See nePxat pratge of for the addiGetionnomical authors Commons, Large or Food Animal and Equine Medicine Commons, Veterinary Microbiology and Immunobiology Commons, and the Veterinary Preventive Medicine, Epidemiology, and Public Health Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ vmpm_pubs/2. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Veterinary Microbiology and Preventive Medicine at Iowa State University Digital Repository. It has been accepted for inclusion in Veterinary Microbiology and Preventive Medicine Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Genome Analysis and Phylogenetic Relatedness of Gallibacterium anatis Strains from Poultry Abstract Peritonitis is the major disease problem of laying hens in commercial table egg and parent stock operations. Despite its importance, the etiology and pathogenesis of this disease have not been completely clarified. Although avian pathogenic Escherichia coli (APEC) isolates have been incriminated as the causative agent of laying hen peritonitis, Gallibacterium anatis are frequently isolated from peritonitis lesions.
  • Bacterioplankton in the Oregon Upwelling System: Distribution, Cell

    Bacterioplankton in the Oregon Upwelling System: Distribution, Cell

    AN ABSTRACT OF THE DISSERTATION OF Krista Longnecker for the degree of Doctor ofPhilosophy in Oceanography presented on July 2, 2004. Title: Bacterioplankton in the Oregon UpwellingSystem: Distribution, Cell-specific Leucine Incorporation, and Diversity Abstract approved: Redacted for privacy Barry F. Sherr Marine bacterioplankton playan important role in global elemental cycles because they return carbon dioxide and nutrientsto the biosphere as they reduce organic matter. Furthermore, marine bacterioplanktonare not unifonnly active, and subpopulations of the in situ communitymay be more or less active at any given time. Defining whether or not a cell is 'active' isnot without difficulty, and the result varies depending on the assay used, since differentassays examine different physiological processes within a cell. Linking the level of activity ofa cell with its phylogenetic identity is an additional important step inexamination of the role of marine prokaryotes in global elemental cycles. In this project,flow cytometry was used in two ways to examine relative cell-specific metabolic activity inbacterioplankton cells: as relative cell-specific nucleic acidcontent via staining with SYBR Green I, andas ability to reduce sufficient 5-cyano-2,3-ditolyltetrazolium chloride (CTC) to be identified as having an active electrontransport system. Based on flow cytometric sorting of cells labeled with 3H-leucine, thehigh nucleic acid (HNA) cells had higher cell-specific leucine incorporation rates than thelow nucleic acid (LNA) cells. The HNA cells were also responsible for proportionatelymore of the leucine incorporation by the total heterotrophic population. Whilethe CTC-positive cells had higheraverage cell-specific leucine incorporation rates than theHNA cells, their low abundances meant that they were responsible for less than 15% ofthe total leucine incorporation.
  • CGM-18-001 Perseus Report Update Bacterial Taxonomy Final Errata

    CGM-18-001 Perseus Report Update Bacterial Taxonomy Final Errata

    report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly. These lists of bacteria originate from 2011, when COGEM petitioned a research project to evaluate the classifications of bacteria in the former GMO regulation and to supplement this list with bacteria that have been classified by other governmental organizations.