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