Maldi-tof and Tandem Ms for Clinical Microbiology

This book highlights the triumph of MALDI-TOF mass spectrometry over the past decade and provides insight into new and expanding technologies through a comprehensive range of short chapters that enable the reader to gauge their current status and how they may progress over the next decade.  This book serves as a platform to consolidate current strengths of the technology and highlight new frontiers in tandem MS/MS that are likely to eventually supersede MALDI-TOF MS. Chapters discuss:
Challenges of Identifying Mycobacterium to the Species level
Identification of Bacteroides and Other Clinically Relevant Anaerobes
Identification of Species in Mixed Microbial Populations
Detection of Resistance Mechanisms
Proteomics as a biomarker discovery and validation platform
Determination of Antimicrobial Resistance using Tandem Mass Spectrometry

EDITORS
Haroun N. Shah, Department of Natural Sciences, Middlesex University, London, UK

Saheer E. Gharbia, Genomic Research, Public Health England, London, UK

List of Contributors xxi

Preface xxix

Part I MALDI-TOF Mass Spectrometry 1

1 A Paradigm Shift from Research to Front�]Line Microbial Diagnostics in MALDI�]TOF and LC�]MS/MS: A Laboratory’s Vision and Relentless Resolve to Help Develop and Implement This New Technology amidst Formidable Obstacles 3
Haroun N. Shah and Saheer E. Gharbia

2 Criteria for Development of MALDI�]TOF Mass Spectral Database 39
Markus Kostrzewa and Thomas Maier

3 Applications of MALDI�]TOF Mass Spectrometry in Clinical Diagnostic Microbiology 55
Onya Opota, Guy Prod’hom and Gilbert Greub

4 The Challenges of Identifying Mycobacterium to the Species Level using MALDI�]TOF MS 93

5 Transformation of Anaerobic Microbiology since the Arrival of MALDI�]TOF Mass Spectrometry 123
Elisabeth Nagy, Mariann Abrok, Edith Urban, A.C.M. Veloo, Arie Jan van Winkelhoff, Itaru Dekio, Saheer E. Gharbia and Haroun N. Shah

6 Differentiation of Closely Related Organisms using MALDI�]TOF MS 147
Mark A. Fisher

7 Identification of Species in Mixed Microbial Populations using MALDI�]TOF MS 167
Pierre Mahe, Maud Arsac, Nadine Perrot, Marie�]Helene Charles, Patrick Broyer, Jay Hyman, John Walsh, Sonia Chatellier, Victoria Girard, Alex van Belkum, and Jean�]Baptiste Veyrieras

8 Microbial DNA Analysis by MALDI�]TOF Mass Spectrometry 187

9 Impact of MALDI�]TOF MS in Clinical Mycology; Progress and Barriers in Diagnostics 211
Cledir R. Santos, Elaine Francisco, Mariana Mazza, Ana Carolina B. Padovan, Arnaldo Colombo and Nelson Lima

10 Development and Application of MALDI�]TOF for Detection of Resistance Mechanisms 231
Stefan Zimmermann and Irene Burckhardt

11 Discrimination of Burkholderia Species, Brucella Biovars, Francisella tularensis and Other Taxa at the Subspecies Level by MALDI�]TOF Mass Spectrometry 249
Axel Karger

12 MALDI�]TOF�]MS Based on Ribosomal Protein Coding in S10�]spc�]alpha Operons for Proteotyping 269
Hiroto Tamura

Part II Tandem MS/MS-Based Approaches to Microbial Characterization 311

13 Tandem Mass Spectrometry Analysis as an Approach to Delineate Genetically Related Taxa 313
Raju V. Misra, Tom Gaulton, Nadia Ahmod, Min Fang, Martin Hornshaw, Jenny Ho, Saheer E. Gharbia and Haroun N. Shah

14 Mapping of the Proteogenome of Clostridium difficile Isolates of Varying Virulence 379
Caroline H. Chilton, Saheer E. Gharbia, Raju V. Misra, Min Fang, Ian R. Poxton, Peter S. Borriello and Haroun N. Shah

15 Determination of Antimicrobial Resistance using Tandem Mass
Spectrometry 399
Ajit J. Shah, Vlad Serafim, Zhen Xu, Hermine Mkrtchyan and Haroun N. Shah

16 Proteotyping: Tandem Mass Spectrometry Shotgun Proteomic Characterization and Typing of Pathogenic Microorganisms 419
Roger Karlsson, Lucia Gonzales�]Siles, Fredrik Boulund, Asa Lindgren, Liselott Svensson�]Stadler, Anders Karlsson, Erik Kristiansson and Edward R.B. Moore

17 Proteogenomics of Pseudomonas aeruginosa in Cystic Fibrosis Infections 451
Liang Yang and Song Lin Chua

18 Top�]Down Proteomics in the Study of Microbial Pathogenicity 493
Joseph Gault, Egor Vorontsov, Mathieu Dupre, Valeria Calvaresi, Magalie Duchateau, Diogo B. Lima, Christian Malosse and Julia Chamot�]Rooke

19 Tandem Mass Spectrometry in Resolving Complex Gut Microbiota Functions 505
Carolin Kolmeder, Kaarina Lahteenmaki, Pirjo Wacklin, Annika Kotovuori, Ilja Ritamo, Jaana Matto, Willem M. de Vos, and Leena Valmu

20 Proteogenomics of Non�]model Microorganisms 529
Jean Armengaud

21A Analysis of MALDI�]TOF MS Spectra using the BioNumerics Software 539
Katleen Vranckx, Katrien De Bruyne and Bruno Pot

21B Subtyping of Staphylococcus spp. Based upon MALDI�]TOF MS Data Analysis 563
Zhen Xu, Ali Olkun, Katleen Vranckx, Hermine V. Mkrtchyan, Ajit J. Shah, Bruno Pot, Ronald R. Cutler and Haroun N. Shah

21C Elucidating the Intra�]Species Proteotypes of Pseudomonas aeruginosa from Cystic Fibrosis 579
Ali Olkun, Ajit J. Shah and Haroun N. Shah

References 588

Index 593

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