Applications of Mass Spectrometry in Microbiology: From Strain Characterization to Rapid Screening for Antibiotic Resistance

336 Pages·2016·9.73 MB·English

by  Plamen Demirev

Applications of Mass Spectrometry in
Microbiology
Plamen Demirev • Todd R. Sandrin
Editors
Applications of Mass
Spectrometry in
Microbiology
From Strain Characterization to Rapid
Screening for Antibiotic Resistance
1 3
Editors
Plamen Demirev Todd R. Sandrin
Applied Physics Laboratory School of Mathematical and Natural Sciences
Johns Hopkins University New College of Interdisciplinary
Laurel, MD Arts & Sciences
USA Arizona State University
Phoenix, AZ
USA
ISBN 978-3-319-26068-6 ISBN 978-3-319-26070-9 (eBook)
DOI 10.1007/978-3-319-26070-9
Library of Congress Control Number: 2015959597
Springer
Springer Cham Heidelberg New York Dordrecht London
© Springer International Publishing Switzerland 2016
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Contents
1 Introduction ................................................................................................ 1
Plamen Demirev and Todd R. Sandrin
Part I Methodology and Techniques
2 Methods and Instrumentation in Mass Spectrometry for the
Differentiation of Closely Related Microorganisms ............................... 13
Franco Basile and Rudolph K. Mignon
3 Sample Preparation Methods for the Rapid MS Analysis of
Microorganisms .......................................................................................... 51
Shobha Devi, Anren Hu and Yen-Peng Ho
4 A dvantages Offered by Proteomic Strategies for Rapid Biodetection ..... 73
Catherine Fenselau
5 B ottom-Up Proteomics Methods for Strain-Level Typing and
Identification of Bacteria ........................................................................... 83
Jacek P. Dworzanski
6 M aximizing the Taxonomic Resolution of MALDI-TOF-MS-Based
Approaches to Bacterial Characterization: From Culture
Conditions Through Data Analysis ........................................................... 147
Lin Zhang and Todd R. Sandrin
Part II Subspecies Discrimination
7 M odulation of the Discriminatory Power of MALDI-TOF
MS Profiling for Distinguishing Between Closely Related
Bacterial Strains ......................................................................................... 185
Ondrej Šedo and Zbyněk Zdráhal
v
vi Contents
8 Discriminatory Power of MALDI-TOF Mass Spectrometry
for Phylogenetically Closely Related Microbial Strains ....................... 203
Peter Lasch, Daniela Jacob, Silke R. Klee and Guido Werner
9 MALDI-TOF MS as a Novel Tool for Dereplication and
Characterization of Microbiota in Bacterial Diversity Studies ........... 235
Freek Spitaels, Anneleen D. Wieme and Peter Vandamme
10 Bacterial Identification at the Serovar Level by Top-Down
Mass Spectrometry .................................................................................. 257
Melinda A. McFarland, Denis Andrzejewski and John H. Callahan
Part III Drug Resistance Monitoring and Assays
11 R apid Profiling of Human Pathogenic Bacteria and
Antibiotic Resistance Employing Specific Tryptic Peptides
as Biomarkers ........................................................................................... 275
David Drissner, René Brunisholz, Ralph Schlapbach and
Maria-Theresia Gekenidis
12   Detection of β-Lactamases and Their Activity Using 
MALDI-TOF MS ..................................................................................... 305
Jaroslav Hrabak, Vladimír Havlicek and Costas C. Papagiannitsis
13 Stable-Isotope-Based Strategies for Rapid Determination of
Drug Resistance by Mass Spectrometry ................................................ 317
Plamen Demirev
Index .................................................................................................................. 327
List of Contributors
Denis Andrzejewski Spectroscopy and Mass Spectrometry Branch, Center for
Food Safety and Applied Nutrition, US Food and Drug Administration, College
Park, MD, USA
Franco Basile Department of Chemistry, Biodetection and Mass Spectrometry
Laboratory, University of Wyoming, Laramie, WY, USA
René Brunisholz Functional Genomics Center Zurich, ETH Zurich and
University of Zurich, Zurich, Switzerland
John H. Callahan Spectroscopy and Mass Spectrometry Branch, Center for Food
Safety and Applied Nutrition, US Food and Drug Administration, College Park,
MD, USA
Plamen Demirev Applied Physics Laboratory Johns Hopkins University, Laurel,
MD, USA
Shobha Devi Department of Chemistry, National Dong Hwa University, Hualien,
Taiwan
David Drissner Agroscope Institute for Food Sciences, Food Microbiology and
Analytics, Waedenswil, Switzerland
Jacek P. Dworzanski Leidos, Inc., Bel Air, MD, USA
Catherine Fenselau Department of Chemistry & Biochemistry, University of
Maryland, College Park, MD, USA
Maria-Theresia Gekenidis Agroscope Institute for Food Sciences, Food
Microbiology and Analytics, Waedenswil, Switzerland
Vladimír Havlicek RCPTM, Department of Analytical Chemistry, Palacky
University, Olomouc, Czech Republic
Yen-Peng Ho Department of Chemistry, National Dong Hwa University, Hualien,
Taiwan
vii
viii List of Contributor
Jaroslav Hrabak Biomedical Center and Department of Microbiology, Charles
University in Prague, Plzen, Czech Republic
Anren Hu Institute of Medical Biotechnology, Tsu-Chi University, Hualien, Taiwan
Daniela Jacob ZBS 2, Highly Pathogenic Microorganisms, Robert Koch-
Institute, Berlin, Germany
Silke R. Klee ZBS 2, Highly Pathogenic Microorganisms, Robert Koch-Institute,
Berlin, Germany
Peter Lasch Proteomics and Spectroscopy at the Centre for Biological Threats
and Special Pathogens (ZBS6), Robert Koch-Institute, Berlin, Germany
Melinda A. McFarland Spectroscopy and Mass Spectrometry Branch, Center for
Food Safety and Applied Nutrition, US Food and Drug Administration, College
Park, MD, USA
Rudolph K. Mignon Department of Chemistry, Biodetection and Mass
Spectrometry Laboratory, University of Wyoming, Laramie, WY, USA
Costas C. Papagiannitsis Biomedical Center and Department of Microbiology,
Charles University in Prague, Plzen, Czech Republic
Todd R. Sandrin School of Mathematical and Natural Sciences, New College of
Interdisciplinary Arts & Sciences, Arizona State University, Phoenix, AZ, USA
Ralph Schlapbach Functional Genomics Center Zurich, ETH Zurich and
University of Zurich, Zurich, Switzerland
Ondrej Šedo Research Group Proteomics, CEITEC—Central European Institute
of Technology, Masaryk University, Brno, Czech Republic
Freek Spitaels Laboratory of Microbiology, Faculty of Sciences, Ghent
University, Ghent, Belgium
Peter Vandamme Laboratory of Microbiology, Faculty of Sciences, Ghent
University, Ghent, Belgium
Guido Werner FG 13, Nosocomial Pathogens and Antibiotic Resistances, Robert
Koch-Institute, Wernigerode, Germany
Anneleen D. Wieme Laboratory of Microbiology, Faculty of Sciences, Ghent
University, Ghent, Belgium
Laboratory of Biochemistry and Brewing, Faculty of Bioscience Engineering,
Ghent University, Ghent, Belgium
Zbyněk Zdráhal Research Group Proteomics, CEITEC—Central European
Institute of Technology, Masaryk University, Brno, Czech Republic
Lin Zhang School of Mathematical and Natural Sciences, Arizona State
University, Phoenix, AZ, USA
Chapter 1
Introduction
Plamen Demirev and Todd R. Sandrin
Mass Spectrometry and Microbiology
Mass spectrometry (MS) is a physical method for analysis introduced more than
100 years ago. During that period, MS applications have successfully proliferated
in almost all areas of science and technology—from early studies of the structure of
atoms and molecules culminating with the discovery of isotopes to characterization
of planetary atmospheres and surfaces and search for extraterrestrial life. MS is an
indispensable tool in organic chemistry and biochemistry for structural elucidation
of various classes of natural products and synthetic compounds. In the last quarter
century, advances in MS methods and instrumentation have been at the forefront
of efforts to map complex biological systems, including the human metabolome,
proteome, and microbiome.
MS was first successfully applied to analysis of intact microorganisms more
than 40 years ago (Anhalt and Fenselau 1975). These efforts have expanded and
have been particularly significant after the introduction of the soft ionization MS
techniques—matrix-assisted laser desorption/ionization (MALDI) and electrospray
ionization (ESI) (Fenn et al. 1989; Tanaka 2003; Karas and Hillenkamp 1988). Both
techniques (recognized by the Nobel Prize in Chemistry in 2002) allow the ion-
ization and transfer into vacuum of large, intact, nonvolatile biomolecules, such
as proteins. Various types of mass analyzers—quadrupole, ion trap, time-of-flight
(TOF)—have been coupled to both MALDI and ESI ion sources, allowing multiple
stages (tandem) MS to be performed for structure elucidation of analytes of interest.
All these instrumental developments have allowed MS to become a well-established
P. Demirev ()
Applied Physics Laboratory Johns Hopkins University Laurel, MD, USA
e-mail: [email protected]
T. R. Sandrin
School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts & Sciences,
Arizona State University, Phoenix, AZ, USA
e-mail: [email protected]
© Springer International Publishing Switzerland 2016 1
P. Demirev, T. R. Sandrin (eds.), Applications of Mass Spectrometry in Microbiology,
DOI 10.1007/978-3-319-26070-9_1
2 P. Demirev and T. R. Sandrin
method for microorganism characterization. MS has demonstrated considerable ad-
vantage as a rapid, precise, and cost-effective method for identification, compared
to conventional phenotypic techniques. The method is ultimately based on detec-
tion of organism-specific “fingerprints” (or “signatures”, i.e., biomarker molecules,
from either intact and/or lysed cells (Fenselau and Demirev 2001; Wilkins et al.
2005; Demirev and Fenselau 2008a, 2008b; Seng et al. 2009; Freivald and Sauer
2009; Shah and Gharbia 2010; Ho and Reddy 2010; Bizzini and Greub 2010; Sauer
and Kliem 2010; Cliff et al. 2011; Welker 2011; Fenselau and Demirev 2011; Crox-
atto et al. 2012; Havlicek et al. 2013; Sandrin et al. 2013; DeMarco and Ford 2013;
Fenselau 2013; Clark et al. 2013; Fagerquist 2013; Calderaro et al. 2014)). Dif-
ferent organisms exhibit different MS signatures allowing differentiation between
organisms to be made. Examples of microorganism-specific biomarkers include
highly expressed intact proteins, their proteolytic products, nonribosomal peptides,
polar and nonpolar lipids, RNA, and DNA. Sequence/structure-specific fragments
for biomarker identification are generated by tandem MS. In top-down proteomics,
these biomarkers are intact proteins, while proteolytic peptides (obtained after enzy-
matic or chemical hydrolysis) are mapped to their precursor proteins in bottom-up/
middle-down approaches. Ultimately microorganism identification relies on map-
ping between spectra of unknowns with signatures of known microorganisms in MS
signature libraries. Such libraries are compiled either by experimentally acquiring
mass spectra of reference organisms and/or by generating in silico signatures from
information in genomic or proteomic databases (Pineda et al. 2000; Demirev et al.
2004).
Thousands of reports on applications of MS for microorganism characterization
in research, clinical microbiology, counter-bioterrorism, food safety, environmental
monitoring, and quality have been published (Havlicek et al. 2013). Regulatory
bodies in Europe, the US (FDA), and elsewhere have approved MS-based assays
for infectious disease diagnostics. As of mid-2015, more than 3300 commercial
MALDI TOF MS systems have been deployed worldwide in hospitals and clinical
laboratories. As interest has increased in this technology, the pace of discovery and
development of new applications has accelerated. The technology has been shown
repeatedly to be effective at rapidly discriminating, identifying, and characterizing
microorganisms at the species level and above. Some of the most promising yet
challenging applications of this technology require microorganism characterization
at the subspecies and strain levels. Categorization of strains sharing similar traits,
differentiation of closely related strains, and/or identification of a single strain by
MS techniques is desired. For example, there is tremendous need in expanding this
approach to rapidly identify strains of antibiotic-resistant microorganisms.
Chapters Included in This Book
While previous work has covered broader approaches to using MS to character-
ize microorganisms at the species level or above, this book focuses on strain-level
and subtyping applications. Innovators, leaders, and practitioners in the field from