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Discriminatory Power of MALDI-TOF Mass Spectrometry for Phylogenetically Closely Related Microbial Strains

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Applications of Mass Spectrometry in Microbiology

Abstract

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a powerful tool for differentiation, identification and classification of microorganisms at the genus and the species levels. In this mini-review, we discuss the challenges and opportunities associated with the application of MALDI-TOF MS for bacterial strain typing below the species level. Based on three examples of important bacterial pathogens, Staphylococcus aureus, Enterococcus faecium and Bacillus cereus sensu lato we explore the strengths and weaknesses of the MS technique. It was found that the taxonomic resolution of MALDI-TOF MS is limited which often prevents reliable strain categorization, or strain identification/typing. Only in selected cases were we able to detect mass spectral biomarkers and fingerprints that allowed for reliable microbial typing and strain differentiation. It was found that typing below the species level requires rigorous standardization, high spectral quality and the application of adequate sample-processing methods, spectra acquisition procedures, and an optimized data analysis pipeline that includes multivariate fingerprinting approaches. However, these conditions cannot be expected in a routine setting. Therefore, future efforts to increase the taxonomic resolution should involve the application of alternative mass spectrometry technologies, ideally in combination with sample pre-processing methods, such as separation techniques. It is hoped that this will open new avenues to further improve the taxonomic resolution of MS-based technologies.

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Abbreviations

ACME:

Arginine catabolic mobile element

ANN:

Artificial neural network

BSL:

Biosafety level

BURP:

Based upon repeat pattern

CA:

Community-Acquired

CC:

Clonal complex

DHB:

2,5-dihydroxybenzoic acid

EntA:

Enterotoxin A

EntB:

Enterotoxin B

HCCA:

α-cyano-4-hydroxycinnamic acid

MALDI-TOF:

Matrix-assisted laser desorption/ionization—time of flight

MLST:

Multilocus sequence typing

MLVA:

Multiple-locus variable number tandem repeat analysis

MRSA:

Methicillin-resistant Staphylococcus aureus

MSSA:

Methicillin-sensitive Staphylococcus aureus

MS:

Mass spectrometry

MSP:

Main spectral projection

MW:

Molecular weight

PFGE:

Pulsed-field gel electrophoresis

PSM:

Phenol-soluble modulins

PVL:

Panton-valentine leukocidin

SASP:

Small, acid-soluble protein

SNR:

Signal-to-noise ratio

TFA:

Trifluoroacetic acid

TSST:

Toxic shock syndrome toxin

VRE:

Vancomycin-resistant Enterococcus

VREfm:

Vancomycin-resistant Enterococcus faecium

VSE:

Vancomycin-sensitive Enterococcus

VSEfm:

Vancomycin-sensitive Enterococcus faecium

UHCA:

Unsupervised hierarchical cluster analysis

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Acknowledgments

The authors wish to thank B. Niederwöhrmeier (Bundeswehr Research Institute for Protective Technologies and NBC Protection in Munster, WIS), M. Ehling-Schulz (University of Veterinary Medicine Vienna), and W. Beyer (Institute for Environmental and Animal Hygiene and Veterinary Medicine at the University of Hohenheim) for providing Bacillus strains. The authors are furthermore grateful to T. Maier, M. Kostrzewa (Bruker Daltonik GmbH), T. Schwecke (RKI Berlin), and R. Dieckmann (Federal Institute for Risk Assessment, Department of Biological Safety) for fruitful discussions and support. Furthermore, the excellent technical assistance of P. Lochau, S. Becker, R. Heinrich, M. Stämmler, A. Brauer, A. Schneider, and S. Herfort (all RKI Berlin) is acknowledged.

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  1. Proteomics and Spectroscopy at the Centre for Biological Threats and Special Pathogens (ZBS6), Robert Koch-Institute, Seestraße 10, 13353, Berlin, Germany

    Dr. Peter Lasch

  2. ZBS 2, Highly Pathogenic Microorganisms, Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany

    Daniela Jacob & Silke R. Klee

  3. FG 13, Nosocomial Pathogens and Antibiotic Resistances, Robert Koch-Institute, 38855, Wernigerode, Burgstraße 37, Germany

    Guido Werner

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Correspondence to Peter Lasch .

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  1. Johns Hopkins University, Applied Physics Laboratory, Laurel, Maryland, USA

    Plamen Demirev

  2. Arizona State University, School of Math and Natural Sciences, Phoenix, Arizona, USA

    Todd R. Sandrin

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Lasch, P., Jacob, D., Klee, S., Werner, G. (2016). Discriminatory Power of MALDI-TOF Mass Spectrometry for Phylogenetically Closely Related Microbial Strains. In: Demirev, P., Sandrin, T. (eds) Applications of Mass Spectrometry in Microbiology. Springer, Cham. https://doi.org/10.1007/978-3-319-26070-9_8

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