Evaluation of MALDI-TOF mass spectroscopy methods for determination of Escherichia coli pathotypes

Clark, Clifford G.; Kruczkiewicz, Peter; Guan, Cai; McCorrister, Stuart; Chong, Patrick; Wylie, John; Caeseele, Paul Van; Tabor, Helen; Snarr, Phillip; Gilmour, Matthew W.; Taboada, Eduardo N.; Westmacott, Garrett

doi:10.1016/j.mimet.2013.06.020

Cited by 73 publications

(43 citation statements)

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“…Presence versus absence, m/z, and (relative) intensity levels are subject to analytical error, biological and technical variation (including complex, sometimes low-level protein expression and posttranslational modification and its regulation), and analyte incorporation in matrix crystals. Thus, some typing schemes, such as the one proposed by Clark et al (11), are largely based on absence of peaks and may thus be more sensitive to technical issues, such as noise in spectra, compared to approaches based on presence of more stable and specific biomarkers.…”

Section: Typing By Maldi-tof Ms: What Can We Learn From Pfge?mentioning

confidence: 99%

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Microbial Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Do We Need Guidance for Data Interpretation?

et al. 2015

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eThe integration of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology has revolutionized species identification of bacteria, yeasts, and molds. However, beyond straightforward identification, the method has also been suggested to have the potential for subspecies-level or even type-level epidemiological analyses. This minireview explores MALDI-TOF MS-based typing, which has already been performed on many clinically relevant species. We discuss the limits of the method's resolution and we suggest interpretative criteria allowing valid comparison of strain-specific data. We conclude that guidelines for MALDI-TOF MS-based typing can be developed along the same lines as those used for the interpretation of data from pulsed-field gel electrophoresis (PFGE). Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been integrated into the routine diagnostic workflow of many industrial, pharmaceutical, and medical microbiology laboratories. It has already been thoroughly evaluated for the identification of clinically relevant bacterial species, including anaerobes, Gram-positive rods and cocci, Enterobacteriaceae, and miscellaneous Gram-negative (including nonfermentative) rods, with adequate to excellent results (1, 2).Species identification, however, is only a first step in the diagnostic workflow. The ability to quickly and reliably distinguish or "type" related bacterial isolates is essential for bacterial transmission studies and larger-scale epidemiological surveillance projects. "Conventional" phenotyping methods, such as multiple-susceptibility testing, phage typing, serotyping, biochemical typing, and several others, have been important contributors to our understanding of the epidemiology of community-and health careassociated infections. However, these methods all have practical limitations which render them largely unsuitable for comprehensive bacterial population analyses as well as for scientifically less ambitious but critical infection surveillance. Furthermore, most phenotypic methods have been developed for individual bacterial taxa and are not transferable to other taxa without considerable adaptation.Hence, over the past 2 decades, phenotyping has been largely replaced by "molecular" genotyping. Clonal reproduction by binary fission imprints the evolutionary history of the organism in genotypic markers amenable to analysis by nucleic acid-mediated methods. However, in practice, the ease with which recombination, transfection, and transformation can take place in bacteria necessitates that data from multiple genetic markers are analyzed in defining a "precise" genotype and even then there is no guarantee that an adequate natural taxonomy will be derived. Polyphasic taxonomy currently uses combinations of different phenotypic and/or genotypic data sets to define genera, species, and entities at or below the subspecies level. Still, all these approaches remain time-consuming and relatively...

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Section: Typing By Maldi-tof Ms: What Can We Learn From Pfge?mentioning

confidence: 99%

“…Thus, the rapid recognition of pathogenic or potentially pathogenic types is of interest. In a study by Clark et al, 136 unrelated strains of E. coli, encompassing six pathotypes, could be grouped by MALDI-TOF MS using an Autoflex III machine (11). One interesting result was the association of E. coli O157:H7 with two specific MS peaks (12).…”

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confidence: 99%

Microbial Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Do We Need Guidance for Data Interpretation?

et al. 2015

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“…MALDI-TOF MS as a tool for classifi cation and identifi cation of bacteria has been systematically used for about ten years (150), and its use as an alternative to conventional methods for identification of food pathogens was described by Schumann and Maier (151). It was also shown that this method can be used as a very effi cient tool for the identifi cation of high-risk toxin-producing E. coli strains (152). The major bott leneck for further implementation of MALDI-TOF MS in food monitoring systems remains sample preparation.…”

Section: Maldi-tof Mass Spectrometrymentioning

confidence: 99%

Foodomics and Food Safety: Where We Are

Andjelković

Gajdošik

Gašo-Sokač

et al. 2017

Food Technol. Biotechnol.

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SummaryThe power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identifi cation, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special att ention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is infl uenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affi nity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affi nity-based methods, are the cross-reactivity between similar molecules and the infl uence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identifi cation and quantifi cation, and for corresponding modeling.

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“…MS-based proteomics therefore becomes an increasingly suitable tool which enables to detect and identify expressed proteins in bacteria. As a prominent example, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF), although in use for several decades, has fairly recently emerged as a rapid and cost-saving method for the identification of microbial species which has been approved for clinical applications (Sauer & Kliem (2010), Neville et al (2011), Clark et al (2013)). While the latter approach processes information at the MS1 level, tandem mass spectrometry (MS/MS)-based proteome analysis techniques decipher amino acid sequences from their fragmentation pattern by matching tandem mass spectra against a provided sequence reference database.…”

Section: Introductionmentioning

confidence: 99%

Hortense: Horizontal gene transfer detection directly from proteomic MS/MS data

Trappe

Wulf

Doellinger

et al. 2017

Preprint

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Horizontal gene transfer (HGT) is a powerful mechanism that allows bacteria to directly transfer long stretches of genomic sequence from one individual to another. The transfer of antimicrobial resistance genes is a prominent example of HGT events in the context of multi-resistant bacteria which pose a high risk to human health. While several approaches for HGT detection exist on the genomic level, to the best of our knowledge, HGT events have not been investigated in a detailed mass spectrometry (MS)-based proteomic study. However, the mere presence of a gene does not necessarily correlate with its expression at the protein level. Consequently, to draw conclusions with respect to the expression of HGT-mediated genes, MS-based proteomics can be employed. We developed a first computational approach -called Hortense -for automated HGT detection directly from shotgun proteomics experiments. We extend the standard database search by a critical cross-validation to unravel potential HGT proteins. A proteogenomic extension gives information about the genomic origin and enables an integration with existing genome-based methods. We successfully validated our approach on simulated data, and further evaluated it on real data from a transgenic organism and a negative control from an organism not harboring a transferred gene. Our results indicate that our method facilitates MS-based analysis for proteomic evidence of HGT events. Especially as an orthogonal approach to genome-based HGT detection methods, our proposed workflow is a first step toward a systematic and large scale analysis of HGT events in, e.g., antimicrobial resistance context. Hortense is publicly available at https://gitlab.com/rki bioinformatics/.

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Evaluation of MALDI-TOF mass spectroscopy methods for determination of Escherichia coli pathotypes

Cited by 73 publications

References 64 publications

Microbial Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Do We Need Guidance for Data Interpretation?

Microbial Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Do We Need Guidance for Data Interpretation?

Foodomics and Food Safety: Where We Are

Hortense: Horizontal gene transfer detection directly from proteomic MS/MS data

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