Targeted Proteomics for Studying Pathogenic Bacteria

Saleh, Sara; Staes, An; Deborggraeve, Stijn; Gevaert, Kris

doi:10.1002/pmic.201800435

Cited by 46 publications

(27 citation statements)

References 102 publications

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“…It is less hampered by multiplexing issues than PCR and immunoassays. Furthermore, results can be obtained rapidly when sample pre-treatment time and organism enrichment can be by-passed or shortened (Charretier et al, 2015; Wang et al, 2017; Saleh et al, 2019; Strich et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Accurate Detection of the Four Most Prevalent Carbapenemases in E. coli and K. pneumoniae by High-Resolution Mass Spectrometry

et al. 2019

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BackgroundAt present, phenotypic growth inhibition techniques are used in routine diagnostic microbiology to determine antimicrobial resistance of bacteria. Molecular techniques such as PCR are often used for confirmation but are indirect as they detect particular resistance genes. A direct technique would be able to detect the proteins of the resistance mechanism itself. In the present study targeted high resolution mass spectrometry assay was developed for the simultaneous detection of KPC, OXA-48-like, NDM, and VIM carbapenemases.MethodsCarbapenemase specific target peptides were defined by comparing available sequences in GenBank. Selected peptide sequences were validated using 62 Klebsiella pneumoniae and Escherichia coli isolates containing: 16 KPC, 21 OXA-48-like, 16 NDM, 13 VIM genes, and 21 carbapenemase negative isolates.ResultsFor each carbapenemase, two candidate peptides were validated. Method validation was performed in a blinded manner for all 83 isolates. All carbapenemases were detected. The majority was detected by both target peptides. All target peptides were 100% specific in the tested isolates and no peptide carry-over was detected.ConclusionThe applied targeted bottom-up mass spectrometry technique is able to accurately detect the four most prevalent carbapenemases in a single analysis.

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Section: Discussionmentioning

confidence: 99%

Accurate Detection of the Four Most Prevalent Carbapenemases in E. coli and K. pneumoniae by High-Resolution Mass Spectrometry

et al. 2019

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“…36 In the last two decades much attention has been paid to study the proteome of different human pathogenic bacteria. 37,38 S. marcescens is one of the pathogenic bacteria and many strains of this bacterium have been sequenced at genome and proteome levels. 10,18,20,22,[39][40][41] To the best of our knowledge, the genome of S. marcescens (ATCC 13880) sequence is available and the proteome of the same is not available till date.…”

Section: Discussionmentioning

confidence: 99%

Proteomic profiling of Serratia marcescens by high-resolution mass spectrometry

2020

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Introduction: Serratia marcescens, an opportunistic human pathogen, is reported as an important cause of nosocomial infection and outbreaks. Although the genome of S. marcescens (ATCC 13880) was completely sequenced by 2014, there are no studies on the proteomic profile of the organism. The objective of the present study is to analyze the protein profile of S. marcescens (ATCC 13880) using a high resolution mass spectrometry (MS). Methods: Serratia marcescens ATCC 13880 strain was grown in Luria-Bertani broth and the protein extracted was subjected to trypsin digestion, followed by basic reverse phase liquid chromatography fractionation. The peptide fractions were then analysed using Orbitrap Fusion Mass Spectrometry and the raw MS data were processed in Proteome Discoverer software. Results: The proteomic analysis identified 15 009 unique peptides mapping to 2541 unique protein groups, which corresponds to approximately 54% of the computationally predicted protein-coding genes. Bioinformatic analysis of these identified proteins showed their involvement in biological processes such as cell wall organization, chaperone-mediated protein folding and ATP binding. Pathway analysis revealed that some of these proteins are associated with bacterial chemotaxis and beta-lactam resistance pathway. Conclusion: To the best of our knowledge, this is the first high-throughput proteomics study of S. marcescens (ATCC 13880). These novel observations provide a crucial baseline molecular profile of the S. marcescens proteome which will prove to be helpful for the future research in understanding the host-pathogen interactions during infection, elucidating the mechanism of multidrug resistance, and developing novel diagnostic markers or vaccine for the disease.

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“…Targeted proteomics applications in the field of pathogenic bacteria have increased substantially in recent years. For example, both SRM and PRM have produced sensitive quantitative results about the proteins associated with bacterial infection, particularly in the fields of clinical diagnosis and antibiotic resistance [84]. Thus, iTRAQ-based quantitative proteomics followed by MRM studies were used to contrast the differentially regulated proteins of Aeromonas veronii.…”

Section: Food Safety In Aquaculture: Biotic Hazardsmentioning

confidence: 99%

Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products

Carrera

Piñeiro

Martı́nez

2020

Foods

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This review presents the primary applications of various proteomic strategies to evaluate the impact of farming conditions on food quality and safety in aquaculture products. Aquaculture is a quickly growing sector that represents 47% of total fish production. Food quality, dietary management, fish welfare, the stress response, food safety, and antibiotic resistance, which are covered by this review, are among the primary topics in which proteomic techniques and strategies are being successfully applied. The review concludes by outlining future directions and potential perspectives.

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Targeted Proteomics for Studying Pathogenic Bacteria

Cited by 46 publications

References 102 publications

Accurate Detection of the Four Most Prevalent Carbapenemases in E. coli and K. pneumoniae by High-Resolution Mass Spectrometry

Accurate Detection of the Four Most Prevalent Carbapenemases in E. coli and K. pneumoniae by High-Resolution Mass Spectrometry

Proteomic profiling of Serratia marcescens by high-resolution mass spectrometry

Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products

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