Proteomics

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Universal antimicrobial resistance detection from clinical bacterial isolates using proteomics


ABSTRACT: Antimicrobial resistance (AMR) is an increasing challenge for therapy and management of bacterial infections. Currently, antimicrobial resistance detection relies on phenotypic assays, which are performed independently of species identification. On the contrary, phenotypic prediction from molecular data using genomics is gaining interest in clinical microbiology and might become a serious alternative in the future. Although, in general protein analysis should be superior to genomics for phenotypic prediction, no untargeted proteomics workflow specifically related to AMR detection has been proposed so far. In this study, we present a universal proteomics workflow to detect the bacterial species and antimicrobial resistance related proteins in the absence of secondary antibiotic cultivation in less than 4 h from a primary culture. The method was validated using a sample cohort of 7 bacterial species and 11 AMR determinants represented by 13 protein isoforms which resulted in a sensitivity of 92 % (100 % with vancomycin inference) and a specificity of 100 % with respect to AMR determinants. This proof-of concept study demonstrates the high potential of untargeted proteomics for clinical microbiology.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Salmonella Enterica Subsp. Enterica Serovar Typhimurium Salmonella Enterica Subsp. Enterica Serovar Infantis Escherichia Coli Enterobacter Cloacae Subsp. Cloacae Enterococcus Faecium Citrobacter Freundii Klebsiella Pneumoniae Subsp. Pneumoniae

SUBMITTER: Christian Blumenscheitc  

LAB HEAD: Robert Koch-Institute

PROVIDER: PXD022425 | Pride | 2021-11-25

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
151-09_K1.raw Raw
151-09_K1_full_Full_Report.csv Csv
151-09_K1_full_Report.pdf Pdf
151-09_K1_full_quant.csv Csv
151-09_K1_whitelisted_Full_Report.csv Csv
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Publications

Unbiased Antimicrobial Resistance Detection from Clinical Bacterial Isolates Using Proteomics.

Blumenscheit Christian C   Pfeifer Yvonne Y   Werner Guido G   John Charlyn C   Schneider Andy A   Lasch Peter P   Doellinger Joerg J  

Analytical chemistry 20211026 44


Antimicrobial resistance (AMR) poses an increasing challenge for therapy and clinical management of bacterial infections. Currently, antimicrobial resistance detection relies on phenotypic assays, which are performed independently from species identification. Sequencing-based approaches are possible alternatives for AMR detection, although the analysis of proteins should be superior to gene or transcript sequencing for phenotype prediction as the actual resistance to antibiotics is almost exclus  ...[more]

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