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PXD022425 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleUniversal antimicrobial resistance detection from clinical bacterial isolates using proteomics
DescriptionAntimicrobial 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterChristian Blumenscheitc
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Enterococcus faecium; NCBI TaxID: 1352; scientific name: Citrobacter freundii; NCBI TaxID: 546; scientific name: Salmonella enterica subsp. enterica serovar Infantis; NCBI TaxID: 595; scientific name: Klebsiella pneumoniae subsp. pneumoniae; NCBI TaxID: 72407; scientific name: Enterobacter cloacae subsp. cloacae; NCBI TaxID: 336306; scientific name: Salmonella enterica subsp. enterica serovar Typhimurium; NCBI TaxID: 90371;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-11-09 03:24:13ID requested
12021-11-25 04:54:28announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: antibiotic resistance mechanism, AMR, LC-MS, proteomics, mass spectrometry, bacteria, data-independent acquisition, carbapenemases, ESBL, mcr
Contact List
Robert Koch-Institute
contact affiliationPeter Lasch, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
contact emaillaschp@rki.de
lab head
Christian Blumenscheitc
contact affiliationRobert Koch-Institut, ZBS6
contact emailchblumenscheit@gmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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