PXD022425

PXD022425 is an original dataset announced via ProteomeXchange.

Title	Universal antimicrobial resistance detection from clinical bacterial isolates using proteomics
Description	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.
HostingRepository	PRIDE
AnnounceDate	2021-11-25
AnnouncementXML	Submission_2021-11-25_04:54:28.536.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian 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;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-09 03:24:13	ID requested
⏵ 1	2021-11-25 04:54:28	announced

Dataset with its publication pending

submitter keyword: antibiotic resistance mechanism, AMR, LC-MS, proteomics, mass spectrometry, bacteria, data-independent acquisition, carbapenemases, ESBL, mcr

Robert Koch-Institute
contact affiliation	Peter Lasch, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
contact email	laschp@rki.de
lab head
Christian Blumenscheitc
contact affiliation	Robert Koch-Institut, ZBS6
contact email	chblumenscheit@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/11/PXD022425

PRIDE project URI

• PRIDE
  1. PXD022425
     1. Label: PRIDE project
     2. Name: Universal antimicrobial resistance detection from clinical bacterial isolates using proteomics