PXD056051-1

PXD056051 is an original dataset announced via ProteomeXchange.

Title	Antibiotic resistance detection and concomitant species identification of ESKAPE pathogens by proteomics
Description	Antimicrobial resistance (AMR) is an increasing challenge for therapy of bacterial infections. Currently, patient treatment is guided by antimicrobial susceptibility testing (AST) using phenotypic assays and species identification by MALDI-ToF biotyping. Bacterial phenotype prediction using omics technologies could offer several advantages over current diagnostic methods. It would allow species identification and AST to be combined in a single measurement, it would eliminate the need for secondary cultivation and could enable the prediction of phenotypes beyond AMR, such as virulence. In this study, the potential of proteomics for clinical microbiology was evaluated in an analysis of 126 clinical isolates covering 16 species including all ESKAPE genera and 30 of the most common AMR determinants. For this purpose, a flexible workflow was developed, which enables to report the AMR phenotype and the species of primary cultures within 2h. Proteomics provided high specificity (99.9%) and sensitivity (94.4 %) for AMR detection, while allowing species identification from very large sequence databases with high accuracy. The results show, that proteomics is well suited for phenotyping clinical bacterial isolates and has the potential to become a valuable diagnostic tool for clinical microbiology in the future.
HostingRepository	PRIDE
AnnounceDate	2026-03-02
AnnouncementXML	Submission_2026-03-02_04:12:57.199.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joerg Doellinger
SpeciesList	scientific name: Klebsiella quasipneumoniae; NCBI TaxID: NEWT:1463165; scientific name: Klebsiella grimontii; NCBI TaxID: NEWT:2058152; scientific name: Staphylococcus aureus; NCBI TaxID: NEWT:1280; scientific name: Acinetobacter baumannii; NCBI TaxID: NEWT:470; scientific name: Klebsiella oxytoca; NCBI TaxID: NEWT:571; scientific name: Pseudomonas aeruginosa PA103; NCBI TaxID: NEWT:1081927; scientific name: Shigella sonnei; NCBI TaxID: NEWT:624; scientific name: Morganella morganii subsp. morganii; NCBI TaxID: NEWT:180434; scientific name: Citrobacter freundii complex; NCBI TaxID: NEWT:1344959; scientific name: Enterobacter cloacae; NCBI TaxID: NEWT:550; scientific name: Enterococcus faecium Com15; NCBI TaxID: NEWT:565663; scientific name: Proteus mirabilis; NCBI TaxID: NEWT:584; scientific name: Escherichia coli; NCBI TaxID: NEWT:562; scientific name: Klebsiella pneumoniae; NCBI TaxID: NEWT:573;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-20 04:28:50	ID requested
⏵ 1	2026-03-02 04:12:57	announced

10.1016/J.MCPRO.2026.101539;

submitter keyword: LC-MS, Public Health,Bacteria, AMR, Proteomics

Joerg Doellinger
contact affiliation	Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
contact email	doellingerj@rki.de
lab head
Joerg Doellinger
contact affiliation	Proteomics and Spectroscopy (ZBS6), Robert Koch-Institute
contact email	doellingerj@rki.de
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/2026/03/PXD056051

PRIDE project URI

• PRIDE
  1. PXD056051
     1. Label: PRIDE project
     2. Name: Antibiotic resistance detection and concomitant species identification of ESKAPE pathogens by proteomics