PXD025365

PXD025365 is an original dataset announced via ProteomeXchange.

Title	Rapid detection of beta-lactam, aminoglycoside and fluoroquinolone resistance mechanisms in blood cultures positive for E. coli or K. pneumoniae using targeted LC-MS/MS
Description	New and rapid antimicrobial susceptibility/resistance testing methods are required for bacteria from positive blood cultures. In the current study we developed and evaluated a targeted LC-MS/MS assay for the detection of beta-lactam, aminoglycoside and fluoroquinolone resistance mechanisms in blood cultures positive for E. coli or K. pneumoniae. Selected targets were the beta-lactamases SHV, TEM, OXA-1-like, CTX-M-1-like, CMY-2-like, chromosomal E. coli AmpC, OXA-48-like, NDM, VIM and KPC, the aminoglycoside modifying enzymes AAC(3)-Ia, AAC(3)-II, AAC(3)-IV, AAC(3)-VI, AAC(6’)-Ib, ANT(2”)-I and APH(3’)-VI, the 16S-RMTases ArmA, RmtB, RmtC and RmtF, the quinolone resistance mechanisms QnrA, QnrB, AAC(6’)-Ib-cr, the wildtype QRDR of GyrA, and for E. coli, the porins OmpC and OmpF. The developed assay was evaluated using 100 prospectively collected positive blood cultures, 100 negative blood cultures inoculated with isolates that were previously collected from blood cultures, and 48 isolates inoculated with isolates carrying genes of less prevalent resistance mechanisms.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:52:19.990.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lennard Dekker
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Acinetobacter sp. PM-14; NCBI TaxID: 1214786; scientific name: Klebsiella pneumoniae JH1; NCBI TaxID: 1037890; scientific name: Klebsiella variicola At-22; NCBI TaxID: 640131;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-13 02:30:41	ID requested
1	2022-07-01 04:16:22	announced
⏵ 2	2023-11-14 08:52:20	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: blood cultures, GyrA, E. coli,Liquid chromatography-mass spectrometry, sepsis, Qnr proteins, parallel reaction monitoring, aminoglycoside modifying enzymes, K. pneumoniae, 16S ribosomal RNA methyltransferases, beta-lactamases, antimicrobial resistance

Theo Luider
contact affiliation	Lab Neuro-oncology Department of Neurology Erasmus MC
contact email	t.luider@erasmusmc.nl
lab head
Lennard Dekker
contact affiliation	Erasmus MC
contact email	l.dekker@erasmusmc.nl
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/2022/07/PXD025365

PRIDE project URI

• PRIDE
  1. PXD025365
     1. Label: PRIDE project
     2. Name: Rapid detection of beta-lactam, aminoglycoside and fluoroquinolone resistance mechanisms in blood cultures positive for E. coli or K. pneumoniae using targeted LC-MS/MS