PXD024339

PXD024339 is an original dataset announced via ProteomeXchange.

Title	Rapid and accurate detection of aminoglycoside modifying enzymes and 16S ribosomal RNA methyltransferases by targeted LC-MS/MS
Description	New and rapid diagnostic methods are needed for the detection of antimicrobial resistance to aid in the curbing of drug-resistant infections. Targeted LC-MS/MS is a method that could serve this purpose, as it can detect specific peptides of resistance mechanisms with high accuracy. In the current study, we aimed to develop an accurate, rapid and high-throughput targeted LC-MS/MS assay based on parallel reaction monitoring for detection of the most prevalent aminoglycoside modifying enzymes and 16S ribosomal RNA methyltransferases in E. coli and K. pneumoniae that confer resistance to the most commonly used aminoglycosides. Specific tryptic peptides needed for detection were selected and validated for AAC(3)-Ia, AAC(3)-II, AAC(3)-IV, AAC(3)-VI, AAC(6’)-Ib, AAC(6’)-Ib-cr, ANT(2”)-I, APH(3’)-VI, ArmA, RmtB, RmtC and RmtF. In total, 205 different isolates containing different aminoglycoside resistance mechanisms that consisted mostly of E. coli and K. pneumoniae were selected for assay development and validation. MS results were automatically analyzed and were compared to WGS results which were regarded as the reference. The average sensitivity and specificity for the detection of the different mechanisms by LC-MS/MS compared to WGS was 95.1 % and 98.0 %, respectively. Furthermore, MS results were also used to predict resistance and susceptibility to gentamicin, tobramycin and amikacin in only the E. coli and K. pneumoniae isolates (n=191). The category interpretations were correctly predicted for gentamicin in 97.4 % of the isolates, for tobramycin in 97.4 % of the isolates, and for amikacin in 82.7 % of the isolates. The current study shows that targeted LC-MS/MS can be applied for accurate and rapid detection of aminoglycoside resistance mechanisms.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:21:37.734.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: Klebsiella pneumoniae BIDMC 40; NCBI TaxID: 1328426;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-24 02:15:24	ID requested
1	2021-04-30 11:25:46	announced
2	2023-11-14 08:52:24	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:21:38	announced	2024-10-22: Updated project metadata.

10.1128/JCM.00464-21;

submitter keyword: E. coli, aminoglycosides, parallel reaction monitoring, aminoglycoside modifying enzymes,Liquid chromatography mass spectrometry, K. pneumoniae, 16S ribosomal RNA methyltransferases, antimicrobial resistance

Theo Luider
contact affiliation	Erasmus MC Neurology Lab. Neuro-Oncology and Clinical and Cancer Proteomics
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/2021/04/PXD024339

PRIDE project URI

• PRIDE
  1. PXD024339
     1. Label: PRIDE project
     2. Name: Rapid and accurate detection of aminoglycoside modifying enzymes and 16S ribosomal RNA methyltransferases by targeted LC-MS/MS