PXD023739

PXD023739 is an original dataset announced via ProteomeXchange.

Title	A systematic exploration of antimicrobial resistance to beta-lactams, aminoglycosides and fluoroquinolones in Escherichia coli and Klebsiella pneumoniae using proteogenomics
Description	Background: Antimicrobial resistance is generally studied using a combination of growth inhibition measurements, sometimes in combination with DNA detection methods. However, the actual proteins that cause resistance such as enzymes, efflux pumps and a lack of porins cannot be detected by these methods. Improvements in liquid chromatography (LC) and mass spectrometry (MS) enabled easier and more comprehensive proteome analysis. In the current study, these three methods are combined into a multi-omics approach to analyze resistance against frequently used antibiotics within the beta-lactam, aminoglycoside and fluoroquinolone group in E. coli and K. pneumoniae. Objectives: We aimed to analyze which currently known antimicrobial resistance genes are detected at the protein level using liquid chromatography-mass spectrometry (LC-MS/MS) and to assess whether these could explain beta-lactam, aminoglycoside, and fluoroquinolone resistance in the studied isolates. Furthermore, we aimed to identify significant protein to resistance correlations which have not yet been described and to correlate the abundance of different porins to resistance. Methods: Whole genome sequencing, high-resolution LC-MS/MS and antimicrobial susceptibility testing by broth microdilution were performed for 187 clinical E. coli and K. pneumoniae isolates. Resistance genes and proteins were identified using the Comprehensive Antibiotic Resistance Database (CARD). All proteins were annotated using the NCBI RefSeq database and Prokka. Results & Conclusion: Proteins of small spectrum beta-lactamases, extended spectrum beta-lactamases, AmpC beta-lactamases, carbapenemases, and proteins of 16S ribosomal RNA methyltransferases and aminoglycoside acetyltransferases can be detected in E. coli and K. pneumoniae by LC-MS/MS. The detected mechanisms could explain phenotypic resistance in most of the studied isolates. Differences in the abundance and the primary structure of other proteins such as porins also correlated with resistance. LC-MS/MS is a different and complementary method which can be used to characterize antimicrobial resistance in detail as not only the primary resistance causing mechanisms are detected, but also secondary enhancing resistance mechanisms.
HostingRepository	PRIDE
AnnounceDate	2021-07-09
AnnouncementXML	Submission_2021-07-09_04:32:50.159.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lennard Dekker
SpeciesList	scientific name: Klebsiella pneumoniae 1162281; NCBI TaxID: 1037908;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-21 08:58:45	ID requested
1	2021-07-09 00:13:29	announced
⏵ 2	2021-07-09 04:32:51	announced	2021-07-09: Updated project metadata.

10.1038/S41598-021-91905-W;

Foudraine DE, Strepis N, Stingl C, Ten Kate MT, Verbon A, Klaassen CHW, Goessens WHF, Luider TM, Dekker LJM, Exploring antimicrobial resistance to beta-lactams, aminoglycosides and fluoroquinolones in E. coli and K. pneumoniae using proteogenomics. Sci Rep, 11(1):12472(2021) [pubmed]

submitter keyword: liquid chromatography, mass spectrometry, aminoglycosides, K. pneumoniae, data dependent acquisition, porins, comprehensive antibiotic resistance database, beta-lactams, fluoroquinolones, minimum inhibitory concentrations,E. coli, whole genome sequencing, antimicrobial resistance

Theo Luider
contact affiliation	Lab. Neuro-oncologie en klinische en kanker proteomics 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

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PRIDE project URI

• PRIDE
  1. PXD023739
     1. Label: PRIDE project
     2. Name: A systematic exploration of antimicrobial resistance to beta-lactams, aminoglycosides and fluoroquinolones in Escherichia coli and Klebsiella pneumoniae using proteogenomics