Exploring antimicrobial resistance to beta-lactams, aminoglycosides and fluoroquinolones in E. coli and K. pneumoniae using proteogenomics

Antimicrobial resistance is mostly studied by means of phenotypic growth inhibition determinations, in combination with PCR confirmations or further characterization by means of whole genome sequencing (WGS). However, the actual proteins that cause resistance such as enzymes and a lack of porins can...

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Bibliographic Details
Published in:Scientific reports Vol. 11; no. 1; pp. 12472 - 18
Main Authors: Foudraine, Dimard E., Strepis, Nikolaos, Stingl, Christoph, ten Kate, Marian T., Verbon, Annelies, Klaassen, Corné H. W., Goessens, Wil H. F., Luider, Theo M., Dekker, Lennard J. M.
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 14.06.2021
Nature Publishing Group
Nature Portfolio
Subjects:
631/326/22/1434
631/337/475
Acetyltransferases - analysis
Acetyltransferases - genetics
Acetyltransferases - metabolism
Amino Acid Sequence
Aminoglycoside antibiotics
Aminoglycosides - pharmacology
Aminoglycosides - therapeutic use
Anti-Bacterial Agents - therapeutic use
Antibiotic resistance
Antibiotics
Antimicrobial agents
Antimicrobial resistance
Bacterial Proteins - analysis
Bacterial Proteins - genetics
Bacterial Proteins - metabolism
beta-Lactamases - analysis
beta-Lactamases - genetics
beta-Lactamases - metabolism
beta-Lactams - pharmacology
beta-Lactams - therapeutic use
Chromatography
Chromatography, High Pressure Liquid - methods
DNA, Bacterial - genetics
DNA, Bacterial - isolation & purification
Drug resistance
Drug Resistance, Bacterial - genetics
E coli
Escherichia coli - drug effects
Escherichia coli - enzymology
Escherichia coli - genetics
Escherichia coli - isolation & purification
Fluoroquinolones
Fluoroquinolones - pharmacology
Fluoroquinolones - therapeutic use
Gene Expression Regulation, Bacterial
Genomes
Humanities and Social Sciences
Klebsiella pneumoniae - drug effects
Klebsiella pneumoniae - enzymology
Klebsiella pneumoniae - genetics
Klebsiella pneumoniae - isolation & purification
Liquid chromatography
Mass spectrometry
Mass spectroscopy
Methyltransferases - analysis
Methyltransferases - genetics
Methyltransferases - metabolism
multidisciplinary
Phenotypes
Porins
Proteins
Proteogenomics - methods
Proteomes
RNA, Ribosomal, 16S - metabolism
rRNA 16S
Science
Science (multidisciplinary)
Scientific imaging
Tandem Mass Spectrometry - methods
Whole Genome Sequencing
β-Lactam antibiotics
ISSN:2045-2322, 2045-2322
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Summary:Antimicrobial resistance is mostly studied by means of phenotypic growth inhibition determinations, in combination with PCR confirmations or further characterization by means of whole genome sequencing (WGS). However, the actual proteins that cause resistance such as enzymes 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, susceptibility testing, WGS and MS 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 . Our aim was to study which currently known mechanisms of resistance can be 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 before and to correlate the abundance of different porins in relation to resistance to different classes of antibiotics. 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. 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 matched with the phenotype in the majority of 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.
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ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-021-91905-w