F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in Human-Associated Commensal Escherichia coli

Stephens, Craig; Arismendi, Tyler; Wright, Megan H.; Hartman, Austin; González, Ainhoa; Gill, Matthew S.; Pandori, Mark; Hess, David

doi:10.1128/msphere.00709-20

Cited by 40 publications

(65 citation statements)

References 51 publications

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“…The ‘success’ of E. coli as a pathogen can be mostly attributed to the wide repertoire of virulence factors that strains may carry [ 6 ] and the increasing fraction of infections caused by multidrug-resistant strains [ 7 ]. Many of the antibiotic resistance genes and virulence factors present in E. coli are commonly encoded on plasmids, mobile genetic elements (MGE) that can be horizontally disseminated [ 8 , 9 , 10 ]. Therefore, precise identification and characterization of E. coli plasmids are highly relevant from an epidemiological and clinical standpoint.…”

Section: Introductionmentioning

confidence: 99%

Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

et al. 2021

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The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP and SCAPP) that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. We found that two thirds (n = 425, 66.3%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (n = 85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (n = 317, 50.23%), and performed best at reconstructing large plasmids (n = 166, 46.37%) and ARG-plasmids (n = 41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (n = 168, 61.54%). Large ARG-plasmids, however, were frequently merged with sequences derived from distinct replicons. Available bioinformatic tools can provide valuable insight into E. coli plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on E. coli plasmids in the absence of long-read sequencing data.

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Section: Introductionmentioning

confidence: 99%

Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

et al. 2021

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“…Indeed, searches of the NCBI database identified carbapenem resistant human E. coli isolate E300, identified in Japan (17), which has an 8 nt insertion, leading to a frameshift in rseA at nucleotide 34 (Accession Number AP022360). Furthermore, two human clinical isolates were found to have a single nucleotide insertion leading to a frameshift in gmhB after nucleotide 126; one from China (Accession Number CP008697) and one from the USA (Accession Number CP072911); and three commensal E. coli from the USA (18) were found to have frameshift mutations at various positions in gmhB (Accession Numbers CP051692, CP054319, and CP054319). Accordingly, we conclude that mutations likely to cause the same phenotypes found in our laboratory-selected cefalexin-resistant mutants are also found in clinical and commensal E. coli from across the world.…”

Section: Resultsmentioning

confidence: 99%

OmpF Downregulation Mediated by Sigma E or OmpR Activation Confers Cefalexin Resistance in Escherichia coli in the Absence of Acquired β-Lactamases

Alzayn

Dulyayangkul

Satapoomin

et al. 2021

Preprint

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Cefalexin is a widely used 1st generation cephalosporin, and resistance in Escherichia coli is caused by Extended-Spectrum (e.g. CTX-M) and AmpC β-lactamase production and therefore frequently coincides with 3rd generation cephalosporin resistance. However, we have recently identified large numbers of E. coli isolates from human infections, and from cattle, where cefalexin resistance is not β-lactamase mediated. Here we show, by studying laboratory selected mutants, clinical isolates, and isolates from cattle, that OmpF porin disruption or downregulation is a major cause of cefalexin resistance in E. coli. Importantly, we identify multiple regulatory mutations that cause OmpF downregulation. In addition to mutation of ompR, already known to downregulate OmpF and OmpC porin production, we find that rseA mutation, which strongly activates the Sigma E regulon, greatly increasing DegP production, which degrades OmpF, OmpC and OmpA porins. Furthermore, we reveal that mutations affecting lipopolysaccharide structure, exemplified by the loss of GmhB, essential for lipopolysaccharide heptosylation, also modestly activate DegP production, resulting in OmpF degradation. Remarkably, given the critical importance attached to such systems for normal E. coli physiology, we find evidence for DegP-mediated OmpF downregulation, gmhB and rseA loss of function mutation in E. coli isolates derived from human infections. Finally, we show that these regulatory mutations enhance the ability of group 1 CTX-M β-lactamase to confer reduced carbapenem susceptibility, particularly those mutations that cause OmpC in addition to OmpF downregulation.

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“…We found that the plasmid-partitioning protein SopA was significantly more abundant in ciprofloxacin resistant E. coli isolates. This protein plays a role in plasmid partitioning of F plasmids which are major carriers of acquired resistance genes in E. coli 32 , 33 . In K. pneumoniae , presence of the outer membrane protein assembly factor BamE was significantly correlated to resistance.…”

Section: Discussionmentioning

confidence: 99%

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

Foudraine

Strepis

Stingl

et al. 2021

Sci Rep

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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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F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in Human-Associated Commensal Escherichia coli

Cited by 40 publications

References 51 publications

Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

OmpF Downregulation Mediated by Sigma E or OmpR Activation Confers Cefalexin Resistance in Escherichia coli in the Absence of Acquired β-Lactamases

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

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