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Presence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing.

ABSTRACT: Transferable linezolid resistance due to optrA, poxtA, cfr and cfr-like genes is increasingly detected in enterococci associated with animals and humans globally. We aimed to characterize the genetic environment of optrA in linezolid-resistant Enterococcus faecalis isolates from Scotland. Six linezolid-resistant E. faecalis isolated from urogenital samples were confirmed to carry the optrA gene by PCR. Short read (Illumina) sequencing showed the isolates were genetically distinct (>13900 core SNPs) and belonged to different MLST sequence types. Plasmid contents were examined using hybrid assembly of short and long read (Oxford Nanopore MinION) sequencing technologies. The optrA gene was located on distinct plasmids in each isolate, suggesting that transfer of a single plasmid did not contribute to optrA dissemination in this collection. pTM6294-2, BX5936-1 and pWE0438-1 were similar to optrA-positive plasmids from China and Japan, while the remaining three plasmids had limited similarity to other published examples. We identified the novel Tn6993 transposon in pWE0254-1 carrying linezolid (optrA), macrolide (ermB) and spectinomycin [ANT(9)-Ia] resistance genes. OptrA amino acid sequences differed by 0-20 residues. We report multiple variants of optrA on distinct plasmids in diverse strains of E. faecalis. It is important to identify the selection pressures driving the emergence and maintenance of resistance against linezolid to retain the clinical utility of this antibiotic.

SUBMITTER: McHugh MP

PROVIDER: S-EPMC8941993 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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Presence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing.

McHugh Martin P MP Parcell Benjamin J BJ Pettigrew Kerry A KA Toner Geoff G Khatamzas Elham E El Sakka Noha N Karcher Anne Marie AM Walker Joanna J Weir Robert R Meunier Danièle D Hopkins Katie L KL Woodford Neil N Templeton Kate E KE Gillespie Stephen H SH Holden Matthew T G MTG

Microbiology (Reading, England) 20220201 2

Transferable linezolid resistance due to optrA, poxtA, cfr and cfr-like genes is increasingly detected in enterococci associated with animals and humans globally. We aimed to characterize the genetic environment of optrA in linezolid-resistant Enterococcus faecalis isolates from Scotland. Six linezolid-resistant E. faecalis isolated from urogenital samples were confirmed to carry the optrA gene by PCR. Short read (Illumina) sequencing showe ...[more]

PMID: 35130141

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Project description:IntroductionThis research aimed to investigate the antibiotic resistance of Enterococcus faecalis from swine farms in Zhejiang Province and the prevalence and transmission mechanism of oxazolidone resistance gene optrA.MethodA total of 226 Enterococcus faecalis were isolated and their resistance to 14 antibiotics was detected by broth microdilution. The resistance genes were detected by PCR.ResultsThe antibiotic resistance rate of 226 isolates to nearly 57% (8/14) of commonly used antibiotics was higher than 50%. The resistance rate of tiamulin was highest (98.23%), that of tilmicosin, erythromycin, tetracycline and florfenicol was higher than 80%, and that of oxazolidone antibiotic linezolid was 38.49%. The overall antibiotics resistance in Hangzhou, Quzhou and Jinhua was more serious than that in the coastal cities of Ningbo and Wenzhou. The result of PCR showed that optrA was the main oxazolidinone and phenicols resistance gene, with a detection rate of 71.68%, and optrA often coexisted with fexA in the isolates. Through multi-locus sequence typing, conjugation transfer, and replicon typing experiments, it was found that the horizontal transmission mediated by RepA_N plasmid was the main mechanism of optrA resistance gene transmission in E. faecalis from Zhejiang Province. Two conjugative multi-resistance plasmids carrying optrA, RepA_N plasmid pHZ318-optrA from Hangzhou and Rep3 plasmid from Ningbo, were sequenced and analyzed. pHZ318-optrA contain two multidrug resistance regions (MDR), which contributed to the MDR profile of the strains. optrA and fexA resistance genes coexisted in IS1216E-fexA-optrA-ferr-erm(A)-IS1216E complex transposon, and there was a partial sequence of Tn554 transposon downstream. However, pNB304-optrA only contain optrA, fexA and an insertion sequence ISVlu1. The presence of mobile genetic elements at the boundaries can possibly facilitate transfer among Enterococcus through inter-replicon gene transfer.DiscussionThis study can provide theoretical basis for ensuring the quality and safety of food of animal origin, and provide scientific guidance for slowing down the development of multi-antibiotic resistant Enterococcus.

Dataset Information

Presence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing.

Publications

Presence of <i>optrA-</i>mediated linezolid resistance in multiple lineages and plasmids of <i>Enterococcus faecalis</i> revealed by long read sequencing.

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