1887

Abstract

Transferable linezolid resistance due to , , and -like genes is increasingly detected in enterococci associated with animals and humans globally. We aimed to characterize the genetic environment of in linezolid-resistant isolates from Scotland. Six linezolid-resistant isolated from urogenital samples were confirmed to carry the 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 gene was located on distinct plasmids in each isolate, suggesting that transfer of a single plasmid did not contribute to dissemination in this collection. pTM6294-2, BX5936-1 and pWE0438-1 were similar to -positive plasmids from China and Japan, while the remaining three plasmids had limited similarity to other published examples. We identified the novel Tn transposon in pWE0254-1 carrying linezolid (), macrolide () and spectinomycin [ANT(9)-Ia] resistance genes. OptrA amino acid sequences differed by 0–20 residues. We report multiple variants of on distinct plasmids in diverse strains of . 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.

Funding
This study was supported by the:
  • Wellcome Trust (Award 105621/Z/14/Z)
    • Principle Award Recipient: NotApplicable
  • Chief Scientist Office, Scottish Government Health and Social Care Directorate (Award SIRN/10)
    • Principle Award Recipient: MatthewTG Holden
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-02-07
2022-05-18
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References

  1. García-Solache M, Rice LB. The Enterococcus: a model of adaptability to its environment. Clin Microbiol Rev 2019; 32:e00058-18 [View Article] [PubMed]
    [Google Scholar]
  2. ECDC Surveillance of antimicrobial resistance in Europe – Annual report of the European Antimicrobial Resistance Surveillance Network (EARS-Net) 2017; 2019 http://www.ecdc.europa.eu/sites/portal/files/documents/EARS-Net-report-2017-update-jan-2019.pdf
  3. Zahedi Bialvaei A, Rahbar M, Yousefi M, Asgharzadeh M, Samadi Kafil H. Linezolid: a promising option in the treatment of Gram-positives. J Antimicrob Chemother 2017; 72:354–364 [View Article] [PubMed]
    [Google Scholar]
  4. Public Health England English surveillance programme for antimicrobial utilisation and resistance (ESPAUR) Report 2018-2019. London, UK: PHE; 2019 https://www.gov.uk/government/publications/english-surveillance-programme-antimicrobial-utilisation-and-resistance-espaur-report
  5. Health Protection Scotland Scottish One Health Antimicrobial Use and Resistance in 2018 Annual Report. Glasgow, UK: HPS; 2019 https://www.hps.scot.nhs.uk/web-resources-container/scottish-one-health-antimicrobial-use-and-antimicrobial-resistance-in-2018
  6. Mendes RE, Deshpande LM, Jones RN. Linezolid update: stable in vitro activity following more than a decade of clinical use and summary of associated resistance mechanisms. Drug Resist Updat 2014; 17:1–12 [View Article] [PubMed]
    [Google Scholar]
  7. Abbo L, Shukla BS, Giles A, Aragon L, Jimenez A et al. Linezolid- and Vancomycin-resistant Enterococcus faecium in solid organ transplant recipients: infection control and antimicrobial stewardship using whole genome sequencing. Clin Infect Dis 2019; 69:259–265 [View Article] [PubMed]
    [Google Scholar]
  8. Antonelli A, D’Andrea MM, Brenciani A, Galeotti CL, Morroni G et al. Characterization of poxtA, a novel phenicol-oxazolidinone-tetracycline resistance gene from an MRSA of clinical origin. J Antimicrob Chemother 2018; 73:1763–1769 [View Article] [PubMed]
    [Google Scholar]
  9. Deshpande LM, Ashcraft DS, Kahn HP, Pankey G, Jones RN et al. Detection of a New cfr-like gene, cfr(B), in Enterococcus faecium isolates recovered from human specimens in the United States as Part of the SENTRY Antimicrobial Surveillance Program. Antimicrob Agents Chemother 2015; 59:6256–6261 [View Article] [PubMed]
    [Google Scholar]
  10. Diaz L, Kiratisin P, Mendes RE, Panesso D, Singh KV et al. Transferable plasmid-mediated resistance to linezolid due to cfr in a human clinical isolate of Enterococcus faecalis. Antimicrob Agents Chemother 2012; 56:3917–3922 [View Article] [PubMed]
    [Google Scholar]
  11. Wang Y, Lv Y, Cai J, Schwarz S, Cui L et al. A novel gene, optrA, that confers transferable resistance to oxazolidinones and phenicols and its presence in Enterococcus faecalis and Enterococcus faecium of human and animal origin. J Antimicrob Chemother 2015; 70:2182–2190 [View Article] [PubMed]
    [Google Scholar]
  12. Pang S, Boan P, Lee T, Gangatharan S, Tan SJ et al. Linezolid-resistant ST872 Enteroccocus faecium harbouring optrA and cfr (D) oxazolidinone resistance genes. Int J Antimicrob Agents 2020; 55:105831 [View Article] [PubMed]
    [Google Scholar]
  13. Long KS, Poehlsgaard J, Kehrenberg C, Schwarz S, Vester B. The Cfr rRNA methyltransferase confers resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A antibiotics. Antimicrob Agents Chemother 2006; 50:2500–2505 [View Article] [PubMed]
    [Google Scholar]
  14. Guerin F, Sassi M, Dejoies L, Zouari A, Schutz S et al. Molecular and functional analysis of the novel cfr(D) linezolid resistance gene identified in Enterococcus faecium. J Antimicrob Chemother 2020; 75:1699–1703 [View Article] [PubMed]
    [Google Scholar]
  15. Deshpande LM, Castanheira M, Flamm RK, Mendes RE. Evolving oxazolidinone resistance mechanisms in a worldwide collection of enterococcal clinical isolates: results from the SENTRY Antimicrobial Surveillance Program. J Antimicrob Chemother 2018; 73:2314–2322 [View Article] [PubMed]
    [Google Scholar]
  16. Health Protection Scotland Oxazolidinone-resistance due to optrA in Enterococcus faecalis. HPS Wkly Rep 2016; 50:230–231
    [Google Scholar]
  17. Cai J, Wang Y, Schwarz S, Zhang G, Chen S et al. High detection rate of the oxazolidinone resistance gene optrA in Enterococcus faecalis isolated from a Chinese anorectal surgery ward. Int J Antimicrob Agents 2016; 48:757–759 [View Article] [PubMed]
    [Google Scholar]
  18. He T, Shen Y, Schwarz S, Cai J, Lv Y et al. Genetic environment of the transferable oxazolidinone/phenicol resistance gene optrA in Enterococcus faecalis isolates of human and animal origin. J Antimicrob Chemother 2016; 71:1466–1473 [View Article] [PubMed]
    [Google Scholar]
  19. EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.0. Version 2018
    [Google Scholar]
  20. Woodford N, Tysall L, Auckland C, Stockdale MW, Lawson AJ et al. Detection of oxazolidinone-resistant Enterococcus faecalis and Enterococcus faecium strains by real-time PCR and PCR-restriction fragment length polymorphism analysis. J Clin Microbiol 2002; 40:4298–4300 [View Article] [PubMed]
    [Google Scholar]
  21. Werner G, Strommenger B, Klare I, Witte W. Molecular detection of linezolid resistance in Enterococcus faecium and Enterococcus faecalis by use of 5’ nuclease real-time PCR compared to a modified classical approach. J Clin Microbiol 2004; 42:5327–5331 [View Article] [PubMed]
    [Google Scholar]
  22. Kehrenberg C, Schwarz S. Distribution of florfenicol resistance genes fexA and cfr among chloramphenicol-resistant Staphylococcus isolates. Antimicrob Agents Chemother 2006; 50:1156–1163 [View Article] [PubMed]
    [Google Scholar]
  23. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
    [Google Scholar]
  24. Loman NJ, Quinlan AR. Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics 2014; 30:3399–3401 [View Article] [PubMed]
    [Google Scholar]
  25. Ponstingl H, Ning Z. SMALT. Wellcome Trust Sanger Institute; 2014 http://www.sanger.ac.uk/science/tools/smalt-0 accessed 21 June 2017
  26. Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genom 2016; 2:e000056 [View Article] [PubMed]
    [Google Scholar]
  27. Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 2014; 6:1–16 [View Article] [PubMed]
    [Google Scholar]
  28. Jolley KA, Maiden MCJ. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010; 11:595 [View Article] [PubMed]
    [Google Scholar]
  29. Ruiz-Garbajosa P, Bonten MJM, Robinson DA, Top J, Nallapareddy SR et al. Multilocus sequence typing scheme for Enterococcus faecalis reveals hospital-adapted genetic complexes in a background of high rates of recombination. J Clin Microbiol 2006; 44:2220–2228 [View Article] [PubMed]
    [Google Scholar]
  30. Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genom 2017; 3:e000131 [View Article] [PubMed]
    [Google Scholar]
  31. Zankari E, Hasman H, Kaas RS, Seyfarth AM, Agersø Y et al. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother 2013; 68:771–777 [View Article] [PubMed]
    [Google Scholar]
  32. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  33. Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI reference sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 2012; 40:D130–5 [View Article] [PubMed]
    [Google Scholar]
  34. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011; 27:1009–1010 [View Article] [PubMed]
    [Google Scholar]
  35. Raven KE, Reuter S, Gouliouris T, Reynolds R, Russell JE et al. Genome-based characterization of hospital-adapted Enterococcus faecalis lineages. Nat Microbiol 2016; 1:15033 [View Article] [PubMed]
    [Google Scholar]
  36. Goodhead I, Darby AC. Taking the pseudo out of pseudogenes. Curr Opin Microbiol 2015; 23:102–109 [View Article] [PubMed]
    [Google Scholar]
  37. Zou J, Tang Z, Yan J, Liu H, Chen Y et al. n.d Dissemination of linezolid resistance through sex pheromone plasmid transfer in Enterococcus faecalis. Front Microbiol 11: [View Article] [PubMed]
    [Google Scholar]
  38. Freitas AR, Finisterra L, Tedim AP, Duarte B, Novais C et al. Linezolid- and multidrug-resistant enterococci in raw commercial dog foodMultidrug-Resistant Enterococci in Raw Commercial Dog Food, Europe, 2019-2020. Emerg Infect Dis 2021; 27:2221–2224 [View Article] [PubMed]
    [Google Scholar]
  39. Iimura M, Hayashi W, Arai E, Natori T, Horiuchi K et al. Identification of a multiresistant mosaic plasmid carrying a new segment of IS1216E-flanked optrA with integrated Tn551-ermB element in linezolid-resistant Enterococcus faecalis human isolate. J Glob Antimicrob Resist 2020; 22:697–699 [View Article] [PubMed]
    [Google Scholar]
  40. Egan SA, Shore AC, O’Connell B, Brennan GI, Coleman DC. Linezolid resistance in Enterococcus faecium and Enterococcus faecalis from hospitalized patients in Ireland: high prevalence of the MDR genes optrA and poxtA in isolates with diverse genetic backgrounds. J Antimicrob Chemother 2020; 75:1704–1711 [View Article] [PubMed]
    [Google Scholar]
  41. Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile genetic elements associated with antimicrobial resistance. Clin Microbiol Rev 2018; 31:e00088-17 [View Article] [PubMed]
    [Google Scholar]
  42. Tansirichaiya S, Rahman MA, Roberts AP. The transposon registry. Mob DNA 2019; 10:40 [View Article] [PubMed]
    [Google Scholar]
  43. Li D, Li X-Y, Schwarz S, Yang M, Zhang S-M et al. Tn 6674, a novel enterococcal optrA -carrying multiresistance transposon of the TN 554 family. Antimicrob Agents Chemother 2019AAC.00809-19, aac;AAC.00809-19v1
    [Google Scholar]
  44. Freitas AR, Tedim AP, Novais C, Lanza VF, Peixe L. Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes. Microb Genom 2020; 6: [View Article] [PubMed]
    [Google Scholar]
  45. Chen L, Han D, Tang Z, Hao J, Xiong W et al. Co-existence of the oxazolidinone resistance genes cfr and optrA on two transferable multi-resistance plasmids in one Enterococcus faecalis isolate from swine. Int J Antimicrob Agents 2020; 56:105993 [View Article] [PubMed]
    [Google Scholar]
  46. Shang Y, Li D, Hao W, Schwarz S, Shan X et al. A prophage and two ICESa2603-family integrative and conjugative elements (ICEs) carrying optrA in Streptococcus suis. J Antimicrob Chemother 2019; 74:2876–2879 [View Article]
    [Google Scholar]
  47. Hao W, Shan X, Li D, Schwarz S, Zhang S-M et al. Analysis of a poxtA- and optrA-co-carrying conjugative multiresistance plasmid from Enterococcus faecalis. J Antimicrob Chemother 2019; 74:1771–1775 [View Article] [PubMed]
    [Google Scholar]
  48. Munk P, Knudsen BE, Lukjancenko O, Duarte ASR et al. Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries. Nat Microbiol 2018; 3:898–908 [View Article] [PubMed]
    [Google Scholar]
  49. Zhao Q, Wang Y, Wang S, Wang Z, Du X et al. Prevalence and abundance of florfenicol and linezolid resistance genes in soils adjacent to swine feedlots. Sci Rep 2016; 6:1–7 [View Article] [PubMed]
    [Google Scholar]
  50. Sassi M, Guérin F, Zouari A, Beyrouthy R, Auzou M et al. Emergence of optrA-mediated linezolid resistance in enterococci from France, 2006-16. J Antimicrob Chemother 2019; 74:1469–1472 [View Article] [PubMed]
    [Google Scholar]
  51. Bender JK, Fleige C, Lange D, Klare I, Werner G. Rapid emergence of highly variable and transferable oxazolidinone and phenicol resistance gene optrA in German Enterococcus spp. clinical isolates. Int J Antimicrob Agents 2018; 52:819–827 [View Article] [PubMed]
    [Google Scholar]
  52. Egan SA, Corcoran S, McDermott H, Fitzpatrick M, Hoyne A et al. Hospital outbreak of linezolid-resistant and vancomycin-resistant ST80 Enterococcus faecium harbouring an optrA-encoding conjugative plasmid investigated by whole-genome sequencing. J Hosp Infect 2020; 105:726–735 [View Article] [PubMed]
    [Google Scholar]
  53. Lazaris A, Coleman DC, Kearns AM, Pichon B, Kinnevey PM et al. Novel multiresistance cfr plasmids in linezolid-resistant methicillin-resistant Staphylococcus epidermidis and vancomycin-resistant Enterococcus faecium (VRE) from a hospital outbreak: co-location of cfr and optrA in VRE. J Antimicrob Chemother 2017; 72:3252–3257 [View Article] [PubMed]
    [Google Scholar]
  54. Cui L, Wang Y, Lv Y, Wang S, Song Y et al. Nationwide surveillance of novel oxazolidinone resistance gene optrA in Enterococcus Isolates in China from 2004 to 2014. Antimicrob Agents Chemother 2016; 60:7490–7493 [View Article] [PubMed]
    [Google Scholar]
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