Genomic Characterization of a Vancomycin-Resistant Strain of Enterococcus faecium Harboring a rep2 Plasmid

References

• Garcia-Solache M, Rice LB. The enterococcus: a model of adaptability to its environment. Clin Microbiol Rev. 2019;32(2):5. PMID: 30700430. PMCID: PMC6431128. doi:10.1128/CMR.00058-18
   Web of Science ®Google Scholar
• Ramos S, Silva V, Dapkevicius MLE, Igrejas G, Poeta P. Enterococci, from harmless bacteria to a pathogen. Microorganisms. 2020;8(8):55. PMID: 32722391. PMCID: PMC7463792. doi:10.3390/microorganisms8081118
   Web of Science ®Google Scholar
• Miller WR, Murray BE, Rice LB, Arias CA. Resistance in vancomycin-resistant enterococci. Infect Dis Clin North Am. 2020;34(4):751–771. PMID: 33131572. PMCID: PMC7640809. doi:10.1016/j.idc.2020.08.004
   PubMed Web of Science ®Google Scholar
• Joshi S, Shallal A, Zervos M. Vancomycin-resistant enterococci: epidemiology, infection prevention, and control. Infect Dis Clin North Am. 2021;35(4):953–968. PMID: 34752227. doi:10.1016/j.idc.2021.07.002
   PubMed Web of Science ®Google Scholar
• De Oliveira DMP, Forde BM, Kidd TJ, et al. Antimicrobial resistance in ESKAPE pathogens. Clin Microbiol Rev. 2020;33(3). PMID: 32404435. PMCID: PMC7227449. doi:10.1128/CMR.00181-19
   PubMed Web of Science ®Google Scholar
• Mascini EM, Bonten MJ. Vancomycin-resistant enterococci: consequences for therapy and infection control. Clin Microbiol Infect. 2005;11(Suppl 4):43–56. PMID: 15953021. doi:10.1111/j.1469-0691.2005.01164.x
   PubMedGoogle Scholar
• Hegstad K, Mikalsen T, Coque TM, Werner G, Sundsfjord A. Mobile genetic elements and their contribution to the emergence of antimicrobial resistant Enterococcus faecalis and Enterococcus faecium. Clin Microbiol Infect. 2010;16(6):541–554. PMID: 20569265. doi:10.1111/j.1469-0691.2010.03226.x
   PubMed Web of Science ®Google Scholar
• Lee T, Pang S, Abraham S, Coombs GW. Antimicrobial-resistant CC17 Enterococcus faecium: the past, the present and the future. J Glob Antimicrob Resist. 2019;16:36–47. PMID: 30149193. doi:10.1016/j.jgar.2018.08.016
   PubMed Web of Science ®Google Scholar
• Cheng VC, Chen JH, Tai JW, et al. Decolonization of gastrointestinal carriage of vancomycin-resistant Enterococcus faecium: case series and review of literature. BMC Infect Dis. 2014;14:514. PMID: 25248287. PMCID: PMC4180964. doi:10.1186/1471-2334-14-514
   PubMed Web of Science ®Google Scholar
• Mutters NT, Mersch-Sundermann V, Mutters R, Brandt C, Schneider-Brachert W, Frank U. Control of the spread of vancomycin-resistant enterococci in hospitals: epidemiology and clinical relevance. Dtsch Arztebl Int. 2013;110(43):725–731. PMID: 24222791. PMCID: PMC3822708. doi:10.3238/arztebl.2013.0725
   PubMed Web of Science ®Google Scholar
• Liu S, Li Y, He Z, Wang Y, Wang J, Jin D. A molecular study regarding the spread of vanA vancomycin-resistant Enterococcus faecium in a tertiary hospital in China. J Glob Antimicrob Resist. 2022;31:270–278. PMID: 36273808. doi:10.1016/j.jgar.2022.10.010
   PubMed Web of Science ®Google Scholar
• Yan MY, He YH, Ruan GJ, Xue F, Zheng B, Lv Y. The prevalence and molecular epidemiology of vancomycin-resistant Enterococcus (VRE) carriage in patients admitted to intensive care units in Beijing, China. J Microbiol Immunol Infect. 2022. PMID: 35922268. doi:10.1016/j.jmii.2022.07.001
   Google Scholar
• Zhang Z, Song Y, Kang J, et al. Epidemiology of patients with central nervous system infections, mainly neurosurgical patients: a retrospective study from 2012 to 2019 in a teaching hospital in China. BMC Infect Dis. 2021;21(1):826. PMID: 34404351. PMCID: PMC8369693. doi:10.1186/s12879-021-06561-2
   PubMed Web of Science ®Google Scholar
• Zhou W, Zhou H, Sun Y, et al. Characterization of clinical enterococci isolates, focusing on the vancomycin-resistant enterococci in a tertiary hospital in China: based on the data from 2013 to 2018. BMC Infect Dis. 2020;20(1):356. PMID: 32517758. PMCID: PMC7285731. doi:10.1186/s12879-020-05078-4
   PubMed Web of Science ®Google Scholar
• Sun L, Xu J, Wang W, He F. Emergence of vanA-type vancomycin-resistant Enterococcus faecium ST 78 strain with a rep2-type plasmid carrying a Tn1546-like element isolated from a urinary tract infection in China. Infect Drug Resist. 2020;13:949–955. PMID: 32308438. PMCID: PMC7135120. doi:10.2147/IDR.S247569
   PubMed Web of Science ®Google Scholar
• Fujiya Y, Harada T, Sugawara Y, et al. Transmission dynamics of a linear vanA-plasmid during a nosocomial multiclonal outbreak of vancomycin-resistant enterococci in a non-endemic area, Japan. Sci Rep. 2021;11(1):14780. PMID: 34285270. PMCID: PMC8292306. doi:10.1038/s41598-021-94213-5
   PubMed Web of Science ®Google Scholar
• Arredondo-Alonso S, Top J, Corander J, Willems RJL, Schurch AC. Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals. Genom Med. 2021;13(1):9. PMID: 33472670. PMCID: PMC7816424. doi:10.1186/s13073-020-00825-3
   Google Scholar
• Hashimoto Y, Kita I, Suzuki M, Hirakawa H, Ohtaki H, Tomita H. First report of the local spread of vancomycin-resistant enterococci ascribed to the interspecies transmission of a vanA gene cluster-carrying linear plasmid. mSphere. 2020;5(2). PMID: 32269153. PMCID: PMC7142295. doi:10.1128/mSphere.00102-20
   PubMed Web of Science ®Google Scholar
• Zheng B, Feng C, Xu H, et al. Detection and characterization of ESBL-producing Escherichia coli expressing mcr-1 from dairy cows in China. J Antimicrob Chemother. 2019;74(2):321–325. PMID: 30418551. doi:10.1093/jac/dky446
   PubMed Web of Science ®Google Scholar
• Zheng B, Xu H, Lv T, et al. Stool samples of acute diarrhea inpatients as a reservoir of ST11 hypervirulent KPC-2-producing Klebsiella pneumoniae. mSystems. 2020;5(3). PMID: 32576652. PMCID: PMC7311318. doi:10.1128/mSystems.00498-20
   Web of Science ®Google Scholar
• Han H, Zhao Z, Lin Y, Lin B, Xu H, Zheng B. Co-production of NDM-1 and OXA-10 beta-lactamase in citrobacter braakii strain causing urinary tract infection. Infect Drug Resist. 2022;15:1127–1133. PMID: 35340671. PMCID: PMC8943965. doi:10.2147/IDR.S347943
   PubMed Web of Science ®Google Scholar
• Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13(6):e1005595. PMID: 28594827. PMCID: PMC5481147. doi:10.1371/journal.pcbi.1005595
   PubMed Web of Science ®Google Scholar
• Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–2069. PMID: 24642063. doi:10.1093/bioinformatics/btu153
   PubMed Web of Science ®Google Scholar
• Florensa AF, Kaas RS, Clausen P, Aytan-Aktug D, Aarestrup FM. ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microb Genom. 2022;8(1). PMID: 35072601. PMCID: PMC8914360. doi:10.1099/mgen.0.000748
   PubMed Web of Science ®Google Scholar
• Carattoli A, Hasman H. PlasmidFinder and in silico pMLST: identification and typing of plasmid replicons in Whole-Genome Sequencing (WGS). Methods Mol Biol. 2020;2075:285–294. PMID: 31584170.
   PubMedGoogle Scholar
• Liu B, Zheng D, Zhou S, Chen L, Yang J. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 2022;50(D1):D912–D7. PMID: 34850947. PMCID: PMC8728188. doi:10.1093/nar/gkab1107
   PubMed Web of Science ®Google Scholar
• Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genom. 2011;12:402. PMID: 21824423. PMCID: PMC3163573. doi:10.1186/1471-2164-12-402
   PubMed Web of Science ®Google Scholar
• Giacobbe DR, Labate L, Tutino S, et al. Enterococcal bloodstream infections in critically ill patients with COVID-19: a case series. Ann Med. 2021;53(1):1779–1786. PMID: 34637370. PMCID: PMC8519517. doi:10.1080/07853890.2021.1988695
   PubMed Web of Science ®Google Scholar
• Xie O, Slavin MA, Teh BW, Bajel A, Douglas AP, Worth LJ. Epidemiology, treatment and outcomes of bloodstream infection due to vancomycin-resistant enterococci in cancer patients in a vanB endemic setting. BMC Infect Dis. 2020;20(1):228. PMID: 32188401. PMCID: PMC7079500. doi:10.1186/s12879-020-04952-5
   PubMed Web of Science ®Google Scholar
• Mu S, Xiang H, Wang Y, et al. The pathogens of secondary infection in septic patients share a similar genotype to those that predominate in the gut. Crit Care. 2022;26(1):68. PMID: 35331299. PMCID: PMC8944137. doi:10.1186/s13054-022-03943-z
   PubMed Web of Science ®Google Scholar
• Yang J, Jiang Y, Guo L, Ye L, Ma Y, Luo Y. Prevalence of diverse clones of vancomycin-resistant Enterococcus faecium ST78 in a Chinese hospital. Microb Drug Resist. 2016;22(4):294–300. PMID: 26652286. doi:10.1089/mdr.2015.0069
   PubMed Web of Science ®Google Scholar
• Sun HL, Liu C, Zhang JJ, Zhou YM, Xu YC. Molecular characterization of vancomycin-resistant enterococci isolated from a hospital in Beijing, China. J Microbiol Immunol Infect. 2019;52(3):433–442. PMID: 30827858. doi:10.1016/j.jmii.2018.12.008
   PubMedGoogle Scholar
• Iseppi R, Di Cerbo A, Messi P, Sabia C. Antibiotic resistance and virulence traits in Vancomycin-Resistant Enterococci (VRE) and Extended-Spectrum beta-Lactamase/AmpC-producing (ESBL/AmpC) Enterobacteriaceae from humans and pets. Antibiotics. 2020;9(4):152. PMID: 32244399. PMCID: PMC7235867. doi:10.3390/antibiotics9040152
   Google Scholar
• Paganelli FL, Willems RJ, Jansen P, et al. Enterococcus faecium biofilm formation: identification of major autolysin AtlAEfm, associated Acm surface localization, and AtlAEfm-independent extracellular DNA Release. mBio. 2013;4(2):e00154. PMID: 23592262. PMCID: PMC3634606. doi:10.1128/mBio.00154-13
   PubMed Web of Science ®Google Scholar
• Xanthopoulou K, Wille J, Zweigner J, et al. Characterization of a vancomycin-resistant Enterococcus faecium isolate and a vancomycin-susceptible E. faecium isolate from the same blood culture. J Antimicrob Chemother. 2021;76(4):883–886. PMID: 33370443. doi:10.1093/jac/dkaa532
   PubMed Web of Science ®Google Scholar