Whole-genome sequencing analysis reveals the spread of a vanB-carrying transposon among different vancomycin-resistant Enterococcus faecium clinical isolates in a non-endemic setting

Abstract

Vancomycin-resistant enterococci (VRE), in particular Enterococcus faecium (VREfm), can cause serious nosocomial infections, and have been responsible for healthcare-associated outbreaks. Spreading of VREfm can occur both clonally and by the dissemination of mobile genetic elements. In this study, we report on prospective analysis of WGS data, including both cgMLST and transposon analysis during a vanB VREfm outbreak. Screening for vanB positive VREfm isolates was performed by real-time PCR on an overnight enriched broth and, if positive, subculture was performed. vanB positive VREfm isolates were whole-genome sequenced. Generated data were used for molecular typing that was performed by cgMLST using SeqSphere. For transposon characterization, sequence data were mapped against the reference sequence of transposon Tn1549 using CLC Genomics workbench or de novo assemblies were used for BLASTN comparisons. A total of 1358 real-time PCRs were performed. Two hundred fifty-one specimens from 207 patients tested PCR positive for vanB, of which 13 specimens obtained from 6 different patients were identified as vanB VREfm positive by culture. These 6 patients harbored 7 unique isolates, belonging to 4 different cluster types: CT118 (n=2), CT2483 (n=3), CT2500 and CT2501. Transposon analysis revealed the presence of an identical vanB-carrying transposon in the isolates cultured from all 6 patients, that could be linked based on epidemiological data. A vanB VREfm outbreak in our hospital occurred, including 6 patients with isolates belonging to 4 different cluster types. In-depth transposon analysis revealed dissemination of the transposon Tn1549 rather than clonal spread being the cause of the outbreak.