The changing landscape of VREfm in Victoria, Australia: a state-wide genomic snapshot

Lee, R. S.; Goncalves da Silva, A.; Baines, S. L.; Strachan, J.; Ballard, S.; Carter, G. P.; Kwong, J. C.; Schultz, M.; Bulach, D.; Seemann, T.; Stinear, T.; Howden, B. P.

doi:10.1101/289975

bioRxiv · 10.1101/289975

The changing landscape of VREfm in Victoria, Australia: a state-wide genomic snapshot

Lee, R. S.·Goncalves da Silva, A.·Baines, S. L.·Strachan, J.·Ballard, S.·Carter, G. P.·Kwong, J. C.·Schultz, M.·Bulach, D.·Seemann, T.·Stinear, T.·Howden, B. P.

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Abstract

Vancomycin-resistant Enterococcus faecium (VREfm) represent a major source of nosocomial infection worldwide. In Australia, the vanB genotype is dominant; however there has been a recent increase in the predominantly plasmid-encoded vanA genotype, prompting investigation into the genomic epidemiology of VREfm in this context.\n\nMaterials and MethodsA cross-sectional study of VREfm in Victoria, Australia (Nov.10th - Dec.9th, 2015). A total of 321 VREfm isolates (from 286 patients) were collected and whole-genome sequenced with Illumina NextSeq. Single nucleotide polymorphisms (SNPs) were used to assess relatedness. Multi-locus sequence types (STs), and genes associated with resistance and virulence were identified. The vanA-harbouring plasmid from an isolate from each ST was assembled using long-read data.\n\nResultsvanA-VREfm comprised 17.8% of isolates. ST203, ST80 and a pstS(-) clade, ST1421, predominated (30.5%, 30.5% and 37.2% of vanA-VREfm, respectively). Most vanB-VREfm were ST796 (77.7%). vanA-VREfm isolates were closely-related within hospitals vs. between them (core SNPs 10 [interquartile range 1-357] vs. 356 [179-416] respectively), suggesting discrete introductions of vanA-VREfm, with subsequent intra-hospital transmission. In contrast, vanB-VREfm had similar core SNP distributions within vs. between hospitals, due to widespread dissemination of ST796. Overall, vanA-harbouring plasmids differed across STs, and with exception of ST78 and ST796, Tn1546 transposons also varied.\n\nConclusionsvanA-VREfm in Victoria is associated with multiple STs, and is not solely mediated by a single shared plasmid/Tn1546 transposon; clonal transmission appears to play an important role, predominantly within, rather than between, hospitals. In contrast, vanB-VREfm appears to be well-established and widespread across Victorian healthcare institutions.

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Lee, R. S., Goncalves da Silva, A., Baines, S. L., Strachan, J., Ballard, S., Carter, G. P., Kwong, J. C., Schultz, M., Bulach, D., Seemann, T., Stinear, T., Howden, B. P.. 2018-03-28. The changing landscape of VREfm in Victoria, Australia: a state-wide genomic snapshot. https://doi.org/10.1101/289975

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