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- Title
Optimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings.
- Authors
Higgs, Charlie; Sherry, Norelle L.; Seemann, Torsten; Horan, Kristy; Walpola, Hasini; Kinsella, Paul; Bond, Katherine; Williamson, Deborah A.; Marshall, Caroline; Kwong, Jason C.; Grayson, M. Lindsay; Stinear, Timothy P.; Gorrie, Claire L.; Howden, Benjamin P.
- Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is a major nosocomial pathogen. Identifying VREfm transmission dynamics permits targeted interventions, and while genomics is increasingly being utilised, methods are not yet standardised or optimised for accuracy. We aimed to develop a standardized genomic method for identifying putative VREfm transmission links. Using comprehensive genomic and epidemiological data from a cohort of 308 VREfm infection or colonization cases, we compared multiple approaches for quantifying genetic relatedness. We showed that clustering by core genome multilocus sequence type (cgMLST) was more informative of population structure than traditional MLST. Pairwise genome comparisons using split k-mer analysis (SKA) provided the high-level resolution needed to infer patient-to-patient transmission. The more common mapping to a reference genome was not sufficiently discriminatory, defining more than three times more genomic transmission events than SKA (3729 compared to 1079 events). Here, we show a standardized genomic framework for inferring VREfm transmission that can be the basis for global deployment of VREfm genomics into routine outbreak detection and investigation. Vancomycin-resistant Enterococcus faecium is an important healthcare-associated pathogen and genomic analyses could inform targeted interventions. Here, the authors optimise an analysis pipeline for identification of putative transmission events using core genome multilocus sequence type clustering and split kmer analysis.
- Subjects
ENTEROCOCCUS faecium; GENOMICS; INFECTIOUS disease transmission; GENE mapping; MEDICAL care
- Publication
Nature Communications, 2022, Vol 13, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-022-28156-4