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Optimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings.
- Source :
-
Nature communications [Nat Commun] 2022 Jan 26; Vol. 13 (1), pp. 509. Date of Electronic Publication: 2022 Jan 26. - Publication Year :
- 2022
-
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.<br /> (© 2022. The Author(s).)
- Subjects :
- Anti-Bacterial Agents
Bacterial Proteins genetics
Bacterial Typing Techniques
Carbon-Oxygen Ligases genetics
Cross Infection epidemiology
Disease Outbreaks
Enterococcus faecium classification
Enterococcus faecium isolation & purification
Genomics
Gram-Positive Bacterial Infections epidemiology
Gram-Positive Bacterial Infections microbiology
Humans
Multilocus Sequence Typing
Phylogeny
Vancomycin
Vancomycin-Resistant Enterococci classification
Vancomycin-Resistant Enterococci isolation & purification
Whole Genome Sequencing
Cross Infection transmission
Delivery of Health Care
Enterococcus faecium genetics
Genome, Bacterial
Gram-Positive Bacterial Infections transmission
Vancomycin-Resistant Enterococci genetics
Subjects
Details
- Language :
- English
- ISSN :
- 2041-1723
- Volume :
- 13
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Nature communications
- Publication Type :
- Academic Journal
- Accession number :
- 35082278
- Full Text :
- https://doi.org/10.1038/s41467-022-28156-4