Optimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings

C Higgs; NL Sherry; T Seemann; K Horan; H Walpola; P Kinsella; K Bond; DA Williamson; C Marshall; JC Kwong; ML Grayson; TP Stinear; CL Gorrie; BP Howden

Journal article

Optimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings

C Higgs, NL Sherry, T Seemann, K Horan, H Walpola, P Kinsella, K Bond, DA Williamson, C Marshall, JC Kwong, ML Grayson, TP Stinear, CL Gorrie, BP Howden

Nature Communications | NATURE PORTFOLIO | Published : 2022

DOI: 10.1038/s41467-022-28156-4

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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 ..

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University of Melbourne Researchers

Norelle Sherry Author

Torsten Seemann Author

Kristy Horan Horan Author

Paul Kinsella Author

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Awarded by State Government of Victoria

Funding Acknowledgements

The authors would like to acknowledge the other members of the Controlling Superbugs Study Group include Robyn Lee (previously MDU, currently University of Toronto), Rhonda Stuart (Infectious Diseases, Monash Health; Medicine, Monash University), Tony Korman (Infectious Diseases and Microbiology, Monash Health; Medicine, Monash University), Caroline Marshall (VIDS, Melbourne Health; Peter Doherty Institute), Hiu Tat (Mark) Chan (Microbiology, Melbourne Health), Maryza Graham (Infectious Diseases and Microbiology, Monash Health; Medicine, Monash University), Marcel Leroi (Microbiology, Austin Health), Caroline Reed (Microbiology, Melbourne Health and Peter MacCallum Cancer Centre), Michael Richards (VIDS, Melbourne Health; Peter Doherty Institute), Monica Slavin and Leon Worth (Infectious Diseases, Peter MacCallum Cancer Centre; National Centre for Infections in Cancer; University of Melbourne), Elizabeth Grabsch (Microbiology, Austin Health), Joanna Price and Carolyn Tullett (Infection Control, Austin Health), Despina Kotsanas (Microbiology, Monash Health), Louise Wright (Infection Control, Monash Health), Suraya Hanim Abdullah Hashim and Jennifer Mitchell (Infectious Diseases, Melbourne Health), Olivia Smibert (Infectious Diseases, Peter MacCallum Cancer Centre), and Carol Wedge (data entry, Austin Health). This work was supported by the Melbourne Genomics Health Alliance (funded by the State Government of Victoria [Australia], Department of Health and Human Services, and the ten member organisations); a National Health and Medical Research Council (Australia) Partnership grant (GNT1149991) and individual grants from National Health and Medical Research Council (Australia) to NLS (GNT1093468), JCK (GNT1142613) and BPH (GNT1196103).