Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis

Norelle L. Sherry; Claire L. Gorrie; Jason C. Kwong; Charlie Higgs; Rhonda L. Stuart; Caroline Marshall; Susan A. Ballard; Michelle Sait; Tony M. Korman; Monica A. Slavin; Robyn S. Lee; Maryza Graham; Marcel Leroi; Leon J. Worth; Hiu Tat Chan; Torsten Seemann; M. Lindsay Grayson; Benjamin P. Howden

The Lancet Regional Health. Western Pacific (Jun 2022)

Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis

Norelle L. Sherry,
Claire L. Gorrie,
Jason C. Kwong,
Charlie Higgs,
Rhonda L. Stuart,
Caroline Marshall,
Susan A. Ballard,
Michelle Sait,
Tony M. Korman,
Monica A. Slavin,
Robyn S. Lee,
Maryza Graham,
Marcel Leroi,
Leon J. Worth,
Hiu Tat Chan,
Torsten Seemann,
M. Lindsay Grayson,
Benjamin P. Howden

Affiliations

Norelle L. Sherry: Microbiological Diagnostic Unit (MDU) Public Health Laboratory, Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia; Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia
Claire L. Gorrie: Microbiological Diagnostic Unit (MDU) Public Health Laboratory, Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia; Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia
Jason C. Kwong: Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia; Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia; Department of Medicine, Austin Health, University of Melbourne, Heidelberg, Victoria, Australia
Charlie Higgs: Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia
Rhonda L. Stuart: Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia; Monash University, Clayton, Victoria, Australia; South East Public Health Unit, Monash Health, Clayton, Victoria, Australia
Caroline Marshall: Infection Prevention & Surveillance, Victorian Infectious Diseases Service, Melbourne Health, Parkville, Victoria, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
Susan A. Ballard: Microbiological Diagnostic Unit (MDU) Public Health Laboratory, Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia
Michelle Sait: Microbiological Diagnostic Unit (MDU) Public Health Laboratory, Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia
Tony M. Korman: Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia; Monash University, Clayton, Victoria, Australia; Department of Microbiology, Monash Health, Clayton, Victoria, Australia
Monica A. Slavin: Department of Infectious Diseases, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia; National Centre for Infections in Cancer, Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
Robyn S. Lee: Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia
Maryza Graham: Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia; Monash University, Clayton, Victoria, Australia; Department of Microbiology, Monash Health, Clayton, Victoria, Australia
Marcel Leroi: Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia; Department of Microbiology, Austin Health, University of Melbourne, Heidelberg, Victoria, Australia
Leon J. Worth: Department of Infectious Diseases, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia; National Centre for Infections in Cancer, Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
Hiu Tat Chan: Department of Microbiology, Melbourne Health, Parkville, Victoria, Australia
Torsten Seemann: Microbiological Diagnostic Unit (MDU) Public Health Laboratory, Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia; Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia
M. Lindsay Grayson: Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia; Department of Medicine, Austin Health, University of Melbourne, Heidelberg, Victoria, Australia; Department of Microbiology, Austin Health, University of Melbourne, Heidelberg, Victoria, Australia
Benjamin P. Howden: Microbiological Diagnostic Unit (MDU) Public Health Laboratory, Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia; Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia; Corresponding author at: Microbiological Diagnostic Unit (MDU) Public Health Laboratory, Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia

Journal volume & issue: Vol. 23
p. 100446

Abstract

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Summary: Background: Current microbiological methods lack the resolution to accurately identify multidrug-resistant organism (MDRO) transmission, however, whole genome sequencing can identify highly-related patient isolates providing opportunities for precision infection control interventions. We investigated the feasibility and potential impact of a prospective multi-centre genomics workflow for hospital infection control. Methods: We conducted a prospective genomics implementation study across eight Australian hospitals over 15 months (2017,2018), collecting all clinical and screening isolates from inpatients with vanA VRE, MRSA, ESBL Escherichia coli (ESBL-Ec), or ESBL Klebsiella pneumoniae (ESBL-Kp). Genomic and epidemiologic data were integrated to assess MDRO transmission. Findings: In total, 2275 isolates were included from 1970 patients, predominantly ESBL-Ec (40·8%) followed by MRSA (35·6%), vanA VRE (15·2%), and ESBL-Kp (8·3%).Overall, hospital and genomic epidemiology showed 607 patients (30·8%) acquired their MDRO in hospital, including the majority of vanA VRE (266 patients, 86·4%), with lower proportions of ESBL-Ec (186 patients, 23·0%), ESBL-Kp (42 patients, 26·3%), and MRSA (113 patients, 16·3%). Complex patient movements meant the majority of MDRO transmissions would remain undetected without genomic data.The genomics implementation had major impacts, identifying unexpected MDRO transmissions prompting new infection control interventions, and contributing to vanA VRE becoming a notifiable condition. We identified barriers to implementation and recommend strategies for mitigation. Interpretation: Implementation of a multi-centre genomics-informed infection control workflow is feasible and identifies many unrecognised MDRO transmissions. This provides critical opportunities for interventions to improve patient safety in hospitals. Funding: Melbourne Genomics Health Alliance (supported by State Government of Victoria, Australia), and National Health and Medical Research Council (Australia).

Published in The Lancet Regional Health. Western Pacific

ISSN: 2666-6065 (Online)
Publisher: Elsevier
Country of publisher: United Kingdom
LCC subjects: Medicine: Public aspects of medicine
Website: https://www.thelancet.com/journals/lanwpc/home

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