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Multi-Site Implementation of Whole Genome Sequencing for Hospital Infection Control: A Prospective Genomic Epidemiological Analysis

37 Pages Posted: 29 Oct 2021

See all articles by Norelle L. Sherry

Norelle L. Sherry

University of Melbourne - Microbiological Diagnostic Unit Public Health Laboratory

Claire L. Gorrie

University of Melbourne

Jason C. Kwong

Austin Health

Charlie Higgs

University of Melbourne

Rhonda L. Stuart

Monash Health

Caroline Marshall

University of Melbourne

Susan A. Ballard

The University of Melbourne at the Peter Doherty Institute of Infection and Immunity - Microbiological Diagnostic Unit Public Health Laboratory

Michelle Sait

University of Melbourne

Tony Korman

Monash Health

Monica A. Slavin

Peter MacCallum Cancer Centre - Department of Infectious Diseases

Robyn S.C. Lee

University of Melbourne

Maryza Graham

Monash Health

Marcel Leroi

Austin Health

Leon J. Worth

Peter MacCallum Cancer Centre

Hiu Tat Chan

Melbourne Health - Department of Microbiology

Torsten Seemann

University of Melbourne

M. Lindsay Grayson

Austin Health

Benjamin Howden

The University of Melbourne at the Peter Doherty Institute of Infection and Immunity - Microbiological Diagnostic Unit Public Health Laboratory; Austin Health - Department of Infectious Diseases; University of Melbourne - Department of Microbiology and Immunology (DMI)

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Abstract

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 1870 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 609 patients (32.6%) acquired their MDRO in hospital, including the majority of vanA VRE (266 patients, 86.4%), with lower proportions of ESBL-Ec (188 patients, 23.2%), 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 significant 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 Information: This work was supported by the Melbourne Genomics Health Alliance (funded by the State Government of Victoria, Department of Health and Human Services, and the 10 member organizations); and individual grants from National Health and Medical Research Council (Australia) to NLS (GNT1093468), JCK (GNT1008549), BPH (GNT1105905), and MAS (GNT1116576).

Declaration of Interests: The authors declare no conflicts of interest.

Ethics Approval Statement: This study was approved by the Melbourne Health Human Research Ethics Committee (HREC/13/MH/326) and endorsed by the corresponding HREC at each participating site.

Keywords: Antimicrobial resistance, whole genome sequencing, infection prevention and control, hospital epidemiology

Suggested Citation

Sherry, Norelle L. and Gorrie, Claire L. and Kwong, Jason C. and Higgs, Charlie and Stuart, Rhonda L. and Marshall, Caroline and Ballard, Susan A. and Sait, Michelle and Korman, Tony and Slavin, Monica A. and Lee, Robyn S.C. and Graham, Maryza and Leroi, Marcel and Worth, Leon J. and Chan, Hiu Tat and Seemann, Torsten and Grayson, M. Lindsay and Howden, Benjamin, Multi-Site Implementation of Whole Genome Sequencing for Hospital Infection Control: A Prospective Genomic Epidemiological Analysis. Available at SSRN: https://ssrn.com/abstract=3952482 or http://dx.doi.org/10.2139/ssrn.3952482

Norelle L. Sherry

University of Melbourne - Microbiological Diagnostic Unit Public Health Laboratory ( email )

185 Pelham Street
Carlton, 3053
Australia

Claire L. Gorrie

University of Melbourne ( email )

185 Pelham Street
Carlton, 3053
Australia

Jason C. Kwong

Austin Health ( email )

145 Studley Rd
Heidelberg VIC 3084
Australia

Charlie Higgs

University of Melbourne ( email )

185 Pelham Street
Carlton, 3053
Australia

Rhonda L. Stuart

Monash Health ( email )

Australia

Caroline Marshall

University of Melbourne ( email )

185 Pelham Street
Carlton, Victoria 3053
Australia

Susan A. Ballard

The University of Melbourne at the Peter Doherty Institute of Infection and Immunity - Microbiological Diagnostic Unit Public Health Laboratory ( email )

185 Pelham Street
Carlton, 3053
Australia

Michelle Sait

University of Melbourne ( email )

185 Pelham Street
Carlton, 3053
Australia

Tony Korman

Monash Health ( email )

Monica A. Slavin

Peter MacCallum Cancer Centre - Department of Infectious Diseases ( email )

305 Grattan Street
Parkville
Melbourne, Victoria
Australia

Robyn S.C. Lee

University of Melbourne ( email )

185 Pelham Street
Carlton, 3053
Australia

Maryza Graham

Monash Health ( email )

Australia

Marcel Leroi

Austin Health ( email )

145 Studley Rd
Heidelberg VIC 3084
Australia

Leon J. Worth

Peter MacCallum Cancer Centre ( email )

305 Grattan Street
Parkville
Melbourne
Australia

Hiu Tat Chan

Melbourne Health - Department of Microbiology ( email )

Parkville, Victoria
Australia

Torsten Seemann

University of Melbourne ( email )

185 Pelham Street
Carlton, 3053
Australia

M. Lindsay Grayson

Austin Health ( email )

145 Studley Rd
Heidelberg VIC 3084
Australia

Benjamin Howden (Contact Author)

The University of Melbourne at the Peter Doherty Institute of Infection and Immunity - Microbiological Diagnostic Unit Public Health Laboratory ( email )

Melbourne
Australia

Austin Health - Department of Infectious Diseases

Heidelberg, Victoria
Australia

University of Melbourne - Department of Microbiology and Immunology (DMI)

Melbourne, 3000
Australia

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