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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
More...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
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