Impact of whole genome sequencing on infection prevention practice and patient outcomes in carbapenemase-producing Enterobacterales outbreaks: a scoping review.

Authors

Louisa Sun, Pearleen Chua Ee-Yong, Shilpa Mukherjee, Kua Jo Ann

Published in

The Journal of hospital infection. Aug 26, 2026. Epub Aug 26, 2026.

Abstract

Whole genome sequencing (WGS) resolves transmission relationships in carbapenemase-producing Enterobacterales (CPE) outbreaks at nucleotide level. Whether this translates into changed infection prevention and control (IPC) practice or improved patient outcomes is unclear.
To review IPC actions and patient outcomes arising from WGS-informed CPE outbreak detection.
We conducted a scoping review, searching MEDLINE, Embase, Web of Science and the Cochrane Library from January 2010 to January 2026. Eligible studies used WGS for CPE outbreak detection or investigation and reported at least one IPC action or clinical outcome. For each, we recorded whether a WGS finding informed the IPC action or whether the action occurred concurrently, without being WGS-driven.
Of 4,114 records, 44 studies met the inclusion criteria. WGS findings informed a documented IPC action or resolved suspected transmission in 16 studies (36%) and generated recommendations in a further 5 (11%); in 21 (48%), IPC actions occurred concurrently with a WGS-characterised outbreak but were not attributable to a WGS finding. Outcomes were variably reported: study-specific mortality in 15 studies (34%), with a crude case-fatality range of 0%-75%. Turnaround time was rarely quantified, and no study compared outcomes between WGS-informed and conventional management. Retrospective application (59%) and absent comparator groups limited causal inference.
WGS for CPE outbreak detection consistently identifies transmission missed by conventional methods, and in a minority of studies demonstrably changed IPC practice. Evidence that it improves patient outcomes remains absent, limited by the lack of comparative designs.

PMID:
42648544
Bibliographic data and abstract were imported from PubMed on 27 Aug 2026.

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