Whole-genome sequencing to investigate transmission of SARS-CoV-2 in the acute healthcare setting: a systematic review.

Autor: Hare D; UCD National Virus Reference Laboratory, University College Dublin, Ireland; School of Medicine, University of Limerick, Limerick, Ireland. Electronic address: daniel.hare@ucd.ie., Dembicka KM; School of Medicine, University of Limerick, Limerick, Ireland., Brennan C; UCD National Virus Reference Laboratory, University College Dublin, Ireland., Campbell C; UCD National Virus Reference Laboratory, University College Dublin, Ireland., Sutton-Fitzpatrick U; UCD National Virus Reference Laboratory, University College Dublin, Ireland., Stapleton PJ; University Hospital Limerick, Limerick, Ireland., De Gascun CF; UCD National Virus Reference Laboratory, University College Dublin, Ireland., Dunne CP; School of Medicine, University of Limerick, Limerick, Ireland; Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.
Jazyk: angličtina
Zdroj: The Journal of hospital infection [J Hosp Infect] 2023 Oct; Vol. 140, pp. 139-155. Date of Electronic Publication: 2023 Aug 09.
DOI: 10.1016/j.jhin.2023.08.002
Abstrakt: Background: Whole-genome sequencing (WGS) has been used widely to elucidate transmission of SARS-CoV-2 in acute healthcare settings, and to guide infection, prevention, and control (IPC) responses.
Aim: To systematically appraise available literature, published between January 1 st , 2020 and June 30 th , 2022, describing the implementation of WGS in acute healthcare settings to characterize nosocomial SARS-CoV-2 transmission.
Methods: Searches of the PubMed, Embase, Ovid MEDLINE, EBSCO MEDLINE, and Cochrane Library databases identified studies in English reporting the use of WGS to investigate SARS-CoV-2 transmission in acute healthcare environments. Publications involved data collected up to December 31 st , 2021, and findings were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement.
Findings: In all, 3088 non-duplicate records were retrieved; 97 met inclusion criteria, involving 62 outbreak analyses and 35 genomic surveillance studies. No publications from low-income countries were identified. In 87/97 (90%), WGS supported hypotheses for nosocomial transmission, while in 46 out of 97 (47%) suspected transmission events were excluded. An IPC intervention was attributed to the use of WGS in 18 out of 97 (18%); however, only three (3%) studies reported turnaround times ≤7 days facilitating near real-time IPC action, and none reported an impact on the incidence of nosocomial COVID-19 attributable to WGS.
Conclusion: WGS can elucidate transmission of SARS-CoV-2 in acute healthcare settings to enhance epidemiological investigations. However, evidence was not identified to support sequencing as an intervention to reduce the incidence of SARS-CoV-2 in hospital or to alter the trajectory of active outbreaks.
(Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)
Databáze: MEDLINE
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