Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

Stirrup, O. et al. (2021) Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. eLife, 10, e65828. (doi: 10.7554/elife.65828) (PMID:34184637) (PMCID:PMC8285103)

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Abstract

Background: Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding potential transmission clusters, but the low mutation rate of SARS-CoV-2 can make interpretation using standard phylogenetic methods difficult. Methods: We developed a novel statistical method and sequence reporting tool (SRT) that combines epidemiological and sequence data in order to provide a rapid assessment of the probability of HCAI among HOCI cases (defined as first positive test >48 hours following admission) and to identify infections that could plausibly constitute outbreak events. The method is designed for prospective use, but was validated using retrospective datasets from hospitals in Glasgow and Sheffield collected February-May 2020. Results: We analysed data from 326 HOCIs. Among HOCIs with time-from-admission >8 days the SRT algorithm identified close sequence matches from the same ward for 160/244 (65.6%) and in the remainder 68/84 (81.0%) had at least one similar sequence elsewhere in the hospital, resulting in high estimated probabilities of within-ward and within-hospital transmission. For HOCIs with time-from-admission 3-7 days, the SRT probability of healthcare acquisition was >0.5 in 33/82 (40.2%). Conclusions: The methodology developed can provide rapid feedback on HOCIs that could be useful for infection prevention and control teams, and warrants further prospective evaluation. The integration of epidemiological and sequence data is important given the low mutation rate of SARS-CoV-2 and its variable incubation period. Funding: COG-UK HOCI funded by COG-UK consortium, supported by funding from UK Research and Innovation, National Institute of Health Research and Wellcome Sanger Institute.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Thomson, Professor Emma and Marek, Dr Aleksandra and Hughes, Dr Joseph and Shepherd, Dr James and Singer, Dr Joshua
Creator Roles:
Hughes, J.Data curation, Formal analysis, Investigation, Visualization, Writing – review and editing
Shepherd, J. G.Data curation, Investigation, Writing – review and editing
Marek, A.Data curation, Investigation, Writing – review and editing
Singer, J. B.Software, Methodology, Writing – review and editing
Thomson, E. C.Conceptualization, Data curation, Supervision, Investigation, Writing – review and editing
Authors: Stirrup, O., Hughes, J., Parker, M., Partridge, D. G., Shepherd, J. G., Blackstone, J., Coll, F., Keeley, A., Lindsey, B. B., Marek, A., Peters, C., Singer, J. B., Tamuri, A., de Silva, T. I., Thomson, E. C., and Breuer, J.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
College of Medical Veterinary and Life Sciences > School of Medicine, Dentistry & Nursing
Journal Name:eLife
Publisher:eLife Sciences Publications
ISSN:2050-084X
ISSN (Online):2050-084X
Copyright Holders:Copyright © 2021 Stirrup et al.
First Published:First published in eLife 10: e65828
Publisher Policy:Reproduced under a Creative Commons License

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