Elsevier

Journal of Infection

Volume 83, Issue 4, October 2021, Pages 473-482
Journal of Infection

Commentary
Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals

https://doi.org/10.1016/j.jinf.2021.07.034Get rights and content
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Highlights

  • Current surveillance definitions underestimate SARS-CoV-2 nosocomial acquisition.

  • Many cases of SARS-CoV-2 diagnosed within the first week of hospital admission were acquired in hospital.

  • Whole genome sequencing revealed most nosocomial transmission occurs from a relatively limited number of highly infectious individuals.

  • The majority of epidemiologically defined outbreaks consisted of multiple genomic introductions.

Abstract

Objectives: Despite robust efforts, patients and staff acquire SARS-CoV-2 infection in hospitals. We investigated whether whole-genome sequencing enhanced the epidemiological investigation of healthcare-associated SARS-CoV-2 acquisition.

Methods: From 17-November-2020 to 5-January-2021, 803 inpatients and 329 staff were diagnosed with SARS-CoV-2 infection at four Oxfordshire hospitals. We classified cases using epidemiological definitions, looked for a potential source for each nosocomial infection, and evaluated genomic evidence supporting transmission.

Results: Using national epidemiological definitions, 109/803(14%) inpatient infections were classified as definite/probable nosocomial, 615(77%) as community-acquired and 79(10%) as indeterminate. There was strong epidemiological evidence to support definite/probable cases as nosocomial. Many indeterminate cases were likely infected in hospital: 53/79(67%) had a prior-negative PCR and 75(95%) contact with a potential source. 89/615(11% of all 803 patients) with apparent community-onset had a recent hospital exposure. Within 764 samples sequenced 607 genomic clusters were identified (>1 SNP distinct). Only 43/607(7%) clusters contained evidence of onward transmission (subsequent cases within ≤ 1 SNP). 20/21 epidemiologically-identified outbreaks contained multiple genomic introductions. Most (80%) nosocomial acquisition occurred in rapid super-spreading events in settings with a mix of COVID-19 and non-COVID-19 patients.

Conclusions: Current surveillance definitions underestimate nosocomial acquisition. Most nosocomial transmission occurs from a relatively limited number of highly infectious individuals.

Keywords

Whole genome sequencing
Epidemiology
SARS-CoV-2
Nosocomial infection

Cited by (0)

1

These authors contributed equally to this work.

2

Membership of the OUH Microbiology laboratory and OUH Infection Prevention and Control teams is provided in the Supplement.