期刊
JOURNAL OF INFECTION
卷 83, 期 4, 页码 473-482出版社
W B SAUNDERS CO LTD
DOI: 10.1016/j.jinf.2021.07.034
关键词
Whole genome sequencing; Epidemiology; SARS-CoV-2; Nosocomial infection
资金
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Oxford University
- Public Health England (PHE), the NIHR Biomedical Research Centre, Oxford [NIHR200915]
- Wellcome Intermediate Fellowship [110,110/Z/15/Z, 214,560/Z/18/Z]
- [MRF-145-00 04-TPG-AVISO]
This study investigated the epidemiological characteristics of healthcare-associated SARS-CoV-2 acquisition. The findings suggest that current surveillance definitions underestimate nosocomial acquisition, with most nosocomial transmission occurring from a relatively limited number of highly infectious individuals.
Objectives: Despite robust efforts, patients and staffacquire 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. (C) 2021 The Authors. Published by Elsevier Ltd on behalf of The British Infection Association.
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