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
Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved..
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.
| Errataetall: |
CommentIn: J Infect. 2022 Feb;84(2):248-288. - PMID 34474059 |
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| Medienart: |
E-Artikel |
| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:83 |
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| Enthalten in: |
The Journal of infection - 83(2021), 4 vom: 12. Okt., Seite 473-482 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Lumley, Sheila F [VerfasserIn] |
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| Links: |
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| Themen: |
Epidemiology |
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| Anmerkungen: |
Date Completed 29.09.2021 Date Revised 02.04.2024 published: Print-Electronic CommentIn: J Infect. 2022 Feb;84(2):248-288. - PMID 34474059 Citation Status MEDLINE |
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| doi: |
10.1016/j.jinf.2021.07.034 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 100 | 1 | |a Lumley, Sheila F |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a 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 |
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| 500 | |a Date Completed 29.09.2021 | ||
| 500 | |a Date Revised 02.04.2024 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a CommentIn: J Infect. 2022 Feb;84(2):248-288. - PMID 34474059 | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved. | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 520 | |a CONCLUSIONS: Current surveillance definitions underestimate nosocomial acquisition. Most nosocomial transmission occurs from a relatively limited number of highly infectious individuals | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Epidemiology | |
| 650 | 4 | |a Nosocomial infection | |
| 650 | 4 | |a SARS-CoV-2 | |
| 650 | 4 | |a Whole genome sequencing | |
| 700 | 1 | |a Constantinides, Bede |e verfasserin |4 aut | |
| 700 | 1 | |a Sanderson, Nicholas |e verfasserin |4 aut | |
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| 700 | 1 | |a Street, Teresa L |e verfasserin |4 aut | |
| 700 | 1 | |a Swann, Jeremy |e verfasserin |4 aut | |
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| 700 | 0 | |a OUH Infection Prevention and Control team |e verfasserin |4 aut | |
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| 700 | 1 | |a Walker, Timothy M |e verfasserin |4 aut | |
| 700 | 1 | |a Stoesser, Nicole E |e verfasserin |4 aut | |
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| 700 | 1 | |a Eyre, David W |e verfasserin |4 aut | |
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