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
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 inpatien...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Elsevier
2021
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| _version_ | 1797070458347061248 |
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| author | Lumley, SF Constantinides, B Sanderson, N Rodger, G Street, TL Swann, J Chau, KK O'Donnell, D Warren, F Hoosdally, S OUH Microbiology laboratory OUH Infection Prevention and Control team O'Donnell, A-M Walker, TM Stoesser, NE Butcher, L Peto, TE Crook, DW Jeffery, K Matthews, PC Eyre, DW |
| author_facet | Lumley, SF Constantinides, B Sanderson, N Rodger, G Street, TL Swann, J Chau, KK O'Donnell, D Warren, F Hoosdally, S OUH Microbiology laboratory OUH Infection Prevention and Control team O'Donnell, A-M Walker, TM Stoesser, NE Butcher, L Peto, TE Crook, DW Jeffery, K Matthews, PC Eyre, DW |
| author_sort | Lumley, SF |
| collection | OXFORD |
| description | 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.
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| first_indexed | 2024-03-06T22:39:07Z |
| format | Journal article |
| id | oxford-uuid:5aec22d4-99c0-47f6-a018-ef2560f10999 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T22:39:07Z |
| publishDate | 2021 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | oxford-uuid:5aec22d4-99c0-47f6-a018-ef2560f109992022-03-26T17:19:03ZEpidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individualsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:5aec22d4-99c0-47f6-a018-ef2560f10999EnglishSymplectic ElementsElsevier2021Lumley, SFConstantinides, BSanderson, NRodger, GStreet, TLSwann, JChau, KKO'Donnell, DWarren, FHoosdally, SOUH Microbiology laboratoryOUH Infection Prevention and Control teamO'Donnell, A-MWalker, TMStoesser, NEButcher, LPeto, TECrook, DWJeffery, KMatthews, PCEyre, DWObjectives: 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. |
| spellingShingle | Lumley, SF Constantinides, B Sanderson, N Rodger, G Street, TL Swann, J Chau, KK O'Donnell, D Warren, F Hoosdally, S OUH Microbiology laboratory OUH Infection Prevention and Control team O'Donnell, A-M Walker, TM Stoesser, NE Butcher, L Peto, TE Crook, DW Jeffery, K Matthews, PC Eyre, DW 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 |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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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