ArticleClinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases2022
Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission.
Article in Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic Review and Meta-Analysis of Inpatient Mortality Associated With Nosocomial and Community COVID-19 Exposes the Vulnerability of Immunosuppressed Adults.Frontiers in immunology · 2021Pooled it
- Beyond traditional outbreak investigation: Using genomic data for enhanced detection of COVID-19 disease clusters in Utah.PloS one · 2026Article
- Analysis of Variants' Dynamic Using the CLIMB Database in COVID-19 Patients Admitted to Hospitals of Barts Health NHS Trust.Journal of medical virology · 2025Article
- SARS-CoV-2 delta variant in African lions (Panthera leo) and humans at Utah's Hogle Zoo, USA, 2021-22.Zoonoses and public health · 2024Article
- The utility of whole-genome sequencing to inform epidemiologic investigations of SARS-CoV-2 clusters in acute-care hospitals.Infection control and hospital epidemiology · 2024Article
- A systematic outbreak investigation of SARS-CoV-2 transmission clusters in a tertiary academic care center.Antimicrobial resistance and infection control · 2023Article
- Real-Time Whole Genome Sequencing to Guide Patient-Tailored Therapy of Severe Acute Respiratory Syndrome Coronavirus 2 Infection.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2023Article
- Dynamics of nosocomial SARS-CoV-2 transmissions: Facing the challenge of variants of concern in a Brazilian reference hospital.Journal of medical virology · 2023Article
- Lessons learned: use of WGS in real-time investigation of suspected intrahospital SARS-CoV-2 outbreaks.The Journal of hospital infection · 2023Article
- Understanding Early Pandemic Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in a Medical Center by Incorporating Public Sequencing Databases to Mitigate Bias.The Journal of infectious diseases · 2022Article
- Article
- Unraveling the hurdles of a large COVID-19 epidemiological investigation by viral genomics.The Journal of infection · 2022Article
- Exploiting genomics to mitigate the public health impact of antimicrobial resistance.Genome medicine · 2022Review
- Article
- SARS-CoV-2 variants with shortened incubation periods necessitate new definitions for nosocomial acquisition.The Journal of infection · 2022Article
- Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK.Frontiers in cellular and infection microbiology · 2022Article
- Real-world deployment of lateral flow SARS-CoV-2 antigen detection in the emergency department to provide rapid, accurate and safe diagnosis of COVID-19.Infection prevention in practice · 2021Article
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Authors and funding
24 authors.
Funding
Abstract
objectivesTo analyse nosocomial transmission in the early stages of the coronavirus 2019 (COVID-19) pandemic at a large multisite healthcare institution. Nosocomial incidence is linked with infection control interventions.
methodsViral genome sequence and epidemiological data were analysed for 574 consecutive patients, including 86 nosocomial cases, with a positive PCR test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the first 19 days of the pandemic.
resultsForty-four putative transmission clusters were found through epidemiological analysis; these included 234 cases and all 86 nosocomial cases. SARS-CoV-2 genome sequences were obtained from 168/234 (72%) of these cases in epidemiological clusters, including 77/86 nosocomial cases (90%). Only 75/168 (45%) of epidemiologically linked, sequenced cases were not refuted by applying genomic data, creating 14 final clusters accounting for 59/77 sequenced nosocomial cases (77%). Viral haplotypes from these clusters were enriched 1-14x (median 4x) compared to the community. Three factors implicated unidentified cases in transmission: (a) community-onset or indeterminate cases were absent in 7/14 clusters (50%), (b) four clusters (29%) had additional evidence of cryptic transmission, and (c) in three clusters (21%) diagnosis of the earliest case was delayed, which may have facilitated transmission. Nosocomial cases decreased to low levels (0-2 per day) despite continuing high numbers of admissions of community-onset SARS-CoV-2 cases (40-50 per day) and before the impact of introducing universal face masks and banning hospital visitors.
conclusionGenomics was necessary to accurately resolve transmission clusters. Our data support unidentified cases-such as healthcare workers or asymptomatic patients-as important vectors of transmission. Evidence is needed to ascertain whether routine screening increases case ascertainment and limits nosocomial transmission.
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