ArticleEmerging infectious diseases2018
Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15.
Article in Emerging infectious diseases, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23.The Journal of infection · 2024Article
- SARS-CoV-2 genomics and impact on clinical care for COVID-19.The Journal of antimicrobial chemotherapy · 2023Article
- Feasibility and clinical utility of local rapid Nanopore influenza A virus whole genome sequencing for integrated outbreak management, genotypic resistance detection and timely surveillance.Microbial genomics · 2023Article
- Nursing home crowding and its association with outbreak-associated respiratory infection in Ontario, Canada before the COVID-19 pandemic (2014-19): a retrospective cohort study.The lancet. Healthy longevity · 2023Article
- Investigating Epidemiologic and Molecular Links Between Patients With Community- and Hospital-Acquired Influenza A: 2017-2018 and 2019-2020, Michigan.Open forum infectious diseases · 2023Article
- From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol.Vaccines · 2022Article
- Article
- Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study.The Lancet. Infectious diseases · 2020Article
- Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014).Influenza and other respiratory viruses · 2019Article
- Use of Whole-Genome Sequencing in the Investigation of a Nosocomial Influenza Virus Outbreak.The Journal of infectious diseases · 2018Article
- Whole Genome Sequencing of Influenza A and B Viruses With the MinION Sequencer in the Clinical Setting: A Pilot Study.Frontiers in microbiology · 2018Article
- Observational
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9 authors.
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Abstract
Adequacy of the current clinical definition of institutional influenza outbreaks is unclear. We performed a retrospective genome sequencing and epidemiologic analysis of institutional influenza outbreaks that occurred during the 2014-15 influenza season in Toronto, Canada. We sequenced the 2 earliest submitted samples positive for influenza A(H3N2) from each of 38 reported institutional outbreaks in long-term care facilities. Genome sequencing showed most outbreak pairs identified by using the current clinical definition were highly related. Inclusion of surveillance samples demonstrated that outbreak sources were likely introductions from broader circulating lineages. Pairwise distance analysis using majority genome and hemagglutinin-specific genes enabled identification of thresholds for discrimination of within and between outbreak pairs; the area under the curve ranged 0.93-0.95. Routine genome sequencing for defining influenza outbreaks in long-term care facilities is unlikely to add significantly to the current clinical definition. Sequencing may prove most useful for investigating sources of outbreak introductions.
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