Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014–15
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 earlies...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Centers for Disease Control and Prevention
2018-03-01
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| Series: | Emerging Infectious Diseases |
| Subjects: | |
| Online Access: | https://wwwnc.cdc.gov/eid/article/24/3/17-1499_article |
| _version_ | 1811263798585065472 |
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| author | Derek R. MacFadden Allison McGeer Taryn Athey Stephen Perusini Romy Olsha Aimin Li Alireza Eshaghi Jonathan B. Gubbay William P. Hanage |
| author_facet | Derek R. MacFadden Allison McGeer Taryn Athey Stephen Perusini Romy Olsha Aimin Li Alireza Eshaghi Jonathan B. Gubbay William P. Hanage |
| author_sort | Derek R. MacFadden |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T19:51:43Z |
| format | Article |
| id | doaj.art-1b91b723cae04047a463aa764b2284c3 |
| institution | Directory Open Access Journal |
| issn | 1080-6040 1080-6059 |
| language | English |
| last_indexed | 2024-04-12T19:51:43Z |
| publishDate | 2018-03-01 |
| publisher | Centers for Disease Control and Prevention |
| record_format | Article |
| series | Emerging Infectious Diseases |
| spelling | doaj.art-1b91b723cae04047a463aa764b2284c32022-12-22T03:18:48ZengCenters for Disease Control and PreventionEmerging Infectious Diseases1080-60401080-60592018-03-0124349249710.3201/eid2403.171499Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014–15Derek R. MacFaddenAllison McGeerTaryn AtheyStephen PerusiniRomy OlshaAimin LiAlireza EshaghiJonathan B. GubbayWilliam P. HanageAdequacy 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.https://wwwnc.cdc.gov/eid/article/24/3/17-1499_articleinfluenzagenomic epidemiologyoutbreakslong-term carehospitalinstitutional outbreak |
| spellingShingle | Derek R. MacFadden Allison McGeer Taryn Athey Stephen Perusini Romy Olsha Aimin Li Alireza Eshaghi Jonathan B. Gubbay William P. Hanage Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014–15 Emerging Infectious Diseases influenza genomic epidemiology outbreaks long-term care hospital institutional outbreak |
| title | Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014–15 |
| title_full | Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014–15 |
| title_fullStr | Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014–15 |
| title_full_unstemmed | Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014–15 |
| title_short | Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014–15 |
| title_sort | use of genome sequencing to define institutional influenza outbreaks toronto ontario canada 2014 15 |
| topic | influenza genomic epidemiology outbreaks long-term care hospital institutional outbreak |
| url | https://wwwnc.cdc.gov/eid/article/24/3/17-1499_article |
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