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 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.