Abstract
BackgroundThe extent of transmission of influenza in hospital settings is poorly understood. Next generation sequencing may improve this by providing information on the genetic relatedness of viral strains.ObjectivesWe aimed to apply next generation sequencing to describe transmission in hospital and compare with methods based on routinely‐collected data.MethodsAll influenza samples taken through routine care from patients at University College London Hospitals NHS Foundation Trust (September 2012 to March 2014) were included. We conducted Illumina sequencing and identified genetic clusters. We compared nosocomial transmission estimates defined using classical methods (based on time from admission to sample) and genetic clustering. We identified pairs of cases with space‐time links and assessed genetic relatedness.ResultsWe sequenced influenza sampled from 214 patients. There were 180 unique genetic strains, 16 (8.8%) of which seeded a new transmission chain. Nosocomial transmission was indicated for 32 (15.0%) cases using the classical definition and 34 (15.8%) based on genetic clustering. Of the 50 patients in a genetic cluster, 11 (22.0%) had known space‐time links with other cases in the same cluster. Genetic distances between pairs of cases with space‐time links were lower than for pairs without spatial links (P < .001).ConclusionsGenetic data confirmed that nosocomial transmission contributes significantly to the hospital burden of influenza and elucidated transmission chains. Prospective next generation sequencing could support outbreak investigations and monitor the impact of infection and control measures.
Highlights
Nosocomial influenza is associated with increased length of hospital stay, severe complications and death.[1]
We found that one in eleven cases of influenza introduced to a hospital seeded a new transmission chain
ACases defined as hospital‐acquired if PCR‐positive influenza sample was taken more than two days after admission; and as community‐ac‐ quired if taken within two days. bCases defined as hospital‐acquired if they were part of a genetically defined cluster; and as community‐acquired if they were index cases or had unique genetic strains. cRow percentages
Summary
Nosocomial influenza is associated with increased length of hospital stay, severe complications and death.[1]. Classical methods assume cases to be “hospital‐acquired” when the time between admission and the first positive sample exceeds the incubation period of the influenza virus. This definition is not always accurate as the incu‐ bation period is variable (0.7 to 2.8 days),[2] early symptoms may not be recorded or recognised as influenza, samples may not be taken at consistent time points within an illness, and systems often fail to capture information on hospital contact prior to admission. Information derived from gen‐ eration sequencing may inform policy and practice for future outbreaks
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