Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014)

the ICONIC group

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10 Citations (Scopus)

Abstract

Background: The 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. Objectives: We aimed to apply next generation sequencing to describe transmission in hospital and compare with methods based on routinely-collected data. Methods: All 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. Results: We 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). Conclusions: Genetic 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.

Original languageEnglish
Pages (from-to)556-563
Number of pages8
JournalInfluenza and other Respiratory Viruses
Volume13
Issue number6
DOIs
Publication statusPublished - 1 Nov 2019

Bibliographical note

Funding Information:
We would like to acknowledge the role of all involved in Infection response through virus genomics (ICONIC). We would like to thank Ms Annette Jeanes, Director of Infection Control and the Infection Control nurses at UCLH for their valuable assistance. This publication presents independent research supported by the Health Innovation Challenge Fund T5‐344 (ICONIC), a parallel funding partnership between the Department of Health and Wellcome Trust. The views expressed in this publication are those of the author(s) and not necessarily those of the Department of Health or Wellcome Trust. EN and BF also receive funding related to this study from the NIHR Biomedical Research Centre and the UCLH/UCL BRC funded NIHR Health Informatics Collaborative study. Where authors are identified as personnel of the International Agency for Research on Cancer / WHO, the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the International Agency for Research on Cancer / WHO. On behalf of the ICONIC group: The ICONIC group includes original grant co‐applicants who contributed to the design of the work program and additional colleagues who made significant contributions to data/specimen collection and interpretation. We thank Jane Kinghorn, Fatima Wurie, Saadia Rahman, Anne Johnson, David Dunn, Andrew Leigh‐Brown, Steven Morris, William Irving, Duncan Clark and Maria Zambon. We also thank and acknowledge the UCLH Clinical Team who supported data collection: De S, Pillay T, Freeman S, Kidd M, Gothard P, Miller R and Brealey D. A.C.H. is a National Institute for Health Research (NIHR) Senior Investigator. The views expressed in this publication are those of the authors and not necessarily those of the NHS, the National Institute for Health Research or the Department of Health and Social Care.

Funding Information:
We would like to acknowledge the role of all involved in Infection response through virus genomics (ICONIC). We would like to thank Ms Annette Jeanes, Director of Infection Control and the Infection Control nurses at UCLH for their valuable assistance. This publication presents independent research supported by the Health Innovation Challenge Fund T5-344 (ICONIC), a parallel funding partnership between the Department of Health and Wellcome Trust. The views expressed in this publication are those of the author(s) and not necessarily those of the Department of Health or Wellcome Trust. EN and BF also receive funding related to this study from the NIHR Biomedical Research Centre and the UCLH/UCL BRC funded NIHR Health Informatics Collaborative study. Where authors are identified as personnel of the International Agency for Research on Cancer / WHO, the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the International Agency for Research on Cancer / WHO. On behalf of the ICONIC group: The ICONIC group includes original grant co-applicants who contributed to the design of the work program and additional colleagues who made significant contributions to data/specimen collection and interpretation. We thank Jane Kinghorn, Fatima Wurie, Saadia Rahman, Anne Johnson, David Dunn, Andrew Leigh-Brown, Steven Morris, William Irving, Duncan Clark and Maria Zambon. We also thank and acknowledge the UCLH Clinical Team who supported data collection: De S, Pillay T, Freeman S, Kidd M, Gothard P, Miller R and Brealey D. A.C.H. is a National Institute for Health Research (NIHR) Senior Investigator. The views expressed in this publication are those of the authors and not necessarily those of the NHS, the National Institute for Health Research or the Department of Health and Social Care.

Publisher Copyright:
© 2019 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

Keywords

  • cross infection
  • disease outbreaks
  • human
  • influenza
  • molecular epidemiology

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