Waleed Javaid1,2, Jordan Ehni2, Ana S Gonzalez-Reiche3, Juan Manuel Carreño4, Elena Hirsch4, Jessica Tan4,5, Zenab Khan3, Divya Kriti3, Thanh Ly6, Bethany Kranitzky7, Barbara Barnett7,8, Freddy Cera9, Lenny Prespa9, Marie Moss1, Randy A Albrecht4,10, Ala Mustafa3, Ilka Herbison1, Matthew M Hernandez4,5, Theodore R Pak3, Hala A Alshammary4, Robert Sebra3,11,12, Melissa L Smith3, Florian Krammer4, Melissa R Gitman6, Emilia Mia Sordillo6, Viviana Simon1,4,10, Harm van Bakel3,11. 1. Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA. 2. Department of Infection Prevention, Mount Sinai Beth Israel, New York, New York, USA. 3. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA. 4. Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA. 5. The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA. 6. Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA. 7. Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA. 8. Department of Emergency Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA. 9. Clinical Laboratory, Mount Sinai Beth Israel, New York, New York, USA. 10. The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA. 11. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA. 12. Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Abstract
BACKGROUND: Nosocomial respiratory virus outbreaks represent serious public health challenges. Rapid and precise identification of cases and tracing of transmission chains is critical to end outbreaks and to inform prevention measures. METHODS: We combined conventional surveillance with influenza A virus (IAV) genome sequencing to identify and contain a large IAV outbreak in a metropolitan healthcare system. A total of 381 individuals, including 91 inpatients and 290 healthcare workers (HCWs), were included in the investigation. RESULTS: During a 12-day period in early 2019, infection preventionists identified 89 HCWs and 18 inpatients as cases of influenza-like illness (ILI), using an amended definition without the requirement for fever. Sequencing of IAV genomes from available nasopharyngeal specimens identified 66 individuals infected with a nearly identical strain of influenza A H1N1pdm09 (43 HCWs, 17 inpatients, and 6 with unspecified affiliation). All HCWs infected with the outbreak strain had received the seasonal influenza virus vaccination. Characterization of 5 representative outbreak viral isolates did not show antigenic drift. In conjunction with IAV genome sequencing, mining of electronic records pinpointed the origin of the outbreak as a single patient and a few interactions in the emergency department that occurred 1 day prior to the index ILI cluster. CONCLUSIONS: We used precision surveillance to delineate a large nosocomial IAV outbreak, mapping the source of the outbreak to a single patient rather than HCWs as initially assumed based on conventional epidemiology. These findings have important ramifications for more-effective prevention strategies to curb nosocomial respiratory virus outbreaks.
BACKGROUND: Nosocomial respiratory virus outbreaks represent serious public health challenges. Rapid and precise identification of cases and tracing of transmission chains is critical to end outbreaks and to inform prevention measures. METHODS: We combined conventional surveillance with influenza A virus (IAV) genome sequencing to identify and contain a large IAV outbreak in a metropolitan healthcare system. A total of 381 individuals, including 91 inpatients and 290 healthcare workers (HCWs), were included in the investigation. RESULTS: During a 12-day period in early 2019, infection preventionists identified 89 HCWs and 18 inpatients as cases of influenza-like illness (ILI), using an amended definition without the requirement for fever. Sequencing of IAV genomes from available nasopharyngeal specimens identified 66 individuals infected with a nearly identical strain of influenza A H1N1pdm09 (43 HCWs, 17 inpatients, and 6 with unspecified affiliation). All HCWs infected with the outbreak strain had received the seasonal influenza virus vaccination. Characterization of 5 representative outbreak viral isolates did not show antigenic drift. In conjunction with IAV genome sequencing, mining of electronic records pinpointed the origin of the outbreak as a single patient and a few interactions in the emergency department that occurred 1 day prior to the index ILI cluster. CONCLUSIONS: We used precision surveillance to delineate a large nosocomial IAV outbreak, mapping the source of the outbreak to a single patient rather than HCWs as initially assumed based on conventional epidemiology. These findings have important ramifications for more-effective prevention strategies to curb nosocomial respiratory virus outbreaks.
Authors: Sean T H Liu; Mohammad Amin Behzadi; Weina Sun; Alec W Freyn; Wen-Chun Liu; Felix Broecker; Randy A Albrecht; Nicole M Bouvier; Viviana Simon; Raffael Nachbagauer; Florian Krammer; Peter Palese Journal: J Clin Invest Date: 2018-10-08 Impact factor: 14.808
Authors: Ruth M Blackburn; Dan Frampton; Catherine M Smith; Ellen B Fragaszy; Simon J Watson; R Bridget Ferns; Špela Binter; Pietro G Coen; Paul Grant; Laura J Shallcross; Zisis Kozlakidis; Deenan Pillay; Paul Kellam; Stéphane Hué; Eleni Nastouli; Andrew C Hayward Journal: Influenza Other Respir Viruses Date: 2019-09-19 Impact factor: 4.380
Authors: P Godoy; N Torner; N Soldevila; C Rius; M Jane; A Martínez; J A Caylà; A Domínguez Journal: BMC Infect Dis Date: 2020-01-28 Impact factor: 3.090
Authors: E Bouza; F Vargas; B Alcázar; T Álvarez; A Asensio; G Cruceta; D Gracia; J Guinea; M A Gil; C Linares; P Muñoz; P Pastor; M L Pedro-Botet; X Querol; J Tovar; I Urrutia; F Villar; E Palomo Journal: Rev Esp Quimioter Date: 2022-03-11 Impact factor: 2.515