tetano
Editor, Senior Moderator
Antimicrob Steward Healthc Epidemiol
. 2023 Mar 8;3(1):e45.
doi: 10.1017/ash.2023.119. eCollection 2023.
On-demand, hospital-based, severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic epidemiology to support nosocomial outbreak investigations: A prospective molecular epidemiology study
Patrick Benoit[SUP] #[/SUP][SUP] 1 [/SUP], Gisèle Jolicoeur[SUP] #[/SUP][SUP] 2 [/SUP], Floriane Point[SUP] #[/SUP][SUP] 3 [/SUP], Chantal Soucy[SUP] 4 [/SUP], Karine Normand[SUP] 4 [/SUP], Philippe Morency-Potvin[SUP] 1 5 [/SUP], Simon Gagnon[SUP] 6 [/SUP], Daniel E Kaufmann[SUP] 2 3 5 [/SUP], Cécile Tremblay[SUP] 1 3 5 [/SUP], François Coutlée[SUP] 1 3 5 6 [/SUP], P Richard Harrigan[SUP] 7 [/SUP], Isabelle Hardy[SUP] 1 3 6 [/SUP], Martin Smith[SUP] 8 [/SUP], Patrice Savard[SUP] #[/SUP][SUP] 1 3 4 5 [/SUP], Simon Grandjean Lapierre[SUP] #[/SUP][SUP] 1 3 5 6 [/SUP]
Affiliations
Abstract
Objectives: We evaluated the added value of infection control-guided, on demand, and locally performed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic sequencing to support outbreak investigation and control in acute-care settings.
Design and setting: This 18-month prospective molecular epidemiology study was conducted at a tertiary-care hospital in Montreal, Canada. When nosocomial transmission was suspected by local infection control, viral genomic sequencing was performed locally for all putative outbreak cases. Molecular and conventional epidemiology data were correlated on a just-in-time basis to improve understanding of coronavirus disease 2019 (COVID-19) transmission and reinforce or adapt control measures.
Results: Between April 2020 and October 2021, 6 outbreaks including 59 nosocomial infections (per the epidemiological definition) were investigated. Genomic data supported 7 distinct transmission clusters involving 6 patients and 26 healthcare workers. We identified multiple distinct modes of transmission, which led to reinforcement and adaptation of infection control measures. Molecular epidemiology data also refuted (n = 14) suspected transmission events in favor of community acquired but institutionally clustered cases.
Conclusion: SARS-CoV-2 genomic sequencing can refute or strengthen transmission hypotheses from conventional nosocomial epidemiological investigations, and guide implementation of setting-specific control strategies. Our study represents a template for prospective, on site, outbreak-focused SARS-CoV-2 sequencing. This approach may become increasingly relevant in a COVID-19 endemic state where systematic sequencing within centralized surveillance programs is not available.
Trial registration: clinicaltrials.gov identifier: NCT05411562.
. 2023 Mar 8;3(1):e45.
doi: 10.1017/ash.2023.119. eCollection 2023.
On-demand, hospital-based, severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic epidemiology to support nosocomial outbreak investigations: A prospective molecular epidemiology study
Patrick Benoit[SUP] #[/SUP][SUP] 1 [/SUP], Gisèle Jolicoeur[SUP] #[/SUP][SUP] 2 [/SUP], Floriane Point[SUP] #[/SUP][SUP] 3 [/SUP], Chantal Soucy[SUP] 4 [/SUP], Karine Normand[SUP] 4 [/SUP], Philippe Morency-Potvin[SUP] 1 5 [/SUP], Simon Gagnon[SUP] 6 [/SUP], Daniel E Kaufmann[SUP] 2 3 5 [/SUP], Cécile Tremblay[SUP] 1 3 5 [/SUP], François Coutlée[SUP] 1 3 5 6 [/SUP], P Richard Harrigan[SUP] 7 [/SUP], Isabelle Hardy[SUP] 1 3 6 [/SUP], Martin Smith[SUP] 8 [/SUP], Patrice Savard[SUP] #[/SUP][SUP] 1 3 4 5 [/SUP], Simon Grandjean Lapierre[SUP] #[/SUP][SUP] 1 3 5 6 [/SUP]
Affiliations
- PMID: 36960087
- PMCID: PMC10028942
- DOI: 10.1017/ash.2023.119
Abstract
Objectives: We evaluated the added value of infection control-guided, on demand, and locally performed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic sequencing to support outbreak investigation and control in acute-care settings.
Design and setting: This 18-month prospective molecular epidemiology study was conducted at a tertiary-care hospital in Montreal, Canada. When nosocomial transmission was suspected by local infection control, viral genomic sequencing was performed locally for all putative outbreak cases. Molecular and conventional epidemiology data were correlated on a just-in-time basis to improve understanding of coronavirus disease 2019 (COVID-19) transmission and reinforce or adapt control measures.
Results: Between April 2020 and October 2021, 6 outbreaks including 59 nosocomial infections (per the epidemiological definition) were investigated. Genomic data supported 7 distinct transmission clusters involving 6 patients and 26 healthcare workers. We identified multiple distinct modes of transmission, which led to reinforcement and adaptation of infection control measures. Molecular epidemiology data also refuted (n = 14) suspected transmission events in favor of community acquired but institutionally clustered cases.
Conclusion: SARS-CoV-2 genomic sequencing can refute or strengthen transmission hypotheses from conventional nosocomial epidemiological investigations, and guide implementation of setting-specific control strategies. Our study represents a template for prospective, on site, outbreak-focused SARS-CoV-2 sequencing. This approach may become increasingly relevant in a COVID-19 endemic state where systematic sequencing within centralized surveillance programs is not available.
Trial registration: clinicaltrials.gov identifier: NCT05411562.