tetano
Editor, Senior Moderator
Infect Control Hosp Epidemiol
. 2023 Dec 22:1-6.
doi: 10.1017/ice.2023.274. Online ahead of print. The utility of whole-genome sequencing to inform epidemiologic investigations of SARS-CoV-2 clusters in acute-care hospitals
Theodore S Rader 4th[SUP] 1 [/SUP], Vatsala R Srinivasa[SUP] 1 2 [/SUP], Marissa P Griffith[SUP] 1 2 [/SUP], Kady Waggle[SUP] 1 2 [/SUP], Lora Pless[SUP] 1 2 [/SUP], Ashley Chung[SUP] 3 [/SUP], Suzanne Wagester[SUP] 3 [/SUP], Lee H Harrison[SUP] 1 2 [/SUP], Graham M Snyder[SUP] 1 4 [/SUP]
Affiliations
Objective: To evaluate the utility of selective reactive whole-genome sequencing (WGS) in aiding healthcare-associated cluster investigations.
Design: Mixed-methods quality-improvement study.
Setting: Thes study was conducted across 8 acute-care facilities in an integrated health system.
Methods: We analyzed healthcare-associated coronavirus disease 2019 (COVID-19) clusters between May 2020 and July 2022 for which facility infection prevention and control (IPC) teams selectively requested reactive WGS to aid the epidemiologic investigation. WGS was performed with real-time results provided to IPC teams, including genetic relatedness of sequenced isolates. We conducted structured interviews with IPC teams on the informativeness of WGS for transmission investigation and prevention.
Results: In total, 8 IPC teams requested WGS to aid the investigation of 17 COVID-19 clusters comprising 226 cases and 116 (51%) sequenced isolates. Of these, 16 (94%) clusters had at least 1 WGS-defined transmission event. IPC teams hypothesized transmission pathways in 14 (82%) of 17 clusters and used data visualizations to characterize these pathways in 11 clusters (65%). The teams reported that in 15 clusters (88%), WGS identified a transmission pathway; the WGS-defined pathway was not one that was predicted by epidemiologic investigation in 7 clusters (41%). WGS changed the understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in 8 clusters (47%) and altered infection prevention interventions in 8 clusters (47%).
Conclusions: Selectively utilizing reactive WGS helped identify cryptic SARS-CoV-2 transmission pathways and frequently changed the understanding and response to SARS-CoV-2 outbreaks. Until WGS is widely adopted, a selective reactive WGS approach may be highly impactful in response to healthcare-associated cluster investigations.
. 2023 Dec 22:1-6.
doi: 10.1017/ice.2023.274. Online ahead of print. The utility of whole-genome sequencing to inform epidemiologic investigations of SARS-CoV-2 clusters in acute-care hospitals
Theodore S Rader 4th[SUP] 1 [/SUP], Vatsala R Srinivasa[SUP] 1 2 [/SUP], Marissa P Griffith[SUP] 1 2 [/SUP], Kady Waggle[SUP] 1 2 [/SUP], Lora Pless[SUP] 1 2 [/SUP], Ashley Chung[SUP] 3 [/SUP], Suzanne Wagester[SUP] 3 [/SUP], Lee H Harrison[SUP] 1 2 [/SUP], Graham M Snyder[SUP] 1 4 [/SUP]
Affiliations
- PMID: 38130169
- DOI: 10.1017/ice.2023.274
Objective: To evaluate the utility of selective reactive whole-genome sequencing (WGS) in aiding healthcare-associated cluster investigations.
Design: Mixed-methods quality-improvement study.
Setting: Thes study was conducted across 8 acute-care facilities in an integrated health system.
Methods: We analyzed healthcare-associated coronavirus disease 2019 (COVID-19) clusters between May 2020 and July 2022 for which facility infection prevention and control (IPC) teams selectively requested reactive WGS to aid the epidemiologic investigation. WGS was performed with real-time results provided to IPC teams, including genetic relatedness of sequenced isolates. We conducted structured interviews with IPC teams on the informativeness of WGS for transmission investigation and prevention.
Results: In total, 8 IPC teams requested WGS to aid the investigation of 17 COVID-19 clusters comprising 226 cases and 116 (51%) sequenced isolates. Of these, 16 (94%) clusters had at least 1 WGS-defined transmission event. IPC teams hypothesized transmission pathways in 14 (82%) of 17 clusters and used data visualizations to characterize these pathways in 11 clusters (65%). The teams reported that in 15 clusters (88%), WGS identified a transmission pathway; the WGS-defined pathway was not one that was predicted by epidemiologic investigation in 7 clusters (41%). WGS changed the understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in 8 clusters (47%) and altered infection prevention interventions in 8 clusters (47%).
Conclusions: Selectively utilizing reactive WGS helped identify cryptic SARS-CoV-2 transmission pathways and frequently changed the understanding and response to SARS-CoV-2 outbreaks. Until WGS is widely adopted, a selective reactive WGS approach may be highly impactful in response to healthcare-associated cluster investigations.