tetano
Editor, Senior Moderator
Open Forum Infect Dis
. 2021 Mar 12;8(10)
fab120.
doi: 10.1093/ofid/ofab120. eCollection 2021 Oct.
Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole-Genome Sequence Analysis
Suzy E Meijer[SUP] 1 2 [/SUP], Noam Harel[SUP] 3 4 [/SUP], Ronen Ben-Ami[SUP] 1 2 [/SUP], Meital Nahari[SUP] 1 2 [/SUP], Michal Yakubovsky[SUP] 1 2 [/SUP], Howard S Oster[SUP] 5 2 [/SUP], Albert Kolomansky[SUP] 5 2 [/SUP], Ora Halutz[SUP] 6 2 [/SUP], Orly Laskar[SUP] 7 [/SUP], Oryan Henig[SUP] 1 2 [/SUP], Adi Stern[SUP] 3 4 [/SUP], Yael Paran[SUP] 1 2 [/SUP]
Affiliations
Abstract
Background: The coronavirus disease 2019 (COVID-19) pandemic poses many epidemiological challenges. The investigation of nosocomial transmission is usually performed via thorough investigation of an index case and subsequent contact tracing. Notably, this approach has a subjective component, and there is accumulating evidence that whole-genome sequencing of the virus may provide more objective insight.
Methods: We report a large nosocomial outbreak in 1 of the medicine departments in our institution. Following intensive epidemiological investigation, we discovered that 1 of the patients involved was suffering from persistent COVID-19 while initially thought to be a recovering patient. She was therefore deemed to be the most likely source of the outbreak. We then performed whole-genome sequencing of the virus of 14 infected individuals involved in the outbreak.
Results: Surprisingly, the results of whole-genome sequencing refuted our initial hypothesis. A phylogenetic tree of the samples showed multiple introductions of the virus into the ward, 1 of which led to a cluster of 10 of the infected individuals. Importantly, the results pointed in the direction of a specific index patient that was different from the 1 that arose from our initial investigation.
Conclusions: These results underscore the important added value of using whole-genome sequencing in epidemiological investigations as it may reveal unexpected connections between cases and aid in understanding transmission dynamics, especially in the setting of a pandemic where multiple possible index cases exist simultaneously.
Keywords: COVID-19; epidemiology; nosocomial; outbreak; sequencing.
. 2021 Mar 12;8(10)
fab120.doi: 10.1093/ofid/ofab120. eCollection 2021 Oct.
Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole-Genome Sequence Analysis
Suzy E Meijer[SUP] 1 2 [/SUP], Noam Harel[SUP] 3 4 [/SUP], Ronen Ben-Ami[SUP] 1 2 [/SUP], Meital Nahari[SUP] 1 2 [/SUP], Michal Yakubovsky[SUP] 1 2 [/SUP], Howard S Oster[SUP] 5 2 [/SUP], Albert Kolomansky[SUP] 5 2 [/SUP], Ora Halutz[SUP] 6 2 [/SUP], Orly Laskar[SUP] 7 [/SUP], Oryan Henig[SUP] 1 2 [/SUP], Adi Stern[SUP] 3 4 [/SUP], Yael Paran[SUP] 1 2 [/SUP]
Affiliations
- PMID: 34631912
- PMCID: PMC7989189
- DOI: 10.1093/ofid/ofab120
Abstract
Background: The coronavirus disease 2019 (COVID-19) pandemic poses many epidemiological challenges. The investigation of nosocomial transmission is usually performed via thorough investigation of an index case and subsequent contact tracing. Notably, this approach has a subjective component, and there is accumulating evidence that whole-genome sequencing of the virus may provide more objective insight.
Methods: We report a large nosocomial outbreak in 1 of the medicine departments in our institution. Following intensive epidemiological investigation, we discovered that 1 of the patients involved was suffering from persistent COVID-19 while initially thought to be a recovering patient. She was therefore deemed to be the most likely source of the outbreak. We then performed whole-genome sequencing of the virus of 14 infected individuals involved in the outbreak.
Results: Surprisingly, the results of whole-genome sequencing refuted our initial hypothesis. A phylogenetic tree of the samples showed multiple introductions of the virus into the ward, 1 of which led to a cluster of 10 of the infected individuals. Importantly, the results pointed in the direction of a specific index patient that was different from the 1 that arose from our initial investigation.
Conclusions: These results underscore the important added value of using whole-genome sequencing in epidemiological investigations as it may reveal unexpected connections between cases and aid in understanding transmission dynamics, especially in the setting of a pandemic where multiple possible index cases exist simultaneously.
Keywords: COVID-19; epidemiology; nosocomial; outbreak; sequencing.