Investigation of healthcare-associated COVID-19 in a large French hospital group by whole-genome sequencing

Valentin Leducq; Jeanne Couturier; Benjamin Granger; Sarah Jolivet; Laurence Morand-Joubert; Jérôme Robert; Michel Denis; Beatrice Salauze; Valérie Goldstein; Karen Zafilaza; Pierre Rufat; Anne-Geneviève Marcelin; Aude Jary; Frédéric Barbut

doi:10.1016/j.micres.2022.127133

Investigation of healthcare-associated COVID-19 in a large French hospital group by whole-genome sequencing

Microbiol Res. 2022 Oct:263:127133. doi: 10.1016/j.micres.2022.127133. Epub 2022 Jul 22.

Authors

Affiliations

¹ Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France. Electronic address: valentin.leducq@sorbonne-universite.fr.
² Unité de Prévention du Risque Infectieux, Hôpital Saint-Antoine, GH Sorbonne Université, AP-HP, Paris, France.
³ Département de Santé Publique, Hôpital de la Pitié-Salpêtrière, GH Sorbonne Université, AP-HP, Paris, France.
⁴ Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, APHP, Hôpital Saint-Antoine, Département de Virologie, Paris, France.
⁵ Equipe Opérationnelle d'Hygiène, Hôpital de la Pitié-Salpêtrière, GH Sorbonne Université, AP-HP, Paris, France.
⁶ Equipe Opérationnelle d'Hygiène, Hôpital Tenon, GH Sorbonne Université, AP-HP, Paris, France.
⁷ Equipe Opérationnelle d'Hygiène, Hôpitaux Trousseau et Rothschild, GH Sorbonne Université, AP-HP, Paris, France.
⁸ Equipe Opérationnelle d'Hygiène Hôpital Charles Foix, GH Sorbonne Université, AP-HP, Ivry, France.
⁹ Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France.
¹⁰ Département d'Information Médicale, Hôpital de la Pitié-Salpêtrière, GH Sorbonne Université, AP-HP, Paris, France.

Abstract

Objectives: Despite the quick implementation of infection prevention and control procedures and the use of personal protective equipment within healthcare facilities, many cases of nosocomial COVID-19 transmission have been reported. We aimed to estimate the frequency and impact of healthcare-associated COVID-19 (HA-COVID-19) and evaluate the contribution of whole-genome sequencing (WGS) in cluster investigation.

Methods: We estimated the frequency and mortality of HA-COVID-19 infections from September 1 to November 30, 2020, with a focus on the evolution of hospitalized community-associated COVID-19 (CA-COVID-19) cases and cases detected among healthcare workers (HCWs) within the Sorbonne University Hospital Group (Paris, France). We thoroughly examined 12 clusters through epidemiological investigations and WGS.

Results: Overall, 209 cases of HA-COVID-19 were reported. Evolution of HA-COVID-19 incidence closely correlated with the incidence of CA-COVID-19 and COVID-19 among HCWs. During the study period, 13.9 % of hospitalized patients with COVID-19 were infected in the hospital and the 30-day mortality rate of HA-COVID-19 was 31.5 %. Nosocomial transmission of SARS-CoV-2 led to clusters involving both patients and HCWs. WGS allowed the exclusion of one-third of cases initially assigned to a cluster.

Conclusions: WGS analysis combined with comprehensive epidemiological investigations is essential to understand transmission routes and adapt the IPC response to protect both patients and HCWs.

Keywords: Epidemiology; Healthcare-Associated infection; Infection control; Severe acute respiratory syndrome coronavirus 2; Whole genome sequencing.

MeSH terms

COVID-19* / epidemiology
Cross Infection* / epidemiology
Delivery of Health Care
Hospitals
Humans
SARS-CoV-2 / genetics