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

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.

Fig. 1

Healthcare-associated COVID-19 weekly incidence. Evolution of the weekly incidence of healthcare-associated COVID-19 cases, community-associated COVID-19 hospitalized patients, and COVID-19 infections among healthcare workers, from ISO week 36 to ISO week 49, 2020. HA-COVID: healthcare-associated COVID-19, CA-COVID: community-acquired COVID-19, HCW: healthcare workers with COVID-19 infection. The X axis represents the time by ISO week from week 36 to week 49 and the Y axis the incidence levels expressed as the number of cases per week.

Fig. 2

Daily growth rate and doubling/halving time of COVID-19 infections healthcare-associated, community-associated and among HCWs. Estimation of the daily growth rate and doubling or halving time according to weekly incidence levels of healthcare-associated COVID-19 cases (A), community-associated COVID-19 hospitalized patients (B), and COVID-19 infections among healthcare workers (C) during the ascending and descending phases on each side of the incidence peak from ISO week 36 to ISO week 49, 2020. BEFORE: ascending phase before the peak of incidence, AFTER: descending phase after the peak of incidence. The X axis represents the time by ISO week from week 36 to week 49 and the Y axis the incidence levels expressed as the number of cases per week.

Fig. 3

Phylogenetic tree. Maximum likelihood phylogenetic tree showing 114 full SARS-CoV-2 genomes sequenced from 58 patients and 56 healthcare workers from the Sorbonne University Hospital Group during the study period and 586 European reference sequences sampled over 2020, extracted from the GISAID database.