Reconstruction of transmission chains of SARS-CoV-2 amidst multiple outbreaks in a geriatric acute-care hospital: a combined retrospective epidemiological and genomic study

Abstract

Background: There is ongoing uncertainty regarding transmission chains and the respective roles of healthcare workers (HCWs) and elderly patients in nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in geriatric settings.

Methods: We performed a retrospective cohort study including patients with nosocomial coronavirus disease 2019 (COVID-19) in four outbreak-affected wards, and all SARS-CoV-2 RT-PCR positive HCWs from a Swiss university-affiliated geriatric acute-care hospital that admitted both Covid-19 and non-Covid-19 patients during the first pandemic wave in Spring 2020. We combined epidemiological and genetic sequencing data using a Bayesian modelling framework, and reconstructed transmission dynamics of SARS-CoV-2 involving patients and HCWs, to determine who infected whom. We evaluated general transmission patterns according to case type (HCWs working in dedicated Covid-19 cohorting wards: HCW_covid; HCWs working in non-Covid-19 wards where outbreaks occurred: HCW_outbreak; patients with nosocomial Covid-19: patient_noso) by deriving the proportion of infections attributed to each case type across all posterior trees and comparing them to random expectations.

Results: During the study period (1 March to 7 May 2020), we included 180 SARS-CoV-2 positive cases: 127 HCWs (91 HCW_covid, 36 HCW_outbreak) and 53 patients. The attack rates ranged from 10% to 19% for patients, and 21% for HCWs. We estimated that 16 importation events occurred with high confidence (4 patients, 12 HCWs) that jointly led to up to 41 secondary cases; in six additional cases (5 HCWs, 1 patient), importation was possible with a posterior probability between 10% and 50%. Most patient-to-patient transmission events involved patients having shared a ward (95.2%, 95% credible interval [CrI] 84.2%-100%), in contrast to those having shared a room (19.7%, 95% CrI 6.7%-33.3%). Transmission events tended to cluster by case type: patient_noso were almost twice as likely to be infected by other patient_noso than expected (observed:expected ratio 2.16, 95% CrI 1.17-4.20, p=0.006); similarly, HCW_outbreak were more than twice as likely to be infected by other HCW_outbreak than expected (2.72, 95% CrI 0.87-9.00, p=0.06). The proportion of infectors being HCW_covid was as expected as random. We found a trend towards a greater proportion of high transmitters (≥2 secondary cases) among HCW_outbreak than patient_noso in the late phases (28.6% vs. 11.8%) of the outbreak, although this was not statistically significant.

Conclusions: Most importation events were linked to HCW. Unexpectedly, transmission between HCW_covid was more limited than transmission between patients and HCW_outbreak. This finding highlights gaps in infection control and suggests the possible areas of improvements to limit the extent of nosocomial transmission.

Funding: This study was supported by a grant from the Swiss National Science Foundation under the NRP78 funding scheme (Grant no. 4078P0_198363).

Keywords: COVID-19; SARS-CoV-2; geriatric hospitals; healthcare-associated infection; infection prevention; infectious disease; medicine; microbiology; nosocomial outbreaks; transmission dynamics; viruses.