Transmission of community- and hospital-acquired SARS-CoV-2 in hospital settings in the UK: A cohort study

Abstract

Background: Nosocomial spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been widely reported, but the transmission pathways among patients and healthcare workers (HCWs) are unclear. Identifying the risk factors and drivers for these nosocomial transmissions is critical for infection prevention and control interventions. The main aim of our study was to quantify the relative importance of different transmission pathways of SARS-CoV-2 in the hospital setting.

Methods and findings: This is an observational cohort study using data from 4 teaching hospitals in Oxfordshire, United Kingdom, from January to October 2020. Associations between infectious SARS-CoV-2 individuals and infection risk were quantified using logistic, generalised additive and linear mixed models. Cases were classified as community- or hospital-acquired using likely incubation periods of 3 to 7 days. Of 66,184 patients who were hospitalised during the study period, 920 had a positive SARS-CoV-2 PCR test within the same period (1.4%). The mean age was 67.9 (±20.7) years, 49.2% were females, and 68.5% were from the white ethnic group. Out of these, 571 patients had their first positive PCR tests while hospitalised (62.1%), and 97 of these occurred at least 7 days after admission (10.5%). Among the 5,596 HCWs, 615 (11.0%) tested positive during the study period using PCR or serological tests. The mean age was 39.5 (±11.1) years, 78.9% were females, and 49.8% were nurses. For susceptible patients, 1 day in the same ward with another patient with hospital-acquired SARS-CoV-2 was associated with an additional 7.5 infections per 1,000 susceptible patients (95% credible interval (CrI) 5.5 to 9.5/1,000 susceptible patients/day) per day. Exposure to an infectious patient with community-acquired Coronavirus Disease 2019 (COVID-19) or to an infectious HCW was associated with substantially lower infection risks (2.0/1,000 susceptible patients/day, 95% CrI 1.6 to 2.2). As for HCW infections, exposure to an infectious patient with hospital-acquired SARS-CoV-2 or to an infectious HCW were both associated with an additional 0.8 infection per 1,000 susceptible HCWs per day (95% CrI 0.3 to 1.6 and 0.6 to 1.0, respectively). Exposure to an infectious patient with community-acquired SARS-CoV-2 was associated with less than half this risk (0.2/1,000 susceptible HCWs/day, 95% CrI 0.2 to 0.2). These assumptions were tested in sensitivity analysis, which showed broadly similar results. The main limitations were that the symptom onset dates and HCW absence days were not available.

Conclusions: In this study, we observed that exposure to patients with hospital-acquired SARS-CoV-2 is associated with a substantial infection risk to both HCWs and other hospitalised patients. Infection control measures to limit nosocomial transmission must be optimised to protect both staff and patients from SARS-CoV-2 infection.

Fig 1. Illustration of assumed incubation periods and the data analysed for 6 example patients.

We assumed that PCR tests were performed 1 day after developing symptoms, which were consistent with COVID-19. In this schematic, an incubation period of 5 days was used. Each hospitalised patient day from admission until (and including) the day of the assumed infection event (i.e., 6 (incubation period plus 1) days prior to the swab leading to the patient’s first positive PCR test) or 6 days prior to the day of discharge or death (whichever occurred first) was considered an observation where the patient was at risk of becoming infected. Each observation, unique to a specific patient on a specific day, therefore corresponds to an outcome 6 days later when the patient could potentially have a swab taken for a SARS-CoV-2 PCR test. An observation had a positive outcome (value of 1) if the patient had a positive PCR test for the first time resulting from a swab taken in the hospital 6 days later, and a negative outcome (value of 0) if the patient did not have a swab taken or had a swab taken resulting in a negative PCR test 6 days later. The risk factors, e.g., ward, number of infectious patients, or HCWs in the same ward, for each observation were taken from the day of the observation itself when the corresponding patient was at risk of becoming infected. COVID-19, Coronavirus Disease 2019; HCW, healthcare worker; SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2.

Fig 2

Weekly sums of SARS-CoV-2 PCR tests performed during March to October 2020 (Panel A). The stacked green bars indicate the number of negative tests. The stacked orange bars indicate the number of positive tests. Percentage of first positive SARS-CoV-2 PCR tests classified by different types of acquisition (Panel B). The colours represent patients who were inpatients on the eighth (red), sixth (orange), and fourth day (yellow) prior to their first positive tests, and who were not hospitalised in the 20 days prior to their first positive tests (blue). These classifications are not mutually exclusive, e.g., a patient who was admitted for 10 days continuously prior to the first positive PCR test would contribute to all first 3 groups. SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2.

Fig 3

Daily transmission risk to susceptible patients (Panel A) and HCWs (Panel B) using a generalised additive model with a logit link. The smooth, nonlinear partial effects of calendar day, infectious patients, and HCWs on the daily risk of nosocomial SARS-CoV-2 infection are presented as coloured lines. These partial effects are the isolated effects of each group of infectious individuals on the binary outcome of assumed acquisition (yes/no) on each day as the dependent variable. Infectious patients and HCWs were both associated with increased risk of nosocomial infection. The presence of more infectious patients or HCWs in a ward on a given day was associated with higher transmission risk. COVID-19, Coronavirus Disease 2019; HCW, healthcare worker; SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2.

Fig 4

Additional risk of suspected nosocomial acquisition of SARS-CoV-2 experienced by a single susceptible patient contributed by (i) infectious patients who acquired SARS-CoV-2 in the community (second row); (ii) infectious patients who acquired SARS-CoV-2 in the hospital (third row); and (iii) infectious HCWs (last row). A generalised mixed model with an identity link was used, with assumed nosocomial acquisition (yes/no) on each day as the dependent variable. Both the intercepts and slopes were allowed to vary by ward. The top row shows the variation of the intercepts of the model, which represent the background infection risk posed by infectious patients and HCWs who are undetected. Each horizontal bar represents the 95% CrI of the estimate. The black crosses in the centre of each bar represent the median of the estimates. CrI, credible interval; HCW, healthcare worker; SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2.

Fig 5

Additional risk of suspected nosocomial acquisition of SARS-CoV-2 experienced by a single susceptible HCW contributed by (i) infectious patients who acquired SARS-CoV-2 in the community (second row); (ii) infectious patients who acquired SARS-CoV-2 in the hospital (third row); and (iii) infectious HCWs (last row). A generalised mixed model with an identity link was used, with assumed nosocomial acquisition (yes/no) on each day as the dependent variable. Both the intercepts and slopes were allowed to vary by ward. The top row shows the variation of the intercepts of the model, which represent the background infection risk posed by infectious patients and HCWs who are undetected. Each horizontal bar represents the 95% CrI of the estimate. The black crosses in the centre of each bar represent the median of the estimates. CrI, credible interval; HCW, healthcare worker; SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2.