Phylogenetic analyses revealed important insights into transmission pathways supporting only 47% of epidemiologically suspected SARS-CoV-2 transmissions within the context of nosocomial outbreak investigation. The remainder of cases most likely reflect community-acquired infection randomly detected by broad screening efforts. These results indicate that calculations of attack rates, not taking sequencing data into account, may result in an overestimation of the transmission risk allocated to specific hospital exposures. Notably, most confirmed transmissions occurred between HCWs, possibly indicating lower perception of the risk of infection among colleagues working together.
Our results indicate that late recognition of infected patients was the main starting point for these four clusters of nosocomial infection as reported by other outbreak investigations [11]. Importantly, complementary analyses of the sequencing data revealed a far more complex picture supporting multiple introductions of distinct strains, some entertaining different sub-clusters among patients and/or HCWs. This is meaningful, since epidemiological work-up would have concluded that all clusters were attributable to few unique sources maintaining onward transmission to patients and HCWs. This finding points to the need to pursue multi-facetted interventions targeting patients and HCWs to break nosocomial transmission chains. Such interventions include strategies for early detection of a- or pre-symptomatic infections but point to the need of enhanced universal precautions, such as mask-wearing and distancing, especially during phases with high-levels of community transmission.
Healthcare workers are at increased occupational risk of acquiring SARS-CoV-2 [12, 13]. This risk has been mainly considered to be resulting from exposures to infectious patients [14, 15]. Our findings suggest that community-acquired infection is the most common route of infection among HCWs, supported by the majority of HCWs being infected with genetically distinct SARS-CoV-2 strains. The importance of community-acquired infection among HCWs has been previously suggested [16–18] and the rate of asymptomatic infection among HCWs has been shown to more likely reflect general community transmission than in-hospital exposure [19]. Our interpretation is supported by our findings that only seven percent of all sequenced strains collected from HCWs in our report were shared between HCWs and patients, while 93% of HCW-strains were either unique (52%) or shared between HCWs (41%, ward-based exposure). Among HCWs reporting a direct exposure to a patient, transmission was ruled out in 78%. This finding suggests that our infection prevention and control measures were suitable to avoid onward transmission from patients by asymptomatic or pre-symptomatic carriers in the majority of cases. Among occupational exposures resulting in confirmed transmission, direct contacts between HCWs were the most common route of transmission. The importance of SARS-CoV-2 transmission between HCWs is supported by previous outbreak investigations involving staff working across different care homes in London [20] and from a large UK NHS Trust [21]. During our outbreak investigations, we commonly identified insufficient social distancing between HCWs during coffee- and meal breaks as a relevant source entertaining transmission between HCWs, especially under tighter space conditions.
It is, however, noteworthy, that HCWs commonly reported patients as the most likely source of infection, suggesting a flawed conception of perceived and actual risk. Among critical care staff, the peak onset of COVID-19 symptoms has been shown to occur two weeks before the peak in COVID-19 patient admissions with staff working in multiple hospital departments, thus exposed to more diverse co-worker encounters or with symptomatic household contacts more likely being infected [22].
Secondary attack rates of 19% have been previously reported for patients sharing the same room with an unrecognized infected patient [23]. It is noteworthy, that direct exposure between patients (defined as sharing the same multi-bedroom for a minimum duration of 15 minutes), resulted in confirmed transmission of SARS-CoV-2 in only 46% of patients testing positive after such exposure, given that most patients were not able to wear masks continuously during their stay in the room and were often exposed to an unrecognized infectious patient for several hours. In contrast, mostly shorter exposures as during HCW-patient interactions or contacts between HCWs resulted in similar transmission rates, suggesting that close contact as encountered during patient care or joint meal breaks result in a higher risk of transmission over time. Close contact to an infected HCW during patient care has been previously reported as an important route of transmission for nosocomial infections of patients [24].
Our findings have several limitations. First, sequencing data was not obtainable for all patients and HCWs involved in the reported infection-clusters. The proportion of successful sequencing in our study (70%) was nevertheless similar to a previous study investigating nosocomial infections in the UK (72%) [11]. Second, data on direct exposures may be flawed by recall-bias and short-term changes to working plans. As these outbreak investigations were performed in November and December 2020, our findings may not be generalizable to in-hospital transmission of other SARS-CoV-2 variants or populations with higher levels of immunity (acquired by infection and/or vaccination, the latter not being available yet for patients and HCWs at that time in Switzerland).