Unexpected details regarding nosocomial transmission revealed by whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2)

Abstract

Objective: Effective infection prevention and control (IPC) measures are key for protecting patients from nosocomial infections and require knowledge of transmission mechanisms in different settings. We performed a detailed outbreak analysis of the transmission and outcome of coronavirus disease 2019 (COVID-19) in a geriatric ward by combining whole-genome sequencing (WGS) with epidemiological data. Design: Retrospective cohort study. Setting: Tertiary care hospital. Participants: Patients and healthcare workers (HCWs) from the ward with a nasopharyngeal sample (NPS) positive for SARS-CoV-2 RNA during the outbreak period. Methods: Patient data regarding clinical characteristics, exposure and outcome were collected retrospectively from medical records. Stored NPS from 32 patients and 15 HCWs were selected for WGS and phylogenetic analysis. Results: Median patient age was 84 years and 17/32 (53%) were male. Fourteen patients (44%) died within 30 days after sampling. Viral load was significantly higher among the deceased. WGS was successful in 28/32 (88%) patient samples and 14/15 (93%) HCW samples. Three separate viral clades were identified, whereof one clade and two subclades among both patient and HCW samples. Integrated epidemiological and genetic analysis revealed six probable transmission events between patients and supported hospital-acquired COVID-19 in 25/32 patients. Conclusion: WGS provided a deep insight into the outbreak dynamics and true extent of nosocomial COVID-19. The extensive transmission between patients and HCWs indicated that current IPC measures were insufficient. We suggest increased use of WGS in outbreak investigations for identification of otherwise unknown transmission links and evaluation of IPC measures.

SARS-CoV-2 Outbreak Investigation Using Contact Tracing and Whole-Genome Sequencing in an Ontario Tertiary Care Hospital

“…Altogether, similar to other studies ( 14 , 21 , 22 ), we show the value of combining contact tracing and genomic epidemiology to understand different aspects of the outbreak that could not be possible with only either contact tracing or genomic epidemiology alone. While we were able to learn about the genomic epidemiology, transmission, and geographical context of this outbreak, there were a few limitations of this study.…”

Outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 in a Rural Community Hospital during Omicron Predominance

“…Limitations of our study include relying solely on epidemiological investigation without whole genome sequencing, which might have resulted in wrongly attributing cases acquired in the community to the outbreak [32]. However, several of these cases occurred close together with clear exposure to persons in the outbreak making this less likely.…”

“…However, several of these cases occurred close together with clear exposure to persons in the outbreak making this less likely. Without WGS, it is unclear if this was a point source outbreak (single index case) or if multiple instances of viral introduction were responsible [32]. We also adopted several outbreak control measures concurrently and, therefore, were unable to discern the relative efficacy of each intervention.…”

State-wide genomic epidemiology investigations of COVID-19 in healthcare workers in 2020 Victoria, Australia: Qualitative thematic analysis to provide insights for future pandemic preparedness

“…Internationally, genomics of SARS-CoV-2 has been a powerful tool for understanding transmission links and outbreaks. 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 Whilst the investigation of HCW infections has traditionally been achieved through epidemiologic assessments, combined genomic and epidemiologic analyses have now emerged as the new standard-of care for these investigations. 20 , 21 …”

“… 6 , 24 Multiple studies document nosocomial transmission and infection in HCWs, tailored infection control investigations and responses. 16 , 17 , 18 , 19 , 20 , 21 , 25 , 26 , 27 , 28 Whole genome sequencing can contribute high resolution data to describe and investigate such transmission networks.…”