Nosocomial or not? A combined epidemiological and genomic investigation to understand hospital-acquired COVID-19 infection on an elderly care ward

Abstract

Background COVID-19 has the potential to cause outbreaks in hospitals. Given the comorbid and elderly cohort of patients hospitalized, hospital-acquired COVID-19 infection is often fatal. Pathogen genome sequencing is becoming increasingly important in infection prevention and control (IPC). Aim To inform the understanding of in-hospital SARS-CoV-2 transmission in order to improve IPC practices and to inform the future development of virological testing for IPC. Methods Patients detected COVID-19 positive by polymerase chain reaction on Ward A in April and May 2020 were included with contact tracing to identify other potential cases. Genome sequencing was undertaken for a subgroup of cases. Epidemiological, genomic, and cluster analyses were performed to describe the epidemiology and to identify factors contributing to the outbreak. Findings Fourteen cases were identified on Ward A. Contact tracing identified 16 further patient cases; in addition, eight healthcare workers (HCWs) were identified as being COVID-19 positive through a round of asymptomatic testing. Genome sequencing of 16 of these cases identified viral genomes differing by two single nucleotide polymorphisms or fewer, with further cluster analysis identifying two groups of infection (a five-person group and a six-person group). Conclusion Despite the temporal relationship of cases, genome sequencing identified that not all cases shared transmission events. However, 11 samples were found to be closely related and these likely represented in-hospital transmission. This included three HCWs, thereby confirming transmission between patients and HCWs.

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

“…There have been many research articles performing SARS-CoV-2 outbreak analyses that use genomic and epidemiologic data ( 2 – 6 ) but only a few sequenced COVID-positive samples from HCWs ( 3 , 4 , 15 – 19 ). Many of these outbreak analyses vary largely in the contact tracing information that they collected, as well as the sequencing breadth (i.e., number of outbreak samples sequenced) and depth (i.e., quality of sequencing).…”

“…Accurate diagnostics combined with contact tracing allow for SARS-CoV-2 outbreak management. With the recent paradigm shift toward next-generation sequencing tools, IPAC clinicians are now also combining whole-genome sequencing with traditional SARS-CoV-2 outbreak management practices ( 2 – 6 ). These advancements have enabled the incorporation of phylogenetics and genomic epidemiology into the understanding of an outbreak.…”

Lessons learned: use of WGS in real-time investigation of suspected intrahospital SARS-CoV-2 outbreaks

“…The use of whole-genome sequencing (WGS) in combination with epidemiological data has been shown to provide a more detailed picture of transmission [ 2 , 5 , [7] , [8] , [9] , [10] , [11] ], and enable rapid phylogenetic analyses leading to timely and improved infection control measures [ 12 , 13 ]. However, previous studies have generally been retrospective and covered short time periods.…”

Combining viral genomics and clinical data to assess risk factors for severe COVID-19 (mortality, ICU admission, or intubation) amongst hospital patients in a large acute UK NHS hospital Trust

“…Large-scale SARS-CoV-2 sequencing programs throughout the pandemic have allowed researchers to explore the role of viral genomics and different variants of the virus. However, whilst genomic epidemiology has been used in a number of studies to understand viral transmission in settings such as hospitals [14][15][16][17], long-term care facilities [18][19][20][21][22], and army barracks [23,24], well-powered studies of patient outcomes with high numbers of cases currently remain limited [25][26][27][28][29][30][31]. One of the largest studies looking at large-scale effects of viral genomics on patient outcomes are papers from the Hospital Onset COVID-19 Infections (HOCI) study in the UK [25,26,28].…”