Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections
About Estée Török
Dr. Estée Török is a Clinician Scientist Fellow and a Senior Research Associate in the Department of Medicine at the University of Cambridge. Her clinical expertise is in Infectious Diseases and Medical Microbiology, and she practices as a Consultant in Infectious Diseases and Microbiology at Cambridge University Hospitals NHS Foundation Trust. She has over 20 years' clinical research experience in infectious diseases in the UK and in south-east Asia. Her current research aims to translate microbial genomics from a research tool into clinical practice, with a particular focus on antimicrobial resistance and healthcare-associated infections. She has published over 100 scientific papers and three books, and is interested in medical education and public engagement.
The burden and impact of healthcare-associated COVID-19 infections is unknown. We aimed to examine the utility of rapid sequencing of SARS-CoV-2 combined with detailed epidemiological analysis to investigate healthcare-associated COVID-19 infections and to inform infection control measures. We set up rapid viral sequencing of SARS-CoV-2 from PCR-positive diagnostic samples using nanopore sequencing, enabling sample-to-sequence in less than 24 hours. We established a rapid review and reporting system with integration of genomic and epidemiological data to investigate suspected cases of healthcare-associated COVID-19. Between 13 March and 24 April 2020, we collected clinical data and samples from 5191 COVID-19 patients in the East of England. We sequenced 1000 samples, producing 747 complete viral genomes. We conducted combined epidemiological and genomic analysis of 299 patients at our hospital and identified 26 genomic clusters involving 114 patients. 66 cases (57.9%) had a strong epidemiological link and 15 cases (13.2%) had a plausible epidemiological link. These results were fed back to clinical, infection control and hospital management teams, resulting in infection control interventions and informing patient safety reporting. We established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and demonstrated the benefit of combined genomic and epidemiological analysis for the investigation of healthcare-associated COVID-19 infections. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection control interventions to reduce further healthcare-associated infections.