Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units – A high risk community-hospital interface. Issue 1 (July 2021)

• Record Type: Journal Article
• Authors: Li, Kathy K.; Woo, Y. Mun; Stirrup, Oliver; Hughes, Joseph; Ho, Antonia; Filipe, Ana Da Silva; Johnson, Natasha; Smollett, Katherine; Mair, Daniel; Carmichael, Stephen; Tong, Lily; Nichols, Jenna; Aranday-Cortes, Elihu; Brunker, Kirstyn; Parr, Yasmin A.; Nomikou, Kyriaki; McDonald, Sarah E.; Niebel, Marc; Asamaphan, Patawee; Sreenu, Vattipally B; Robertson, David L.; Taggart, Aislynn; Jesudason, Natasha; Shah, Rajiv; Shepherd, James; Singer, Josh; Taylor, Alison H.M.; Cousland, Zoe; Price, Jonathan; Lees, Jennifer S.; Jones, Timothy P.W.; Lopez, Carlos Varon; MacLean, Alasdair; Starinskij, Igor; Gunson, Rory; Morris, Scott T.W.; Thomson, Peter C.; Geddes, Colin C.; Traynor, Jamie P.; Breuer, Judith; Thomson, Emma C.; Mark, Patrick B.;
• Is Part Of: Journal of infection. Volume 83:Issue 1(2021)
• Page Start: 96
• Page End: 103
• Publication Date: 2021-07
• Subjects: SARS-CoV-2 -- COVID-19 -- Haemodialysis -- Renal dialysis unit -- Infection control -- Rapid sequencing -- Outbreak -- Nosocomial; Infection -- Periodicals; Bacterial Infections -- Periodicals; Communicable Diseases -- Periodicals; Electronic journals; 616.905
• DOI: 10.1016/j.jinf.2021.04.020
• Languages: English
• ISSNs: 0163-4453

Abstract

Highlights: Haemodialysis patients are at increased risk of severe disease and mortality from COVID-19 disease. Phylogenetic analysis using whole genome sequencing of SARS-CoV-2 provides limited information on transmission events. Addition of Bayesian statistical reporting tool can help to resolve transmission and introduction events in renal dialysis units for targeted infection control measures. Transferability to other community-hospital interface for targeting infection control measures. Abstract: Objectives: Patients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data generated by the COG-UK consortium. Methods: We combined geographical, temporal and genomic sequence data from the community and hospital to estimate the probability of infection originating from within the dialysis unit, the hospital or the community using Bayesian statistical modelling and compared these results to the details of epidemiological investigations. Results: Of 671 patients, 60 (8.9%) became infected with SARS-CoV-2, of whom 16 (27%) died. Within-unit and community transmission were both evident and an instance of transmission from the wider hospital setting was also demonstrated. Conclusions: Near-real-time SARS-CoV-2 sequencing data can facilitate tailored infection prevention and control measures, which can be targeted at reducing risk in these settings.