Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission.
Jamie M EllingfordRyan GeorgeJohn H McDermottShazaad AhmadJonathan J EdgerleyDavid GokhaleWilliam G NewmanStephen BallNicholas MachinGraeme Cm BlackPublished in: eLife (2021)
Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. We integrated patient movement and staff location data into the analysis of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples. Incorporation of HCW location further increased the number of individuals within PCCs and identified additional links in SARS-CoV-2 transmission pathways. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location. SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters. This dynamic approach can support infection control management strategies within the healthcare setting.
Keyphrases
- sars cov
- healthcare
- respiratory syndrome coronavirus
- end stage renal disease
- ejection fraction
- case report
- newly diagnosed
- chronic kidney disease
- electronic health record
- randomized controlled trial
- systematic review
- prognostic factors
- copy number
- big data
- peritoneal dialysis
- escherichia coli
- gene expression
- dna methylation
- genome wide
- staphylococcus aureus
- drug resistant
- single cell
- machine learning
- cystic fibrosis
- acinetobacter baumannii
- long term care
- genetic diversity