Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.
Stirrup, Oliver Blackstone, James Mapp, Fiona MacNeil, Alyson Panca, Monica Holmes, Alison Machin, Nicholas Shin, Gee Yen Mahungu, Tabitha Saeed, Kordo
Stirrup, Oliver
Blackstone, James
Mapp, Fiona
MacNeil, Alyson
Panca, Monica
Holmes, Alison
Machin, Nicholas
Shin, Gee Yen
Mahungu, Tabitha
Saeed, Kordo
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Affiliation
University College London; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust; Sandwell and West Birmingham NHS Trust
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Publication date
2022-09-13
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Abstract
A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p=0.14) or rapid (0.85, 0.48-1.50; p=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources.
Citation
Stirrup, O., Blackstone, J., Mapp, F., MacNeil, A., Panca, M., Holmes, A., Machin, N., Shin, G. Y., Mahungu, T., Saeed, K., Saluja, T., Taha, Y., Mahida, N., Pope, C., Chawla, A., Cutino-Moguel, M. T., Tamuri, A., Williams, R., Darby, A., Robertson, D. L., … Breuer, J. (2022). Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study. eLife, 11, e78427. https://doi.org/10.7554/eLife.78427
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Article