National surveillance of bacterial and fungal co- and secondary infection in COVID-19 patients in England – Lessons from the first wave

Gerver, Sarah M.; Guy, Rebecca; Wilson, Kate; Thelwall, Simon; Nsonwu, Olisaeloka; Rooney, Graeme; Brown, Colin S.; Muller-Pebody, Berit; Hope, Russell; Hall FFPH, Victoria

OBJECTIVES: The impact of bacterial/fungal infections on the morbidity and mortality of persons with COVID-19 remains unclear. We have investigated the incidence and impact of key bacterial/fungal infections in COVID-19 persons in England. METHODS: We extracted laboratory-confirmed SARS-CoV-2 cases (01/01/2020-02/06/2020) and blood and lower-respiratory specimens positive for 24 genera/species of clinical relevance (01/01/2020-30/06/2020) from Public Health England’s national laboratory surveillance system. We defined coinfection and secondary infection as a culture-positive key organism, isolated within 1-day, or 2-27 days, respectively of the SARS-CoV-2 positive date. We described the incidence and timing of bacterial/fungal infections and compared characteristics of COVID-19 patients with and without bacterial/fungal infection. RESULTS: One-percent (n=2,279/223,413) of COVID-19 persons in England had co/secondary infection, >65% were bloodstream infections. The most common causative organisms were Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae. Cases with co/secondary infections were older than without (median 70-years [IQR:58-81] vs 55-years [IQR:38-77]), and a higher percentage of cases with secondary infection were of Black or Asianst ethnicity than cases without (6·7% vs 4·1%, and 9·9% vs 8·2%, respectively, p<0·001). Age-sex-adjusted case fatality rates were higher in COVID-19 cases with a coinfection (23·0% [95%CI:18·8%-27·6%] or secondary infection (26·5% [95%CI:14·5%-39·4%]), than those without (7·6% [95%CI:7·5%-7·7%])(p<0·005). CONCLUSIONS: Co/secondary bacterial/fungal infections were rare in non-hospitalised and hospitalised persons with COVID-19, varied by ethnicity and age, and were associated with higher mortality. However, the inclusion of non-hospitalized persons with asymptomatic/mild COVID-19 likely underestimated the rate of secondary bacterial/fungal infections. This should inform diagnostic testing and antibiotic prescribing strategy.