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.