National surveillance of bacterial and fungal coinfection and secondary infection in COVID-19 patients in England: lessons from the first wave

Abstract

Objectives: The impact of bacterial/fungal infections on the morbidity and mortality of persons with coronavirus disease 2019 (COVID-19) remains unclear. We have investigated the incidence and impact of key bacterial/fungal infections in persons with COVID-19 in England.

Methods: We extracted laboratory-confirmed cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (1st January 2020 to 2nd June 2020) and blood and lower-respiratory specimens positive for 24 genera/species of clinical relevance (1st January 2020 to 30th June 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: 1% of persons with COVID-19 (2279/223413) in England had coinfection/secondary infection, of which >65% were bloodstream infections. The most common causative organisms were Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae. Cases with coinfection/secondary infections were older than those without (median 70 years (IQR 58-81) versus 55 years (IQR 38-77)), and a higher percentage of cases with secondary infection were of Black or Asian ethnicity than cases without (6.7% versus 4.1%, and 9.9% versus 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 in those without (7.6% (95%CI 7.5-7.7%)) (p < 0.005).

Conclusions: Coinfection/secondary bacterial/fungal infections were rare in non-hospitalized and hospitalized 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.

Keywords: Bacterial; COVID-19; Coinfection; England; Fungal; National; SARS-CoV-2; Surveillance.

Fig. 1

Description of definitions used to categorize bacterial/fungal infections by timing of diagnosis.

Fig. 2

Counts and percentage of coinfections/secondary infections in persons with coronavirus disease 2019 (COVID-19) diagnosed in England, January to May 2020^a, by week. (2a) Weekly totals of persons with COVID-19 also with a key bacterial/fungal coinfection or secondary infection, and weekly totals of COVID-19, by week of SARS-CoV-2 laboratory confirmation. (2b) Percentage of all persons with COVID-19 also with a key bacterial/fungal coinfection or secondary infection, by week of first coinfection/secondary infection diagnosis. Fig 2a. The count is of coinfection/secondary infection cases plotted against week of COVID-19 diagnosis and not the coinfection/secondary infection diagnosis. Arrows indicate timing of testing policy change: (1) reduced testing in the community; (2) testing available to front-line National Health Service (NHS) staff with symptoms; (3) testing available to all essential workers and members of their household with symptoms; (4) testing available to everyone in England (over the age of 5 years) with symptoms. Fig 2b. The percentage of persons with COVID-19 and a coinfection/secondary infection is plotted against the week of the first bacterial/fungal infection diagnosis and not the week of COVID-19 diagnosis. This is to show the distribution of secondary infections over time in the first wave of the COVID-19 pandemic in England, for consideration of infection prevention control/treatment processes over time. These data differ from those in (Fig. 2a). ^aData are for weeks 1–22 inclusive, so incorporate COVID-19 diagnoses between 1st January 2020 and 2nd June 2020.