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

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1658-1665
Number of pages8
JournalClinical Microbiology and Infection
Volume27
Issue number11
Early online date8 Jun 2021
DOIs
Publication statusPublished - Nov 2021

Bibliographical note

Funding Information: No funding information.

Open Access: Free to read, but no Open Access licence.

Publisher Copyright: Crown Copyright ©2021 Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. All rights reserved.

Citation: Sarah M. Gerver, Rebecca Guy, Kate Wilson, Simon Thelwall, Olisaeloka Nsonwu, Graeme Rooney, Colin S. Brown, Berit Muller-Pebody, Russell Hope, Victoria Hall, National surveillance of bacterial and fungal coinfection and secondary infection in COVID-19 patients in England: lessons from the first wave,
Clinical Microbiology and Infection, Volume 27, Issue 11, 2021, Pages 1658-1665, ISSN 1198-743X.

DOI: https://doi.org/10.1016/j.cmi.2021.05.040.

Keywords

  • Bacterial
  • COVID-19
  • Coinfection
  • England
  • Fungal
  • National
  • SARS-CoV-2
  • Surveillance

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