Low frequency of community-acquired bacterial co-infection in patients hospitalized for COVID-19 based on clinical, radiological and microbiological criteria: a retrospective cohort study

  1. Sophie Coenen
  2. Jara R. de la Court
  3. David T. P. Buis
  4. Lilian J. Meijboom
  5. Rogier P. Schade
  6. Caroline E. Visser
  7. Reinier van Hest
  8. Marianne Kuijvenhoven
  9. Jan M. Prins
  10. Suzan F. M. Nijman
  11. Elske Sieswerda
  12. Kim C. E. Sigaloff

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

Background

We defined the frequency of respiratory community-acquired bacterial co-infection in patients with COVID-19, i.e. patients with a positive SARS-CoV-2 PCR or a COVID-19 Reporting and Data System (CO-RADS) score ≥ 4, based on a complete clinical assessment, including prior antibiotic use, clinical characteristics, inflammatory markers, chest computed tomography (CT) results and microbiological test results.

Methods

Our retrospective study was conducted within a cohort of prospectively included patients admitted for COVID-19 in our tertiary medical centres between 1-3-2020 and 1-6-2020. A multidisciplinary study team developed a diagnostic protocol to retrospectively categorize patients as unlikely, possible or probable bacterial co-infection based on clinical, radiological and microbiological parameters in the first 72 h of admission. Within the three categories, we summarized patient characteristics and antibiotic consumption.

Results

Among 281 included COVID-19 patients, bacterial co-infection was classified as unlikely in 233 patients (82.9%), possible in 35 patients (12.4%) and probable in 3 patients (1.1%). Ten patients (3.6%) could not be classified due to inconclusive data. Within 72 h of hospital admission, 81% of the total study population and 78% of patients classified as unlikely bacterial co-infection received antibiotics.

Conclusions

COVID-19 patients are unlikely to have a respiratory community-acquired bacterial co-infection. This study underpins recommendations for restrictive use of antibacterial drugs in patients with COVID-19.

Article activity feed

  1. Version published to 10.1186/s13756-021-01024-4
  2. ScreenIT

    SciScore for 10.1101/2021.06.23.21259020: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: This study was approved by the Medical Ethics Committee VUmc (Amsterdam, the Netherlands); All necessary patient consent has been obtained and archived.
    Consent: This study was approved by the Medical Ethics Committee VUmc (Amsterdam, the Netherlands); All necessary patient consent has been obtained and archived.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationContamination: Relevant tests included blood and sputum cultures, bronchoalveolar lavage (BAL) and tracheal fluids, PCRs for Mycoplasma pneumoniae, Legionella pneumophila and Chlamydia pneumonia, and Legionella and pneumococcal urinary antigen tests.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    By means of this study, we addressed the limitation of previous reports, i.e. co-infection is not confirmed or ruled out by microbiological test results alone (19). Indeed, we found that only 11/38 (29%) patients classified as possible or probable co-infection had positive microbiological test results. Conversely, 4/15 (27%) positive microbiological test results were considered contamination, colonization or were due to extra-pulmonary infection. One recent study by Karaba et al. also included clinical and radiological criteria to assess the frequency of co-infection and concluded that co-infection was proven in 0.3%, probable in 1.1% and possible in 48% of patients (12). In contrast to our study, the authors found co-infection unlikely in only 51% of patients. This large difference could be explained by the different criteria used for co-infection. Karaba et al. classified patients meeting one clinical criterion (with the exception of hypoxia) or patients with positive radiological criteria on chest radiograph or chest CT as possible co-infection. This approach is likely to lead to overestimation of possible co-infection. We combined multiple clinical criteria with radiological and microbiological findings and a final classification by an expert panel. Furthermore, Karaba et al. included both chest radiograph and chest CT while chest CT has a higher sensitivity and specificity for bacterial CAP compared to chest radiograph (20). Chest CT was an important factor in our catego...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.06.23.21259020v1 on medRxiv