Secondary bacterial infections and antimicrobial resistance in COVID-19: comparative evaluation of pre-pandemic and pandemic-era, a retrospective single center study

Ann Clin Microbiol Antimicrob. 2021 Aug 5;20(1):51. doi: 10.1186/s12941-021-00454-7.


Purpose: In this study, we aimed to evaluate the epidemiology and antimicrobial resistance (AMR) patterns of bacterial pathogens in COVID-19 patients and to compare the results with control groups from the pre-pandemic and pandemic era.

Methods: Microbiological database records of all the COVID-19 diagnosed patients in the Ege University Hospital between March 15, 2020, and June 15, 2020, evaluated retrospectively. Patients who acquired secondary bacterial infections (SBIs) and bacterial co-infections were analyzed. Etiology and AMR data of the bacterial infections were collected. Results were also compared to control groups from pre-pandemic and pandemic era data.

Results: In total, 4859 positive culture results from 3532 patients were analyzed. Fifty-two (3.59%) patients had 78 SBIs and 38 (2.62%) patients had 45 bacterial co-infections among 1447 COVID-19 patients. 22/85 (25.88%) patients died who had bacterial infections. The respiratory culture-positive sample rate was 39.02% among all culture-positive samples in the COVID-19 group. There was a significant decrease in extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (8.94%) compared to samples from the pre-pandemic (20.76%) and pandemic era (20.74%) (p = 0.001 for both comparisons). Interestingly, Acinetobacter baumannii was the main pathogen in the respiratory infections of COVID-19 patients (9.76%) and the rate was significantly higher than pre-pandemic (3.49%, p < 0.002) and pandemic era control groups (3.11%, p < 0.001).

Conclusion: Due to the low frequency of SBIs reported during the ongoing pandemic, a more careful and targeted antimicrobial prescription should be taken. While patients with COVID-19 had lower levels of ESBL-producing Enterobacterales, the frequency of multidrug-resistant (MDR) A. baumannii is higher.

Keywords: Antimicrobial resistance; COVID-19; Co-infections; Secondary bacterial infections.

Publication types

  • Comparative Study

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • Anti-Bacterial Agents / pharmacology
  • Bacterial Infections / drug therapy
  • Bacterial Infections / epidemiology
  • Bacterial Infections / microbiology*
  • COVID-19 / epidemiology
  • COVID-19 / microbiology*
  • COVID-19 Nucleic Acid Testing
  • Child
  • Child, Preschool
  • Coinfection / epidemiology
  • Coinfection / microbiology*
  • Drug Resistance, Bacterial / drug effects*
  • Female
  • Humans
  • Infant
  • Male
  • Microbial Sensitivity Tests
  • Middle Aged
  • Retrospective Studies
  • Turkey / epidemiology
  • Young Adult


  • Anti-Bacterial Agents