Respiratory Bacterial and Fungal Superinfections During the Third Surge of the COVID-19 Pandemic in Iran

Objective: We characterized bacterial and fungal superinfection and evaluated the antimicrobial resistance profile against the most common superinfection-causing pathogens ( Klebsiella pneumoniae , Acinetobacter baumannii , and Staphylococcus aureus ). Methods: In a cross-sectional study, 192 respiratory samples were collected from patients with and without SARS-COV-2 admitted to a teaching hospital in Tehran. Superinfection proportions and the antibiotic resistance profile were assessed and compared with demographic, comorbidities, and other clinical factors. Results: Superinfection rate was 60% among COVID-19 patients ( p = 0.629). Intensive care unit admission ( p = 0.017), mortality rate ( p ≤ 0.001), and antiviral and corticosteroid therapy ( p ≤ 0.001) were significantly more common among patients with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). The most common superinfections were caused by K. pneumoniae (42.7%, 82/192), A. baumannii (14.6%, 28/192), and S. aureus (13%, 25/192 ). A. baumannii isolates exhibited greater antibiotic resistance. Forty-four percent (11/25) of S. aureus isolates were cefoxitin resistant and also confirmed as methicillin-resistant S. aureus by PCR. Conclusion: The rise of difficult-to-treat infections with a high burden of antibiotic resistance, coupled with an increase in mortality rate of SARS-COV-2 superinfected individuals, illustrates the impact of the COVID-19 pandemic on antimicrobial resistance. Post-pandemic antimicrobial resistance crisis management requires precise microbiological diagnosis, drug susceptibility testing, and prescription of antimicrobials appropriate for the patient's condition.