Bacterial Superinfections After SARS-CoV-2 Pneumonia: Antimicrobial Resistance Patterns, Impact on Inflammatory Profiles, Severity Scores, and Clinical Outcomes

Abstract

Background and Objectives: Secondary bacterial pneumonia can substantially worsen the clinical trajectory of patients hospitalized for Coronavirus Disease 2019 (COVID-19). This study aimed to characterize bacterial superinfections in COVID-19, including pathogen profiles, resistance patterns, inflammatory responses, severity scores, and ICU admission risk. Methods: In a retrospective cohort design, we reviewed 141 patients admitted to a single tertiary-care hospital between February 2021 and December 2024. A total of 58 patients had laboratory-confirmed bacterial superinfection by sputum, bronchoalveolar lavage, or blood cultures (superinfection group), whereas 83 had COVID-19 without any documented bacterial pathogens (COVID-only group). We collected detailed microbiological data from sputum, bronchoalveolar lavage (BAL), and blood cultures. Antibiotic sensitivity testing was performed using standard breakpoints for multidrug resistance (MDR). Inflammatory markers (C-reactive protein, procalcitonin, neutrophil-to-lymphocyte ratio, and systemic immune-inflammation index) and the severity indices Acute Physiology and Chronic Health Evaluation (APACHE) II, Confusion, Urea, Respiratory rate, Blood pressure (CURB), and National Early Warning Score (NEWS) were measured at admission. Primary outcomes included intensive care unit (ICU) admission, mechanical ventilation, and mortality. Results: Patients in the superinfection group showed significantly elevated inflammatory markers and severity scores compared to the COVID-only group (mean APACHE II of 17.2 vs. 13.8; p < 0.001). Pathogens most frequently isolated from sputum and BAL included Klebsiella pneumoniae (27.6%) and Pseudomonas aeruginosa (20.7%). Multidrug-resistant strains were documented in 32.8% of isolates. The superinfection group had higher ICU admissions (37.9% vs. 19.3%; p = 0.01) and more frequent mechanical ventilation (25.9% vs. 9.6%; p = 0.01). Mortality trended higher among superinfected patients (15.5% vs. 7.2%; p = 0.09). A total of 34% of the cohort had prior antibiotic use, which independently predicted MDR (aOR 2.6, p = 0.01). The presence of MDR pathogens such as Klebsiella pneumoniae (OR 2.8), Pseudomonas aeruginosa (OR 2.5), and Staphylococcus aureus (OR 2.1) significantly increases the risk of ICU admission. Conclusions: Bacterial superinfection exacerbates inflammation and worsens outcomes in COVID-19 patients, such as a higher risk of ICU admission.

Keywords: COVID-19; antimicrobial resistance; bacterial infections; intensive care unit; pneumonia.

Figure 1

Clinical severity scores.

Figure 2

Risk factor assessment for ICU admission.