Secondary infection in severe COVID-19 patients: clinical and microbial patterns at a tertiary hospital in Vietnam

COVID-19 predisposes patients to secondary infection, resulting in increased mortality worldwide. It is thus crucial to identify the causes of secondary infection and their clinical outcomes to devise future prevention and control strategies. This study aimed to report the clinical and microbiological features of bacterial and fungal secondary infections in severe COVID-19 patients during the peak of the pandemic in Vietnam. We collected data from 3,789 confirmed COVID-19 patients hospitalized at the Hospital for Tropical Diseases in Ho Chi Minh City between 2020 and 2021. Demographics, infection pathogens, treatment characteristics, and patient outcomes were recorded. Univariate and multivariate analyses were performed to identify risk factors associated with mortality. Microbiologically confirmed secondary infection was identified in 17.7% (651/3,682) of hospitalized COVID-19 patients. The most frequent comorbidities were cardiovascular diseases (74.9%), hypertension (65.9%), and diabetes (54.5%). The overall survival rate was 83.5% (3,075/3,682), highest in patients without secondary infection (97.2%), and dropped dramatically to 35.6% in those with microbiologically confirmed secondary infection. Out of 2,649 pathogens identified, Gram-negative bacteria accounted for 53.8% of isolates, followed by fungi (32.5%) and Gram-positive bacteria (13.7%). Notably, the predominant bacterial (A. baumannii, K. pneumoniae, P. aeruginosa) and fungal pathogens (C. tropicalis, C. albicans) exhibited high resistance rates to last-resort antibiotics (carbapenems, colistin) and antifungal drugs (fluconazole), respectively. Regression analyses found that secondary infection, older age, chronic kidney disease, cardiovascular disease and mechanical ventilation were the independent predictors of mortality. Secondary infection in COVID-19 patients was predominantly caused by highly resistant Gram-negative bacteria, and was associated with older patients who had comorbidities and underwent invasive procedures. Patients with secondary infection experienced higher mortality. Our work underscores the need for strengthening infection prevention measures and antibiotic stewardship programs to prevent nosocomial infections and better prepare for future epidemics.