Bacterial and fungal secondary infections in patients with severe SARS-CoV-2 pneumonitis: Prevalence, epidemiology and resistance profile

Background: Coronavirus disease (COVID19) is an infectious disease caused by the SARS-CoV-2 virus. Most people infected with the virus present with mild to severe respiratory illness requiring care in an intensive care unit. However, critically ill patients are likely to develop secondary bacterial infections such as secondary pneumonia, bloodstream infection of unknown origin and catheter-related sepsis. The aim of this study was to investigate the prevalence and potential risk factors for secondary infections, and to identify the incriminating pathogens and their resistance profiles in critically ill patients infected with SARS-CoV-2. Methods. We conducted a single-center retrospective observational study over a 15-month period at the Mohammed V Military Hospital. Clinical specimens were identified using standard microbiological methods. Antimicrobial susceptibility testing was performed using a range of antibiotics recommended by CA-SFM/EUCAST 2021. Results. We collected 138 patients who met our inclusion criteria, 102 of whom developed a secondary infection, i.e. a prevalence of 74%. The most frequent secondary infection was pneumonia (56%), followed by bacteremia (31%) and catheter-related infection (13%). Age, length of stay in intensive care, corticosteroid treatment, diabetes, chronic lung disease and smoking were statistically associated with the acquisition of secondary infections. Secondary fungal infection represented 10%. Secondary infection was dominated by Gram-negative bacilli. Conclusion. In our study, the prevalence of microbial secondary infection was very high. Gram-negative bacilli were the most common germs, with alarmingly high rates of resistance, complicating the therapeutic management of these patients.