Secondary bacterial infections in patients with COVID-19

The COVID-19 was considered a mild upper respiratory tract disease in a significant number of individuals, with an estimated hospitalization rate exceeding 8%, possibly reaching up to 20% in the high-risk population. Many patients required admission to intensive care units (ICUs), where mortality rates reached 50% among those needing mechanical ventilation. Viral respiratory infections predisposed patients to secondary bacterial infections, which contributed to worsened prognosis and were associated with increased mortality in severe COVID-19 cases that endured extended periods in ICUs and underwent mechanical ventilation. Various bacterial species were identified as the cause of ventilator-associated pneumonia in COVID-19 patients, including bacterial strains resistant to antimicrobials used in ICUs.In the context of the pandemic, the impact of antimicrobial resistance (AMR) on patient care was questioned, given the widespread use of broad-spectrum antimicrobials in COVID-19 patients (up to 70% of patients received broad-spectrum antimicrobials, promoting the selection and increased prevalence of AMR). Empirical or prolonged use of antimicrobial therapy also raised the risk of healthcare-associated infections. Consequently, an increase in multidrug-resistant (MDR) organisms was observed during the pandemic.The Hospital de Base de Sao Jose do Rio Preto (HB) was a tertiary hospital providing care to over 2 million residents from 102 municipalities. Since March 2020, HB had demonstrated exemplary care for COVID-19 patients and continued to serve as a reference center for COVID-19 treatment. Therefore, it was crucial to understand the diversity of etiological agents of major secondary infections in COVID-19 patients within the institution. This information was essential for designing management and treatment strategies, as well as infection control and prevention measures within the institution, to enhance patient safety and improve prognosis. For this, isolates of Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa were sequenced.