Burkholderia species are opportunistic bacteria encountered in clinical settings, most frequently affecting individuals with cystic fibrosis. In our observations, members of the Burkholderia cepacia complex (Bcc) were also detected in patients with respiratory infections caused by viruses such as H7N9 influenza and SARS-CoV-2. Nevertheless, systematic investigation of Bcc co-infections with respiratory viruses remains limited. Accordingly, this study aimed to characterize COVID-19–Bcc and H7N9–Bcc co-infections by analyzing their genomic features, antimicrobial resistance profiles, and virulence-related traits. A retrospective study was conducted on 49 clinical isolates of the Burkholderia cepacia complex (Bcc) obtained from patients treated at a tertiary hospital in Zhejiang Province during outbreaks of H7N9 influenza and COVID‑19. Among these isolates, 42 were recovered from H7N9 cases, while the remaining 7 were recovered from individuals infected with SARS-CoV-2. All isolates were subjected to antimicrobial susceptibility testing, virulence assessment using the Galleria mellonella larval infection model, and whole-genome sequencing to enable comprehensive molecular characterization of Bcc strains associated with COVID-19. Among the 49 Bcc strains tested, those recovered from COVID-19 patients accounted for 57.1% of all multidrug-resistant isolates. Analysis of median survival time in G. mellonella larvae revealed that COVID‑19‑associated Bcc strains killed the larvae more quickly and exhibited greater virulence compared to H7N9‑associated Bcc (P < 0.05). Phylogenetic analysis suggested that COVID‑19‑related Bcc may have originated from H7N9‑related Bcc through evolutionary changes. This study is the first to identify co-infection with Burkholderia cepacia complex (Bcc) in a substantial number of patients with respiratory tract infections, specifically those with H7N9 influenza and COVID-19. Our findings also suggest that Bcc strains associated with COVID‑19 likely evolved from H7N9‑linked Bcc and exhibit both enhanced virulence and multidrug resistance.
