COVID-19 infection may predispose to secondary
bacterial infection which is associated with poor clinical outcome especially among
critically ill patients. We aimed to characterize the lower respiratory tract bacterial microbiome of
COVID-19 critically ill patients in comparison to COVID-19-negative patients. We performed a
16S rRNA profiling on bronchoalveolar lavage (BAL) samples collected between April and May 2020 from 24
COVID-19 critically ill subjects and 24 patients with non-COVID-19
pneumonia. Lung microbiome of
critically ill patients with
COVID-19 was characterized by a different bacterial diversity (PERMANOVA on weighted and unweighted UniFrac Pr(> F) = 0.001) compared to COVID-19-negative patients with
pneumonia. Pseudomonas alcaligenes, Clostridium hiranonis, Acinetobacter schindleri, Sphingobacterium spp., Acinetobacter spp. and Enterobacteriaceae, characterized lung microbiome of
COVID-19 critically ill patients (LDA score > 2), while COVID-19-negative patients showed a higher abundance of lung commensal bacteria (Haemophilus influenzae, Veillonella dispar, Granulicatella spp., Porphyromonas spp., and Streptococcus spp.). The incidence rate (IR) of
infections during
COVID-19 pandemic showed a significant increase of
carbapenem-resistant Acinetobacter baumannii (CR-Ab)
infection. In conclusion,
SARS-CoV-2 infection and
antibiotic pressure may predispose
critically ill patients to bacterial
superinfection due to opportunistic multidrug resistant pathogens.