Acute SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa in the nose

Rhoades, Nicholas S.; Pinski, Amanda N.; Monsibais, Alisha N.; Jankeel, Allen; Doratt, Brianna M.; Cinco, Isaac R.; Ibraim, Izabela; Messaoudi, Ilhem

Research conducted on SARS-CoV-2 pathogenesis and COVID-19 has focused on the systemic host response, especially that generated by severely ill patients with few studies investigating the impact of acute SARS-CoV-2 at the site of infection. We show that the nasal microbiome of SARS-CoV-2 positive patients (CoV+, n=68) at the time of diagnosis was unique compared to CoV- healthcare workers (n=45) and CoV- outpatients (n=21). This shift was marked by an increased abundance of bacterial pathogens including Pseudomonas aeruginosa which was also positively associated with viral RNA load. Additionally, we observed a robust host transcriptional response in the nasal epithelia of CoV+ patients, indicative of an antiviral innate immune repones and neuronal damage. These data suggest that the inflammatory response caused by SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens in the nasal cavity that could contribute to increased incidence of secondary bacterial infections.