Co-infections with COVID-19

The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused sharply increased cases and deaths worldwide. Between January 27 and February 26, 2020, we collected 68 clinical specimens (sputum, nasal and throat swab, anal swab and feces) from 24 patients hospitalized with SARS-CoV-2 infection, in Guangdong, China. We extracted total RNA, applied ultra-deep metatranscriptomic sequencing in combination with laboratory technologies, and uncovered co-infection rates, the prevalence and abundance of viruses, bacteria and fungi in these SARS-CoV-2 patients. Compared to mild cases, severe cases with ICU admission had much higher co-detection rates of respiratory viruses (30.8% vs 0%) and fungi (15.4% vs 0%), and greater expression levels of clinically relevant bacterial pathogens including Burkholderia cepacia complex (BCC), Staphylococcus epidermidis and Mycoplasma spp. More importantly, we demonstrated a time-dependent secondary and systemic infection of B. cenocepacia with expressions of multiple virulence genes in one ventilated patient, which might be the primary cause of his death after 1-month ICU admission. Our findings characterized a comprehensive spectrum of co-infections with SARS-CoV-2 and multiple respiratory pathogens that were distinct between hospitalized patients with different disease severity. Detection and tracking of BCC-associated secondary infections are recommended to inform the pre-emptive treatment regimen and prevent fatal outcomes of hospitalized patients during the current SARS-CoV-2 pandemic.