Co-occurrence of SARS-CoV-2 and Respiratory Pathogens in the Frail Elderly

Baunoch, D.; Wolfe, A.; Wang, D.; Gnewuch, R.; Zhao, X.; Halverson, T.; Cacdac, P.; Huang, S.; Lauterbach, T.; Luke, N.

Background: Elderly SARS-CoV-2 patients are associated with higher hospitalization and mortality. Co-infection is critical in the severity of respiratory diseases. It is largely understudied for SARS-CoV-2. Methods: Between March 24th and April 27th, 2020, nasopharyngeal and oropharyngeal swabs from 3,348 patients from nursing homes and assisted living facilities in 22 states in the US were tested by Capstone Healthcare for SARS-CoV-2, 24 other respiratory viruses, and 8 respiratory bacteria. Total nucleic acid was extracted with MagMAXTM Viral/Pathogen Ultra nucleic acid isolation kit. SARS-Co-V-2 was detected with the CDC 2019-novel coronavirus (2019-nCoV) diagnostic panel. Total nucleic acid was pre-amplified before analysis for other respiratory pathogens with Taqman OpenArrayTM Respiratory Tract Microbiota Plate. Results: Patients mean age was 76.9 years. SARS-CoV-2 was detected in 1,413 patients (42.2%). Among them, 1,082 (76.6%) and 737 (43.7%) patients were detected with at least one bacterium or another virus, respectively. SARS-CoV-2-positive patients were more likely to have bacterial co-occurrences (76.6%) than SARS-CoV-2-negative patients (70.0%) (p<0.0001). The most common co-occurring bacteria were Staphylococcus aureus and Klebsiella pneumonia, detected in 55.8% and 40.1% SARS-CoV-2-positive patients, respectively. Staphylococcus aureus was associated with SARS-CoV-2, with higher detection rates in SARS-CoV-2-positive patients (55.8%) than SARS-CoV-2-negative patients (46.2%) (p<0.0001). Human herpes virus 6 (HHV6) also was common and associated with SARS-CoV-2, with higher detection rates in SARS-CoV-2-positive patients (26.6%) than SARS-CoV-2-negative patients (19.1%) (p<0.0001). Conclusions: SARS-CoV-2-positive patients are more likely to be positive for certain respiratory bacteria and viruses. This observation may help explain high hospitalization and mortality rates in older patients.