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Prevalence and Characterization of Bacteria Present in the Nasopharynx of Outpatients with and without SARS-CoV-2

COVID-19 has emerged as a highly contagious and debilitating disease caused by the SARS-CoV-2 virus and has claimed the lives of over 6.8 million people worldwide. Bacterial co-infections are one of many co-morbidities that have been suggested to impact the outcome of COVID-19 in patients. The primary goal of this study was to assess the prevalence of bacterial co-infections and to describe any trends observed during the height of the COVID-19 pandemic. To do this, we investigated SARS-CoV-2 and bacterial co-infections from outpatient RT-PCR testing in Texas. The results indicate Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae were the most frequently detected bacterial pathogens in both SARS-CoV-2 positive and SARS-CoV-2 negative patients and that these bacterial pathogens were present in these two patient populations at similar proportions. We also detected Staphylococcus aureus in a significantly larger proportion of males relative to females and people under 65 years of age relative to those 65 and over. Finally, we found that Hispanics were 75% more likely to be SARS-CoV-2 positive than non-Hispanics. The results suggest that COVID-19 patients may benefit from rapid diagnostic tests for bacterial pathogens and that this information could help delineate targeted antimicrobial therapy.