Detection of Viral and Bacterial Respiratory Pathogens Identified by Molecular Methods in COVID-19 Hospitalized Patients and Its Impact on Mortality and Unfavorable Outcomes

Alonso Soto,1,2 Dante M Quiñones-Laveriano,1 Faviola Valdivia,3 Eduardo Juscamayta-López,3 Johan Azañero-Haro,2 Liliana Chambi,2 Helen Horna,3 Gladys Patiño,4 Elizabet Guzman,4 Jhony A De la Cruz-Vargas1 1Instituto de Investigaciones en Ciencias Biomédicas, Universidad Ricardo Palma, Lima, Perú; 2Department of Medicine, Hospital Nacional Hipólito Unanue, Lima, Peru; 3Department of Public Health, Instituto Nacional de Salud, Lima, Peru; 4Department of Clinical Pathology, Hospital Nacional Hipólito Unanue, Lima, PeruCorrespondence: Alonso SotoInstituto de Investigaciones en Ciencias Biomédicas, Universidad Ricardo Palma, Av. Alfredo Benavides 5440, Santiago de Surco, Lima, 15039, Per&#x00FATel +051 996128953Email alonso.soto@urp.edu.pePurpose: The purpose of this study is to evaluate the frequency of viral and bacterial respiratory pathogens detected by molecular methods in sputum samples of patients hospitalized for COVID-19 and to evaluate its impact on mortality and unfavorable outcomes (in-hospital death or mechanical ventilation).Patients and Methods: The prospective cohort included patients with diagnosis of COVID-19 hospitalized at Hospital Nacional Hipólito Unanue. Sociodemographic and clinical data were collected from clinical records. Sputum samples were analyzed with the Biofire Filmarray Pneumonia plus® respiratory panel. Crude and adjusted associations with unfavorable outcomes were evaluated using logistic regression models.Results: Ninety-three patients who were able to collect sputum samples were recruited between September 8 and December 28, 2020. The median age was 61.7 years (IQR 52.3– 69-8) and 66 (71%) were male. The most frequent symptoms were dyspnea, cough, fever, and general malaise found in 80 (86%), 76 (82%), 45 (48%), and 34 (37%) patients, respectively. Fifty-three percent of patients had comorbidities. Seventy-six (82%) patients received antibiotics prior to admission and 29 (31%) developed unfavorable outcome. Coinfection was evidenced in 38 (40.86%) cases. The most frequently found bacteria were Staphylococcus aureus, Streptococcus agalactiae, Haemophilus influenzae and Klebsiella pneumoniae in 11 (11.83%), 10 (10.75%), 10 (10.75%), and 8 (8.6%) cases, respectively. Streptococcus pneumoniae was found in one case (1.08%). We neither identify atypical bacteria nor influenza virus. No association was found between the presence of viral or bacterial microorganisms and development of unfavorable outcomes (OR 1.63; 95% CI 0.45– 5.82).Conclusion: A high frequency of respiratory pathogens was detected by molecular methods in patients with COVID-19 pneumonia but were not associated with unfavorable outcomes. No atypical agents or influenza virus were found. The high use antibiotics before admission is a concern. Our data suggest that the use of drug therapy against atypical bacteria and viruses would not be justified in patients hospitalized for COVID-19.Keywords: SARS-CoV-2, coinfection, molecular biology, mortality, COVID-1