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

• Published in: Infection and drug resistance 2021-01, Vol.14, p.2795-2807
• Main Authors: Soto, Alonso, Quinones-Laveriano, Dante M, Valdivia, Faviola, Juscamayta-Lopez, Eduardo, Azanero-Haro, Johan, Chambi, Liliana, Horna, Helen, Patino, Gladys, Guzman, Elizabet, De la Cruz-Vargas, Jhony A
• Format: Article
• Language: English
• Subjects: Antibiotics; Bacteria; Bacterial pneumonia; Cardiovascular disease; coinfection; Comorbidity; Coronaviruses; Cough; COVID-19; Dehydrogenases; Diabetes; Drug therapy; Dyspnea; Fever; Genes; Hospital patients; Hospitalization; Hospitals; Hypertension; Influenza; Influenza viruses; Laboratories; Mechanical ventilation; Medical records; Methods; Molecular biology; Mortality; Original Research; Pandemics; Pathogenic microorganisms; Pathogens; Patient outcomes; Patients; Pneumonia; Polymerase chain reaction; Regression analysis; Respiration; Respiratory diseases; RNA polymerase; Sample size; sars-cov-2; Severe acute respiratory syndrome coronavirus 2; Software; Sputum; Streptococcus infections; Ventilators; Viruses
• ISSN: 1178-6973; 1178-6973
• DOI: 10.2147/IDR.S306439

Purpose: 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 Hipolito Unanue. Sociodemographic and clinical data were collected from clinical records. Sputum samples were analyzed with the Biofire Filmarray Pneumonia plus[R] 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-19