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; Dante M Quiñones-Laveriano; Faviola Valdivia; Eduardo Juscamayta-López; Johan Azañero-Haro; Liliana Chambi; Helen Horna; Gladys Patiño; Elizabet Guzman; Jhony A De la Cruz-Vargas

doi:10.2147/IDR.S306439

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

Infect Drug Resist. 2021 Jul 21:14:2795-2807. doi: 10.2147/IDR.S306439. eCollection 2021.

Affiliations

¹ Instituto de Investigaciones en Ciencias Biomédicas, Universidad Ricardo Palma, Lima, Perú.
² Department of Medicine, Hospital Nacional Hipólito Unanue, Lima, Peru.
³ Department of Public Health, Instituto Nacional de Salud, Lima, Peru.
⁴ Department of Clinical Pathology, Hospital Nacional Hipólito Unanue, Lima, Peru.

Abstract

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 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: COVID-19; SARS-CoV-2; coinfection; molecular biology; mortality.

Grants and funding

The research was funded by FONDECYT through the project “Coinfección por patógenos respiratorios virales y bacterianos detectados por métodos moleculares en pacientes hospitalizados por COVID-19 y su impacto en la mortalidad y desenlaces desfavorables” (Convenio N° 044-2020-FONDECYT) and Research Vice-chancellor of Universidad Ricardo Palma.