Identification of Co-Infections by Viral and Bacterial Pathogens in Covid-19 Hospitalized Patients in Peru: Molecular Diagnosis and Clinical Characteristics

Purpose: The impact of respiratory coinfections in COVID-19 is still not well understood. This study sought to identify the respiratory pathogens causing coinfections in patients with moderate/severe SARS-CoV-2 pneumonia from a hospital in Peru. Also, to describe the clinical characteristics and outcomes of coinfected and non-coinfected patients. Methods & Materials: A descriptive study was conducted on hospitalized patients with a confirmed diagnosis of moderate/severe pneumonia due to SARS-CoV-2 infection. The selection criteria included patients older than 18 years of age who were admitted to the Guillermo Almenara Irigoyen Hospital in Lima, Peru during the period July-November 2020. Pregnant women were excluded from the study. A nasopharyngeal swab sample was obtained from the patients included in the study. Diagnosis of SARS-CoV-2 infection was performed by reverse-transcriptase polymerase chain reaction (RT-PCR). The detection of the following respiratory viruses was performed by RT-PCR: Influenza A and B, Respiratory syncitial virus (RSV) A and B; and Adenovirus. The detection of atypical bacteria, Mycoplasma pneumoniae and Chlamydia pneumoniae was carried out using conventional polymerase chain reaction. Results: A total of 295 patients with confirmed SARS-CoV-2 infection were enrolled during the study period. A coinfection with one or more respiratory pathogen was detected in 154 (52.20%) patients at hospital admission. The most common coinfections were Mycoplasma pneumoniae (28.12%), Chlamydia pneumoniae (8.81%) and with both bacteria (11.53%); followed by Adenovirus (1.70%), Mycoplasma pneumoniae/Adenovirus (0.71%), Chlamydia pneumoniae/Adenovirus (0.71%), RSV-B/Chlamydia pneumoniae (0.32%), Mycoplasma pneumoniae/Chlamydia pneumoniae/Adenovirus (0.32%). Sepsis was more frequent among coinfected patients than non coinfected (33.12% vs 20.57%, p = 0.018). Expectoration was less frequent in coinfected individuals compared to non coinfected (5.84% vs 12.77%, p = 0.045). We could highlight that the majority of patients were administered an antibiotic (69.50%). The correlation between the empirical use of macrolides in patients with Mycoplasma pneumoniae and Chlamydia pneumoniae was observed in 41% of the cases. Conclusion: Mycoplasma pneumoniae and Chlamydia pneumoniae were the main microorganisms associated with SARS-CoV-2 coinfection at hospital admission. The presence of multiple coinfections was described in some patients. Antibiotics should be carefully prescribed, as high rates of antibiotic use was found, particularly with macrolides.