Etiology of Community-Acquired Pneumonia during the Epidemic Spread of COVID-19 and Healthcare-Associated Pneumonia Risk Assessment

Introduction. In 2020, the COVID-19 pandemic contributed to the epidemiology of respiratory tract infections. The importance of timely differential diagnosis of COVID-19 and seasonal acute respiratory diseases is hard to overestimate. Patients with the novel coronavirus disease are at risk of developing hospital-acquired pneumonia. The analysis of specific features of circulation of various strains of pathogens of nosocomial infections resistant to antibacterial chemotherapeutic agents is relevant.
Our objective was to study the etiological structure of community-acquired pneumonia during the epidemic spread of COVID-19 and to assess risks of developing healthcare-associated pneumonia.
Materials and methods. Biological specimens from 446 inpatients and outpatients diagnosed with community-acquired pneumonia in the city of Rostov-on-Don were tested. Verification of respiratory viruses, including RNA of SARS-CoV-2, M. pneumoniae, C. pneumoniae, and L. pneumophila, was performed by polymerase chain reaction in nasopharyngeal swab specimens. Bacteriological analysis of sputum was carried out using differential diagnostic media, and isolated pathogens were then identified by time-of-flight mass spectrometry on an Autoflex instrument (Bruker Daltonics GmbH, Germany) using the MALDI BioTyperR 3.0 software.
Results and discussion. In December 2020, the proportion of SARS-CoV-2 positive test results among patients diagnosed with community-acquired pneumonia was 35.6 %. The frequency of mixed viral infections in patients with a confirmed diagnosis of COVID-19 was not significantly different from that in patients tested negative (25.9 % and 26.2 %, respectively). The microbiota in pneumonia unrelated to SARS-CoV-2 was dominated by Candida fungi and plasma-coagulating staphylococci while cultures of non-fermenting gram-negative bacteria were significantly more often isolated from COVID-19 cases. Secondary infection presumably induced by environmental contamination or disease transmission from healthcare personnel was registered in 51.6 % of inpatients. Transmission of nosocomial infections between patients was not observed.

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