Etiology of community-acquired and hospital-acquired pneumonia associated with COVID-19

PURPOSE: The COVID-19 pandemic is accompanied by a high incidence of community-acquired pneumonia (CAP). Patients with a new coronavirus infection have an increased risk of developing hospital-acquired pneumonia. Aim: to study the etiological structure of CAP during the epidemic spread of COVID-19, to assess the risks of joining the pathogens of pneumonia associated with the provision of medical care. METHODS & MATERIALS: Biological material from 1085 hospitalized patients with CAP was conducted from August 2020 - June 2021 in Rostov-on-Don (Russia). Verification of respiratory viruses including SARS-CoV-2 RNA was performed by polymerase chain reaction in nasopharyngeal smears. Bacteriological analysis of sputum was performed via classical methods, identification of isolated pathogens was carried out using time-of-flight mass spectrometry on an Autoflex (Bruker Daltonics) with BioTyper 3.0 software. RESULTS: Cases of type 3 parainfluenza virus (7.8±0.9%), other types of coronaviruses (HKU-1, OC43, HL-63 and 229Е) (2.7±0.5%), respiratory syncytial virus (1.9±0.5%) were detected in patients with COVID-19. Fungi of the genus Candida (35.6±1.8%) and Staphylococcus aureus (9.1±1.1%) were prevailing in the microbiota structure. Should be noted that the number of Streptococcus pneumoniae cultures decreased from 5.5 % in August 2020 to 1.1 % in June 2021, possibly due to pneumococcal vaccination. Gramm-negative enterobacteria were presented predominantly by Klebsiella pneumoniae (3.5±0.7%), Escherichia coli (2.9±0.6%), and non-fermenting Gramm-negative bacteria – Pseudomonas aeruginosa (1.5±0.5%) and Acinetobacter baumannii (1.2±0.4%). In 30.6% of patients treated in the hospital there was a secondary infection probably associated with compromised immune system and the transmission of infection from the hospital environment. Secondary infection with Candida spp., non-fermenting Gramm-negative bacteria (A. baumannii, and P. aeruginosa) and K. pneumoniae, including those characterized by multiple drug-resistance, prevailed. The most frequently registered resistance to penicillins, cephalosporins of 3rd generation. CONCLUSION: A feature of CAP in patients with laboratory-confirmed COVID-19 is a higher incidence of mixed infection of both viral and bacterial etiology. Patients with COVID-19 represent a high risk group for the development of mycotic lung lesions, possibly against the background of treatment with antibacterial drugs. There is a significant risk of the formation of nosocomial infections in patients.