The impact of COVID-19 on respiratory tract microbiota pattern in patients with severe pneumonia

COVID-19 weakens the body’s immune system and predisposes to bacterial infections. It has been increasingly evident about changes in the etiological pattern of pneumonia pathogens due to altered lung microbiota after viral pneumonia, the effect of SARS-CoV-2 on the immune system, and antibiotics taking as part of preventing secondary bacterial infection. Our study was aimed to analyze the dynamic change in the pattern of the respiratory tract microbiota in patients with severe pneumonia in the years from 2019 to 2023. There were enrolled 304 patients with pneumonia diagnosed after X-ray examination assessed from January 2019 to December 2023 inclusive. During the pandemic, all the investigated patients had a positive SARS-CoV-2 PCR result, and in the period after the pandemic all the examined patients were negative. Sputum samples delivered to the laboratory, where we performed microbiological culture with identification by MALDI-ToF mass spectrometry. In the pre-COVID-19 pandemic, 62 sputum samples were analyzed, among which Klebsiella pneumoniae and Stenotrophomonas maltophilia were the most common found in 21% and 17.7%, respectively. Both Acinetobacter baumanii and Staphylococcus aureus were isolated in 14.5% cases. Streptococcus pneumoniae was found in 8.1% cases. During the COVID-19 pandemic, 122 samples were evaluated allowing to observe that K. pneumoniae accounted for half of all isolated microorganisms. The second most common was A. baumannii (23.8%). In the post-pandemic period, 120 samples were analyzed, from which K. pneumoniae was mainly identified (31.7%). The next most frequent among pathogens were S. aureus and A. baumannii — 23.3% and 18.3%, respectively. In this way, there was a statistically significant change in the frequency of detection of Gram-positive and Gram-negative microorganisms in ICU patients during the study periods. Before the COVID-19 pandemic, the proportion of Gram-negative microorganisms in the pattern of pathogens was 67.7%, during the pandemic — 91.0%, in the post-pandemic period — approached the values of 2019–2020 and amounted to 70.0% (p < 0.001). K. pneumoniae and A. baumannii were the most frequently found, however, the statistical significance of the changes was observed only for K. pneumoniae (p < 0.005). An insignificant decline in the detection rate of pneumococcus was established as well. The frequency of staphylococcal discharge after coronavirus infection exceeded the pre-pandemic magnitude (p < 0.001).