Changes in the microbial landscape and antimicrobial resistance in patients of an infectious disease hospital during the COVID-19 pandemic

The aim of the study was to assess changes in the microbial landscape in patients of an infectious disease hospital during the pre-pandemic and pandemic periods, taking into account the respiratory tract, sterile sites, and gastrointestinal tract, as well as to trace the dynamics of antimicrobial resistance of key clinically significant pathogens. A retrospective-prospective analysis of microbiological studies performed in 2019–2024 was conducted. Clinically significant isolates recovered from respiratory samples, blood, cerebrospinal fluid, and intestinal contents were studied. The dynamics of antimicrobial resistance of the main nosocomial pathogens were analyzed separately. The COVID–19 pandemic was accompanied by a significant restructuring of the microbial landscape. In the respiratory tract, the proportion of gram-negative hospital pathogens, primarily Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, increased. In the intestinal biotope, a statistically significant decrease in pathogenic enterobacteria was observed, with a simultaneous increase in opportunistic and hospital flora. In sterile sites, a marked increase in the number of isolates was noted, mainly due to K. pneumoniae, Escherichia coli, and A. baumannii. At the same time, a deterioration in antimicrobial resistance profiles was observed, including an increase in carbapenem resistance of A. baumannii, the emergence of colistin–resistant K. pneumoniae, MRSA, and VRE. The obtained data substantiate the need for regular microbiological monitoring, local antimicrobial resistance audits, and revision of empirical antibacterial therapy regimens.