Population structure of Pseudomonas aeruginosa in the Russian Federation: role of high-risk clones in spread of carbapenemases and carbapenem resistance

Objective. To determine the population structure of clinical P. aeruginosa isolates recovered from hospitals in different regions of Russia and to assess the role of high-risk clones in the dissemination of carbapenemases and carbapenem resistance. Materials and Methods. The study included consecutive, non-duplicate clinical isolates of P. aeruginosa (N = 1379) obtained from 55 hospitals across 30 Russian cities over a 24-month period. Species identification was performed using MALDI-TOF mass-spectrometry. Antimicrobial susceptibility testing was carried out by broth microdilution. The presence of acquired carbapenemase genes (VIM, IMP, NDM, GES-2/-5) was determined by real-time PCR. Subspecies typing and assignment to known sequence types (STs) and clonal complexes (CCs) were performed by identifying single nucleotide polymorphisms (SNPs) in seven chromosomal loci used in the multilocus sequence typing (MLST) scheme. Whole-genome sequencing (WGS) and resistance gene annotation were performed for selected isolates representing the main high-risk clones. Results. All P. aeruginosa isolates were assigned to 264 genetic lineages, among which four clonal complexes corresponding to internationally recognized high-risk clones were predominant: CC235 (13.05%), CC244 (7.11%), CC654 (5.51%), and CC357 (4.21%). Three of these lineages – CC235, CC357, and CC654 – showed significantly higher levels of resistance to most antibiotics, including carbapenems, and were more frequently associated with nosocomial than communityacquired infections. Carbapenemase production was detected in 14.5% of isolates (VIM, 11.02%; GES-5, 2.61%; IMP, 0.44%; NDM, 0.44%), with the majority of carbapenemase-producing strains belonging to CC235 (52.0%) and CC654 (35.0%). WGS data revealed that CC235 isolates collected from different regions of Russia exhibited the greatest diversity of resistance determinants, including carbapenemase genes VIM-2, GES-5, and IMP-1. In contrast, all CC654 isolates carried the VIM-2 metallo-β-lactamase gene and shared similar genotypic and phenotypic resistance profiles to various antibiotic classes. Compared with previous surveillance data from the Russia, a decreasing trend was observed in the proportion of CC235 isolates, including carbapenemase producers, while the prevalence of other high-risk clones within the P. aeruginosa population remained stable. Conclusions. Despite a decline in carbapenemase production frequency and overall carbapenem resistance, the data show that high-risk clones continue to serve as the main reservoirs and drivers of resistance dissemination, underscoring the importance of maintaining systematic molecular surveillance and control of their circulation.