Molecular and genetic monitoring of clinical isolates of K. pneumoniae ST395 in the Russian Federation based on whole-genome sequencing data

Relevance. Globally disseminated genetic lineages of Klebsiella pneumoniae characterized by the presence and rapid acquisition of multiple antimicrobial resistance determinants and virulence factors are known as epidemic clones or clonal groups of high risk. At present, sequence type ST395 represents the predominant epidemic clone of K. pneumoniae circulating in the Russian Federation.

Aims. To investigate the genetic diversity of K. pneumoniae strains isolated in hospitals from different regions of the Russian Federation using whole-genome sequencing data, with particular emphasis on the dominant epidemic clone ST395.

Materials and Methods. Whole-genome sequencing data from 162 clinical K. pneumoniae isolates collected in six medical institutions located in Moscow, Barnaul, and Orenburg were analyzed.

Results. Among the 162 isolates examined, the most prevalent genetic lineage was ST395 (62/162; 38 %), which was detected in all participating hospitals. All analyzed K. pneumoniae isolates harbored a broad repertoire of genomic resistance determinants to at least nine classes of antibacterial agents, including aminoglycosides, beta-lactams (including carbapenems), phenicols, trimethoprim, fosfomycin, macrolides, fluoroquinolones, sulfonamides, and tetracyclines. A substantial proportion of ST395 isolates (77.7 %, 49/63) carried combinations of three or more distinct betalactamase genes, and the most interesting fact was the co-occurrence of blaNDM with blaCTX and blaTEM. Phylogenetic analysis demonstrated the formation of several clusters comprising isolates from different medical institutions. Isolates from one hospital in Moscow and one isolate from Barnaul were assigned to the same epidemic clone.

Conclusion. Genomically closely related, and in some cases apparently identical, strains were identified in geographically distant medical institutions. These findings underscore the importance of assigning isolates to epidemic clones, as such classification enables a more accurate assessment of their epidemic potential.

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