| Summary: | <i>Elizabethkingia anophelis</i> is an emerging multidrug-resistant pathogen that causes severe nosocomial and community-acquired infections worldwide. We report the first case of <i>E. anophelis</i> isolation in Russia and the first isolation from raw cow’s milk. The ML-44 demonstrated resistance to 28 antimicrobials of 33 tested in the disk-diffusion test. Whole genome-based phylogeny showed ML-44 strain clustered together with the F3201 strain isolated from a human patient in Kuwait in 1982. Both strains were a part of the “<i>endophytica</i>” clade. Another clade was formed by subsp. <i>anophelis</i> strains. Each of the <i>E. anophelis</i> compared genomes carried 18 to 21 antibiotic resistance determinants. The ML-44 chromosome harbored nine efflux system genes and three beta-lactamase genes, along with six other antimicrobial resistance genes. In total, 72 virulence genes were revealed. The set of virulence factors was quite similar between different <i>E. anophelis</i> strains and included LPS and capsule encoded genes, type IV pili, oxidative stress response genes, and genes encoding TIVSS and TVISS effectors. The particular interest caused the <i>mip</i> and <i>zmp</i>1 gene homologs, which can be essential for intracellular survival. In sum, our findings suggest that raw milk might be a source of <i>E. anophelis</i> harboring a set of virulence factors and a broad resistance to generally used antimicrobials.
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