Molecular-Genetic Characteristics of Polyresistant Listeria monocytogenes Strains and Identification of New Sequence Types

L. monocytogenes is a causative agent of listeriosis with a lethality rate of up to 21%. The goal of this paper is to study the genotypes and phenotypes of 30 L. monocytogenes strains isolated in eight regions of the Russian Federation in 2015-2018 from human beings, food, and wastewater. Susceptibility to antimicrobials for L. monocytogenes strains; serotyping; MLST-typing; whole-genome sequencing; identification of antibiotic resistance genes, virulence genes, and stress-survival-islet genes; and phylogenetic analysis were done. All strains are classified as multidrug-resistant (MDR); resistance genes fosX, pbp-like, lin, norB, and sul were identified; and their allelic profiles were determined. Sixteen L. monocytogenes sequence types (ST) were identified: 4 STs belonging to evolutionary line I and 12 STs to evolutionary line II, including 13 previously known STs (ST1, ST2, ST5, ST7, ST9, ST14, ST16, ST20, ST26, ST121, ST155, ST425, and ST451) and three novel STs (ST1453, ST1455, and ST1454). Five serogroups were revealed: 1-2a-3a, 1/2c-3c, 4b, 4a-4c, and 1/2b-3b-7. An LIPI-1 pathogenicity island (prfA, hly, plcA, plcB, mpl, actA) and LIPI-2 pathogenicity island (inlABCJ) were identified in the genomes of all strains. An LIPI-3 pathogenicity island (llsAXGHBYDP) was identified in two strains of the evolutionary line I. SSI-1 and SSI-2 stress-survival islets were found in nine and one strains, respectively. Allelic profiles of virulence and stress-resistance genes were determined. Phylogenetic analysis revealed a large genetic diversity of the strains. L. monocytogenes MDR strains belonging to widespread and highly virulent sequence types were identified in the study, and three new sequence types were described.