Whole genome sequencing reveals circulation of potentially virulent Listeria innocua strains with novel genomic features in cattle farm environments in Dhaka, Bangladesh

Through the last decade, Listeria spp. has been detected in food and environmental samples in Bangladesh. However, the genomic information of this bacterium that prevails in the country remains scarce. This study analyzed the complete genome sequences of two Listeria spp. isolates obtained from cow dung and their drinking water collected from a cattle farm in Dhaka, Bangladesh. Both the isolates were identified as Listeria innocua, which shared almost identical genomic features. The genome sequences demonstrated the presence of 13 virulence genes associated with invasion (iap/cwhA, gtcA, and lpeA), surface protein anchoring (lspA), adherence (fbpA, and lap), intracellular survival (lplA1, and prsA2), peptidoglycan modification (oatA, and pdgA), and heat stress (clpC, clpE, and clpP). Additionally, the gene fosX, conferring resistance to fosfomycin, and two copper resistance-associated genes, copC and csoR, were identified in both. The genome sequences also revealed two plasmid replicons, rep25 and rep32, along with three insertion sequences [ISLmo3 (CP022021), ISLmo7 (CP006611), ISS1N (M37395)]. Notably, a composite transposon [CN_8789_ISS1N (M37395)], was detected in both L. innocua isolates, representing the first documented occurrence of this particular composite transposon in any reported Listeria species. Furthermore, the genomes contained four prophage regions [Listeria phage LP-030-2 (NC_021539), Listeria phage vB_LmoS_188 (NC_028871), Listeria phage A118 (NC_003216) and Escherichia phage RCS47 (NC_042128)]. Two CRISPR arrays were also identified, one belonging to the family type II-A. Multilocus Sequence Typing (MLST) analysis classified the L. innocua isolates of the same sequence type, ST-637. Single nucleotide polymorphism (SNP) analysis uncovered the presence of 231-340 SNPs between the L. innocua isolates and their closely related global lineage. In contrast, only 42 SNPs were identified between the two isolates, suggesting a potential transmission of L. innocua between cow dung and cattle farm water. The presence of L. innocua isolates harboring virulence genes associated with ruminant infection in the cattle farm environment of Bangladesh raises significant concerns about the potential presence of other human and animal pathogens. This poses a serious threat to the cattle farming industry. Additionally, the genomic analysis of the L. innocua isolates enhances our understanding of the evolutionary dynamics of Listeria species.