124. Genomic Analysis of Salmonella Enterica Serovar Lubbock from Liver Abscesses: Virulence Potential Assessment and Comparative Analysis with Strains from Lymph Nodes and Feces of Feedlot Cattle.

Abstract

Salmonella Lubbock, a relatively novel serotype, was first isolated from subiliac lymph nodes of beef cattle, collected at slaughter, and subsequently reported to be a frequent isolate from liver abscesses (LA) of feedlot cattle. However, the contribution of S. Lubbock to the development of LA has not been determined. Thus, our objective was to utilize whole genome sequence analysis of S. Lubbock strains isolated from LA of beef cattle (n = 45) to assess virulence potential and comparatively analyze with genome sequences of strains from lymph nodes (n = 42) and feces (n = 81) of feedlot cattle available in NCBI database. Mean genome size of S. Lubbock strains were 4.96 Mbp (LA), 5.02 Mbp (lymph nodes) and 5.02 Mbp (feces). Pan-genome analysis revealed a total of 6,113 genes across all strains, with 4,428 were core genes. Virulence genes analysis revealed that 151 of 173 genes queried were conserved (100 % prevalence) across all strains. The conserved core of virulence genes included Salmonella-associated pathogenicity islands, SPI-1 and SPI-2, type III secretion system apparatus and effectors, fimbrial effectors, complete flagellar assembly genes, two-component regulatory systems (PhoP/Q, PmrA/B) involved in signal transduction and intramacrophage survival, iron acquisition cluster along with type VI secretion system-associated genes. Additionally, among the 22 variable virulence genes, siiE (SPI-4 associated adhesin factor) showed the highest variability, being present in 100 % and 96.3 % of the LA and fecal strains, respectively, followed by a prevalence of 92.7 %) in lymph nodes. Genome-wide association study using pangenome showed that a total of 81 genes were significantly associated with liver abscess strains (P < 0.05) than that of lymph node or fecal strains. The 81 liver-abscess-associated genes included genes functionally enriched in anaerobic metabolism (oadA, adhE and dmsB) and metal efflux system (cusA). Comparative analysis of antimicrobial resistance (AMR) profiles indicated a highly conserved AMR gene repertoire, such as OmpA, marA, mdsC, mdtB, mdtC and AMPH genes across all S. Lubbock strains. Phylogenetic analysis, based on single nucleotide polymorphism differences, of 168 S. Lubbock strains by maximum-likelihood method revealed several distinct clades. Lymph node and fecal strains were intermixed, indicating similar lineages. However, LA strains formed a single cluster distinct from lymph node and fecal strains, indicating presence of a specific lineage colonizing liver abscesses. Our findings indicate that a majority of S. Lubbock strains from LA represented a clonal population distinct from lymph node and fecal strains with a conserved repertoire of virulence and AMR genes across colonization sites.