Deciphering the landscape of human pathogenome in non-typhoidal Salmonella through multidimensional genomics

Abstract

Non-typhoidal Salmonella (NTS) is a leading foodborne pathogen causing severe gastrointestinal and systemic infections, posing a significant global health burden. This study employed a genomic approach to investigate the functional and distribution characteristics of human pathogenome in NTS, aiming to provide molecular targets and a theoretical foundation for novel anti-salmonellosis strategies. Analysis of eight NTS strains revealed 2,000 virulence genes encoding 263 factors, predominantly effector delivery systems (41%), of which type III secretion system (T3SS) genes constituted the majority (66.3%). A total of 217 partial sequences from 13 salmonella pathogenicity islands (SPIs) were identified, with SPI-2 (26.7%), SPI-1 (24%), and SPI-13 (10.6%) being most prevalent. Key virulence genes in SPI-1 (35 T3SS1-related genes), SPI-2 (30 T3SS2-related genes), and SPI-5 ( sopB/sigD , pipB ) were conserved across all strains. We identified 7,868 human pathogenicity-related genes, functionally enriched in metabolic/cellular processes, catalytic activity, and binding. Human pathogenicity-related virulence genes were mainly classified as delivery systems, adhesion factors, and nutrient metabolism factors. Enzymatic analysis showed human pathogenicity-related protease genes were primarily serine, cysteine, and metallopeptidases, while human pathogenicity-related carbohydrase-active genes were associated with glycoside hydrolases, glycosyltransferases, and carbohydrate esterases. Functional annotation with the Kyoto Encyclopedia of Genes and Genomes indicated human pathogenicity-related protease genes enrichment in signaling, cellular, metabolic, and genetic information processing pathways, particularly in antibiotic resistance and infectious diseases, while human pathogenicity-related carbohydrase-active genes were enriched in carbohydrate metabolism and glycan biosynthesis. A structurally conserved, metal-chelating non-ribosomal peptide metallophore (NRP-metallophore) gene cluster was present in all strains, containing biosynthetic virulence genes ( entA , entC , entF , entB , entE , fes ) and transport-related virulence genes ( fep family, entS ). Functional type I-E clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems with variable numbers of CRISPR arrays but conserved direct repeats were identified in most strains. NTS strains carried conserved T3SS effectors, human pathogenicity-related factors enriched in metabolism, catalysis, antibiotic resistance, and infection pathways, a conserved NRP-metallophore gene cluster for iron acquisition, and a functional type I-E CRISPR-Cas system, collectively defining key genetic determinants for pathogenesis.