Pangenome and Comparative Genomics Analyses Reveal Patterns of Quorum Sensing and Antimicrobial Resistance in Salmonella Lineages from African Food Chains

Abstract

Salmonella enterica is a major public health concern in Africa because of its increasing antimicrobial resistance (AMR) to multiple antibiotics that threatens effective treatment and control. In this study, we analyzed 135 publicly available AMR Salmonella genomes from African food sources. Using a pangenome analysis approach, we identified 15,269 genes, including a core genome of ∼3.5 Mbp with 3350 core genes (99–100% prevalence) and a substantial accessory genome comprising 183 soft-core, 1441 shell, and 10,295 cloud genes. We found substantial genomic diversity among the AMR-positive S. enterica isolates. AMR profiling revealed widespread distribution of resistance genes, with aac(6′)-laa_1 present in nearly all genomes, and tet(A), sul2, and fosA71 frequently co-occurring. Core virulence genes such as invA, ssaL, and steA were nearly universally conserved, suggesting essential roles in pathogenesis. Sporadic rare virulence genes such as papE, tcpC, and ybtP were present in the genome, pointing to lineage-specific patterns. The presence of macrolide inactivation genes (ereA) points to a huge risk of resistance to the globally important antibiotic azithromycin. Quorum-sensing genes, including the AI-2 system (luxS, lsrA-D, lsrK), and biofilm formation genes were widely conserved across the isolates, highlighting their potential role in adaptation and the spread of antimicrobial resistance in foodborne Salmonella in Africa. Hierarchical clustering based on core genome multilocus sequence typing (cgMLST) revealed monophyletic clades for major serovars such as Enteritidis and Infantis. Shannon diversity indices revealed geographical variation in AMR gene richness, with Burkina Faso, South Africa, and Tunisia showing high intracountry diversity. Our analysis identified lineage-associated accessory genes, hence providing potential markers for surveillance. This study offers valuable insights into the genomic architecture and AMR landscape of Salmonella in Africa and underscores the need for expanded genomic surveillance across diverse geographic and food production contexts.