Clonal and Plasmid-Mediated Dissemination of Multidrug-Resistant Salmonella Enteritidis in Chicken Production, Northeastern Thailand

Background: The global dissemination of multidrug-resistant (MDR) Salmonella poses a persistent and serious threat to food safety systems. As a leading poultry-exporting country, Thailand requires a comprehensive understanding of how resistance plasmids spread among Salmonella populations within its chicken production chain. Methods: Between March 2023 and February 2024, 223 Salmonella isolates were collected from chicken slaughterhouses and markets in northeastern Thailand. From these, 19 representative MDR Salmonella enterica isolates, selected based on distinct spatiotemporal distributions, underwent whole-genome sequencing. Genomic analyses included sequence typing, core-genome phylogenetics, and screening for antimicrobial resistance genes. Plasmid replicons were identified, and functional annotation was performed using the COG database. Results: Phylogenetic analysis revealed 11 distinct sequence types within the population. Among these, ST1541 and ST50 showed clear evidence of clonal transmission across different production stages, with a notable clustering pattern observed during the winter season. All sequenced isolates exhibited an MDR phenotype. Plasmids were detected in 78.9% of isolates, with conjugative plasmids being the most frequent type (57.9%). The β-lactamase gene blaTEM-60 was the most prevalent (78.9%) and showed a strong correlation (r ≥ 0.7) with resistance to both ampicillin and cefotaxime. Functional annotation further revealed an abundance of genes involved in carbohydrate and amino acid metabolism across all isolates. Conclusions: These findings indicate that MDR Salmonella dissemination is driven by two synergistic mechanisms: the clonal expansion of fit lineages and the horizontal transfer of conjugative plasmids harboring β-lactamase genes. We identified IncI-gamma-K1 and Col-related plasmids as key vectors in this process. This study advocates for targeted interventions, guided by a One Health approach, that specifically aim to disrupt plasmid transmission at critical control points, such as slaughterhouses, to curb the spread of antimicrobial resistance.