Detection and Preliminary Genomic Characterization of Poultry-Derived Salmonella enterica from Southern Kazakhstan

<b>Background/Objectives</b>: <i>Salmonella enterica</i> is a major cause of foodborne infection globally, with poultry acting as an important reservoir. However, data from Central Asia remain limited. This study provides preliminary phenotypic and genomic characterization of <i>S. enterica</i> isolates recovered from poultry farms in southern Kazakhstan, focusing on antimicrobial resistance (AMR), serotypes/sequence types and phylogenetic relationships. <b>Methods</b>: In October 2024, 335 poultry and environmental samples were collected from three regions of southern Kazakhstan using a cross-sectional, detection-focused sampling strategy. Isolation of <i>Salmonella enterica</i> followed enrichment and selective culturing, with confirmation by biochemical assays, slide agglutination serology and real-time PCR. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method and interpreted according to CLSI veterinary breakpoints (VET01/VET08) and CLSI M100 where veterinary criteria were unavailable. Whole-genome sequencing (Illumina) was used for in silico serotyping, MLST, AMR gene detection, plasmid replicon typing and SNP-based phylogenetic reconstruction. <b>Results</b>: Nine <i>S. enterica</i> isolates were confirmed (overall yield 2.7%; 9/335), comprising <i>S.</i> Enteritidis (ST11; <i>n</i> = 4), <i>S.</i> Infantis (ST32; <i>n</i> = 3) and ST68 <i>(n</i> = 2; Choleraesuis/Paratyphi C lineage). All isolates were resistant to ciprofloxacin, and most displayed resistance to ampicillin, gentamicin and trimethoprim-sulfamethoxazole. Plasmid-associated AMR determinants, including <i>blaTEM-116</i>, <i>tet(A)</i>, <i>sul1</i> and <i>dfrA14</i>, were frequently identified on IncF-type replicons. Phylogenetic analysis revealed that the isolates clustered with previously described Eurasian poultry-associated lineages. <b>Conclusions</b>: In this small, exploratory sample from poultry farms in southern Kazakhstan, all recovered <i>S. enterica</i> isolates were multidrug-resistant, with universal fluoroquinolone resistance and frequent plasmid-borne AMR genes. These preliminary findings provide baseline genomic evidence and highlight the need for broader, harmonized AMR surveillance in the regional poultry sector.