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

Bolat Yespembetov, Zhumagul Kirkimbaeva, Akbope A. Abdykalyk, Assel Akhmetova, Alexandr Shevtsov, Nazym Syrymkyzy Syrym, Sabira E. Alpysbayeva, Makhpal K. Sarmykova, Azamat R. Abdimukhtar, Aktoty M. Anarbekova

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Bekzat Yerzhigit, Andrey Shestakov, Nurlan Kozhabergenov, Bekbolat S. Usserbayev, Yerbol A. Bulatov, Alinur T. Toleukhan

Antibiotics, 2025

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DOI 10.3390/antibiotics14121195
Data confidence 85 high
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Abstract

Background/Objectives: Salmonella enterica 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 S. enterica isolates recovered from poultry farms in southern Kazakhstan, focusing on antimicrobial resistance (AMR), serotypes/sequence types and phylogenetic relationships. Methods: 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 Salmonella enterica 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. Results: Nine S. enterica isolates were confirmed (overall yield 2.7%; 9/335), comprising S. Enteritidis (ST11; n = 4), S. Infantis (ST32; n = 3) and ST68 (n = 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 blaTEM-116, tet(A), sul1 and dfrA14, were frequently identified on IncF-type replicons. Phylogenetic analysis revealed that the isolates clustered with previously described Eurasian poultry-associated lineages. Conclusions: In this small, exploratory sample from poultry farms in southern Kazakhstan, all recovered S. enterica 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.