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.

Outbreaks of hemorrhagic septicemia (HS) caused by Pasteurella multocida serogroup B are endemic in Kazakhstan. These outbreaks have repeatedly led to mass mortality events among wild saigas and economic losses to farms. The aim of this study was to conduct the first whole-genome sequencing (WGS) and analysis of P. multocida genomes associated with HS cases in saigas and livestock in Kazakhstan. In this study, WGS was performed on 22 P. multocida isolates obtained from saigas and livestock. A comparative genomic analysis of P. multocida isolates from Kazakhstan and publicly available genomes was performed. All isolates belonged to the B:2:ST122 genotype and formed distinct phylogenetic clusters based on outbreaks in saiga populations and livestock. Clustering also corresponded to identified mutations in virulence genes. Isolates recovered from the 2015 mass mortality of saigas in the Betpak-Dala population were found to have a deletion of the flp1 gene. This observation emphasizes the study of the role of Flp pili in HS pathogenesis. Comparison of the P. multocida B:L2:ST122 genomes revealed low virulence gene diversity and an open pangenome. Prophage annotation did not identify virulence or pathogenicity genes. The obtained results will be useful for future studies of HS pathogenesis.

Bovine babesiosis is a tick-borne disease of major veterinary and economic importance, yet molecular epidemiological data from Kazakhstan remain limited. This study investigated the prevalence, distribution, and species composition of Babesia spp. in cattle across all 17 administrative regions of Kazakhstan. A total of 6455 cattle blood samples from 171 villages were screened by nested PCR targeting the cytochrome b (cytb) gene, and positive samples were characterized by sequencing and phylogenetic analysis. The overall positive rate for Babesia spp. were 3.87% (95% CI: 3.41–4.37%). Of 250 PCR-positive samples, 215 yielded high-quality sequences and were assigned to four species: Babesia major (31.2%), B. occultans (29.6%), B. bigemina (18.0%), and B. bovis (7.2%). Marked regional heterogeneity was observed, with B. major and B. occultans predominating across most regions, whereas B. bigemina was dominant in Atyrau. Turkistan was the only region where all four species co-circulated. First molecular evidence of B. bovis and B. bigemina was obtained for Atyrau, Akmola, and West Kazakhstan regions. These findings expand current knowledge of bovine babesiosis in Kazakhstan and reveal a species composition dominated by B. major and B. occultans, contrasting with the B. bovis/B. bigemina-dominated patterns commonly reported elsewhere. The detection of pathogenic Babesia species in previously unsurveyed regions highlights the need for continued molecular surveillance.

Enteroviral infection is a common cause of aseptic meningitis, herpangina, and hand, foot, and mouth disease in children. Limited data are available on the enteroviral subtypes associated with hospitalization for these conditions in Kazakhstan. We collected cerebrospinal fluid (CSF) and nasopharyngeal swabs (NSW) from children (N=152, median age=8 years) hospitalized with symptoms of aseptic meningitis (AM, N=139) or herpangina (HA, N=13) disease. We then genotyped enteroviral subtypes associated with AM (n=50) and HA (n=9) using next-generation sequencing (NGS) on the viral protein 1 (VP1), followed up by whole-genome sequencing of the isolated viral species. All identified EVs were species B EV, consisting of five echovirus (E6, E9, E11, E21 and E25) and three coxsackievirus (CVA9, CVB3 and CVB5) serotypes within the cohort. The most abundant EVs were CVA9 (38.5%), CVB5 (21.5%) and E6 (13.8%). Most HA samples (6/9) were genotyped with coxsackievirus CVA9, while AM was associated with a variety of both echovirus and coxsackievirus serotypes. The results suggest that coxsackievirus CVA9 may be the dominant serotype circulating in the HA population, while AM is more diverse in terms of circulating echovirus and coxsackievirus serotypes. Further studies are needed to determine the clinical implications of these findings and to investigate potential differences in disease severity or outcomes associated with different EV serotypes.

Background/Objectives: Bovine mastitis is a common infection in cattle causing significant economic losses globally in the dairy industry. While bacterial profiles and antimicrobial resistance (AMR) patterns are generally consistent worldwide, comprehensive epidemiological and AMR data from Kazakhstan are lacking. This study characterized mastitis-associated bacterial isolates and their AMR profiles from a single commercial Simmental dairy herd in the Akmola Region, Kazakhstan. Milk samples from 41 cows with clinical mastitis and documented treatment histories were collected. Methods: Bacterial identification was performed using MALDI-TOF MS, and antimicrobial susceptibility was tested phenotypically following EUCAST criteria. Whole genome sequencing (WGS) on a subset of isolates analyzed resistance and plasmid content using AMRFinderPlus v3.11.14 and Abricate v1.4.0, with the ResFinder and PlasmidFinder databases, respectively. Results: All samples yielded bacterial growth, resulting in 58 isolates across 11 species and five genera, from which Staphylococci predominated (50.0%), followed by Streptococci (28.0%), Escherichia coli (19%), one Aerococcus (1.72%) and one Corynebacterium (1.72%) strain. Phenotypic resistance to at least one antimicrobial class was found in 65.5% of tested isolates. Tetracycline resistance was the most frequent (71.7% of tested isolates), with multidrug resistance detected in 6.9%. WGS of a randomly selected subset of 33 isolates revealed that 27 (82%) carried at least one acquired AMR gene, predominantly tetracycline resistance genes (26/33), followed by lincosamide/macrolide (12 and 11 isolates) and aminoglycoside resistance genes (9 isolates). Plasmid replicon screening identified plasmid replicons in 21 of the 33 sequenced isolates, mainly of the repUS43 and repUS76 staphylococcal replicon families, suggesting a potential role of plasmids in AMR gene dissemination within the herd. Conclusions: This study offers a comprehensive phenotypic and genomic characterization of mastitis-associated pathogens and their AMR determinants within this single herd, highlighting the co-circulation of tetracycline, lincosamide/macrolide, and aminoglycoside resistance genes. As this study was limited to a single dairy herd, these findings should be regarded as descriptive, farm-level observations rather than being representative of the Akmola Region or Kazakhstan more broadly. These findings support farm-level mastitis surveillance that combines species identification, phenotypic AMR testing, and targeted molecular screening.

Mammalian tuberculosis (TB) in cattle, caused mostly by Mycobacterium bovis, has a significant impact on veterinary public health, animal welfare, trade, and farming economies. Diagnosis and laboratory confirmation are crucial for disease surveillance and effective control strategies in animals. The relatively low sensitivity of current ante- and postmortem tests for TB often leads to undetected infections in animals. In the absence of a “gold standard”, bacteriological culture of M. bovis is considered the reference standard for confirmation, but it has a long turnaround time and relatively low sensitivity. In reference laboratories there has been a move towards the more rapid turnaround PCR-based testing, with equivalent sensitivity to culture. Although current molecular diagnostic techniques are based on the detection of M. bovis DNA, 16S rRNA offers detection with high sensitivity while also serving as a marker of bacterial viability. In this pilot study, we evaluated the ability of the mycobacterial load assay (MBLA), a PCR-based method quantifying viable Mycobacterium tuberculosis complex organisms, to rapidly detect M. bovis 16S rRNA directly from culture-positive bovine tissue samples. We assessed the efficacy of MBLA to detect M. bovis in comparison to the reference method, bacteriological culture. We also evaluated the association of MBLA-determined bacterial load to tissue weight, presence or absence of visible lesions, lesion scores, and M. bovis molecular types. MBLA detected M. bovis in 89.7% of culture positive tissue samples. Quantification was possible in 72.9% of positive samples, with bacterial loads ranging from 3.11x102 CFU/g to 1.09x106 CFU/g. No significant associations were found between bacterial load and tissue weight, lesion status, lesion scores, or molecular types. This study is the first to utilize MBLA to detect and quantify M. bovis 16S rRNA bacterial loads directly from infected bovine tissues. MBLA demonstrated promising potential for rapid, robust and reliable quantitative detection of M. bovis in infected bovine tissues. Further research is needed to evaluate its applicability to detect M. bovis in other cattle sample types, environmental samples and tissues from other host species.