Fire blight of fruit crops is one of the most dangerous diseases for apple trees and other plants of the Rosaceae family, and in Kazakhstan, it is subject to quarantine. To study the spread of fire blight, a phytopathological evaluation of 59 apple varieties of domestic and foreign breeds was carried out in various regions of the south and southeast of Kazakhstan while also considering climatic conditions. The susceptibility of an apple tree to fire blight is influenced by the climatic conditions prevailing in a particular fruit region of Kazakhstan. Samples were collected from various varieties of apple trees with fire blight symptoms for molecular genetic analysis. The phytopathological evaluation and results of the PCR analysis made it possible to identify the causative agent of the disease and its spread to apple varieties in the main fruit regions of Kazakhstan. A molecular study of the resistance to the fire blight pathogen was carried out using the most effective molecular markers. A set of 10 (FBE-1_Y320; FBE-2_Y192; FBE-2_Y495; FBE-2_Y551; FB-MR5-K35; FB-MRS-R240; FB-MR5-R249; FB-MR5-rp16k15_M106; RLP1a; and RLP1b) SNPs was selected, including SNPs reported to be associated with three trait loci, as well as the two markers AE10-375 and GE-8019. Interestingly, the SNP analysis revealed that for all ten markers linked to fire blight resistance, the genotypes of all 59 apple cultivars were identical. No differences in the presence or absence of these markers were observed among the studied varieties. The 26 apple varieties of domestic and foreign breeds most resistant to fire blight were identified in the molecular analysis using the markers AE-375 and GE-8019. Among the studied 59 apple varieties, 23 varieties were identified using the AE-375 marker and 7 varieties with the GE-8019 marker. Samuret, Honeycrisp, Pinova, and Red Topaz were found to be resistant using markers AE-375 and GE-8019. The most promising apple varieties for further breeding for resistance to fire blight programs were selected.

Background/Objectives: Acinetobacter baumannii is an increasingly significant nosocomial pathogen causing severe infections globally. The emergence of multidrug-resistant A. baumannii strains has raised concerns about the efficacy of current treatment options. This study aimed to investigate the molecular epidemiology and antimicrobial resistance patterns of A. baumannii isolates from Kazakhstan. Methods: We collected nine A. baumannii isolates in 2022–2023 in Karaganda, Kazakhstan, which were then subjected to whole-genome sequencing (WGS) using the IonTorrent platform for genome characterization. Multilocus sequence typing (MLST) was used to classify the isolates into distinct clonal complexes. In addition, antibiotic susceptibility testing was conducted using the standard methods for a range of antibiotics commonly used against A. baumannii. Results: Our results revealed a high degree of genomic diversity among isolates from Kazakhstan, with multiple distinct classes identified: ST78 (n = 4, 44.4%), ST15 (n = 2, 22.2%), ST2 (n = 2, 22.2%), and ST193 (n = 1, 11%). MLST analysis showed that ST78^Pas/1104^Oxf (harboring blaOXA-72 and blaOXA-90 genes) were prevalent among the multidrug-resistant isolates. Based on the results of MLST, KL, and OCL, the analyzed isolates were assigned to specific international clones: IC2—ST2(Pas)-KL2/168-OCL1, IC4—ST15(Pas)-KL9-OCL7, and IC6—ST78(Pas)-KL49-OCL1. Notably, these isolates exhibited resistance to multiple antibiotics including meropenem, imipenem, gentamicin, amikacin, and ciprofloxacin. Conclusions: This study highlighted the complex molecular epidemiology of A. baumannii in Kazakhstan over a two-year period, underscoring the need for targeted surveillance strategies to monitor antimicrobial resistance patterns. The emergence and dissemination of multidrug-resistant strains within this timeframe emphasizes the importance of whole-genome sequencing as a diagnostic tool and underscores the challenges posed by these infections.

Background and Aim: Equine influenza (EI) is a highly contagious disease that causes fever and upper respiratory tract inflammation. It is caused by influenza virus A, belonging to the Orthomyxoviridae family, with subtypes H3N8 and H7N7. This study presents data on the development of a real-time polymerase chain reaction (RT-PCR) assay using TaqMan probes to detect the H3 subtype of EI virus (EIV). Materials and Methods: The evaluation of the developed RT-PCR assay involved five strains of EIV as positive controls and ten nasopharyngeal swab samples collected from horses. RNA was isolated using the GeneJet Viral DNA and RNA Purification Kit, and primers and probes were designed using the Integrated DNA Technology PrimerQuest Tool. The assay was optimized by investigating the annealing temperature, primer and probes concentrations, sensitivity, and specificity. Sequencing was performed using the Thermo Fisher 3130 Genetic Analyzer, and the evolutionary history was inferred using the Neighbor-Joining method. Results: The designed primers and probes, targeting the H3 gene, were found to be specific to the EIV. The RT-PCR assay was capable of detecting as low as 50 femtogram (f) or 3 × 103 copies of genomic RNA. No cross-reactions were observed with other respiratory viral and bacterial pathogens, indicating the high specificity of the assay. To evaluate its effectiveness, ten nasopharyngeal swab samples collected from farms in North Kazakhstan regions during disease monitoring were analyzed. The accuracy of the analysis was confirmed by comparing the results with those obtained from a commercial RT-PCR assay for EI identification. The developed RT-PCR assay exhibited high sensitivity and specificity for detecting the EIV. Conclusion: The results demonstrate that the developed RT-PCR assay is suitable for diagnosing EI. This simple, highly sensitive, and specific assay for detecting H3 EIV can be a reliable tool for diagnosing and surveilling EI. Implementing this RT-PCR assay in veterinary practice will enhance and expedite the timely response to potential outbreaks of EI, thus positively impacting the overall epizootic well-being of EI in Kazakhstan. Keywords: equine influenza, hemagglutinin, horses, primers, probe, real-time polymerase chain reaction assay, virus.

Background/Objectives: Staphylococcus aureus, particularly methicillin-resistant strains, is a leading cause of severe pneumonia. Understanding local molecular epidemiology, including virulence gene profiles and antimicrobial resistance (AMR) mechanisms, is crucial for effective infection control. This pilot study aimed to characterize S. aureus isolates from pneumonia patients in Karaganda, Kazakhstan. Methods: We collected 48 respiratory samples from patients with pneumonia across three medical institutions. Bacterial identification was performed using MALDI-TOF MS. Antimicrobial susceptibility testing (AST) was carried out using European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Whole-genome sequencing of S. aureus isolates was conducted on an Ion Torrent S5 platform. Genomic analysis included multilocus sequence typing (MLST), identification of virulence and AMR genes, and phylogenetic reconstruction. Results: S. aureus was identified in 14.6% (n = 7) of pneumonia cases included in this study. All isolates (100%, n = 7) were phenotypically resistant to benzylpenicillin. The mecA gene was detected in 57.1% of isolates (n = 4), while phenotypic resistance to methicillin was observed in 28.6% (n = 2) of the isolates. Resistance to azithromycin (57.1%, n = 4) and levofloxacin (42.9%, n = 3) was observed among the isolates. Two isolates (28.6%) were multidrug-resistant (MDR). Genomic analysis revealed the prevalence of the ST22 clone (57.1%, n = 4) in the studied cohort. Other sequence types were ST97, ST8, and ST45 (14.3% each). Phylogenetic analysis showed clustering consistent with MLST profiles. All isolates carried a conserved core virulence arsenal, including hemolysin (hla, hlg), biofilm-forming genes (icaADBC), immune evasion genes (sak, scn), and iron acquisition genes (isd). The Panton–Valentine leukocidin (PVL) genes were detected in three isolates. AMR gene analysis revealed the ubiquitous presence of mepA and tetracycline efflux pump genes, along with regulatory genes (arlRS, mepR, mgrA). The blaZ and ermA genes were not detected despite high phenotypic resistance to penicillin and macrolides. Conclusions: This study reports the identification of the virulent and resistant ST22 S. aureus clone in pneumonia cases in Karaganda, Kazakhstan. The discordance between phenotypic and genotypic AMR profiles underscores the necessity for integrated diagnostic approaches.

Background and Aim. The collection, transport, and preservation of fecal and intestinal samples from wild animals are critical steps in microbiome research, particularly in studies of the saiga antelope microbiome using 16S rRNA sequencing to investigate complex host microbial interactions The aim of this study was to compare four methods for the transport and preservation of saiga fecal and intestinal samples in order to evaluate their effectiveness in maintaining microbial DNA integrity for subsequent 16S rRNA sequencing. Materials and Methods. The research was conducted in the Bokeyorda State Nature Reserve, located in the West Kazakhstan region of Kazakhstan, with permission from the Ministry of Ecology and Natural Resources of the Republic of Kazakhstan. The animals were captured for study without harm to their health. Biological material in the form of feces from live saigas was collected using a non-invasive method into sterile test tubes. The autopsy of dead saigas was performed in clean field conditions using sterile instruments. All samples were immediately frozen in liquid nitrogen. Additionally, they were cooled to 4 °C, stored at room temperature, and preserved with RNAlater for subsequent analysis. Results. A total of 37 samples were collected from two dead female saigas from different sections of the gastrointestinal tract, as well as fresh fecal samples and rectal swabs obtained from two live females and one male. Upon arrival at the laboratory, all samples were stored at −80 °C until the start of laboratory studies. The study demonstrated that sample storage conditions significantly affect the preservation of the saiga faecal microbiota structure. Samples stored at −80 °C showed the greatest stability in both alpha diversity and taxonomic composition of microbial communities. These findings are particularly relevant for microbiota research and RNA sequencing in remote and inaccessible regions of the saiga habitat. Conclusion. The results suggest that in field conditions where strict cold-chain maintenance is not possible, particularly when sampling from wild and remote saiga populations, the use of liquid nitrogen or RNAlater provides an effective and practical alternative to rapid freezing.

Background and Aim. Whole-genome sequencing is a powerful tool for studying the genetic structure of livestock populations. Effective implementation of WGS is largely determined by the quality of the source genomic DNA. Sheep ear notches obtained in the field are a convenient source of biomaterial; however, their high connective tissue density makes DNA extraction challenging. The aim of this study was to compare the CTAB method and the commercial PureLink Genomic DNA Kit for DNA extraction from ear notches of Kazakh fat-tailed sheep.Materials and Methods. The study was conducted in two stages. CTAB lysis buffer was used in the first stage, and the commercial PureLink Genomic DNA Kit (Thermo Fisher Scientific) was used in the second stage. Quality control was performed using a NanoDrop2000 spectrophotometer and gel electrophoresis.Results. The average DNA concentration isolated by the CTAB method was 293 ng/μl, and the A260/280 ratio ranged from 1.70 to 1.86 (mean 1.78 ± 0.04), indicating heterogeneous purity. The PureLink kit demonstrated consistently high quality: concentration 350.2 ± 96.9 ng/μl, A260/280 1.86± 0.01, and A260/230 2.13 ± 0.08.Conclusion. The commercial PureLink Genomic DNA Kit is recommended for DNA extraction from sheep ear notches, as it provides consistent quantitative and qualitative data that meet WGS requirements.