Project/program objectives:

1) Isolation and identification of bacterial isolates of the main foodborne pathogens of the Enterobacteriaceae family (Escherichia coli, Salmonella spp., Shigella spp., Yersinia enterocolitica), Campylobacter spp. and Staphylococcus aureus from biological materials of animals and animal products in the West Kazakhstan, Kostanay, and Akmola regions.

2) Optimization and standardization of the laboratory protocol for determining the genetic factors that cause resistance to antimicrobial drugs in bacterial isolates using the polymerase chain reaction (PCR) method.

3) Determination of the resistance of bacterial isolates to antimicrobial drugs using microbiological methods.

4) Confirmation of genetic factors of resistance to antimicrobial drugs by polymerase chain reaction.

5) Whole-genome sequencing of isolates with broad resistance to antimicrobial drugs and isolates with unidentified genetic factors of resistance.

6) Bioinformatic analysis of whole-genome data to identify factors determining resistance to antimicrobial drugs and virulence factors, and assessment of the genetic diversity of circulating isolates of pathogens causing major foodborne infections.

Results and novelty:

The scientific novelty of the program lies in the fact that, for the first time, comprehensive studies will be conducted on the antimicrobial resistance of the most common foodborne pathogens isolated from farm animals and animal products.  Large-scale studies will be carried out on the isolation and identification of AMR pathogens, as well as the identification of genetic factors of their resistance to antimicrobial drugs using PCR and whole-genome sequencing methods. The results of these studies will make it possible to identify the main factors of antibiotic resistance in bacterial pathogens and to assess the genetic diversity of circulating isolates of foodborne pathogens based on whole-genome data.

The practical significance of the program is confirmed by the fact that the planned studies are aimed at solving the pressing problems outlined in the following strategic and program documents of the Republic of Kazakhstan, which are aimed at ensuring biosafety and combating antimicrobial resistance (AMR) and improving public health.

Scientific impact:

Expanding knowledge about the mechanisms and pathways of resistance gene spread among different hosts, in the environment, and in the food chain. The One Health approach allows antibiotic resistance to be considered in the context of human, animal, and environmental interactions. Obtaining data on resistant genes opens up opportunities for developing new strategies to combat antibiotic-resistant pathogens.

Improving the effectiveness of monitoring and controlling the spread of resistant bacterial strains. These measures will provide a better understanding of how bacteria develop resistance to antibiotics in different environments. The One Health approach integrates data from different sectors.

Economic impact:

Optimizing the use of antibiotics in medical, veterinary, and agricultural practices will reduce the cost of treating infections and preventing their spread. The One Health approach helps coordinate efforts across different sectors, which can improve the economic efficiency of antibiotic use.

Social impact:

Improved protection of human and animal health from infections caused by resistant bacteria. Improved quality of life, reduced morbidity and mortality. The One Health approach promotes interdisciplinary cooperation, which increases society's overall readiness to combat antibiotic resistance. Increased education and awareness of the population about the problems of antibiotic resistance. Introduction of scientific and technical achievements into educational programs, which contributes to the formation of a new generation of specialists capable of effectively combating AMR.

The expected results of the program aimed at studying the resistance of microorganisms and the genetic factors that cause resistance are highly competitive both at the level of the Republic of Kazakhstan and in the global context. The program addresses several key areas that are relevant for the development of effective measures to combat antimicrobial resistance in agriculture and healthcare.

Expected results:

- Genetic approach to studying resistance. Creation of a database of genetic factors determining resistance. The data obtained from this approach is an important step, as polymerase chain reaction (PCR) allows for the accurate identification of genes associated with antimicrobial resistance, which will enable effective tracking and prediction of the spread of resistant strains.

- Whole-genome data and genetic diversity. Using whole-genome data to evaluate circulating isolates and identify resistance and virulence factors provides a deeper understanding of the mechanisms of resistance spread and allows for a more accurate assessment of the threats associated with foodborne infections.

- Formation of reference strain panels. The creation of panels of strains with established antibiotic resistance, as well as panels of DNA samples with known resistance, for interlaboratory comparative testing is of great importance for standardizing diagnostics and improving the quality of interlaboratory studies. This will increase the accuracy and comparability of data.

- Recommendations and preventive measures. The development of methodological recommendations for determining genetic resistance factors using PCR will be an important step in standardizing diagnostics

- Nine (9) articles and/or reviews will be published in peer-reviewed scientific journals in the scientific field of the program, included in the first (1), second (2), and (or) 3 (third) quartile by impact factor in the Web of Science database and (or) having a CiteScore percentile in the Scopus database of at least 50 (fifty),

- 10 (ten) articles in journals recommended by KOKNVO.

Prospective publications for publishing results in scientific journals in the scientific field of the program, included in the 1st (first), 2nd (second) and (or) 3 (third) quartile by impact factor in the Web of Science database and (or) having a CiteScore percentile in the Scopus database of at least 50 (fifty): Microorganism, PlosOne, Frontiers in microbiology, BMC infectious diseases, Antibiotics (CiteScore in the Scopus database -94), Pathogens (CiteScore in the Scopus database -74) and other journals; Scientific journals recommended by KOKNVO: “Ғылым және Білім” and other journals.

- One (1) monograph or textbook will be published by Kazakhstani publishers recommended by the scientific council and/or scientific and technical council of the applicant's organization;

- During the project implementation period (2025–2027), five intellectual property objects (patents) will be obtained, registered with the National Institute of Intellectual Property of the Republic of Kazakhstan.

- Scientific and technical documentation will be developed for a “real-time PCR test for the detection and species identification of C. coli and C. jejuni.”

- A pilot implementation of antibiotic resistance monitoring methods will be carried out in veterinary laboratories in the West Kazakhstan, Kostanay, and Akmola regions.

- Seminars and training sessions will be organized for veterinary service specialists, farmers, and other target users, and the research results will be presented at international conferences to inform the scientific community.

- An electronic database will be created with characteristics of isolates, including whole genome data and resistance data. A reference panel of strains will be developed to standardize laboratory research. New analysis methods will be introduced into laboratory practice in the region.

• List of goods, works and services for the BR28712545 project dated 09.23.2025
• Updated list of goods, works and services for the BR28712545 project dated 11.20.2025