{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T09:07:06Z","timestamp":1789376826040,"version":"build-2803163510"},"reference-count":39,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T00:00:00Z","timestamp":1789171200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Science and Higher Education of the Republic of Kazakhstan","award":["BR28712545"],"award-info":[{"award-number":["BR28712545"]}]},{"award":["BR28712545"],"award-info":[{"award-number":["BR28712545"]}],"id":[{"id":"https:\/\/ror.org\/05tyne317","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>Data on the prevalence of bacteria and antimicrobial resistance (AMR) among food-producing animals in Kazakhstan remain limited in scope. As part of this regional cross-sectional descriptive study, specific bacterial taxa and AMR were characterized in farm animals in the West Kazakhstan Region. Between September 2025 and July 2026, samples were collected from 974 individual animals at 48 farms located in 12 administrative districts. Targeted bacteriological isolation was performed for Escherichia coli, presumptive Shigella spp., Salmonella spp., Yersinia enterocolitica, Campylobacter spp., and Staphylococcus aureus, followed by specific real-time PCR. Antimicrobial susceptibility was assessed in 214 E. coli isolates using the EUCAST disk diffusion method, and five selected isolates underwent exploratory screening by quantitative PCR (qPCR) for the presence of determinants associated with antimicrobial resistance. A total of 311 bacterial isolates were identified. The predominant taxon was E. coli, detected in 22.0% of the animals from which samples were collected and accounting for 68.8% of the isolates; followed by S. aureus (3.2% of animals), presumptive Shigella spp. (2.9%), Salmonella spp. (1.5%), Campylobacter spp. (1.5%), and Y. enterocolitica (0.8%). Corresponding molecular targets were detected in 303 of 311 presumptively identified isolates (97.4%). No clear age-related gradient in the prevalence of E. coli was observed, and this taxon was detected in all three study areas. Phenotypic resistance to at least one antimicrobial agent with an applicable clinical breakpoint according to EUCAST was detected in 2 of 214 E. coli isolates (0.9%), including resistance to ceftriaxone or amoxicillin with clavulanic acid. Molecular screening of five selected isolates revealed various determinants associated with antimicrobial resistance and mobile genetic elements, with blaCMY, mphA, qepA_1_2, catA1, and intI1F165_clinical being the most frequently detected. These results establish a regional baseline for comprehensive monitoring of bacteria associated with animal husbandry and antimicrobial resistance in Western Kazakhstan.<\/jats:p>","DOI":"10.3390\/biology15181612","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T08:10:23Z","timestamp":1789373423000},"page":"1612","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Prevalence, Identification, and Antimicrobial Resistance of Bacterial Pathogens in Farm Animals from Western Kazakhstan"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7557-5894","authenticated-orcid":false,"given":"Laura","family":"Dushayeva","sequence":"first","affiliation":[{"name":"Veterinary and Agro Technology Institute, Noncommercial Joint Stock Company \u201cZhangir Khan West Kazakhstan Agrarian-Technical University\u201d, 51 Zhangir Khan St., Uralsk 090009, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Askar","family":"Nametov","sequence":"additional","affiliation":[{"name":"Veterinary and Agro Technology Institute, Noncommercial Joint Stock Company \u201cZhangir Khan West Kazakhstan Agrarian-Technical University\u201d, 51 Zhangir Khan St., Uralsk 090009, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Aiman","family":"Ichshanova","sequence":"additional","affiliation":[{"name":"Veterinary and Agro Technology Institute, Noncommercial Joint Stock Company \u201cZhangir Khan West Kazakhstan Agrarian-Technical University\u201d, 51 Zhangir Khan St., Uralsk 090009, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2565-3107","authenticated-orcid":false,"given":"Rashid","family":"Karmaliyev","sequence":"additional","affiliation":[{"name":"Veterinary and Agro Technology Institute, Noncommercial Joint Stock Company \u201cZhangir Khan West Kazakhstan Agrarian-Technical University\u201d, 51 Zhangir Khan St., Uralsk 090009, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Raushan","family":"Rychshanova","sequence":"additional","affiliation":[{"name":"Research Institute of Innovative Technologies, Noncommercial Joint Stock Company \u201cAkhmet Baitursynuly Kostanay Regional University\u201d, 47 A. Baitursynov St., Building 1, Kostanay 110000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0307-1053","authenticated-orcid":false,"given":"Alexandr","family":"Shevtsov","sequence":"additional","affiliation":[{"name":"Laboratory of Applied Genetics, National Center for Biotechnology LLP, 13\/5 Korgalzhyn Avenue, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Kenzhebek","family":"Murzabayev","sequence":"additional","affiliation":[{"name":"Veterinary and Agro Technology Institute, Noncommercial Joint Stock Company \u201cZhangir Khan West Kazakhstan Agrarian-Technical University\u201d, 51 Zhangir Khan St., Uralsk 090009, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Dosmukan","family":"Gabdullin","sequence":"additional","affiliation":[{"name":"Veterinary and Agro Technology Institute, Noncommercial Joint Stock Company \u201cZhangir Khan West Kazakhstan Agrarian-Technical University\u201d, 51 Zhangir Khan St., Uralsk 090009, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Adilbay","family":"Karagulov","sequence":"additional","affiliation":[{"name":"Veterinary and Agro Technology Institute, Noncommercial Joint Stock Company \u201cZhangir Khan West Kazakhstan Agrarian-Technical University\u201d, 51 Zhangir Khan St., Uralsk 090009, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Balaussa","family":"Yertleuova","sequence":"additional","affiliation":[{"name":"Veterinary and Agro Technology Institute, Noncommercial Joint Stock Company \u201cZhangir Khan West Kazakhstan Agrarian-Technical University\u201d, 51 Zhangir Khan St., Uralsk 090009, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Ainur","family":"Tolegen","sequence":"additional","affiliation":[{"name":"Veterinary and Agro Technology Institute, Noncommercial Joint Stock Company \u201cZhangir Khan West Kazakhstan Agrarian-Technical University\u201d, 51 Zhangir Khan St., Uralsk 090009, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,12]]},"reference":[{"key":"ref_1","first-page":"743","article-title":"Antimicrobial resistance: One Health approach","volume":"15","year":"2022","journal-title":"Vet. World"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Al-Khalaifah, H., Rahman, M.H., Al-Surrayai, T., Al-Dhumair, A., and Al-Hasan, M. (2025). A One-Health Perspective on Antimicrobial Resistance (AMR): Human, Animal, and Environmental Health. Life, 15.","DOI":"10.3390\/life15101598"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"100748","DOI":"10.1016\/j.onehlt.2024.100748","article-title":"The Impacts of Animal Agriculture on One Health\u2014Bacterial Zoonoses, Antimicrobial Resistance, and Beyond","volume":"18","author":"Zhang","year":"2024","journal-title":"One Health"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Dantas Palmeira, J., and Ferreira, H.M.N. (2020). Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in cattle production\u2014A threat around the world. Heliyon, 6.","DOI":"10.1016\/j.heliyon.2020.e03206"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Zhang, H., Zhao, M., Hu, S., Ma, K., Li, J., Zhao, J., Wei, X., Tong, L., and Li, S. (2023). Establishment of a Real-Time Recombinase Polymerase Amplification Assay for Rapid Detection of Pathogenic Yersinia enterocolitica. Pathogens, 12.","DOI":"10.3390\/pathogens12020226"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Olvera-Ram\u00edrez, A.M., McEwan, N.R., Stanley, K., Nava-Diaz, R., and Aguilar-Tipacam\u00fa, G. (2023). A Systematic Review on the Role of Wildlife as Carriers and Spreaders of Campylobacter spp.. Animals, 13.","DOI":"10.3390\/ani13081334"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Sun, S., and Zhang, X. (2023). Genetic characteristics and integration specificity of Salmonella enterica temperate phages. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1199843"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Li, Y., Shi, Z., Hu, A., Cui, J., Yang, K., Liu, Y., Deng, G., Zhu, C., and Zhu, L. (2022). Rapid One-Tube RPA-CRISPR\/Cas12 Detection Platform for Methicillin-Resistant Staphylococcus aureus. Diagnostics, 12.","DOI":"10.3390\/diagnostics12040829"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Zhang, S., Bai, Z., Wang, Z., Wang, X., Wang, W., Li, H., and Dong, Q. (2022). Molecular characterization and phylogeny of Shiga toxin-producing Escherichia coli derived from a cattle farm. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.950065"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Silva, A., Silva, V., Pereira, J.E., Maltez, L., Igrejas, G., Valent\u00e3o, P., Falco, V., and Poeta, P. (2023). Antimicrobial resistance and clonal lineages of Escherichia coli in meat-producing animals. Antibiotics, 12.","DOI":"10.3390\/antibiotics12061061"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"161","DOI":"10.14202\/IJOH.2024.161-171","article-title":"Antimicrobial resistance at the \u201chuman\u2013animal\u2013environment\u201d interface: A focus on the dynamics of transmission of antimicrobial-resistant Escherichia coli strains, clinical implications, and future directions","volume":"10","author":"Fatokun","year":"2024","journal-title":"Int. J. One Health"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Abo-Almagd, E.E., Sabala, R.F., Abd-Elghany, S.M., Jackson, C.R., Ramadan, H., Imre, K., Morar, A., Herman, V., and Sallam, K.I. (2023). \u03b2-Lactamase Producing Escherichia coli Encoding blaCTX-M and blaCMY Genes in Chicken Carcasses from Egypt. Foods, 12.","DOI":"10.3390\/foods12030598"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Mei, C.Y., Jiang, Y., Ma, Q.C., Lu, M.J., Wu, H., Wang, Z.Y., Jiao, X., and Wang, J. (2024). Low prevalence of mcr-1 in Escherichia coli from food-producing animals and food products in China. BMC Vet. Res., 20.","DOI":"10.1186\/s12917-024-03891-6"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Garcias, B., Flores, M.A., Fern\u00e1ndez, M., Monteith, W., Pascoe, B., Sheppard, S.K., Mart\u00edn, M., Cortey, M., and Darwich, L. (2024). Global Variation in Escherichia coli mcr-1 Genes and Plasmids from Animal and Human Genomes Following Colistin Usage Restrictions in Livestock. Antibiotics, 13.","DOI":"10.3390\/antibiotics13080759"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Jiang, H., Ran, M., Wang, X., Chen, Q., Wang, J., Ruan, Z., Wang, J., Tang, B., and Fang, J. (2025). Prevalence and characterization of class I integrons in multidrug-resistant Escherichia coli isolates from humans and food-producing animals in Zhejiang Province, China. BMC Microbiol., 25.","DOI":"10.1186\/s12866-025-03794-y"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Lencina, F.A., Bertona, M., Stegmayer, M.A., Olivero, C.R., Frizzo, L.S., Zimmermann, J.A., Signorini, M.L., Soto, L.P., and Zbrun, M.V. (2024). Prevalence of colistin-resistant Escherichia coli strains in food products and in animals used for food production throughout the food chain: A global systematic review and meta-analysis. Heliyon, 10.","DOI":"10.1016\/j.heliyon.2024.e26579"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Wang, C., Fang, W., Chang, J., Jiang, Z., Han, Y., Wang, M., Jing, B., Zhao, A., and Yin, X. (2024). Development and application of a one-step multiplex real-time PCR assay for the detection of three major pathogens associated with bovine neonatal diarrhea. Front. Cell. Infect. Microbiol., 14.","DOI":"10.3389\/fcimb.2024.1367385"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Huang, Y., Gu, D., Xue, H., Yu, J., Tang, Y., Huang, J., Zhang, Y., and Jiao, X. (2021). Rapid and Accurate Campylobacter jejuni Detection Using CRISPR-Cas12b Based on Newly Identified Campylobacter jejuni-Specific and -Conserved Genomic Signatures. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.649010"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Xiao, Y., Ren, H., Hu, P., Wang, Y., Wang, H., Li, Y., Feng, K., Wang, C., Cao, Q., and Guo, Y. (2022). Ultra-Sensitive and Rapid Detection of Pathogenic Yersinia enterocolitica Based on the CRISPR\/Cas12a Nucleic Acid Identification Platform. Foods, 11.","DOI":"10.3390\/foods11142160"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Oon, Y.-L., Oon, Y.-S., Ayaz, M., Deng, M., Li, L., and Song, K. (2023). Waterborne pathogens detection technologies: Advances, challenges, and future perspectives. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1286923"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Alekseyuk, P.G., Bogoyavlensky, A.P., Moldakhanov, Y.S., Akanova, K.S., Manakbaeva, A.N., Kerimov, T., Berezin, V.E., and Alekseuk, M.S. (2025). Genomic and antimicrobial resistance profiles of multidrug-resistant Escherichia coli strains isolated from cattle in Kazakhstan. Pathogens, 14.","DOI":"10.3390\/pathogens14010090"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Dushaeva, L., Murzabaev, K., Karagulov, A., Mlaga, K.D., Karmaliev, R., Nametov, A., Sidikhov, B., Ichshanova, A., Sidikhov, R., and Demeugalieva, G. (2026). Prevalence and antimicrobial resistance profiles of Escherichia coli isolated from a commercial poultry farm in the West Kazakhstan Region. Biology, 15.","DOI":"10.3390\/biology15110877"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"419","DOI":"10.52578\/3134-8114-2026-3-419-428","article-title":"Analysis of the microbiocenotic structure of biomaterials from farm animals and the prevalence of bacteria in the West Kazakhstan Region","volume":"82","author":"Dushaeva","year":"2026","journal-title":"Anim. Health Biosaf."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/S0167-7012(02)00150-1","article-title":"Application of the fluorogenic probe technique (TaqMan PCR) to the detection of Enterococcus spp. and Escherichia coli in water samples","volume":"52","author":"Frahm","year":"2003","journal-title":"J. Microbiol. Methods"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Kasturi, K.N., and Drgon, T. (2017). Real-Time PCR Method for Detection of Salmonella spp. in Environmental Samples. Appl. Environ. Microbiol., 83.","DOI":"10.1128\/AEM.00644-17"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"221","DOI":"10.4315\/0362-028X-73.2.221","article-title":"A quantitative PCR assay for rapid detection of Shigella species in fresh produce","volume":"73","author":"Lin","year":"2010","journal-title":"J. Food Prot."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"4443","DOI":"10.1128\/JCM.02528-14","article-title":"Real-Time TaqMan PCR for Yersinia enterocolitica Detection Based on the ail and foxA Genes","volume":"52","author":"Wang","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/S0378-1097(03)00845-0","article-title":"Applicability of a rapid duplex real-time PCR assay for the speciation of Campylobacter jejuni and Campylobacter coli directly from culture plates","volume":"229","author":"Best","year":"2003","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"32092","DOI":"10.1038\/s41598-025-17272-y","article-title":"An ddPCR method for the simultaneous detection and quantification of Salmonella enterica, Staphylococcus aureus, Listeria monocytogenes, and Bacillus cereus in foods","volume":"15","author":"Sun","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_30","unstructured":"EUCAST (Breakpoint Tables for Interpretation of MICs and Zone Diameters, 2026). Breakpoint Tables for Interpretation of MICs and Zone Diameters, Version 16.0."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"fiy130","DOI":"10.1093\/femsec\/fiy130","article-title":"Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements","volume":"94","author":"Stedtfeld","year":"2018","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: An international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"102905","DOI":"10.1016\/j.psj.2023.102905","article-title":"A systematic review and meta-analysis of Campylobacter sources in poultry production (pre-slaughter) and their relative contribution to the microbiological risk of poultry meat","volume":"102","author":"Wang","year":"2023","journal-title":"Poult. Sci."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1038\/s41467-024-45111-7","article-title":"Global surveillance of antimicrobial resistance in food animals using priority drugs maps","volume":"15","author":"Zhao","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1007\/s42770-024-01560-2","article-title":"Cumulative prevalence of phenotypic and genotypic profiles of antimicrobial resistance in Escherichia coli in poultry: A systematic review and meta-analysis","volume":"56","author":"Limeira","year":"2025","journal-title":"Braz. J. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Messele, Y.E., Alkhallawi, M., Veltman, T., Trott, D.J., McMeniman, J.P., Kidd, S.P., Lowe, W.Y., and Petrovski, K.R. (2022). Phenotypic and genotypic analysis of antimicrobial resistance in Escherichia coli isolated from beef cattle at feedlots in Australia. Animals, 12.","DOI":"10.3390\/ani12172256"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predicting phenotypes based on genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"143808","DOI":"10.1016\/j.chemosphere.2024.143808","article-title":"Antimicrobial resistance genes and associated mobile genetic elements in Escherichia coli isolated from humans, animals, and the environment","volume":"369","author":"Rana","year":"2024","journal-title":"Chemosphere"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1093\/jac\/dkaa443","article-title":"Prevalence of Antimicrobial Resistance Genes and Its Association with Restricted Use of Antimicrobials in Animals Raised for Meat: A Systematic Review and Meta-Analysis","volume":"76","author":"Nobrega","year":"2021","journal-title":"J. Antimicrob. Chemother."}],"container-title":["Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-7737\/15\/18\/1612\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T08:51:09Z","timestamp":1789375869000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-7737\/15\/18\/1612"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,12]]},"references-count":39,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["biology15181612"],"URL":"https:\/\/doi.org\/10.3390\/biology15181612","relation":{},"ISSN":["2079-7737"],"issn-type":[{"value":"2079-7737","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,12]]}}}