{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T21:52:16Z","timestamp":1791582736838,"version":"4.3.4"},"reference-count":56,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T00:00:00Z","timestamp":1768003200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Veterinary Sciences"],"abstract":"<jats:p>Pneumonia caused by the facultative intracellular pathogen Rhodococcus equi stands out as one of the most significant infections associated with a notably high mortality rate in foals worldwide. Limited therapeutic options and inadequate control and prevention measures result in substantial economic losses, underscoring the need for enhanced interventions. A cross-sectional, multi-province study was conducted on racehorse-breeding farms in T\u00fcrkiye to estimate prevalence and index virulence, assess relatedness, and summarize antimicrobial susceptibility within a farm management context. Nasal and fecal swabs and environmental samples (soil and water) were cultured and confirmed; virulence was assessed with vapA-specific PCR, genetic relationship determined with PFGE, and antimicrobial susceptibility using disk diffusion. R. equi was detected in 10% of nasal swabs, 22.9% of fecal swabs, 29.4% of soil samples, and 5.9% of water samples; 46.2% of confirmed isolates were vapA-positive. Susceptibility patterns were favorable overall, with frequent ampicillin resistance, infrequent resistance to macrolides and rifampin, rare multidrug resistance, and no vancomycin resistance was detected. PFGE demonstrated substantial genotypic diversity, with 12 clusters and 29 distinct pulsotypes. Farm-level observations were exploratory. More frequent mechanical paddock cleaning coincided with the absence of foal deaths, and vapA-positive isolates were observed on farms with prior infection. Taken together, these findings support routine paddock hygiene, prompt isolation of clinically affected foals, culture-guided therapy, and continued surveillance, and they indicate a need for longitudinal and genomic studies to evaluate the impact.<\/jats:p>","DOI":"10.3390\/vetsci13010072","type":"journal-article","created":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T09:13:01Z","timestamp":1768209181000},"page":"72","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["From Paddock to Foal: Prevalence and Genotypic Diversity of Rhodococcus equi on Stud Farms in T\u00fcrkiye"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6895-2727","authenticated-orcid":false,"given":"Zeynep","family":"Yerlikaya","sequence":"first","affiliation":[{"name":"Department of Microbiology, Faculty of Veterinary Medicine, Firat University, Elazig 23200, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6628-4515","authenticated-orcid":false,"given":"Burcu","family":"Karag\u00fclle","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Veterinary Medicine, Firat University, Elazig 23200, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6220-0521","authenticated-orcid":false,"given":"Bar\u0131\u015f","family":"Otlu","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Medicine, \u0130n\u00f6n\u00fc University, Malatya 44280, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adile","family":"Muz","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Veterinary Medicine, Firat University, Elazig 23200, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/mmi.14267","article-title":"The pathogenic actinobacterium Rhodococcus equi: What\u2019s in a name?","volume":"112","author":"Meijer","year":"2019","journal-title":"Mol. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"3310","DOI":"10.1099\/ijsem.0.003481","article-title":"On the status of the names Corynebacteriales Goodfellow and Jones 2015, Mycobacteriales Janke 1924 (Approved Lists 1980) and Mycobacteriales Cavalier-Smith 2002","volume":"69","author":"Tindall","year":"2019","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_3","unstructured":"(2025, December 18). List of Prokaryotic Names with Standing in Nomenclature (LPSN). Rhodococcus equi. Available online: https:\/\/lpsn.dsmz.de\/species\/rhodococcus-equi."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1111\/evj.14135","article-title":"Science-in-brief: The 6th Havemeyer Workshop on Rhodococcus equi-A decade-long journey in advancing research into a major equine pathogen (2012\u20132023)","volume":"56","year":"2024","journal-title":"Equine Vet. J."},{"key":"ref_5","first-page":"006679","article-title":"Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi","volume":"75","author":"Duquesne","year":"2025","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.14737\/journal.aavs\/2015\/3.1.1.10","article-title":"Current understanding of Rhodococcus equi infection and its zoonotic implications","volume":"3","author":"Khurana","year":"2015","journal-title":"Adv. Anim. Vet. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.tvjl.2011.08.014","article-title":"Rhodococcus equi pneumonia in the foal\u2014Part 1: Pathogenesis and epidemiology","volume":"192","author":"Muscatello","year":"2012","journal-title":"Vet. J."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1111\/j.1740-8261.2012.01964.x","article-title":"Association between radiographic pattern and outcome in foals with pneumonia caused by Rhodococcus equi","volume":"53","author":"Roberts","year":"2012","journal-title":"Vet. Radiol. Ultrasound"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Rakowska, A., Cywinska, A., and Witkowski, L. (2020). Current Trends in Understanding and Managing Equine Rhodococcosis. Animals, 10.","DOI":"10.3390\/ani10101910"},{"key":"ref_10","first-page":"5570186","article-title":"Rhodococcus equi, an Unusual Human Pathogen That Causes Cavitating Pneumonia in Patients with AIDS","volume":"2024","author":"Vandersnickt","year":"2024","journal-title":"Case Rep. Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"108568","DOI":"10.1016\/j.vetmic.2019.108568","article-title":"Antimicrobial susceptibility patterns of Rhodococcus equi from necropsied foals with rhodococcosis","volume":"242","author":"Erol","year":"2020","journal-title":"Vet. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"6152","DOI":"10.1128\/AEM.00495-06","article-title":"Associations between the ecology of virulent Rhodococcus equi and the epidemiology of R. equi pneumonia on Australian thoroughbred farms","volume":"72","author":"Muscatello","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"385","DOI":"10.2460\/ajvr.69.3.385","article-title":"Association of soil concentrations of Rhodococcus equi and incidence of pneumonia attributable to Rhodococcus equi in foals on farms in central Kentucky","volume":"69","author":"Cohen","year":"2008","journal-title":"Am. J. Vet. Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"404","DOI":"10.2460\/javma.2005.226.404","article-title":"Farm characteristics and management practices associated with development of Rhodococcus equi pneumonia in foals","volume":"226","author":"Cohen","year":"2005","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Miranda-CasoLuengo, R., Yerlikaya, Z., Luo, H., Cheng, C., Blanco, A., Haas, A., and Meijer, W.G. (2024). The N-terminal domain is required for cell surface localisation of VapA, a member of the Vap family of Rhodococcus equi virulence proteins. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0298900"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"109919","DOI":"10.1016\/j.vetmic.2023.109919","article-title":"Short review: Geographical distribution of equine-associated pVAPA plasmids in Rhodococcus equi in the world","volume":"287","author":"Takai","year":"2023","journal-title":"Vet. Microbiol."},{"key":"ref_17","unstructured":"American Association of Equine Practitioners (AAEP) (2025, December 27). Rhodococcus equi Disease Guidelines. Available online: https:\/\/aaep.org\/wp-content\/uploads\/2017\/01\/Rhodococcus-equi-Disease-Guidelines-Final.pdf."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.cveq.2016.11.002","article-title":"Treatment of Infections Caused by Rhodococcus equi","volume":"33","author":"Giguere","year":"2017","journal-title":"Vet. Clin. N. Am. Equine Pract."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.cveq.2022.11.002","article-title":"Rhodococcus equi-What is New This Decade?","volume":"39","author":"Sanz","year":"2023","journal-title":"Vet. Clin. N. Am. Equine Pract."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1111\/evj.13567","article-title":"Rhodococcus equi foal pneumonia: Update on epidemiology, immunity, treatment and prevention","volume":"54","author":"Bordin","year":"2022","journal-title":"Equine Vet. J."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e02665-18","DOI":"10.1128\/AEM.02665-18","article-title":"Effect of Macrolide and Rifampin Resistance on the Fitness of Rhodococcus equi","volume":"85","author":"Berghaus","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Kalinowski, M., Gr\u0105dzki, Z., Jarosz, \u0141.S., Kato, K., Hieda, Y., Kakuda, T., and Takai, S. (2016). Plasmid Profiles of Virulent Rhodococcus equi Strains Isolated from Infected Foals in Poland. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0152887"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"417","DOI":"10.3906\/vet-1505-25","article-title":"Isolation of virulent Rhodococcus equi from Arabian horses in Sanliurfa, Turkey","volume":"40","author":"Tel","year":"2016","journal-title":"Turk. J. Vet. Anim. Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"103935","DOI":"10.1016\/j.meegid.2019.103935","article-title":"Pulsed-field gel electrophoresis (PFGE): A review of the \u201cgold standard\u201d for bacteria typing and current alternatives","volume":"74","author":"Neoh","year":"2019","journal-title":"Infect. Genet. Evol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1089\/fpd.2019.2634","article-title":"PulseNet: Entering the Age of Next-Generation Sequencing","volume":"16","author":"Ribot","year":"2019","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Song, Y., Xu, X., Huang, Z., Xiao, Y., Yu, K., Jiang, M., Yin, S., Zheng, M., Meng, H., and Han, Y. (2022). Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.807610"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Ghielmetti, G., Stevens, M.J.A., Schmitt, S., Kittl, S., Cernela, N., Biggel, M., Schulthess, B., Keller, P.M., Schrenzel, J., and Stephan, R. (2025). Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering. BMC Microbiol., 25.","DOI":"10.1186\/s12866-025-04152-8"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2887","DOI":"10.1128\/jcm.29.12.2887-2889.1991","article-title":"Prevalence of virulent Rhodococcus equi in isolates from soil and feces of horses from horse-breeding farms with and without endemic infections","volume":"29","author":"Takai","year":"1991","journal-title":"J. Clin. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1111\/j.1472-765X.1996.tb00033.x","article-title":"Identification of Rhodococcus equi using the polymerase chain reaction","volume":"23","author":"Bell","year":"1996","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1642","DOI":"10.1128\/jcm.35.6.1642-1644.1997","article-title":"Prevalence of the virulence-associated gene of Rhodococcus equi in isolates from infected foals","volume":"35","author":"Haites","year":"1997","journal-title":"J. Clin. Microbiol."},{"key":"ref_31","unstructured":"Clinical and Laboratory Standards Institute (CLSI) (2013). Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated from Animals. Approved Standard, Clinical and Laboratory Standards Institute. [4th ed.]. CLSI Document VET01-A4."},{"key":"ref_32","unstructured":"Clinical and Laboratory Standards Institute (CLSI) (2015). Performance Standards for Antimicrobial Susceptibility Testing. Twenty-Fifth Informational Supplement, Clinical and Laboratory Standards Institute. CLSI Document M100-S25."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1023\/A:1001791509073","article-title":"Diversity of isolates of Rhodococcus equi from Australian thoroughbred horse farms","volume":"74","author":"Morton","year":"1998","journal-title":"Antonie Van. Leeuwenhoek"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Witkowski, L., Rzewuska, M., Cisek, A.A., Chrobak-Chmiel, D., Kizerwetter-Swida, M., Czopowicz, M., Welz, M., and Kita, J. (2015). Prevalence and genetic diversity of Rhodococcus equi in wild boars (Sus scrofa), roe deer (Capreolus capreolus) and red deer (Cervus elaphus) in Poland. BMC Microbiol., 15.","DOI":"10.1186\/s12866-015-0445-1"},{"key":"#cr-split#-ref_35.1","unstructured":"EFSA Panel on Animal Health and Welfare (AHAW), Nielsen, S.S., Bicout, D.J., Calistri, P., Canali, E., Drewe, J.A., Garin-Bastuji, B., Gonzales Rojas, J.L., Gort\u00e1zar, C., and Herskin, M. (2022). Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation"},{"key":"#cr-split#-ref_35.2","unstructured":"(EU) No 2016\/429): Antimicrobial-resistant Rhodococcus equi in horses. EFSA J., 20, e07081."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1111\/evj.12804","article-title":"Prevalence of Rhodococcus equi from the nasal cavity of 1010 apparently healthy horses","volume":"50","author":"Gressler","year":"2018","journal-title":"Equine Vet. J."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"623","DOI":"10.14202\/vetworld.2013.623-627","article-title":"The study of aerobic bacterial flora of the upper respiratory tract of equines from Jammu and Kashmir region of India","volume":"6","author":"Kumar","year":"2013","journal-title":"Vet. World"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"246","DOI":"10.18683\/germs.2021.1261","article-title":"Comparative performance of commercial Amies transport media with and without charcoal for Neisseria gonorrhoeae culture for gonococcal isolation and antimicrobial resistance monitoring in Ukraine","volume":"11","author":"Boiko","year":"2021","journal-title":"Germs"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"22512","DOI":"10.1038\/s41598-022-27084-z","article-title":"Feasibility, acceptability, and bacterial recovery for community-based sample collection to estimate antibiotic resistance in commensal gut and upper respiratory tract bacteria","volume":"12","author":"Tran","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1112","DOI":"10.1292\/jvms.25-0267","article-title":"Isolation of vapA-positive Rhodococcus equi from soil and fecal samples in Mongolia","volume":"87","author":"Ganbaatar","year":"2025","journal-title":"J. Vet. Med. Sci."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1111\/jvim.13828","article-title":"Use of Serial Quantitative PCR of the vapA Gene of Rhodococcus equi in Feces for Early Detection of R. equi Pneumonia in Foals","volume":"30","author":"Madrigal","year":"2016","journal-title":"J. Vet. Intern. Med."},{"key":"ref_42","first-page":"49","article-title":"Management of Rhodococcus equi pneumonia in foals","volume":"4","author":"Johns","year":"2013","journal-title":"Vet. Med. Res. Rep."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1016\/j.jevs.2011.03.002","article-title":"Associations between the Exposure to Airborne Virulent Rhodococcus equi and the Incidence of R. equi Pneumonia among Individual Foals","volume":"31","author":"Kuskie","year":"2011","journal-title":"J. Equine Vet. Sci."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2912","DOI":"10.1111\/jvim.16294","article-title":"Randomized, Controlled Trial Comparing Rhodococcus equi and Poly-N-Acetyl Glucosamine Hyperimmune Plasma to Prevent R. equi Pneumonia in Foals","volume":"35","author":"Kahn","year":"2021","journal-title":"J. Vet. Intern. Med."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1111\/evj.13858","article-title":"Transfusion of Hyperimmune Plasma for Protecting Foals against Rhodococcus equi Pneumonia","volume":"55","author":"Kahn","year":"2023","journal-title":"Equine Vet. J."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.vetimm.2009.12.004","article-title":"Current Understanding of the Equine Immune Response to Rhodococcus equi: An Immunological Review of R. equi Pneumonia","volume":"135","author":"Dawson","year":"2010","journal-title":"Vet. Immunol. Immunopathol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/S0168-1605(00)00172-0","article-title":"Resistance of Rhodococcus equi to acid pH","volume":"55","author":"Benoit","year":"2000","journal-title":"Int. J. Food Microbiol."},{"key":"ref_48","unstructured":"American Association of Equine, P (2022). AAEP Biosecurity Guidelines, American Association of Equine Practitioners."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"121","DOI":"10.54846\/jshap\/300","article-title":"Evaluation of the efficacy of a peroxygen compound, Virkon (R) S, as a boot bath disinfectant","volume":"9","author":"Amass","year":"2001","journal-title":"J. Swine Health Prod."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2715","DOI":"10.1007\/s10068-024-01618-9","article-title":"Effectiveness of organic acids for inactivating pathogenic bacteria inoculated in laboratory media and foods: An updated minireview","volume":"33","author":"Yoon","year":"2024","journal-title":"Food Sci. Biotechnol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"95","DOI":"10.2460\/AJVR.2002.63.95","article-title":"Association of pneumonia in foals caused by Rhodococcus equi with farm soil geochemistry","volume":"63","author":"Martens","year":"2002","journal-title":"Am. J. Vet. Res."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"2167","DOI":"10.1128\/AEM.67.5.2167-2175.2001","article-title":"Epidemiology of Rhodococcus equi strains on Thoroughbred horse farms","volume":"67","author":"Morton","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1177\/104063871002200419","article-title":"Detection of strain variation in isolates of Rhodococcus equi from an affected foal using repetitive sequence-based polymerase chain reaction","volume":"22","author":"Bolton","year":"2010","journal-title":"J. Vet. Diagn. Invest."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.3201\/eid2809.220222","article-title":"International Spread of Multidrug-Resistant Rhodococcus equi","volume":"28","author":"Darcy","year":"2022","journal-title":"Emerg. Infect. Dis."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"108571","DOI":"10.1016\/j.vetmic.2019.108571","article-title":"Comparing PFGE, MLST, and WGS in Monitoring the Spread of Macrolide and Rifampin Resistant Rhodococcus equi in Horse Production","volume":"242","author":"Logue","year":"2020","journal-title":"Vet. Microbiol."}],"container-title":["Veterinary Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-7381\/13\/1\/72\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T09:45:50Z","timestamp":1768211150000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-7381\/13\/1\/72"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,10]]},"references-count":56,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["vetsci13010072"],"URL":"https:\/\/doi.org\/10.3390\/vetsci13010072","relation":{},"ISSN":["2306-7381"],"issn-type":[{"value":"2306-7381","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,10]]}}}