{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T16:35:57Z","timestamp":1789144557206,"version":"build-2803163510"},"reference-count":79,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T00:00:00Z","timestamp":1762905600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005019","name":"Beef Cattle Research Council","doi-asserted-by":"publisher","award":["ANH.18.19"],"award-info":[{"award-number":["ANH.18.19"]}],"id":[{"id":"10.13039\/501100005019","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013480","name":"Beef Farmers of Ontario","doi-asserted-by":"publisher","award":["20-04 WaldnerFunk"],"award-info":[{"award-number":["20-04 WaldnerFunk"]}],"id":[{"id":"10.13039\/100013480","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Genomic ASSETS (Antimicrobial Stewardship Systems from Evidence-based Treatment Strategies) for Livestock"},{"DOI":"10.13039\/501100010788","name":"Genome Prairie","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100010788","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100010787","name":"Genome Alberta","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100010787","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100008921","name":"Saskatchewan Agriculture Development Fund","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100008921","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100008920","name":"University of Saskatchewan","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100008920","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Veterinary Sciences"],"abstract":"<jats:p>Macrolides are crucial for the management and treatment of bovine respiratory disease (BRD). However, antimicrobial resistance (AMR) threatens the efficacy of these and other antimicrobials. We developed real-time recombinase polymerase amplification (RPA) assays targeting three clinically relevant macrolide antimicrobial resistance genes (ARGs)\u2014msrE-mphE and erm42\u2014in \u226430 min using extracted DNA. A set of 199 deep nasopharyngeal swabs (DNPS) collected from feedlot calves near the time of arrival were selected based on bacterial culture (BC) results for Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni and antimicrobial susceptibility testing (AST) for tulathromycin, tilmicosin, tildipirosin, or gamithromycin. Samples were also tested for the same targets using RPA and polymerase chain reaction (PCR). In samples that were culture-positive for one or more macrolide-resistant BRD-associated bacteria (n = 101), msrE-mphE and\/or erm42 were detected in 95% of cases using RPA. The remaining 98 samples were either culture-negative, or the recovered bacteria were macrolide-susceptible: 43% of these were RPA-positive for at least one macrolide ARG. Together with BC-AST and PCR, Bayesian latent class modelling estimated the clinical sensitivity of RPA for macrolide ARGs to be 95% and specificity to be 58%, with moderate agreement between RPA and BC-AST (\u03ba = 0.52) or PCR (\u03ba = 0.55). The estimated sensitivity of the RPA multiplex assay for the targeted macrolide ARGs was very good, although estimated specificity was limited. However, Sanger sequencing confirmed RPA detection of msrE-mphE in BC-AST\/PCR-negative samples (n = 23), reflecting the presence of this locus in non-target bacteria, as well as potential ARG variants among BRD bacteria. These findings support the potential of RPA for rapid ARG detection from extracted DNA. Continued assay optimization and evaluation for detection of respiratory bacteria and ARGs will further enhance its diagnostic utility.<\/jats:p>","DOI":"10.3390\/vetsci12111079","type":"journal-article","created":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T10:56:47Z","timestamp":1762945007000},"page":"1079","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Novel Recombinase Polymerase Amplification Assay Is Sensitive for Detection of Macrolide Resistance Genes Relevant to Bovine Respiratory Disease Management in Feedlot Calves"],"prefix":"10.3390","volume":"12","author":[{"given":"Tara","family":"Funk","sequence":"first","affiliation":[{"name":"Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lianne","family":"McLeod","sequence":"additional","affiliation":[{"name":"Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9066-469X","authenticated-orcid":false,"given":"Cheyenne C.","family":"Conrad","sequence":"additional","affiliation":[{"name":"Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3307-4666","authenticated-orcid":false,"given":"Rahat","family":"Zaheer","sequence":"additional","affiliation":[{"name":"Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3270-4032","authenticated-orcid":false,"given":"Simon J. G.","family":"Otto","sequence":"additional","affiliation":[{"name":"HEAT-AMR (Human-Environment-Animal Transdisciplinary AMR) Research Group, School of Public Health, University of Alberta, Edmonton, AB T6G 2G7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7152-4261","authenticated-orcid":false,"given":"Cheryl L.","family":"Waldner","sequence":"additional","affiliation":[{"name":"Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8266-6513","authenticated-orcid":false,"given":"Tim A.","family":"McAllister","sequence":"additional","affiliation":[{"name":"Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Andr\u00e9s-Lasheras, S., Jelinski, M., Zaheer, R., and McAllister, T.A. (2022). Bovine Respiratory Disease: Conventional to Culture-Independent Approaches to Studying Antimicrobial Resistance in North America. Antibiotics, 11.","DOI":"10.3390\/antibiotics11040487"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Klima, C.L., Holman, D.B., Cook, S.R., Conrad, C.C., Ralston, B.J., Allan, N., Anholt, R.M., Niu, Y.D., Stanford, K., and Hannon, S.J. (2020). Multidrug Resistance in Pasteurellaceae Associated With Bovine Respiratory Disease Mortalities in North America From 2011 to 2016. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.606438"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1017\/S1466252314000115","article-title":"BRD in 2014: Where Have We Been, Where Are We Now, and Where Do We Want to Go?","volume":"15","author":"Hilton","year":"2014","journal-title":"Anim. Health Res. Rev."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1017\/S146625232000016X","article-title":"Bovine Respiratory Disease Treatment Failure: Definition and Impact","volume":"21","author":"Booker","year":"2020","journal-title":"Anim. Health Res. Rev."},{"key":"ref_5","first-page":"754","article-title":"Laboratory Test Descriptions for Bovine Respiratory Disease Diagnosis and Their Strengths and Weaknesses: Gold Standards for Diagnosis, Do They Exist?","volume":"53","author":"Fulton","year":"2012","journal-title":"Can. Vet. J."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.cvfa.2010.04.001","article-title":"Pathogenesis and Pathology of Bovine Pneumonia","volume":"26","author":"Panciera","year":"2010","journal-title":"Vet. Clin. N. Am. Food Anim. Pract."},{"key":"ref_7","first-page":"163","article-title":"Infection of Calves with In-Vivo Passaged Bovine Parainfluenza-3 Virus, Alone or in Combination with Bovine Respiratory Syncytial Virus and Bovine Coronavirus","volume":"84","author":"Ellis","year":"2020","journal-title":"Can. J. Vet. Res."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Brault, S.A., Hannon, S.J., Gow, S.P., Warr, B.N., Withell, J., Song, J., Williams, C.M., Otto, S.J.G., Booker, C.W., and Morley, P.S. (2019). Antimicrobial Use on 36 Beef Feedlots in Western Canada: 2008\u20132012. Front. Vet. Sci., 6.","DOI":"10.3389\/fvets.2019.00329"},{"key":"ref_9","first-page":"1095","article-title":"The Epidemiology of Bovine Respiratory Disease: What Is the Evidence for Predisposing Factors?","volume":"51","author":"Taylor","year":"2010","journal-title":"Can. Vet. J."},{"key":"ref_10","first-page":"1351","article-title":"The Epidemiology of Bovine Respiratory Disease: What Is the Evidence for Preventive Measures?","volume":"51","author":"Taylor","year":"2010","journal-title":"Can. Vet. J."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/j.cvfa.2015.05.008","article-title":"Use of Antimicrobial Metaphylaxis for the Control of Bovine Respiratory Disease in High-Risk Cattle","volume":"31","author":"Ives","year":"2015","journal-title":"Vet. Clin. N. Am. Food Anim. Pract."},{"key":"ref_12","unstructured":"(2025, January 31). Health Canada Categorization of Antimicrobial Drugs Based on Importance in Human Medicine. Available online: https:\/\/www.canada.ca\/en\/health-canada\/services\/drugs-health-products\/veterinary-drugs\/antimicrobial-resistance\/categorization-antimicrobial-drugs-based-importance-human-medicine.html."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.vetmic.2019.06.012","article-title":"Genetic Characterization of Susceptible and Multi-Drug Resistant Mannheimia haemolytica Isolated from High-Risk Stocker Calves Prior to and after Antimicrobial Metaphylaxis","volume":"235","author":"Snyder","year":"2019","journal-title":"Vet. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Stanford, K., Zaheer, R., Klima, C., McAllister, T., Peters, D., Niu, Y.D., and Ralston, B. (2020). Antimicrobial Resistance in Members of the Bacterial Bovine Respiratory Disease Complex Isolated from Lung Tissue of Cattle Mortalities Managed with or without the Use of Antimicrobials. Microorganisms, 8.","DOI":"10.3390\/microorganisms8020288"},{"key":"ref_15","first-page":"140","article-title":"Macrolide Antibiotic Interaction and Resistance on the Bacterial Ribosome","volume":"4","author":"Douthwaite","year":"2003","journal-title":"Curr. Opin. Investig. Drugs"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2475","DOI":"10.1128\/AAC.00092-11","article-title":"Molecular Basis of Macrolide, Triamilide, and Lincosamide Resistance in Pasteurella multocida from Bovine Respiratory Disease","volume":"55","author":"Kadlec","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"12702","DOI":"10.1016\/S0021-9258(17)44232-3","article-title":"Site of Action of a Ribosomal RNA Methylase Responsible for Resistance to Erythromycin and Other Antibiotics","volume":"258","author":"Skinner","year":"1983","journal-title":"J. Biol. Chem."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1111\/j.1574-6968.2008.01145.x","article-title":"Update on Macrolide-Lincosamide-Streptogramin, Ketolide, and Oxazolidinone Resistance Genes","volume":"282","author":"Roberts","year":"2008","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s13100-022-00275-1","article-title":"Genomic Analysis Reveals the Role of Integrative and Conjugative Elements in Plant Pathogenic Bacteria","volume":"13","author":"Fernandes","year":"2022","journal-title":"Mob. DNA"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1139\/cjm-2021-0349","article-title":"Examination of the Horizontal Gene Transfer Dynamics of an Integrative and Conjugative Element Encoding Multidrug Resistance in Histophilus somni","volume":"69","author":"Farghaly","year":"2023","journal-title":"Can. J. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1093\/jac\/dkae040","article-title":"Identification and Evolution of ICE-PmuST394: A Novel Integrative Conjugative Element in Pasteurella multocida ST394","volume":"79","author":"Chowdhury","year":"2024","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1128\/JCM.02485-13","article-title":"Pathogens of Bovine Respiratory Disease in North American Feedlots Conferring Multidrug Resistance via Integrative Conjugative Elements","volume":"52","author":"Klima","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Bhatt, K., Timsit, E., Rawlyk, N., Potter, A., and Liljebjelke, K. (2018). Integrative Conjugative Element ICEHs1 Encodes for Antimicrobial Resistance and Metal Tolerance in Histophilus somni. Front. Vet. Sci., 5.","DOI":"10.3389\/fvets.2018.00153"},{"key":"ref_24","unstructured":"Volkov, S. (2024). WHO List of Medically Important Antimicrobials a Risk Management Tool for Mitigating Antimicrobial Resistance Due to Non-Human Use."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.trac.2017.10.015","article-title":"Recombinase Polymerase Amplification: Basics, Applications and Recent Advances","volume":"98","author":"Lobato","year":"2018","journal-title":"TrAC-Trends Anal. Chem."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1371\/journal.pbio.0040204","article-title":"DNA Detection Using Recombination Proteins","volume":"4","author":"Piepenburg","year":"2006","journal-title":"PLoS Biol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Conrad, C.C., Daher, R.K., Stanford, K., Amoako, K.K., Boissinot, M., Bergeron, M.G., Alexander, T., Cook, S., Ralston, B., and Zaheer, R. (2020). A Sensitive and Accurate Recombinase Polymerase Amplification Assay for Detection of the Primary Bacterial Pathogens Causing Bovine Respiratory Disease. Front. Vet. Sci., 7.","DOI":"10.3389\/fvets.2020.00208"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Nelson, M.M., Waldron, C.L., and Bracht, J.R. (2019). Rapid Molecular Detection of Macrolide Resistance. BMC Infect. Dis., 19.","DOI":"10.1186\/s12879-019-3762-4"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Conrad, C.C., Funk, T., Andr\u00e9s-Lasheras, S., Yevtushenko, C., Claassen, C., Otto, S.J.G., Waldner, C., Zaheer, R., and McAllister, T.A. (2024). Improving the Detection of Integrative Conjugative Elements in Bovine Nasopharyngeal Swabs Using Multiplex Recombinase Polymerase Amplification. J. Microbiol. Methods, 221.","DOI":"10.1016\/j.mimet.2024.106943"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Zhao, G., He, H., and Wang, H. (2019). Use of a Recombinase Polymerase Amplification Commercial Kit for Rapid Visual Detection of Pasteurella multocida. BMC Vet. Res., 15.","DOI":"10.1186\/s12917-019-1889-6"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Jiang, L., Zhang, G., Wang, P., Niu, X., Liu, Q., Zhang, S., Gao, W., and Li, Y. (2024). Simultaneous Detection of Bovine Viral Diarrhea Virus (BVDV) and Bovine Herpesvirus 1 (BoHV-1) Using Recombinase Polymerase Amplification. Sci. Rep., 14.","DOI":"10.1038\/s41598-024-56869-7"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.prevetmed.2006.04.006","article-title":"Bayesian Estimation of Sensitivity and Specificity of Serum ELISA and Faecal Culture for Diagnosis of Paratuberculosis in Greek Dairy Sheep and Goats","volume":"76","author":"Kostoulas","year":"2006","journal-title":"Prev. Vet. Med."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/1742-7622-9-9","article-title":"A tutorial in estimating the prevalence of disease in humans and animals in the absence of a gold standard diagnostic","volume":"9","author":"Lewis","year":"2012","journal-title":"Emerg. Themes Epidemiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"e00502-24","DOI":"10.1128\/aem.00502-24","article-title":"Identification of Genetic Markers of Resistance to Macrolide Class Antibiotics in Mannheimia haemolytica Isolates from a Saskatchewan Feedlot","volume":"90","author":"Deschner","year":"2024","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Klima, C.L., Cook, S.R., Zaheer, R., Laing, C., Gannon, V.P., Xu, Y., Rasmussen, J., Potter, A., Hendrick, S., and Alexander, T.W. (2016). Comparative Genomic Analysis of Mannheimia haemolytica from Bovine Sources. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0149520"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Beker, M., Rose, S., Lykkebo, C.A., and Douthwaite, S. (2018). Integrative and Conjugative Elements (ICEs) in Pasteurellaceae Species and Their Detection by Multiplex PCR. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.01329"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1093\/jac\/dkr411","article-title":"ICEPmu1, an Integrative Conjugative Element (ICE) of Pasteurella multocida: Structure and Transfer","volume":"67","author":"Michael","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Andr\u00e9s-Lasheras, S., Ha, R., Zaheer, R., Lee, C., Booker, C.W., Dorin, C., Van Donkersgoed, J., Deardon, R., Gow, S., and Hannon, S.J. (2021). Prevalence and Risk Factors Associated With Antimicrobial Resistance in Bacteria Related to Bovine Respiratory Disease\u2014A Broad Cross-Sectional Study of Beef Cattle at Entry Into Canadian Feedlots. Front. Vet. Sci., 8.","DOI":"10.3389\/fvets.2021.692646"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1093\/jac\/dkab395","article-title":"Macrolides Mediate Transcriptional Activation of the Msr(E)-Mph(E) Operon through Histone-like Nucleoid-Structuring Protein (HNS) and CAMP Receptor Protein (CRP)","volume":"77","author":"Duan","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_40","first-page":"920","article-title":"Changes in the Phenotypic Susceptibility of Mannheimia haemolytica Isolates to Macrolide Antimicrobials during the Early Feeding Period Following Metaphylactic Tulathromycin Use in Western Canadian Feedlot Calves","volume":"63","author":"Younes","year":"2022","journal-title":"Can. Vet. J."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Abi Younes, J.N., Campbell, J.R., Otto, S.J.G., Gow, S.P., Woolums, A.R., Jelinski, M., Lacoste, S., and Waldner, C.L. (2024). Variation in Pen-Level Prevalence of BRD Bacterial Pathogens and Antimicrobial Resistance Following Feedlot Arrival in Beef Calves. Antibiotics, 13.","DOI":"10.3390\/antibiotics13040322"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Freeman, C.N., Herman, E.K., Abi Younes, J., Ramsay, D.E., Erikson, N., Stothard, P., Links, M.G., Otto, S.J.G., and Waldner, C. (2022). Evaluating the Potential of Third Generation Metagenomic Sequencing for the Detection of BRD Pathogens and Genetic Determinants of Antimicrobial Resistance in Chronically Ill Feedlot Cattle. BMC Vet. Res., 18.","DOI":"10.1186\/s12917-022-03269-6"},{"key":"ref_43","unstructured":"Gow, S., Bergen, R., Booker, C., Butters, A., Dorin, C., Dimmers, G., Erickson, N., Hannon, S., Hendrick, S., and Ramsay, D. (2021, January 7\u20139). National Surveillance of Antimicrobial Use and Antimicrobial Resistance in Canadian Feedlots. Proceedings of the AABP 54th Annual Conference; American Association of Bovine Practitioners, Salt Lake City, UT, USA. Available online: https:\/\/bovine-ojs-tamu.tdl.org\/AABP\/article\/view\/8291."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/j.vetmic.2010.11.018","article-title":"Genetic Characterization and Antimicrobial Susceptibility of Mannheimia haemolytica Isolated from the Nasopharynx of Feedlot Cattle","volume":"149","author":"Klima","year":"2011","journal-title":"Vet. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1177\/1040638718800170","article-title":"Development of a Multiplex Real-Time PCR Assay Using Two Thermocycling Platforms for Detection of Major Bacterial Pathogens Associated with Bovine Respiratory Disease Complex from Clinical Samples","volume":"30","author":"Loy","year":"2018","journal-title":"J. Vet. Diagn. Investig."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Dutta, E., Loy, J.D., Deal, C.A., Wynn, E.L., Clawson, M.L., Clarke, J., and Wang, B. (2021). Development of a Multiplex Real-Time PCR Assay for Predicting Macrolide and Tetracycline Resistance Associated with Bacterial Pathogens of Bovine Respiratory Disease. Pathogens, 10.","DOI":"10.3390\/pathogens10010064"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Herman, E.K., Lacoste, S.R., Freeman, C.N., Otto, S.J.G., McCarthy, E.L., Links, M.G., Stothard, P., and Waldner, C.L. (2024). Bacterial Enrichment Prior to Third-Generation Metagenomic Sequencing Improves Detection of BRD Pathogens and Genetic Determinants of Antimicrobial Resistance in Feedlot Cattle. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1386319"},{"key":"ref_48","unstructured":"Hornik, K., Leisch, F., and Zeileis, A. (2003, January 20\u201322). JAGS: A Program for Analysis of Bayesian Graphical Models Using Gibbs Sampling. Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), Vienna, Austria."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v071.i09","article-title":"Runjags: An R Package Providing Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS","volume":"71","author":"Denwood","year":"2016","journal-title":"J. Stat. Softw."},{"key":"ref_50","unstructured":"R Core Team (2021). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing."},{"key":"ref_51","unstructured":"Waldner, C. Personal Communication."},{"key":"ref_52","unstructured":"Dohoo, I.R., Martin, S.W., and Stryhn, H. (2014). Veterinary Epidemiologic Research, VER, Inc.. [2nd ed.]."},{"key":"ref_53","unstructured":"(2025, March 27). Canadian Feedlot AMU\/AMR Surveillance Program Injectable Antimicrobial Use (AMU) in Canadian Feedlot Cattle 2019\u20132022 (Veterinarians). Available online: https:\/\/cfaasp.ca\/resources\/cfaasp-resources\/Injectable-Antimicrobial-Use-AMU-In-2022-in-Canadian-Feedlot-Cattle-2019-2022-Veterinarians."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1111\/nyas.14058","article-title":"Critically Important Antibiotics: Criteria and Approaches for Measuring and Reducing Their Use in Food Animal Agriculture","volume":"1441","author":"Scott","year":"2019","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.prevetmed.2017.01.006","article-title":"STARD-BLCM: Standards for the Reporting of Diagnostic Accuracy Studies That Use Bayesian Latent Class Models","volume":"138","author":"Kostoulas","year":"2017","journal-title":"Prev. Vet. Med."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.prevetmed.2018.10.023","article-title":"Design, Statistical Analysis and Reporting Standards for Test Accuracy Studies for Infectious Diseases in Animals: Progress, Challenges and Recommendations","volume":"162","author":"Gardner","year":"2019","journal-title":"Prev. Vet. Med."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"350","DOI":"10.2460\/ajvr.78.3.350","article-title":"Comparison of the Diagnostic Performance of Bacterial Culture of Nasopharyngeal Swab and Bronchoalveolar Lavage Fluid Samples Obtained from Calves with Bovine Respiratory Disease","volume":"78","author":"Capik","year":"2017","journal-title":"Am. J. Vet. Res."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Holman, D.B., Timsit, E., Amat, S., Abbott, D.W., Buret, A.G., and Alexander, T.W. (2017). The Nasopharyngeal Microbiota of Beef Cattle before and after Transport to a Feedlot. BMC Microbiol., 17.","DOI":"10.1186\/s12866-017-0978-6"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Limmathurotsakul, D., Jamsen, K., Arayawichanont, A., Simpson, J.A., White, L.J., Lee, S.J., Wuthiekanun, V., Chantratita, N., Cheng, A., and Day, N.P.J. (2010). Defining the True Sensitivity of Culture for the Diagnosis of Melioidosis Using Bayesian Latent Class Models. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0012485"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1111\/jvim.12547","article-title":"Mannheimia haemolytica in Feedlot Cattle: Prevalence of Recovery and Associations with Antimicrobial Use, Resistance, and Health Outcomes","volume":"29","author":"Noyes","year":"2015","journal-title":"J. Vet. Intern. Med."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"214","DOI":"10.3168\/jdsc.2022-0329","article-title":"In Vitro Evaluation of the Effect of Transport Medium, Temperature, and Time on the Recovery of Mannheimia haemolytica and Pasteurella multocida","volume":"4","author":"Garzon","year":"2023","journal-title":"JDS Commun."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Van Driessche, L., De Neve, C., Haesebrouck, F., Van Leenen, K., Boyen, F., and Pardon, B. (2020). Storage Time and Temperature Affect the Isolation Rate of Mannheimia haemolytica and Pasteurella multocida from Bovine Bronchoalveolar Lavage Samples. BMC Vet. Res., 16.","DOI":"10.1186\/s12917-020-02456-7"},{"key":"ref_63","first-page":"15","article-title":"Histophilosis as a Natural Disease","volume":"351","author":"Sondgeroth","year":"2015","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1177\/1040638715597724","article-title":"Characterization of Mannheimia haemolytica in Beef Calves via Nasopharyngeal Culture and Pulsed-Field Gel Electrophoresis","volume":"27","author":"Capik","year":"2015","journal-title":"J. Vet. Diagn. Investig."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Carter, H.F., Wills, R.W., Scott, M.A., Thompson, A.C., Singer, R.S., Loy, J.D., Karisch, B.B., Epperson, W.B., and Woolums, A.R. (2022). Assessment of Diversity of Antimicrobial Resistance Phenotypes and Genotypes of Mannheimia haemolytica Isolates From Bovine Nasopharyngeal Swabs. Front. Vet. Sci., 9.","DOI":"10.3389\/fvets.2022.883389"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.cvfa.2010.04.004","article-title":"Bacterial Pathogens of the Bovine Respiratory Disease Complex","volume":"26","author":"Griffin","year":"2010","journal-title":"Vet. Clin. North. Am. Food Anim. Pract."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s13567-021-01020-x","article-title":"Bovine Respiratory Microbiota of Feedlot Cattle and Its Association with Disease","volume":"53","author":"Chai","year":"2022","journal-title":"Vet. Res."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.vetmic.2018.09.019","article-title":"Evolution of the Nasopharyngeal Bacterial Microbiota of Beef Calves from Spring Processing to 40 Days after Feedlot Arrival","volume":"225","author":"McMullen","year":"2018","journal-title":"Vet. Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Centeno-Delphia, R.E., Glidden, N., Long, E., Ellis, A., Hoffman, S., Mosier, K., Ulloa, N., Cheng, J.J., Davidson, J.L., and Mohan, S. (2025). Nasal Pathobiont Abundance Is a Moderate Feedlot-Dependent Indicator of Bovine Respiratory Disease in Beef Cattle. Anim. Microbiome, 7.","DOI":"10.1186\/s42523-025-00387-y"},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Cameron, A., Zaheer, R., and McAllister, T.A. (2019). Emerging Variants of the Integrative and Conjugant Element ICEMh1 in Livestock Pathogens: Structural Insights, Potential Host Range, and Implications for Bacterial Fitness and Antimicrobial Therapy. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.02608"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1039\/C8AN01621F","article-title":"Review: A Comprehensive Summary of a Decade Development of the Recombinase Polymerase Amplification","volume":"144","author":"Li","year":"2019","journal-title":"Analyst"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"2565","DOI":"10.1021\/ac403750z","article-title":"Nucleic Acid Test to Diagnose Cryptosporidiosis: Lab Assessment in Animal and Patient Specimens","volume":"86","author":"Crannell","year":"2014","journal-title":"Anal. Chem."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Zaheer, R., Cook, S.R., Klima, C.L., Stanford, K., Alexander, T., Topp, E., Read, R.R., and McAllister, T.A. (2013). Effect of Subtherapeutic vs. Therapeutic Administration of Macrolides on Antimicrobial Resistance in Mannheimia haemolytica and Enterococci Isolated from Beef Cattle. Front. Microbiol., 4.","DOI":"10.3389\/fmicb.2013.00133"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1093\/jac\/dku361","article-title":"Analysis and Comparative Genomics of ICEMh1, a Novel Integrative and Conjugative Element (ICE) of Mannheimia haemolytica","volume":"70","author":"Eidam","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1093\/jac\/dkr406","article-title":"ICEPmu1, an Integrative Conjugative Element (ICE) of Pasteurella multocida: Analysis of the Regions That Comprise 12 Antimicrobial Resistance Genes","volume":"67","author":"Michael","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"e2219827120","DOI":"10.1073\/pnas.2219827120","article-title":"A Neglected and Emerging Antimicrobial Resistance Gene Encodes for a Serine-Dependent Macrolide Esterase","volume":"120","author":"Dhindwal","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1016\/j.tim.2023.08.008","article-title":"Macrolide Esterases: Current Threats and Opportunities","volume":"31","author":"Dhindwal","year":"2023","journal-title":"Trends Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Lin, J., Lv, H., Wang, T., Tao, H., Zhong, Y., Zhou, Y., Tang, Y., Xie, F., Zhuang, G., and Xu, C. (2024). The Global Distribution of the Macrolide Esterase EstX from the Alpha\/Beta Hydrolase Superfamily. Commun. Biol., 7.","DOI":"10.1038\/s42003-024-06473-2"},{"key":"ref_79","first-page":"38","article-title":"Characterization of Mannheimia haemolytica Isolated from Feedlot Cattle That Were Healthy or Treated for Bovine Respiratory Disease","volume":"78","author":"Klima","year":"2014","journal-title":"Can. J. Vet. Res."}],"container-title":["Veterinary Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-7381\/12\/11\/1079\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T05:28:25Z","timestamp":1763098105000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-7381\/12\/11\/1079"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,12]]},"references-count":79,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2025,11]]}},"alternative-id":["vetsci12111079"],"URL":"https:\/\/doi.org\/10.3390\/vetsci12111079","relation":{},"ISSN":["2306-7381"],"issn-type":[{"value":"2306-7381","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,12]]}}}