{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T14:51:38Z","timestamp":1792162298937,"version":"4.4.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1012797","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T00:00:00Z","timestamp":1755820800000}}],"reference-count":69,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2025,8,13]],"date-time":"2025-08-13T00:00:00Z","timestamp":1755043200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"crossref","award":["R35GM134934"],"award-info":[{"award-number":["R35GM134934"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIH","award":["F30OD030022"],"award-info":[{"award-number":["F30OD030022"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    <jats:italic>Campylobacter spp.<\/jats:italic>\n                    resistant to fluoroquinolones and macrolides are serious public health threats. Studies aiming to identify risk factors for drug-resistant\n                    <jats:italic>Campylobacter<\/jats:italic>\n                    have narrowly focused on antimicrobial use at the farm level. Using chain graphs, we quantified risk factors for fluoroquinolones- and macrolide-resistance in\n                    <jats:italic>Campylobacter coli<\/jats:italic>\n                    isolated from two distinctive swine production systems, conventional and antibiotic-free (ABF). The chain graphs were learned using genotypic and antimicrobial susceptibility data from 1082 isolates and host exposures obtained through surveys for 14 cohorts of pigs. The gyrA T86I point mutation alone explained at least 58% of the variance in ciprofloxacin minimum inhibitory concentration (MIC) for ABF and 79% in conventional farms. For macrolides, genotype and host exposures explained similar variance in azithromycin and erythromycin MIC. Among host exposures, heavy metal exposures were identified as risk factors in both conventional and ABF. Chain graph models can generate insights into the complex epidemiology of antimicrobial resistance by characterizing context-specific risk factors and facilitating causal discovery.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1012797","type":"journal-article","created":{"date-parts":[[2025,8,13]],"date-time":"2025-08-13T18:37:07Z","timestamp":1755110227000},"page":"e1012797","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Risk factors for fluoroquinolone- and macrolide-resistance among swine Campylobacter coli using multi-layered chain graphs"],"prefix":"10.1371","volume":"21","author":[{"given":"Christine A.","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William J.","family":"Love","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel","family":"Jara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnoud H. 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resistance","volume":"387","author":"AH Holmes","year":"2016","journal-title":"Lancet."},{"issue":"4","key":"pcbi.1012797.ref012","doi-asserted-by":"crossref","first-page":"567","DOI":"10.3390\/antibiotics4040567","article-title":"Co-selection of resistance to antibiotics, biocides and heavy metals, and its relevance to foodborne pathogens","volume":"4","author":"AD Wales","year":"2015","journal-title":"Antibiotics (Basel)."},{"issue":"3","key":"pcbi.1012797.ref013","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1111\/1541-4337.12438","article-title":"Antimicrobial resistance on farms: a review including biosecurity and the potential role of disinfectants in resistance selection","volume":"18","author":"R Davies","year":"2019","journal-title":"Compr Rev Food Sci Food Saf."},{"issue":"5","key":"pcbi.1012797.ref014","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1111\/j.1574-6976.2011.00289.x","article-title":"Persistence of antibiotic resistance in bacterial populations","volume":"35","author":"DI Andersson","year":"2011","journal-title":"FEMS Microbiol Rev."},{"issue":"5","key":"pcbi.1012797.ref015","doi-asserted-by":"crossref","DOI":"10.1128\/aac.01687-21","article-title":"Genomic screening of antimicrobial resistance markers in UK and US Campylobacter isolates highlights stability of resistance over an 18-year period","volume":"66","author":"AH van Vliet","year":"2022","journal-title":"Antimicrob Agents Chemother."},{"issue":"9","key":"pcbi.1012797.ref016","first-page":"000875","article-title":"Emerging patterns of fluoroquinolone resistance in Campylobacter jejuni in the UK","volume":"8","author":"D Veltcheva","year":"2022","journal-title":"Microb Genom."},{"issue":"1","key":"pcbi.1012797.ref017","doi-asserted-by":"crossref","first-page":"22608","DOI":"10.1038\/s41598-023-47862-7","article-title":"Global trends in antimicrobial resistance on organic and conventional farms","volume":"13","author":"EO Ager","year":"2023","journal-title":"Sci Rep."},{"issue":"1","key":"pcbi.1012797.ref018","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.femsle.2004.12.017","article-title":"The chloramphenicol resistance gene cmlA is disseminated on transferable plasmids that confer multiple-drug resistance in swine Escherichia coli","volume":"243","author":"KM Bischoff","year":"2005","journal-title":"FEMS Microbiol Lett."},{"issue":"6","key":"pcbi.1012797.ref019","first-page":"356","article-title":"Sequencing-based methods and resources to study antimicrobial resistance","volume":"20","author":"M Boolchandani","year":"2019","journal-title":"Nat Rev Genet."},{"issue":"4","key":"pcbi.1012797.ref020","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1007\/s10985-007-9065-x","article-title":"Generalized linear mixed models: a review and some extensions","volume":"13","author":"CB Dean","year":"2007","journal-title":"Lifetime Data 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Probabilistic graphical models: principles and techniques. MIT Press; 2009."},{"key":"pcbi.1012797.ref023","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1146\/annurev-statistics-060116-053803","article-title":"Structure learning in graphical modeling","volume":"4","author":"M Drton","year":"2017","journal-title":"Annu Rev Stat Appl."},{"key":"pcbi.1012797.ref024","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1186\/s12859-016-1039-0","article-title":"Learning mixed graphical models with separate sparsity parameters and stability-based model selection","volume":"17","author":"AJ Sedgewick","year":"2016","journal-title":"BMC Bioinformatics."},{"key":"pcbi.1012797.ref025","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.3389\/fgene.2019.01381","article-title":"Heterogeneous multi-layered network model for omics data integration and analysis","volume":"10","author":"B Lee","year":"2020","journal-title":"Front Genet."},{"key":"pcbi.1012797.ref026","first-page":"1","article-title":"Penalized maximum likelihood estimation of multi-layered Gaussian graphical models","volume":"17","author":"J Lin","year":"2016","journal-title":"J Mach Learn Res."},{"issue":"1","key":"pcbi.1012797.ref027","first-page":"1","article-title":"Joint estimation and inference for data integration problems based on multiple multi-layered gaussian graphical models","volume":"23","author":"S Majumdar","year":"2022","journal-title":"J Mach Learn Res."},{"issue":"3","key":"pcbi.1012797.ref028","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.artmed.2003.11.003","article-title":"Understanding tuberculosis epidemiology using structured statistical models","volume":"30","author":"L Getoor","year":"2004","journal-title":"Artif Intell Med."},{"issue":"4","key":"pcbi.1012797.ref029","article-title":"Identifying patient-level risk factors associated with non-\u03b2-lactam resistance outcomes in invasive MRSA infections in the United States using chain graphs","volume":"4","author":"WJ Love","year":"2022","journal-title":"JAC Antimicrob Resist."},{"issue":"8","key":"pcbi.1012797.ref030","doi-asserted-by":"crossref","first-page":"2698","DOI":"10.1128\/AEM.07723-11","article-title":"Longitudinal study of the persistence of antimicrobial-resistant campylobacter strains in distinct Swine production systems on farms, at slaughter, and in the environment","volume":"78","author":"MP Quintana-Hayashi","year":"2012","journal-title":"Appl Environ Microbiol."},{"issue":"1","key":"pcbi.1012797.ref031","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-021-91456-0","article-title":"AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence","volume":"11","author":"M Feldgarden","year":"2021","journal-title":"Sci Rep."},{"issue":"4","key":"pcbi.1012797.ref032","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1086\/324626","article-title":"Mechanisms of resistance 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Campylobacter coli","volume":"58","author":"A Gibreel","year":"2006","journal-title":"J Antimicrob Chemother."},{"issue":"11","key":"pcbi.1012797.ref039","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1038\/nrmicro1265","article-title":"The bacterial ribosome as a target for antibiotics","volume":"3","author":"J Poehlsgaard","year":"2005","journal-title":"Nat Rev Microbiol."},{"issue":"1","key":"pcbi.1012797.ref040","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.ijantimicag.2005.08.019","article-title":"An investigation of the molecular mechanisms contributing to high-level erythromycin resistance in Campylobacter","volume":"27","author":"D Corcoran","year":"2006","journal-title":"Int J Antimicrob Agents."},{"issue":"2","key":"pcbi.1012797.ref041","article-title":"Antimicrobial resistance, interspecies gene transfer in Campylobacter coli, Campylobacter jejuni isolated from food animals, poultry processing and retail meat in North Carolina 2018 \u20132019","volume":"16","author":"DM Hull","year":"2021","journal-title":"PLoS One."},{"key":"pcbi.1012797.ref042","unstructured":"FDA. 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Rep."},{"issue":"2","key":"pcbi.1012797.ref048","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1089\/fpd.2020.2835","article-title":"Modeling the effect of tylosin phosphate on macrolide-resistant enterococci in feedlots and reducing resistance transmission","volume":"18","author":"GS Stapleton","year":"2021","journal-title":"Foodborne Pathog Dis."},{"key":"pcbi.1012797.ref049","doi-asserted-by":"crossref","DOI":"10.1146\/annurev-micro-041522-102707","article-title":"From petri dishes to patients to populations: scales and evolutionary mechanisms driving antibiotic resistance","volume":"78","author":"C Souque","year":"2024","journal-title":"Annu Rev Microbiol."},{"key":"pcbi.1012797.ref050","doi-asserted-by":"crossref","first-page":"142702","DOI":"10.1016\/j.scitotenv.2020.142702","article-title":"Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments","volume":"755","author":"SH Mazhar","year":"2021","journal-title":"Sci Total Environ."},{"key":"pcbi.1012797.ref051","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1016\/j.scitotenv.2017.10.106","article-title":"Feed additives shift gut microbiota and enrich antibiotic resistance in swine gut","volume":"621","author":"Y Zhao","year":"2018","journal-title":"Sci Total Environ."},{"key":"pcbi.1012797.ref052","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.fm.2016.12.009","article-title":"Antimicrobial resistance and its association with tolerance to heavy metals in agriculture production","volume":"64","author":"Z Yu","year":"2017","journal-title":"Food Microbiol."},{"issue":"7","key":"pcbi.1012797.ref053","doi-asserted-by":"crossref","first-page":"2124","DOI":"10.1128\/AAC.46.7.2124-2131.2002","article-title":"CmeABC functions as a multidrug efflux system in Campylobacter jejuni","volume":"46","author":"J Lin","year":"2002","journal-title":"Antimicrob Agents 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