{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T18:39:38Z","timestamp":1788374378573,"version":"build-2803163510"},"reference-count":30,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2020,3,1]],"date-time":"2020-03-01T00:00:00Z","timestamp":1583020800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2020,3,1]],"date-time":"2020-03-01T00:00:00Z","timestamp":1583020800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"}],"funder":[{"DOI":"10.13039\/100001250","name":"Morris Animal Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001250","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Veterinary Microbiology"],"published-print":{"date-parts":[[2020,3]]},"DOI":"10.1016\/j.vetmic.2019.108571","type":"journal-article","created":{"date-parts":[[2019,12,28]],"date-time":"2019-12-28T11:26:42Z","timestamp":1577532402000},"page":"108571","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":7,"special_numbering":"C","title":["Comparing PFGE, MLST, and WGS in monitoring the spread of macrolide and rifampin resistant Rhodococcus equi in horse production"],"prefix":"10.1016","volume":"242","author":[{"given":"Sonsiray","family":"\u00c1lvarez-Narv\u00e1ez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine M.","family":"Logue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolle Lima","family":"Barbieri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Londa J.","family":"Berghaus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steeve","family":"Gigu\u00e8re","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.vetmic.2019.108571_bib0005","doi-asserted-by":"crossref","first-page":"59","DOI":"10.2460\/javma.2002.220.59","article-title":"Evaluation of a commercially available hyperimmune plasma product for prevention of naturally acquired pneumonia caused by Rhodococcus equi in foals","volume":"220","author":"Giguere","year":"2002","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"10.1016\/j.vetmic.2019.108571_bib0010","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1111\/j.1939-1676.2011.00804.x","article-title":"Rhodococcus equi: clinical manifestations, virulence, and immunity","volume":"25","author":"Giguere","year":"2011","journal-title":"J. Vet. Intern. Med."},{"key":"10.1016\/j.vetmic.2019.108571_bib0015","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. North Am. Equine Pract."},{"key":"10.1016\/j.vetmic.2019.108571_bib0020","doi-asserted-by":"crossref","first-page":"74","DOI":"10.2460\/javma.237.1.74","article-title":"Determination of the prevalence of antimicrobial resistance to macrolide antimicrobials or rifampin in Rhodococcus equi isolates and treatment outcome in foals infected with antimicrobial-resistant isolates of R equi","volume":"237","author":"Giguere","year":"2010","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"10.1016\/j.vetmic.2019.108571_bib0025","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1016\/j.vetmic.2019.07.010","article-title":"Prevalence and risk factors associated with emergence of Rhodococcus equi resistance to macrolides and rifampicin in horse-breeding farms in Kentucky, USA","volume":"235","author":"Huber","year":"2019","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.vetmic.2019.108571_bib0030","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.01714-18","article-title":"Emergence of Resistance to Macrolides and Rifampin in Clinical Isolates of Rhodococcus equi from Foals in Central Kentucky, 1995 to 2017","volume":"63","author":"Huber","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.vetmic.2019.108571_bib0035","series-title":"Demographics of the U.S. Equine Population","author":"Veterinary Services, C. f. E. a. A. H","year":"2017"},{"key":"10.1016\/j.vetmic.2019.108571_bib0040","first-page":"306","article-title":"Rhodococcus equi infections in animals and humans","volume":"64","author":"Witkowski","year":"2011","journal-title":"Wiad. Lek."},{"key":"10.1016\/j.vetmic.2019.108571_bib0045","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1093\/cid\/cix059","article-title":"World health organization ranking of antimicrobials according to their importance in human medicine","volume":"64","author":"Cohen","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.vetmic.2019.108571_bib0050","doi-asserted-by":"crossref","first-page":"1834","DOI":"10.3201\/eid2110.140633","article-title":"Influenza virus surveillance in coordinated swine production systems, United States","volume":"21","author":"Kaplan","year":"2015","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.vetmic.2019.108571_bib0055","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0115815","article-title":"European surveillance network for influenza in pigs: surveillance programs, diagnostic tools and Swine influenza virus subtypes identified in 14 European countries from 2010 to 2013","volume":"9","author":"Simon","year":"2014","journal-title":"PLoS One"},{"issue":"Suppl 3","key":"10.1016\/j.vetmic.2019.108571_bib0060","doi-asserted-by":"crossref","first-page":"S135","DOI":"10.1086\/381579","article-title":"Dramatic decrease in the incidence of Salmonella serotype Enteritidis infections in 5 FoodNet sites: 1996-1999","volume":"38","author":"Marcus","year":"2004","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.vetmic.2019.108571_bib0065","first-page":"3184","article-title":"Novel transferable erm(46) determinant responsible for emerging macrolide resistance in Rhodococcus equi","volume":"70","author":"Anastasi","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.vetmic.2019.108571_bib0070","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.vetmic.2017.08.010","article-title":"Development of a multilocus sequence typing scheme for Rhodococcus equi","volume":"210","author":"Duquesne","year":"2017","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.vetmic.2019.108571_bib0075","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02260-19","article-title":"Clonal confinement of a highly mobile resistance element driven by combination therapy in Rhodococcus equi","volume":"10","author":"Alvarez-Narvaez","year":"2019","journal-title":"MBio"},{"key":"10.1016\/j.vetmic.2019.108571_bib0080","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s12864-016-3407-6","article-title":"Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods","volume":"18","author":"Ahrenfeldt","year":"2017","journal-title":"BMC Genomics"},{"key":"10.1016\/j.vetmic.2019.108571_bib0085","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.vetmic.2019.108571_bib0090","doi-asserted-by":"crossref","first-page":"2784","DOI":"10.1128\/JCM.39.8.2784-2787.2001","article-title":"Characterization of mutations in the rpoB gene associated with rifampin resistance in Rhodococcus equi isolated from foals","volume":"39","author":"Fines","year":"2001","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.vetmic.2019.108571_bib0095","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":"10.1016\/j.vetmic.2019.108571_bib0100","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1294\/jes.16.29","article-title":"Genotypic characterization of virulent Rhodococcus equi isolated from the environment of Hokkaido native horses in Hakodate, Hokkaido","volume":"16","author":"Takai","year":"2005","journal-title":"J. Equine Sci."},{"key":"10.1016\/j.vetmic.2019.108571_bib0105","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1089\/fpd.2006.3.59","article-title":"Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet","volume":"3","author":"Ribot","year":"2006","journal-title":"Foodborne Pathog. Dis."},{"key":"10.1016\/j.vetmic.2019.108571_bib0110","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1093\/jac\/dkv072","article-title":"Investigation of a possible outbreak of carbapenem-resistant Acinetobacter baumannii in Odense, Denmark using PFGE, MLST and whole-genome-based SNPs","volume":"70","author":"Hammerum","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.vetmic.2019.108571_bib0115","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1111\/jam.12977","article-title":"Multilocus sequence typing of Arcobacter butzleri isolates collected from dairy plants and their products, and comparison with their PFGE types","volume":"120","author":"De Cesare","year":"2016","journal-title":"J. Appl. Microbiol."},{"key":"10.1016\/j.vetmic.2019.108571_bib0120","article-title":"Laboratory investigation of Salmonella enterica serovar Poona Outbreak in California: comparison of pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) results","volume":"8","author":"Kozyreva","year":"2016","journal-title":"PLoS Curr."},{"key":"10.1016\/j.vetmic.2019.108571_bib0125","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3201\/eid0703.017303","article-title":"PulseNet: The molecular subtyping network for foodborne bacterial bisease burveillance, United States","volume":"7","author":"Swaminathan","year":"2001","journal-title":"Emerging Infect. Dis."},{"key":"10.1016\/j.vetmic.2019.108571_bib0130","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/s12866-015-0445-1","article-title":"Prevalence and genetic diversity of Rhodococcus equi in wild boars (Sus scrofa), roe deer (Capreolus capreolus) and red deer (Cervus elaphus) in Poland","volume":"15","author":"Witkowski","year":"2015","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.vetmic.2019.108571_bib0135","doi-asserted-by":"crossref","first-page":"153","DOI":"10.2460\/ajvr.2003.64.153","article-title":"Epidemiologic study of results of pulsed-field gel electrophoresis of isolates of Rhodococcus equi obtained from horses and horse farms","volume":"64","author":"Cohen","year":"2003","journal-title":"Am. J. Vet. Res."},{"key":"10.1016\/j.vetmic.2019.108571_bib0140","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1292\/jvms.68.249","article-title":"Molecular typing of VapA-positive Rhodococcus equi isolates from Jeju native horses, Korea","volume":"68","author":"Son","year":"2006","journal-title":"J. Vet. Med. Sci."},{"key":"10.1016\/j.vetmic.2019.108571_bib0145","doi-asserted-by":"crossref","first-page":"3140","DOI":"10.1093\/gbe\/evw222","article-title":"Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi","volume":"8","author":"Anastasi","year":"2016","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.vetmic.2019.108571_bib0150","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1128\/JCM.41.4.1499-1506.2003","article-title":"Influence of transferable genetic determinants on the outcome of typing methods commonly used for Enterococcus faecium","volume":"41","author":"Werner","year":"2003","journal-title":"J. Clin. Microbiol."}],"container-title":["Veterinary Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0378113519310880?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0378113519310880?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T23:05:07Z","timestamp":1759878307000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0378113519310880"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,3]]},"references-count":30,"alternative-id":["S0378113519310880"],"URL":"https:\/\/doi.org\/10.1016\/j.vetmic.2019.108571","relation":{},"ISSN":["0378-1135"],"issn-type":[{"value":"0378-1135","type":"print"}],"subject":[],"published":{"date-parts":[[2020,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Comparing PFGE, MLST, and WGS in monitoring the spread of macrolide and rifampin resistant Rhodococcus equi in horse production","name":"articletitle","label":"Article Title"},{"value":"Veterinary Microbiology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.vetmic.2019.108571","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2020 Elsevier B.V. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"108571"}}