{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T10:24:37Z","timestamp":1777544677707,"version":"3.51.4"},"reference-count":32,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2019,3,21]],"date-time":"2019-03-21T00:00:00Z","timestamp":1553126400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Department of Agriculture Project number","award":["CA-V-PHR-4707-AH407 and CA-V-PHR-4048-H"],"award-info":[{"award-number":["CA-V-PHR-4707-AH407 and CA-V-PHR-4048-H"]}]},{"name":"USDA National Institute of Food and Agriculture (NIFA) project number","award":["201567030238928"],"award-info":[{"award-number":["201567030238928"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:sec>\n<jats:title>Background<\/jats:title>\n<jats:p>In this study cull dairy cows from six California dairy herds were sampled seasonally over the course of a year. The objectives were to determine the prevalence of antimicrobial resistant (AMR) <jats:italic>Salmonella<\/jats:italic> spp. shed in cull cow feces, and the factors associated with fecal shedding of AMR and multidrug resistant (MDR) <jats:italic>Salmonella<\/jats:italic>.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Methods<\/jats:title>\n<jats:p>Six dairy farms located in the San Joaquin Valley of California were identified and enrolled as a convenience sample. On each dairy, and once during each of the four seasons, 10 cull cows were randomly selected for fecal sampling on the day of their removal from the herd. In addition, study personnel completed a survey based on responses of the herd manager to questions related to the previous 4 month\u2019s herd management and the specific cattle sampled. Fecal samples were submitted to the California Animal Health and Food Safety laboratory for <jats:italic>Salmonella<\/jats:italic> isolation. Antimicrobial resistance was evaluated using broth microdilution method and a gram-negative assay plate following Clinical Laboratory Standards Institute (CLSI) guidelines and breakpoint references. All statistical models were survey adjusted for number of animals on sampling day.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>A total of 62 <jats:italic>Salmonella<\/jats:italic> were isolated from 60 of the 239 fecal samples collected. For 12% (95% confidence interval (CI) [3\u201320]) of fecal samples a multidrug resistant <jats:italic>Salmonella<\/jats:italic> was isolated. The survey-weighted results for the two most common drug classes for which isolates were resistant were tetracycline (39%; 95% CI [27\u201351]) and ampicillin (18%; 95% CI [9\u201327]). An important finding was the identification of cephalosporin as the third most common drug class for which isolates were resistant, with ceftriaxone (10%; 95% CI [2\u201317]) being the most common drug associated with resistance in that class. At the cow-level, reason for culling, prior treatment with antimicrobial drugs as the reason for culling was associated with higher odds of isolating an AMR <jats:italic>Salmonella<\/jats:italic> isolate. At the herd-level, percent of animals monthly culled on the farm as well as number of milking cows in the herd were associated with isolation of antimicrobial resistant <jats:italic>Salmonella<\/jats:italic> in cull cows.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Discussion<\/jats:title>\n<jats:p><jats:italic>Salmonella<\/jats:italic> isolated from fecal samples from cull cows were resistant to important antimicrobials, such as ceftriaxone. The most common drug classes for which isolates were resistant were tetracyclines and beta-lactams, with ampicillin, ceftriaxone and ceftiofur being the three most common drugs within the latter. Cow and herd level factors were associated with isolating antimicrobial resistant <jats:italic>Salmonella<\/jats:italic> that should be further investigated for their potential role in promoting occurrence of AMR <jats:italic>Salmonella<\/jats:italic>. Our results also highlight the importance of monitoring dairy cattle sent to slaughter for shedding of <jats:italic>Salmonella<\/jats:italic> resistant to medically important antimicrobial drugs.<\/jats:p>\n<\/jats:sec>","DOI":"10.7717\/peerj.6546","type":"journal-article","created":{"date-parts":[[2019,3,21]],"date-time":"2019-03-21T05:41:39Z","timestamp":1553146899000},"page":"e6546","source":"Crossref","is-referenced-by-count":13,"title":["Association between herd management practices and antimicrobial resistance in <i>Salmonella<\/i> spp. from cull dairy cattle in Central California"],"prefix":"10.7717","volume":"7","author":[{"given":"Richard","family":"Pereira","sequence":"first","affiliation":[{"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7534-732X","authenticated-orcid":true,"given":"Deniece R.","family":"Williams","sequence":"additional","affiliation":[{"name":"Veterinary Medicine Teaching and Research Center, University of California, Davis, Tulare, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Rossitto","sequence":"additional","affiliation":[{"name":"Veterinary Medicine Teaching and Research Center, University of California, Davis, Tulare, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Adaska","sequence":"additional","affiliation":[{"name":"California Animal Health and Food Safety Laboratory System, University of California, Davis, Tulare, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emmanuel","family":"Okello","sequence":"additional","affiliation":[{"name":"Veterinary Medicine Teaching and Research Center, University of California, Davis, Tulare, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Champagne","sequence":"additional","affiliation":[{"name":"Veterinary Medicine Teaching and Research Center, University of California, Davis, Tulare, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0896-3939","authenticated-orcid":true,"given":"Terry W.","family":"Lehenbauer","sequence":"additional","affiliation":[{"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA"},{"name":"Veterinary Medicine Teaching and Research Center, University of California, Davis, Tulare, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xunde","family":"Li","sequence":"additional","affiliation":[{"name":"Western Institute for Food Safety and Security, University of California, Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2812-979X","authenticated-orcid":true,"given":"Jennifer","family":"Chase","sequence":"additional","affiliation":[{"name":"Western Institute for Food Safety and Security, University of California, Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tran","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Western Institute for Food Safety and Security, University of California, Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9326-0298","authenticated-orcid":true,"given":"Alda F. A.","family":"Pires","sequence":"additional","affiliation":[{"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edward R.","family":"Atwill","sequence":"additional","affiliation":[{"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA"},{"name":"Western Institute for Food Safety and Security, University of California, Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0330-5013","authenticated-orcid":true,"given":"Sharif S.","family":"Aly","sequence":"additional","affiliation":[{"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA"},{"name":"Veterinary Medicine Teaching and Research Center, University of California, Davis, Tulare, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"4443","published-online":{"date-parts":[[2019,3,21]]},"reference":[{"key":"10.7717\/peerj.6546\/ref-1","doi-asserted-by":"publisher","first-page":"e2386","DOI":"10.7717\/peerj.2386","article-title":"Epidemiology of Salmonella sp. in California cull dairy cattle: prevalence of fecal shedding and diagnostic accuracy of pooled enriched broth culture of fecal samples","volume":"4","author":"Abu Aboud","year":"2016","journal-title":"PeerJ"},{"key":"10.7717\/peerj.6546\/ref-2","doi-asserted-by":"publisher","first-page":"211","DOI":"10.2147\/JMDH.S104807","article-title":"Information bias in health research: definition, pitfalls, and adjustment methods","volume":"9","author":"Althubaiti","year":"2016","journal-title":"Journal of Multidisciplinary Healthcare"},{"issue":"12","key":"10.7717\/peerj.6546\/ref-3","doi-asserted-by":"publisher","first-page":"e00140","DOI":"10.1128\/AEM.00140-17","article-title":"Whole-genome sequencing of drug-resistant Salmonella enterica isolates from dairy cattle and humans in New York and Washington states reveals source and geographic associations","volume":"83","author":"Carroll","year":"2017","journal-title":"Applied and Environmental Microbiology"},{"key":"10.7717\/peerj.6546\/ref-4","article-title":"Antibiotic resistance threats in the United States","author":"Centers for Disease Control and Prevention (CDC)","year":"2013"},{"key":"10.7717\/peerj.6546\/ref-5","article-title":"Reports of selected Salmonella outbreak investigations","author":"Centers for Disease Control and Prevention (CDC)","year":"2017"},{"key":"10.7717\/peerj.6546\/ref-6","article-title":"2016 California dairy statistics annual","author":"California Department of Food and Agriculture","year":"2017"},{"key":"10.7717\/peerj.6546\/ref-7","volume-title":"Performance standards for antimicrobial disk and dilution susceptibility tests for bacteria isolated from animals approved standard. VET01","author":"Clinical & Laboratory Standards Institute (CLSI)","year":"2014","edition":"4"},{"key":"10.7717\/peerj.6546\/ref-8","volume-title":"M100 Performance standards for antimicrobial susceptibility testing","author":"Clinical & Laboratory Standards Institute (CLSI)","year":"2018","edition":"28"},{"issue":"4","key":"10.7717\/peerj.6546\/ref-9","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1089\/fpd.2012.1285","article-title":"Antimicrobial resistance trends among Salmonella isolates obtained from dairy cattle in the northeastern United States, 2004\u20132011","volume":"10","author":"Cummings","year":"2013","journal-title":"Foodborne Pathogens and Disease"},{"key":"10.7717\/peerj.6546\/ref-10","volume-title":"Rebhun\u2019s diseases of dairy cattle","year":"2008","edition":"2"},{"key":"10.7717\/peerj.6546\/ref-11","article-title":"Extralabel use and antimicrobials","author":"Food and Drug Administration (FDA)","year":"2017"},{"issue":"6","key":"10.7717\/peerj.6546\/ref-12","doi-asserted-by":"publisher","first-page":"1896","DOI":"10.3168\/jds.S0022-0302(06)72257-3","article-title":"Invited review: culling: nomenclature, definitions, and recommendations","volume":"89","author":"Fetrow","year":"2006","journal-title":"Journal of Dairy Science"},{"issue":"9","key":"10.7717\/peerj.6546\/ref-13","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1089\/fpd.2012.1149","article-title":"Farm-level associations with the shedding of Salmonella and antimicrobial-resistant Salmonella in U.S. dairy cattle","volume":"9","author":"Habing","year":"2012","journal-title":"Foodborne Pathogens and Disease"},{"key":"10.7717\/peerj.6546\/ref-14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.prevetmed.2017.09.015","article-title":"Culling from the actors\u2019 perspectives\u2014decision-making criteria for culling in Quebec dairy herds enrolled in a veterinary preventive medicine program","volume":"148","author":"Haine","year":"2017","journal-title":"Preventive Veterinary Medicine"},{"issue":"17","key":"10.7717\/peerj.6546\/ref-15","doi-asserted-by":"publisher","first-page":"5947","DOI":"10.1128\/AEM.00377-10","article-title":"The prevalence of multidrug resistance is higher among bovine than human Salmonella enterica serotype Newport, Typhimurium, and 4,5,12:i:- isolates in the United States but differs by serotype and geographic region","volume":"76","author":"Hoelzer","year":"2010","journal-title":"Applied and Environmental Microbiology"},{"issue":"Pt_11","key":"10.7717\/peerj.6546\/ref-16","doi-asserted-by":"publisher","first-page":"1743","DOI":"10.1099\/jmm.0.062729-0","article-title":"Co-selection may explain high rates of ciprofloxacin non-susceptible Escherichia coli from retail poultry reared without prior fluoroquinolone exposure","volume":"62","author":"Ingram","year":"2013","journal-title":"Journal of Medical Microbiology"},{"issue":"1","key":"10.7717\/peerj.6546\/ref-17","doi-asserted-by":"publisher","first-page":"5100","DOI":"10.1038\/srep05100","article-title":"Impact of treatment strategies on cephalosporin and tetracycline resistance gene quantities in the bovine fecal metagenome","volume":"4","author":"Kanwar","year":"2014","journal-title":"Scientific Reports"},{"issue":"1","key":"10.7717\/peerj.6546\/ref-18","doi-asserted-by":"publisher","first-page":"264","DOI":"10.3168\/jds.S0022-0302(98)75575-4","article-title":"Dairy cow culling strategies: making economical culling decisions","volume":"81","author":"Lehenbauer","year":"1998","journal-title":"Journal of Dairy Science"},{"issue":"1","key":"10.7717\/peerj.6546\/ref-19","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1097\/01.mop.0000192520.48411.fa","article-title":"The use of fluoroquinolones in children","volume":"18","author":"Leibovitz","year":"2006","journal-title":"Current Opinion in Pediatrics"},{"issue":"1","key":"10.7717\/peerj.6546\/ref-20","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1089\/fpd.2007.0018","article-title":"Antimicrobial drug resistance of fecal Escherichia coli and Salmonella spp. isolates from United States dairy cows","volume":"5","author":"Lundin","year":"2008","journal-title":"Foodborne Pathogens and Disease"},{"issue":"3","key":"10.7717\/peerj.6546\/ref-21","doi-asserted-by":"publisher","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":"8","author":"Magiorakos","year":"2012","journal-title":"Clinical Microbiology and Infection"},{"issue":"1","key":"10.7717\/peerj.6546\/ref-22","doi-asserted-by":"publisher","first-page":"29","DOI":"10.3201\/eid2301.160771","article-title":"Estimated incidence of antimicrobial drug\u2013resistant nontyphoidal Salmonella infections, United States, 2004\u20132012","volume":"23","author":"Medalla","year":"2016","journal-title":"Emerging Infectious Diseases"},{"key":"10.7717\/peerj.6546\/ref-23","article-title":"Economic Opportunities For Dairy Cow Culling Management Options","author":"Ott","year":"1996"},{"issue":"4","key":"10.7717\/peerj.6546\/ref-24","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.prevetmed.2003.08.003","article-title":"Association between bovine-leukosis virus seroprevalence and herd-level productivity on US dairy farms","volume":"61","author":"Ott","year":"2003","journal-title":"Preventive Veterinary Medicine"},{"issue":"2","key":"10.7717\/peerj.6546\/ref-25","doi-asserted-by":"publisher","first-page":"317","DOI":"10.2307\/1403631","article-title":"The role of sampling weights when modeling survey data","volume":"61","author":"Pfeffermann","year":"1993","journal-title":"International Statistical Review\/Revue Internationale de Statistique"},{"issue":"2\u20134","key":"10.7717\/peerj.6546\/ref-26","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1016\/j.prevetmed.2006.12.001","article-title":"Prevalence of antimicrobial resistance among Salmonella on midwest and northeast USA dairy farms","volume":"79","author":"Ray","year":"2007","journal-title":"Preventive Veterinary Medicine"},{"key":"10.7717\/peerj.6546\/ref-27","article-title":"Stratified sampling","author":"SAS","year":"2018"},{"key":"10.7717\/peerj.6546\/ref-28","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3201\/eid1701.P11101","article-title":"Foodborne illness acquired in the United States\u2014major pathogens","volume":"17","author":"Scallan","year":"2011","journal-title":"Emerging Infectious Diseases"},{"issue":"9","key":"10.7717\/peerj.6546\/ref-29","doi-asserted-by":"publisher","first-page":"1212","DOI":"10.2460\/javma.2001.219.1212","article-title":"Prevalence of Salmonella spp in cull (market) dairy cows at slaughter","volume":"219","author":"Troutt","year":"2001","journal-title":"Journal of the American Veterinary Medical Association"},{"issue":"2","key":"10.7717\/peerj.6546\/ref-30","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1086\/505084","article-title":"Highly resistant Salmonella Newport-MDRAmpC transmitted through the domestic US food supply: a foodnet case-control study of sporadic Salmonella Newport infections, 2002\u20132003","volume":"194","author":"Varma","year":"2006","journal-title":"Journal of Infectious Diseases"},{"issue":"8","key":"10.7717\/peerj.6546\/ref-31","doi-asserted-by":"publisher","first-page":"e42919","DOI":"10.1371\/journal.pone.0042919","article-title":"The co-selection of fluoroquinolone resistance genes in the gut flora of Vietnamese children","volume":"7","author":"Vien","year":"2012","journal-title":"PLOS ONE"},{"issue":"1","key":"10.7717\/peerj.6546\/ref-32","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/S0167-5877(96)01061-6","article-title":"Factors associated with mortality to 21 days of life in dairy heifers in the United States","volume":"29","author":"Wells","year":"1996","journal-title":"Preventive Veterinary Medicine"}],"container-title":["PeerJ"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/peerj.com\/articles\/6546.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/6546.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/6546.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/6546.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,3,21]],"date-time":"2019-03-21T05:41:47Z","timestamp":1553146907000},"score":1,"resource":{"primary":{"URL":"https:\/\/peerj.com\/articles\/6546"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3,21]]},"references-count":32,"alternative-id":["10.7717\/peerj.6546"],"URL":"https:\/\/doi.org\/10.7717\/peerj.6546","archive":["CLOCKSS","LOCKSS","Portico"],"relation":{},"ISSN":["2167-8359"],"issn-type":[{"value":"2167-8359","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,3,21]]},"article-number":"e6546"}}