{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T22:26:42Z","timestamp":1788906402110,"version":"build-2803163510"},"reference-count":51,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,11,3]],"date-time":"2022-11-03T00:00:00Z","timestamp":1667433600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>In the USA, <jats:italic>Salmonella enterica<\/jats:italic> subspecies <jats:italic>enterica<\/jats:italic> serovar Senftenberg is among the top five serovars isolated from food and the top 11 serovars isolated from clinically ill animals. Human infections are associated with exposure to farm environments or contaminated food. The objective of this study was to characterize <jats:italic>S.<\/jats:italic> Senftenberg isolates from production animals by analyzing phenotypic antimicrobial resistance profiles, genomic features and phylogeny.<\/jats:p><jats:p><jats:italic>Salmonella<\/jats:italic> Senftenberg isolates (n\u2009=\u200994) from 20 US states were selected from NVSL submissions (2014\u20132017), tested against 14 antimicrobial drugs, and resistance phenotypes determined. Resistance genotypes were determined using whole genome sequencing analysis with AMRFinder and the NCBI and ResFinder databases with ABRicate. Plasmids were detected using PlasmidFinder. Integrons were detected using IntFinder and manual alignment with reference genes. Multilocus-sequence-typing (MLST) was determined using ABRicate with PubMLST database, and phylogeny was determined using vSNP.<\/jats:p><jats:p>Among 94 isolates, 60.6% were resistant to at least one antimicrobial and 39.4% showed multidrug resistance. The most prevalent resistance findings were for streptomycin (44.7%), tetracycline (42.6%), ampicillin (36.2%) and sulfisoxazole (32.9%). The most commonly found antimicrobial resistance genes were <jats:italic>aac<\/jats:italic>(6\u2032)-Iaa (100%), <jats:italic>aph<\/jats:italic>(3\u2033)-Ib and <jats:italic>aph<\/jats:italic>(6)-Id (29.8%) for aminoglycosides, followed by <jats:italic>bla<\/jats:italic><jats:sub>TEM-1<\/jats:sub> (26.6%) for penicillins, <jats:italic>sul<\/jats:italic>1 (25.5%) and <jats:italic>sul<\/jats:italic>2 (23.4%) for sulfonamides and <jats:italic>tet<\/jats:italic>A (23.4%) for tetracyclines. Quinolone-resistant isolates presented mutations in <jats:italic>gyr<\/jats:italic>A and\/or <jats:italic>par<\/jats:italic>C genes. Class 1 integrons were found in 37 isolates. Thirty-six plasmid types were identified among 77.7% of the isolates. Phylogenetic analysis identified two distinct lineages of <jats:italic>S.<\/jats:italic> Senftenberg that correlated with the MLST results. Isolates were classified into two distinct sequence types (ST): ST14 (97.9%) and ST 185 (2.1%). The diversity of this serotype suggests multiple introductions into animal populations from outside sources.<\/jats:p><jats:p>This study provided antimicrobial susceptibility and genomic characteristics of <jats:italic>S.<\/jats:italic> Senftenberg clinical isolates from production animals in the USA during 2014 to 2017. This study will serve as a base for future studies focused on the phenotypic and molecular antimicrobial characterization of <jats:italic>S.<\/jats:italic> Senftenberg isolates in animals. Monitoring of antimicrobial resistance to detect emergence of multidrug-resistant strains is critical.<\/jats:p>","DOI":"10.3389\/fmicb.2022.979790","type":"journal-article","created":{"date-parts":[[2022,11,3]],"date-time":"2022-11-03T04:51:15Z","timestamp":1667451075000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":17,"title":["Antimicrobial resistance and genomic characterization of Salmonella enterica serovar Senftenberg isolates in production animals from the United States"],"prefix":"10.3389","volume":"13","author":[{"given":"Mariela E.","family":"Srednik","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brenda R.","family":"Morningstar-Shaw","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica A.","family":"Hicks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tonya A.","family":"Mackie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda K.","family":"Schlater","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,11,3]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"256","DOI":"10.3390\/genes9050256","article-title":"Characterization of antimicrobial resistance determinants and class 1 and class 2 Integrons in Salmonella enterica spp., multidrug-resistant isolates from pigs","volume":"9","author":"Arg\u00fcello","year":"2018","journal-title":"Genes (Basel)"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"e35782","DOI":"10.1371\/journal.pone.0035782","article-title":"Heterogeneity of Persistence of Salmonella enterica Serotype Senftenberg strains could explain the emergence of this serotype in poultry flocks","volume":"7","author":"Boumart","year":"2012","journal-title":"PLoS One"},{"key":"ref800","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"e00853","DOI":"10.1128\/mBio.00853-19","article-title":"Identification of novel mobilized colistin resistance gene mcr-9 in a multidrug-resistant, colistin-susceptible Salmonella enterica serotype Typhimurium isolate","volume":"10","author":"Carroll","year":"2019","journal-title":"MBio"},{"key":"ref4","year":""},{"key":"ref5","year":"2010"},{"key":"ref6","year":"2016"},{"key":"ref7","year":"2022"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1111\/1462-2920.14858","article-title":"Emergence of new variants of antibiotic resistance genomic islands among multidrug-resistant Salmonella enterica in poultry","volume":"22","author":"Cohen","year":"2020","journal-title":"Environ. Microbiol."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12941-015-0100-6","article-title":"Resistance integrons: class 1, 2 and 3 integrons","volume":"14","author":"Deng","year":"2015","journal-title":"Ann. Clin. Microbiol. Antimicrob."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"779","DOI":"10.4315\/0362-028x-63.6.779","article-title":"Review of studies on the thermal resistance of Salmonellae","volume":"63","author":"Doyle","year":"1999","journal-title":"J. Food Prot."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-4939-1625-2_1","article-title":"Luminex(\u00ae) multiplex bead suspension arrays for the detection and serotyping of Salmonella spp","volume":"1225","author":"Dunbar","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"2014","DOI":"10.1128\/JCM.00052-16","article-title":"Genomic and phenotypic analyses reveal the emergence of an atypical Salmonella enterica Serovar Senftenberg variant in China","volume":"54","author":"El Ghany","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"e00483","DOI":"10.1128\/AAC.00483-19","article-title":"Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates","volume":"63","author":"Feldgarden","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"2877","DOI":"10.1093\/bioinformatics\/btv271","article-title":"kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome","volume":"31","author":"Gardner","year":"2015","journal-title":"Bioinformatics"},{"key":"ref16","volume-title":"Antigenic Formulae of the","author":"Grimont","year":"2007"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"e0259471","DOI":"10.1371\/journal.pone.0259471","article-title":"Genomic evidence of environmental and resident Salmonella Senftenberg and Montevideo contamination in the pistachio supply-chain","volume":"16","author":"Haendiges","year":"2019","journal-title":"PLoS One"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"e265","DOI":"10.1017\/S0950268819001547","article-title":"Multistate outbreaks of Salmonella infections linked to imported Maradol papayas \u2013 United States, December 2016\u2013September 2017","volume":"147","author":"Hassan","year":"2019","journal-title":"Epidemiol. Infect."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1128\/JCM.02227-12","article-title":"Extremely drug-resistant Salmonella enterica Serovar Senftenberg infections in patients in Zambia","volume":"51","author":"Hendriksen","year":"2013","journal-title":"J. Clin. Microbiol."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"886","DOI":"10.3390\/antibiotics9120886","article-title":"Genomic characteristics of Colistin-resistant Salmonella enterica subsp. enterica Serovar Infantis from poultry farms in the republic of Serbia","volume":"9","author":"Jov\u010di\u0107","year":"2020","journal-title":"Antibiotics (Basel)."},{"key":"ref100","doi-asserted-by":"publisher","first-page":"7674","DOI":"10.1038\/s41598-018-26073-5","article-title":"Genomic and functional characterisation of IncX3 plasmids encoding blaSHV-12 in Escherichia coli from human and animal origin","volume":"8","author":"Liakopoulos","year":"2018","journal-title":"Sci. Rep."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1089\/fpd.2011.1083","article-title":"Surveillance of Salmonella prevalence in animal feeds and characterization of the Salmonella isolates by serotyping and antimicrobial susceptibility","volume":"9","author":"Li","year":"2012","journal-title":"Foodborne Pathog. Dis."},{"key":"ref400","author":"Loaiza","year":"2020"},{"key":"ref22","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":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"5515","DOI":"10.1128\/AAC.01030-16","article-title":"Whole-genome sequencing for detecting antimicrobial resistance in Nontyphoidal Salmonella","volume":"60","author":"McDermott","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"832","DOI":"10.3389\/fmicb.2019.00832","article-title":"Antimicrobial resistance genes, cassettes, and plasmids present in Salmonella enterica associated with United States food animals","volume":"10","author":"McMillan","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"167","DOI":"10.3390\/foods7100167","article-title":"Antibiotic-resistant Salmonella in the food supply and the potential role of antibiotic alternatives for control","volume":"7","author":"Nair","year":"2018","journal-title":"Foods (Basel, Switzerland)."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1186\/s12866-019-1598-0","article-title":"Characterization of Salmonella Dublin isolated from bovine and human hosts","volume":"19","author":"Paudyal","year":"2019","journal-title":"BMC Microbiol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1128\/AAC.37.4.761","article-title":"The 3\u2032 conserved segment of integrons contains a gene associated with multidrug resistance to antiseptics and disinfectants","volume":"37","author":"Paulsen","year":"1993","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1080\/03079450802216561","article-title":"Persistence of Salmonella Senftenberg in poultry production environments and investigation of its resistance to desiccation","volume":"37","author":"Pedersen","year":"2008","journal-title":"Avian Pathol."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"16120","DOI":"10.1038\/nmicrobiol.2016.120","article-title":"Assess drug-resistance phenotypes, not just genotypes","volume":"1","author":"Piddock","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"001386","DOI":"10.1099\/jmm.0.001386","article-title":"Fluoroquinolone resistance in non-typhoidal Salmonella enterica isolated from slaughtered pigs in Thailand","volume":"70","author":"Poomchuchit","year":"2021","journal-title":"J. Med. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"7359","DOI":"10.1038\/s41598-020-64346-0","article-title":"Discovery of seven novel mutations of gyrB, parC and pare in Salmonella Typhi and Paratyphi strains from Jiangsu Province of China","volume":"10","author":"Qian","year":"2020","journal-title":"Sci. Rep."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"e00009","DOI":"10.1128\/mSystems.00009-16","article-title":"Is the evolution of Salmonellaenterica subsp. enterica linked to restriction-modification systems?","volume":"1","author":"Roer","year":"2016","journal-title":"mSystems"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1093\/jac\/dkg168","article-title":"Mutations in gyrA and parC genes in nalidixic acid-resistant Escherichia coli strains from food products, humans and animals","volume":"51","author":"S\u00e1enz","year":"2003","journal-title":"J. Antimicrob. Chemother."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"1733","DOI":"10.1089\/mdr.2020.0230","article-title":"Antimicrobial resistance phenotypes and genotypes of Salmonella spp. isolated from commercial duck meat production in Thailand and their minimal inhibitory concentration of disinfectants","volume":"27","author":"Sinwat","year":"2021","journal-title":"Microb. Drug Resist."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"417","DOI":"10.33073\/pjm-2019-055","article-title":"Colistin resistance in Enterobacterales strains \u2013 A current view","volume":"68","author":"Stefaniuk","year":"2019","journal-title":"Pol. J. Microbiol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/1471-2180-11-153","article-title":"Molecular and comparative analysis of Salmonella enterica Senftenberg from humans and animals using PFGE, MLST and NERMS","volume":"11","author":"Stepan","year":"2011","journal-title":"BMC Microbiol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1111\/j.1574-6976.2011.00273.x","article-title":"Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into gram-negative pathogens","volume":"35","author":"Stokes","year":"2011","journal-title":"FEMS Microbiol. Rev."},{"key":"ref42","author":"Switt","year":"2019"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"e00573","DOI":"10.1128\/AAC.00573-20","article-title":"The mcr-9 gene of Salmonella and Escherichia coli is not associated with Colistin resistance in the United States","volume":"64","author":"Tyson","year":"2020","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref44","year":"2014"},{"key":"ref700","year":"2021"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1080\/20477724.2019.1574112","article-title":"Extensive drug resistant Salmonella enterica serovar Senftenberg carrying blaNDM encoding plasmid p5558 (IncA\/C) from India","volume":"113","author":"Veeraraghavan","year":"2019","journal-title":"Pathogens Global Health"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.ijantimicag.2006.05.027","article-title":"Antibiotic resistance, integrons and Salmonella genomic island 1 among non-typhoidal Salmonella serovars in The Netherlands","volume":"28","author":"Vo","year":"2006","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"1681","DOI":"10.3201\/eid1311.061438","article-title":"Human Salmonella and concurrent decreased susceptibility to quinolones and extended-Spectrum Cephalosporins","volume":"13","author":"Whichard","year":"2007","journal-title":"Emerg. Infect. Dis."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1016\/j.jiph.2019.06.011","article-title":"Genomic and antimicrobial resistance genes diversity in multidrug CTX-M-positive isolates of Escherichia coli at a health care facility in Jeddah","volume":"13","author":"Yasir","year":"2020","journal-title":"J. Infect. Public Health"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"2764","DOI":"10.1093\/jac\/dkx217","article-title":"PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens","volume":"72","author":"Zankari","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"2644","DOI":"10.1093\/jac\/dku197","article-title":"Presence of disinfectant resistance genes in Escherichia coli isolated from retail meats in the USA","volume":"69","author":"Zou","year":"2014","journal-title":"J. Antimicrob. Chemother."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.979790\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,3]],"date-time":"2022-11-03T04:51:20Z","timestamp":1667451080000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.979790\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,3]]},"references-count":51,"alternative-id":["10.3389\/fmicb.2022.979790"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2022.979790","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,3]]},"article-number":"979790"}}