{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:18:37Z","timestamp":1787026717692,"version":"build-2736575974"},"reference-count":83,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,3,16]],"date-time":"2023-03-16T00:00:00Z","timestamp":1678924800000},"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>\n                    The presence of mobile genetic elements in\n                    <jats:italic>Salmonella<\/jats:italic>\n                    isolated from a chicken farm constitutes a potential risk for the appearance of emerging bacteria present in the food industry. These elements contribute to increased pathogenicity and antimicrobial resistance through genes that are related to the formation of biofilms and resistance genes contained in plasmids, integrons, and transposons. One hundred and thirty-three\n                    <jats:italic>Salmonella<\/jats:italic>\n                    isolates from different stages of the production line, such as feed manufacturing, hatchery, broiler farm, poultry farm, and slaughterhouse, were identified, serotyped and sequenced. The most predominant serotype was\n                    <jats:italic>Salmonella<\/jats:italic>\n                    Infantis. Phylogenetic analyses demonstrated that the diversity and spread of strains in the pipeline are serotype-independent, and that isolates belonging to the same serotype are very closely related genetically. On the other hand,\n                    <jats:italic>Salmonella<\/jats:italic>\n                    Infantis isolates carried the pESI IncFIB plasmid harboring a wide variety of resistance genes, all linked to mobile genetic elements, and among carriers of these plasmids, the antibiograms showed differences in resistance profiles and this linked to a variety in plasmid structure, similarly observed in the diversity of\n                    <jats:italic>Salmonella<\/jats:italic>\n                    Heidelberg isolates carrying the IncI1-I\u03b1 plasmid. Mobile genetic elements encoding resistance and virulence genes also contributed to the differences in gene content. Antibiotic resistance genotypes were matched closely by the resistance phenotypes, with high frequency of tetracycline, aminoglycosides, and cephalosporins resistance. In conclusion, the contamination in the poultry industry is described throughout the entire production line, with mobile genetic elements leading to multi-drug resistant bacteria, thus promoting survival when challenged with various antimicrobial compounds.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2023.1072793","type":"journal-article","created":{"date-parts":[[2023,3,16]],"date-time":"2023-03-16T03:12:48Z","timestamp":1678936368000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":30,"title":["Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line"],"prefix":"10.3389","volume":"14","author":[{"given":"Gabriel I.","family":"Kr\u00fcger","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Coral","family":"Pardo-Est\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phillippi","family":"Zepeda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge","family":"Olivares-Pacheco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Galleguillos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcia","family":"Suarez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Castro-Severyn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis","family":"Alvarez-Thon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"Tello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge H.","family":"Valdes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia P.","family":"Saavedra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,3,16]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000365","article-title":"Molecular epidemiology of salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid","volume":"6","author":"Alba","year":"2020","journal-title":"Microb. Genom."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/nar\/gkz935\/5608993","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref3","first-page":"403","article-title":"Basic local alignment search tool","volume-title":"J. Mol. Biol.","author":"Altschul","year":"1990"},{"key":"ref4","volume-title":"FastQC: A Quality Control Tool for High Throughput Sequence Data","author":"Andrews","year":"2010"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1111\/1462-2920.12351","article-title":"A unique megaplasmid contributes to stress tolerance and pathogenicity of an emergent S almonella enterica serovar Infantis strain","volume":"16","author":"Aviv","year":"2014","journal-title":"Environ. Microbiol."},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.12834\/VetIt.2269.13773.1","article-title":"High prevalence of clonally related multiple resistant salmonella Infantis carrying class 1 integrons in broiler farms","volume":"57","author":"Badouei","year":"2021","journal-title":"Vet. Ital."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a New genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"104972","DOI":"10.1016\/j.micinf.2022.104974","article-title":"Genomic characterization of a multi-drug resistant, CTX-M-65-producing clinical isolate of salmonella Infantis isolated in Brazil","volume":"24","author":"Bertani","year":"2022","journal-title":"Microbes Infect."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1016\/j.micpath.2018.03.039","article-title":"Biofilm formation by salmonella Enteritidis and salmonella typhimurium isolated from avian sources is partially related with their in vivo pathogenicity","volume":"118","author":"Borges","year":"2018","journal-title":"Microb. Pathog."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"2284","DOI":"10.3201\/eid2412.180500","article-title":"CTX-M-65 extended-Spectrum \u03b2-lactamase\u2013producing salmonella enterica serotype Infantis, united States1","volume":"24","author":"Brown","year":"2018","journal-title":"Emerg. Infect. Dis."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"2431","DOI":"10.3389\/fmicb.2018.02431","article-title":"Genomic characterization of extended-Spectrum cephalosporin-resistant salmonella enterica in the Colombian poultry chain","volume":"9","author":"Castellanos","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"2070","DOI":"10.14202\/vetworld.2020.2070-2084","article-title":"Antibiotic resistance in salmonella spp. isolated from poultry: a global overview","volume":"13","author":"Castro-Vargas","year":"2020","journal-title":"Vet. World"},{"key":"ref01","article-title":"Performance standards for antimicrobial susceptibility testing. 28th ed","year":"2018","journal-title":"CLSI supplement M100"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1499.e7","DOI":"10.1016\/j.cmi.2022.05.029","article-title":"The emergence of a multidrug resistant salmonella Muenchen in Israel is associated with horizontal acquisition of the epidemic pESI plasmid","volume":"28","author":"Cohen","year":"2022","journal-title":"Clin. Microbiol. Infect."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"184","DOI":"10.3389\/fpls.2017.00184","article-title":"Analysis of plant pan-genomes and transcriptomes with GET_HOMOLOGUES-EST, a clustering solution for sequences of the same species","volume":"8","author":"Contreras-Moreira","year":"2017","journal-title":"Front. Plant Sci."},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"3293","DOI":"10.1128\/AEM.02588-10","article-title":"Genotypic-phenotypic discrepancies between antibiotic resistance characteristics of Escherichia coli isolates from calves in management settings with high and low antibiotic use","volume":"77","author":"Davis","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"109091","DOI":"10.1016\/j.ijfoodmicro.2021.109091","article-title":"Genomic investigation of antimicrobial resistance determinants and virulence factors in salmonella enterica serovars isolated from contaminated food and human stool samples in Brazil","volume":"343","author":"de Melo","year":"2021","journal-title":"Int. J. Food Microbiol."},{"key":"ref18","first-page":"107","article-title":"Inhibiting bacterial cooperation is an evolutionarily robust anti-biofilm strategy","volume-title":"Nat. Commun.","author":"Dieltjens","year":"2020"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1111\/zph.12819","article-title":"Molecular characterization and antimicrobial resistance profiles of salmonella Heidelberg isolates from poultry","volume":"68","author":"Dominguez","year":"2021","journal-title":"Zoonoses Publ. Health"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"104112","DOI":"10.1016\/j.fm.2022.104112","article-title":"Large-scale genomic analysis reveals the pESI-like megaplasmid presence in salmonella Agona, Muenchen, Schwarzengrund, and Senftenberg","volume":"108","author":"dos Santos","year":"2022","journal-title":"Food Microbiol."},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.2903\/j.efsa.2018.5500","article-title":"The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2017","volume":"16","year":"2018","journal-title":"EFSA J."},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.2903\/j.efsa.2019.5926","article-title":"The European Union one health 2018 Zoonoses report","volume":"17","year":"2019","journal-title":"EFSA J."},{"key":"ref23","article-title":"Non Typhoidal salmonella in food products. Nutrition and food","volume":"2","author":"Fazza","year":"2021","journal-title":"Technology"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"e0125621","DOI":"10.1128\/spectrum.01256-21","article-title":"WHO critical priority Escherichia coli as one health challenge for a post-pandemic scenario: genomic surveillance and analysis of current trends in Brazil","volume":"10","author":"Fuga","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"D195","DOI":"10.1093\/nar\/gky1050","article-title":"PLSDB: a resource of complete bacterial plasmids","volume":"47","author":"Galata","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"104716","DOI":"10.1016\/j.meegid.2021.104716","article-title":"The plasmidome of multidrug-resistant emergent salmonella serovars isolated from poultry","volume":"89","author":"Galetti","year":"2021","journal-title":"Infect. Genet. Evol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"780","DOI":"10.3390\/microorganisms10040780","article-title":"Food is reservoir of MDR salmonella: prevalence of ESBLs profiles and resistance genes in strains isolated from food","volume":"10","author":"Gambino","year":"2022","journal-title":"Microorganisms"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1093\/jac\/dkq481","article-title":"IncA\/C plasmids mediate antimicrobial resistance linked to virulence genes in the Spanish clone of the emerging salmonella enterica serotype 4,[5],12:i:\u2212","volume":"66","author":"Garc\u00eda","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"101157","DOI":"10.1016\/j.psj.2021.101157","article-title":"Mapping foodborne pathogen contamination throughout the conventional and alternative poultry supply chains","volume":"100","author":"Golden","year":"2021","journal-title":"Poult. Sci."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1186\/s12864-019-6260-6","article-title":"WGS based study of the population structure of salmonella enterica serovar Infantis","volume":"20","author":"Gymoese","year":"2019","journal-title":"BMC Genomics"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast genome-wide functional annotation through Orthology assignment by eggNOG-mapper","volume":"34","author":"Huerta-Cepas","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"109821","DOI":"10.1016\/j.ijfoodmicro.2022.109821","article-title":"Multidrug resistance and virulence genes carried by mobile genomic elements in salmonella enterica isolated from live food animals, processed, and retail meat in North Carolina, 2018\u20132019","volume":"378","author":"Hull","year":"2022","journal-title":"Int. J. Food Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref36","doi-asserted-by":"publisher","DOI":"10.1111\/jfs.12852","article-title":"Prevalence of salmonella serotypes S. Enteritidis and S. Typhimurium in poultry and poultry products","volume":"40","author":"Karabasanavar","year":"2020","journal-title":"J. Food Saf."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"108964","DOI":"10.1016\/j.foodcont.2022.108964","article-title":"Antibiofilm effects of quercetin against salmonella enterica biofilm formation and virulence, stress response, and quorum-sensing gene expression","volume":"137","author":"Kim","year":"2022","journal-title":"Food Control"},{"key":"ref38","volume-title":"Trim galore: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files","author":"Krueger","year":"2012"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"108956","DOI":"10.1016\/j.ijfoodmicro.2020.108956","article-title":"Whole-genome sequence analysis of salmonella Infantis isolated from raw chicken meat samples and insights into pESI-like megaplasmid","volume":"337","author":"K\u00fcrekci","year":"2021","journal-title":"Int. J. Food Microbiol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"1049","DOI":"10.3390\/ani10061049","article-title":"Phenotypic and genotypic characterization of virulence factors and susceptibility to antibiotics in salmonella Infantis strains isolated from chicken meat: first findings in Chile","volume":"10","author":"Lapierre","year":"2020","journal-title":"Animals"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.5851\/kosfa.2020.e75","article-title":"Etiological agents implicated in foodborne illness world wide","volume":"41","author":"Lee","year":"2021","journal-title":"Food Sci. Anim. Resour."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"6031","DOI":"10.1016\/j.psj.2020.07.038","article-title":"Prevalence and characteristics of salmonella isolates recovered from retail raw chickens in Shaanxi Province","volume":"99","author":"Li","year":"2020","journal-title":"Chin. Poult. Sci."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"e0266443","DOI":"10.1371\/journal.pone.0266443","article-title":"Highly prevalent MDR, frequently carrying virulence genes and antimicrobial resistance genes in salmonella enterica serovar 4,[5],12:i:-isolates from Guizhou Province, China","volume":"17","author":"Long","year":"2022","journal-title":"PLoS One"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1111\/j.1574-695X.2012.00960.x","article-title":"The interconnection between biofilm formation and horizontal gene transfer","volume":"65","author":"Madsen","year":"2012","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e0134848","DOI":"10.1371\/journal.pone.0134848","article-title":"Cleanroom maintenance significantly reduces abundance but not diversity of indoor microbiomes","volume":"10","author":"Mahnert","year":"2015","journal-title":"PLoS One"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1086\/650733","article-title":"The global burden of Nontyphoidal salmonella gastroenteritis","volume":"50","author":"Majowicz","year":"2010","journal-title":"Clin. Infect. Dis."},{"key":"ref48","first-page":"4647","article-title":"Zdobnov EM. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume-title":"Mol. Biol. Evol.","author":"Manni","year":"2021"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"101968","DOI":"10.1016\/j.psj.2022.101968","article-title":"Research note: persistent salmonella problems in slaughterhouses related to clones linked to poultry companies","volume":"101","author":"Marin","year":"2022","journal-title":"Poult. Sci."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"691","DOI":"10.3389\/fvets.2020.547891","article-title":"Genomic epidemiology of salmonella Infantis in Ecuador: from poultry farms to human infections","volume":"7","author":"Mej\u00eda","year":"2020","journal-title":"Front. Vet. Sci."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"94","DOI":"10.21608\/zvjz.2021.81722.1144","article-title":"Antimicrobial resistance, virulence associated genes and biofilm formation of salmonella species isolated from different sources","volume":"49","author":"Mohamed","year":"2021","journal-title":"Zagazig Vet. J."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"1096","DOI":"10.1093\/bioinformatics\/btp105","article-title":"Correia a. INTEGRALL: a database and search engine for integrons, integrases and gene cassettes","volume":"25","author":"Moura","year":"2009","journal-title":"Bioinformatics"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"109120","DOI":"10.1016\/j.vetmic.2021.109120","article-title":"Prevalence, risk factors and genetic traits of salmonella Infantis in Dutch broiler flocks","volume":"258","author":"Mughini-Gras","year":"2021","journal-title":"Vet. Microbiol."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"108539","DOI":"10.1016\/j.foodcont.2021.108539","article-title":"Public health impact of salmonella spp. on raw poultry: current concepts and future prospects in the United States","volume":"132","author":"O\u2019Bryan","year":"2022","journal-title":"Food Control"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"100195","DOI":"10.1016\/j.japr.2021.100195","article-title":"Antimicrobial tolerance, biofilm formation, and molecular characterization of salmonella isolates from poultry processing equipment","volume":"30","author":"Obe","year":"2021","journal-title":"J. Appl. Poult. Res."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/j.ijfoodmicro.2012.12.028","article-title":"Biocide tolerance in bacteria","volume":"162","author":"Ortega Morente","year":"2013","journal-title":"Int. J. Food Microbiol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1111\/risa.13563","article-title":"Salmonella prevalence alone is not a good indicator of poultry food safety","volume":"41","author":"Oscar","year":"2021","journal-title":"Risk Anal."},{"key":"ref59","first-page":"038190","article-title":"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments","author":"Page","year":"2016","journal-title":"bioRxiv"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"2370","DOI":"10.3390\/microorganisms9112370","article-title":"Genetic characterization of salmonella Infantis with multiple drug resistance profiles isolated from a poultry-farm in Chile","volume":"9","author":"Pardo-Est\u00e9","year":"2021","journal-title":"Microorganisms"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1016\/j.fm.2013.10.002","article-title":"Current and emerging technologies for rapid detection and characterization of salmonella in poultry and poultry products","volume":"38","author":"Park","year":"2014","journal-title":"Food Microbiol."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref63","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00088-17","article-title":"Mobile genetic elements associated with antimicrobial resistance","volume":"31","author":"Partridge","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"ref64","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics11070876","article-title":"Multi-Drug Resistance to Salmonella spp. When isolated from raw meat products","volume":"11","author":"P\u0142awi\u0144ska-Czarnak","year":"2022","journal-title":"Antibiotics."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"e0206021","DOI":"10.1128\/mBio.02060-21","article-title":"TnCentral: a prokaryotic transposable element database and web portal for transposon analysis","volume":"12","author":"Ross","year":"2021","journal-title":"MBio"},{"key":"ref66","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1186\/s12864-022-08725-z","article-title":"Differences between the global transcriptomes of salmonella enterica serovars Dublin and Cerro infecting bovine epithelial cells","volume":"23","author":"Salaheen","year":"2022","journal-title":"BMC Genomics"},{"key":"ref67","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1017\/S1466252317000020","article-title":"Types and prevalence of extended\u2013spectrum beta\u2013lactamase producing Enterobacteriaceae in poultry","volume":"18","author":"Saliu","year":"2017","journal-title":"Anim. Health Res. Rev."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref69","doi-asserted-by":"publisher","first-page":"687","DOI":"10.3382\/ps\/pew342","article-title":"Population dynamics and antimicrobial resistance of the most prevalent poultry-associated salmonella serotypes","volume":"96","author":"Shah","year":"2017","journal-title":"Poult. Sci."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"D32","DOI":"10.1093\/nar\/gkj014","article-title":"ISfinder: the reference centre for bacterial insertion sequences","volume":"34","author":"Siguier","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1089\/mdr.2018.0175","article-title":"Disinfectant resistance profiles and biofilm formation capacity of Escherichia coli isolated from retail chicken","volume":"25","author":"Sun","year":"2019","journal-title":"Microb. Drug Resist."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"2757","DOI":"10.3390\/foods10112757","article-title":"The prevalence and epidemiology of salmonella in retail raw poultry meat in China: a systematic review and meta-analysis","volume":"10","author":"Sun","year":"2021","journal-title":"Foods"},{"key":"ref73","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00488-17","article-title":"Comparative analysis of extended-Spectrum-\u03b2-lactamase CTX-M-65-producing salmonella enterica Serovar Infantis isolates from humans, food animals, and retail chickens in the United States","volume":"61","author":"Tate","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"792","DOI":"10.1089\/mdr.2020.0389","article-title":"A multidrug-resistant salmonella Infantis clone is spreading and recombining in the United States","volume":"27","author":"Tyson","year":"2021","journal-title":"Microb. 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