{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T12:06:03Z","timestamp":1753877163150,"version":"3.41.2"},"reference-count":66,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,15]],"date-time":"2022-12-15T00:00:00Z","timestamp":1671062400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","award":["#303437\/2017\u20130","#405644\/2018\u20133"],"award-info":[{"award-number":["#303437\/2017\u20130","#405644\/2018\u20133"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"CAPES","doi-asserted-by":"publisher","award":["001"],"award-info":[{"award-number":["001"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018802","name":"UFPB","doi-asserted-by":"publisher","award":["88881.311776\/2018\u201301"],"award-info":[{"award-number":["88881.311776\/2018\u201301"]}],"id":[{"id":"10.13039\/501100018802","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Salmonella enterica subsp. enterica serovar Enteritidis (SE) has become the prevalent serovar isolated from gastroenteritis cases in Brazil since the 1990s. To better understand the genomic diversity and phylogenetic relationship amongst SE epidemic isolates from Brazil, 30 SE isolates from a variety of implicated foods and case patients of outbreaks between 1999 and 2006 were selected for genome comparison analyses. SE genomes were also compared against publicly available Brazilian SE isolates from pre- and postepidemic period. MLST analysis revealed that all isolates belong to sequence type (ST) 11. A total of seven Salmonella pathogenicity islands (SPIs) (SPI-1, SPI-3\u20135, SPI-13, SPI14, and C63PI) were identified in the evaluated genomes and all studied SE genomes carried similar prophage profiling. Resistome analysis revealed the presence of resistance genes to aminoglycosides [aac(6\u2019)laa, aph(3\u201d)-lb, aph(6)-ld], as well as point mutations in gyrA. Phylogenetic analysis demonstrated that certain isolates have circulated in Brazil for years and been involved in distinct outbreaks.<\/jats:p>","DOI":"10.1093\/lambio\/ovac045","type":"journal-article","created":{"date-parts":[[2024,4,8]],"date-time":"2024-04-08T13:43:42Z","timestamp":1712583822000},"source":"Crossref","is-referenced-by-count":2,"title":["Genomic and phylogenetic analysis of <i>Salmonella enterica<\/i> serovar Enteritidis strains linked to multiple outbreaks in Brazil"],"prefix":"10.1093","volume":"76","author":[{"given":"Guojie","family":"Cao","sequence":"first","affiliation":[{"name":"Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, MD, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Balkey","sequence":"additional","affiliation":[{"name":"Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, MD, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qing","family":"Jin","sequence":"additional","affiliation":[{"name":"Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, MD, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Brown","sequence":"additional","affiliation":[{"name":"Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, MD, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Allard","sequence":"additional","affiliation":[{"name":"Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, MD, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adma Nadja Ferreira","family":"de\u00a0Melo","sequence":"additional","affiliation":[{"name":"Laboratory of Microbial Processes in Foods, Department of Food Engineering, Federal University of Para\u00edba , Jo\u00e3o Pessoa, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geany Targino de Souza","family":"Pedrosa","sequence":"additional","affiliation":[{"name":"Laboratory of Microbial Processes in Foods, Department of Food Engineering, Federal University of Para\u00edba , Jo\u00e3o Pessoa, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tereza Cristina Rocha Moreira","family":"de\u00a0Oliveira","sequence":"additional","affiliation":[{"name":"Department of Food Science, State University of Londrina , Rodovia Celso Garcia Cid, Cidade Universit\u00e1ria, Londrina, Paran\u00e1 State, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marciane","family":"Magnani","sequence":"additional","affiliation":[{"name":"Laboratory of Microbial Processes in Foods, Department of Food Engineering, Federal University of Para\u00edba , Jo\u00e3o Pessoa, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dumitru","family":"Macarisin","sequence":"additional","affiliation":[{"name":"Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, MD, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,12,15]]},"reference":[{"key":"2024040813410632900_bib1","doi-asserted-by":"crossref","first-page":"e0007485","DOI":"10.1371\/journal.pntd.0007485","article-title":"Emergence of phylogenetically diverse and fluoroquinolone resistant Salmonella Enteritidis as a cause of invasive nontyphoidal Salmonella disease in Ghana","volume":"13","author":"Aldrich","year":"2019","journal-title":"PLoS NeglTrop Dis"},{"key":"2024040813410632900_bib2","doi-asserted-by":"crossref","first-page":"384","DOI":"10.5455\/javar.2019.f358","article-title":"Detection of Salmonella pathogenicity island and Salmonella plasmid virulence genes in Salmonella Enteritidis originated from layer and broiler farms in Java Island","volume":"6","author":"Andesfha","year":"2019","journal-title":"J Adv Vet Anim Res"},{"key":"2024040813410632900_bib3","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: a better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024040813410632900_bib4","doi-asserted-by":"crossref","first-page":"5671","DOI":"10.3390\/ijerph19095671","article-title":"Characterisation of Salmonella Enteritidis ST11 and ST1925 associated with human intestinal and extra-intestinal infections in Singapore","volume":"19","author":"Aung","year":"2022","journal-title":"Int J Environ Res Pub Health"},{"key":"2024040813410632900_bib5","doi-asserted-by":"crossref","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":"2024040813410632900_bib6","doi-asserted-by":"crossref","first-page":"2413","DOI":"10.1128\/JCM.02137-09","article-title":"Prevalence of Salmonella enterica in poultry and eggs in Uruguay during an epidemic due to Salmonella enterica serovar Enteritidis","volume":"48","author":"Betancor","year":"2010","journal-title":"J Clin Microbiol"},{"key":"2024040813410632900_bib7","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2024040813410632900_bib8","doi-asserted-by":"crossref","first-page":"158","DOI":"10.4315\/0362-028X.JFP-16-299","article-title":"Spread of a major clone of Salmonella enterica serotype Enteritidis in poultry and in salmonellosis outbreaks in southern Brazil","volume":"80","author":"Borges","year":"2017","journal-title":"J Food Prot"},{"key":"2024040813410632900_bib10","doi-asserted-by":"crossref","first-page":"151","DOI":"10.4103\/ijmr.IJMR_830_18","article-title":"A systematic review of antimicrobial resistance of typhoidal Salmonella in India","volume":"149","author":"Britto","year":"2019","journal-title":"Ind J Med Res"},{"key":"2024040813410632900_bib9","doi-asserted-by":"crossref","first-page":"e01450","DOI":"10.1128\/MRA.01450-18","article-title":"Complete genome sequences of four Salmonella enterica strains (including those of serotypes Montevideo, Mbandaka, and Lubbock) isolated from peripheral lymph nodes of healthy cattle","volume":"8","author":"Bugarel","year":"2019","journal-title":"Microbiol Resour Announc"},{"key":"2024040813410632900_bib11","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/0168-1605(94)90195-3","article-title":"Salmonella enteritidis in Argentina","volume":"21","author":"Caffer","year":"1994","journal-title":"Int J Food Microbiol"},{"key":"2024040813410632900_bib13","doi-asserted-by":"crossref","first-page":"10478","DOI":"10.1038\/s41598-018-28844-6","article-title":"Changing of the genomic pattern of Salmonella Enteritidis strains isolated in Brazil over a 48 year-period revealed by whole genome SNP analyses","volume":"8","author":"Campioni","year":"2018","journal-title":"Sci Rep"},{"key":"2024040813410632900_bib14","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1007\/s42770-020-00392-0","article-title":"Phenotypic analyses of Salmonella enterica serovar Enteritidis strains isolated in the pre- and post-epidemic period in Brazil","volume":"52","author":"Campioni","year":"2021","journal-title":"Braz J Microbiol"},{"key":"2024040813410632900_bib66_1670786774980","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/j.fm.2012.06.008","article-title":"Genetic diversity, virulence genes and antimicrobial resistance of Salmonella Enteritidis isolated from food and humans over a 24-year period in Brazil","volume":"32","author":"Campioni","year":"2012","journal-title":"Food Microbiol"},{"key":"2024040813410632900_bib15","doi-asserted-by":"crossref","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":"2024040813410632900_bib12","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.jiph.2015.10.013","article-title":"Distribution and factors associated with Salmonella enterica genotypes in a diverse population of humans and animals in Qatar using multi-locus sequence typing (MLST)","volume":"9","author":"Chang","year":"2016","journal-title":"J Infect Pub Heal"},{"key":"2024040813410632900_bib16","doi-asserted-by":"crossref","first-page":"109055","DOI":"10.1016\/j.ijfoodmicro.2021.109055","article-title":"Highly prevalent multidrug resistance and QRDR mutations in Salmonella isolated from chicken, pork and duck meat in Southern China, 2018\u20132019","volume":"340","author":"Chen","year":"2021","journal-title":"Int J Food Microbiol"},{"key":"2024040813410632900_bib17","doi-asserted-by":"crossref","first-page":"e20","DOI":"10.7717\/peerj-cs.20","article-title":"CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data","volume":"1","author":"Davis","year":"2015","journal-title":"Peer J Comput Sci"},{"key":"2024040813410632900_bib18","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.ijfoodmicro.2004.04.022","article-title":"Antimicrobial resistance in Salmonella Enteritidis strains isolated from broiler carcasses, food, human and poultry-related samples","volume":"97","author":"De\u00a0Oliveira","year":"2005","journal-title":"Int J Food Microbiol"},{"key":"2024040813410632900_bib20","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s40659-017-0109-8","article-title":"Differential roles for pathogenicity islands SPI-13 and SPI-8 in the interaction of Salmonella Enteritidis and Salmonella Typhi with murine and human macrophages","volume":"50","author":"Espinoza","year":"2017","journal-title":"Biol Res"},{"article-title":"Joint ECDC-EFSA rapid outbreak assessment - Salmonella Enteritidis ST11 infections linked to eggs and egg products","year":"2022","author":"European Centre for Disease Prevention and Control (ECDC)","key":"2024040813410632900_bib19"},{"key":"2024040813410632900_bib21","first-page":"544","article-title":"Salmonella Enteritidis, un pat\u00f3geno emergente en Chile [Salmonella enteritidis, an emergent pathogen in Chile]","volume":"125","author":"Fica","year":"1997","journal-title":"Rev Med Chil"},{"key":"2024040813410632900_bib22","doi-asserted-by":"crossref","first-page":"1147e61","DOI":"10.1099\/mic.0.058115-0","article-title":"Functions of the Salmonella pathogenicity island 2 (SPI-2) type III secretion system effectors","volume":"158","author":"Figueira","year":"2012","journal-title":"Microbiology"},{"key":"2024040813410632900_bib24","article-title":"Virulence determinants of non-typhoidal Salmonellae","volume-title":"Microorganisms","author":"Gao","year":"2019"},{"key":"2024040813410632900_bib23","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/nrg.2017.88","article-title":"Towards a genomics-informed, real-time, global pathogen surveillance system","volume":"19","author":"Gardy","year":"2018","journal-title":"Nat Rev Genet"},{"key":"2024040813410632900_bib25","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.3382\/ps\/pew037","article-title":"Colonization of internal organs by Salmonella Enteritidis in experimentally infected laying hens housed in enriched colony cages at different stocking densities","volume":"95","author":"Gast","year":"2016","journal-title":"Poult Sci"},{"key":"2024040813410632900_bib26","first-page":"251","article-title":"Iranian clonal population of Salmonella enterica serovar Enteritidis, characterized by multi-locus sequence typing (MLST) method","volume":"7","author":"Ghaderi","year":"2015","journal-title":"Iran J Microbiol"},{"key":"2024040813410632900_bib27","doi-asserted-by":"crossref","first-page":"29","DOI":"10.3389\/fvets.2020.00029","article-title":"Prevalence of Salmonella isolates and their distribution based on whole-genome sequence in a chicken slaughterhouse in Jiangsu, China","volume":"7","author":"Gu","year":"2020","journal-title":"Front Vet Sci"},{"key":"2024040813410632900_bib28","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1093\/bioinformatics\/btx610","article-title":"Phandango: an interactive viewer for bacterial population genomics","volume":"34","author":"Hadfeld","year":"2017","journal-title":"Bioinformatics"},{"key":"2024040813410632900_bib30","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.phrp.2012.12.005","article-title":"A comparison of subtyping methods for differentiating Salmonella enterica serovar Enteritidis isolates obtained from food and human sources","volume":"4","author":"Hyeon","year":"2013","journal-title":"Osong Pub Health Res Perspect"},{"key":"2024040813410632900_bib31","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1017\/S0950268816001941","article-title":"Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis","volume":"145","author":"Inns","year":"2017","journal-title":"Epidemiol Infect"},{"key":"2024040813410632900_bib32","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.resmic.2019.01.001","article-title":"LoiA directly represses lon gene expression to activate the expression of Salmonella pathogenicity island-1 genes","volume":"170","author":"Jiang","year":"2019","journal-title":"Res Microbiol"},{"key":"2024040813410632900_bib33","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.diagmicrobio.2011.05.004","article-title":"Occurrence of IncFII plasmids carrying the blaCTX-M-15 gene in Salmonella enterica serovar Enteritidis sequence type 11 in Korea","volume":"71","author":"Kim","year":"2011","journal-title":"Diagn Microbiol Infect Dis"},{"key":"2024040813410632900_bib34","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1099\/jmm.0.028597-0","article-title":"Molecular characterization and resistance profile of Salmonella Enteritidis PT4 and PT9 strains isolated in Brazil","volume":"60","author":"Kottwitz","year":"2011","journal-title":"J Med Microbiol"},{"key":"2024040813410632900_bib35","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":"2024040813410632900_bib36","article-title":"Salmonella - a re-emerging pathogen: fluoroquinolone resistance in Salmonella: mechanisms, fitness, and virulence","volume-title":"Microorganisms","author":"Li","year":"2018"},{"key":"2024040813410632900_bib37","doi-asserted-by":"crossref","first-page":"108191","DOI":"10.1016\/j.foodcont.2021.108191","article-title":"Molecular characterisation of antimicrobial resistance determinants and class 1 integrons of Salmonella enterica subsp. enterica serotype Enteritidis strains from retail food in China","volume":"128","author":"Li","year":"2021","journal-title":"Food Cont"},{"key":"2024040813410632900_bib38","doi-asserted-by":"crossref","first-page":"270","DOI":"10.3389\/fcimb.2019.00270","article-title":"Salmonella pathogenicity island 1 (SPI-1) and its complex regulatory network","volume":"9","author":"Lou","year":"2019","journal-title":"Front Cell Infect Microbiol"},{"key":"2024040813410632900_bib39","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.ijfoodmicro.2018.09.022","article-title":"High-levels of resistance to quinolone and cephalosporin antibiotics in MDR-ACSSuT Salmonella enterica serovar Enteritidis mainly isolated from patients and foods in Shanghai, China","volume":"286","author":"Ma","year":"2018","journal-title":"Int J Food Microbiol"},{"key":"2024040813410632900_bib40","doi-asserted-by":"crossref","first-page":"108831","DOI":"10.1016\/j.ijfoodmicro.2020.108831","article-title":"Prediction of Salmonella serovars isolated from clinical and food matrices in Lebanon and genomic-based investigation focusing on Enteritidis serovar","volume":"333","author":"Mansour","year":"2020","journal-title":"Int J Food Microbiol"},{"key":"2024040813410632900_bib41","doi-asserted-by":"crossref","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":"Melo","year":"2021","journal-title":"Int J Food Microbiol"},{"article-title":"Coordination of surveillance of waterborne and foodborne diseases. Epidemiological analysis of foodborne disease outbreaks in Brazil","year":"2018","author":"Ministry of Health, Health Surveillance Department","key":"2024040813410632900_bib42"},{"key":"2024040813410632900_bib44","doi-asserted-by":"crossref","first-page":"2049","DOI":"10.1007\/s42770-020-00372-4","article-title":"Highly clonal relationship among Salmonella Enteritidis isolates in a commercial chicken production chain, Brazil","volume":"51","author":"Monte","year":"2020","journal-title":"Braz J Microbiol"},{"key":"2024040813410632900_bib43","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.ijfoodmicro.2015.08.003","article-title":"Antibiotic resistance determinants and genetic analysis of Salmonella enterica isolated from food in Morocco","volume":"215","author":"Murgia","year":"2015","journal-title":"Int J Food Microbiol"},{"key":"2024040813410632900_bib45","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/j.micinf.2016.02.001","article-title":"New insights about excisable pathogenicity islands in Salmonella and their contribution to virulence","volume":"18","author":"Nieto","year":"2016","journal-title":"Microbes Infect"},{"key":"2024040813410632900_bib46","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1751-0147-53-38","article-title":"Multi-locus sequence typing of Salmonella enterica subsp. enterica serovar Enteritidis strains in Japan between 1973 and 2004","volume":"53","author":"Noda","year":"2011","journal-title":"Acta Vet Scand"},{"key":"2024040813410632900_bib47","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"2024040813410632900_bib48","first-page":"e000056","article-title":"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments","volume":"2","author":"Page","year":"2016","journal-title":"Microb Genom"},{"key":"2024040813410632900_bib49","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1016\/S1473-3099(19)30047-7","article-title":"An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study","volume":"19","author":"Pijnacker","year":"2019","journal-title":"Lancet Infect Dis"},{"key":"2024040813410632900_bib50","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3390\/antibiotics11010001","article-title":"Evaluation of antibiotic resistance of Salmonella serotypes and whole-genome sequencing of multiresistant strains isolated from food products in Russia","volume":"11","author":"Rakitin","year":"2022","journal-title":"Antibiotics"},{"key":"2024040813410632900_bib51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fmicb.2015.00464","article-title":"Genetic and phenotypic evidence of the Salmonella enterica serotype Enteritidis human-animal interface in Chile","volume":"6","author":"Retamal","year":"2015","journal-title":"Front Microbiol"},{"key":"2024040813410632900_bib52","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.3201\/eid1807.120063","article-title":"Potential international spread of multidrug-resistant invasive Salmonella enterica Serovar Enteritidis","volume":"18","author":"Rodr\u00edguez","year":"2012","journal-title":"Emerg Infect Dis"},{"key":"2024040813410632900_bib54","doi-asserted-by":"crossref","first-page":"e59","DOI":"10.1002\/cpmb.59","article-title":"Overview of next-generation sequencing technologies","volume":"122","author":"Slatko","year":"2018","journal-title":"Curr Protoc Mol Biol"},{"key":"2024040813410632900_bib55","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1099\/jmm.0.46257-0","article-title":"Detection of virulence determinants in clinical strains of Salmonella enterica serovar Enteritidis and mapping on macrorestriction profiles","volume":"55","author":"Soto","year":"2006","journal-title":"J Med Microbiol"},{"key":"2024040813410632900_bib53","doi-asserted-by":"crossref","first-page":"e58449","DOI":"10.1371\/journal.pone.0058449","article-title":"Virulence gene profiling and pathogenicity characterization of non-typhoidal Salmonella accounted for invasive disease in humans","volume":"8","author":"Suez","year":"2013","journal-title":"PLoS ONE"},{"key":"2024040813410632900_bib56","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"Tatusova.","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024040813410632900_bib57","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1590\/S0036-46651996000200006","article-title":"The role of public health laboratory in the problem of salmonellosis in Sao Paulo, Brazil","volume":"38","author":"Taunay","year":"1996","journal-title":"Rev Inst Med Trop Sao Paulo"},{"key":"2024040813410632900_bib58","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1111\/mmi.14167","article-title":"Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?","volume":"111","author":"Wahl","year":"2019","journal-title":"Mol Microbiol"},{"key":"2024040813410632900_bib59","first-page":"1","article-title":"Salmonella virulence and immune scape","volume":"8","author":"Wang","year":"2020","journal-title":"Microorganisms"},{"article-title":"Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics","year":"2017","author":"World Health Organization","key":"2024040813410632900_bib60"},{"key":"2024040813410632900_bib61","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.ijregi.2022.04.003","article-title":"Antimicrobial susceptibility and genomic profiling of Salmonella enterica from bloodstream infections at a tertiary referral hospital in Lusaka, Zambia, 2018\u20132019","volume":"3","author":"Yamba","year":"2022","journal-title":"IJID Reg"},{"key":"2024040813410632900_bib62","doi-asserted-by":"crossref","first-page":"6812","DOI":"10.1128\/AEM.00497-10","article-title":"Differential phenotypic diversity among epidemic-spanning Salmonella enterica serovar Enteritidis isolates from humans or animals","volume":"76","author":"Yim","year":"2010","journal-title":"Appl Environ Microbiol"},{"key":"2024040813410632900_bib63","doi-asserted-by":"crossref","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":"2024040813410632900_bib64","doi-asserted-by":"crossref","first-page":"2384","DOI":"10.1016\/S2095-3119(21)63888-1","article-title":"Weighted gene co-expression network analysis identifies potential regulators in response to Salmonella Enteritidis challenge in the reproductive tract of laying ducks","volume":"21","author":"Zhang","year":"2022","journal-title":"J Integr Agric"},{"key":"2024040813410632900_bib65","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1093\/gbe\/evx065","article-title":"Whole-genome comparative analysis of Salmonella enterica serovar Newport strains reveals lineage-specific divergence","volume":"9","author":"Zheng.","year":"2017","journal-title":"Genome Biol Evol"},{"volume-title":"Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum-likelihood criterion","year":"2006","author":"Zwickl","key":"2024040813410632900_bib66"}],"container-title":["Letters in Applied Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/lambio\/article-pdf\/76\/1\/ovac045\/55388605\/ovac045.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/lambio\/article-pdf\/76\/1\/ovac045\/55388605\/ovac045.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,8]],"date-time":"2024-04-08T13:44:23Z","timestamp":1712583863000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/lambio\/article\/doi\/10.1093\/lambio\/ovac045\/6912254"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,15]]},"references-count":66,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,23]]}},"URL":"https:\/\/doi.org\/10.1093\/lambio\/ovac045","relation":{},"ISSN":["1472-765X"],"issn-type":[{"type":"electronic","value":"1472-765X"}],"subject":[],"published-other":{"date-parts":[[2023,1]]},"published":{"date-parts":[[2022,12,15]]},"article-number":"ovac045"}}