{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T02:52:57Z","timestamp":1790304777220,"version":"4.1.0"},"reference-count":57,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2020,6,30]],"date-time":"2020-06-30T00:00:00Z","timestamp":1593475200000},"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."],"DOI":"10.3389\/fmicb.2020.01483","type":"journal-article","created":{"date-parts":[[2020,6,30]],"date-time":"2020-06-30T05:39:18Z","timestamp":1593495558000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":44,"title":["NAuRA: Genomic Tool to Identify Staphylococcal Enterotoxins in Staphylococcus aureus Strains Responsible for FoodBorne Outbreaks"],"prefix":"10.3389","volume":"11","author":[{"given":"D\u00e9borah","family":"Merda","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnaud","family":"Felten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"No\u00e9mie","family":"Vingadassalon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Denayer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yacine","family":"Titouche","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucia","family":"Decastelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernadette","family":"Hickey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christos","family":"Kourtis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hristo","family":"Daskalov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michel-Yves","family":"Mistou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacques-Antoine","family":"Hennekinne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2020,6,30]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"139","DOI":"10.9734\/bmrj\/2013\/2913","article-title":"Prevalence of seg, seh and sei Genes among Clinical and Nasal Staphylococcus aureus Isolates in Palestine.","volume":"3","author":"Adwan","year":"2013","journal-title":"Br. Microbiol. Res. J."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1751","DOI":"10.3390\/toxins2071751","article-title":"Food poisoning and Staphylococcus aureus enterotoxins.","volume":"2","author":"Argud\u00edn","year":"2010","journal-title":"Toxins"},{"key":"B3","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.ijfoodmicro.2011.05.007","article-title":"Prevalence of staphylococcal enterotoxins, toxin genes and genetic-relatedness of foodborne Staphylococcus aureus strains isolated in the Marmara Region of Turkey.","volume":"148","author":"Aydin","year":"2011","journal-title":"Int. J. Food Microbiol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0168-1605(00)00377-9","article-title":"Staphylococcal enterotoxins.","volume":"61","author":"Balaban","year":"2000","journal-title":"Int. J. Food Microbiol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1016\/j.ijfoodmicro.2005.10.013","article-title":"Distribution of newly described enterotoxin-like genes in Staphylococcus aureus from food.","volume":"108","author":"Bania","year":"2006","journal-title":"Int. J. Food Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1111\/lam.12182","article-title":"Enterotoxin gene profiles of Staphylococcus aureus isolated from milk and dairy products in Italy.","volume":"58","author":"Bianchi","year":"2014","journal-title":"Lett. Appl. Microbiol."},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00362","article-title":"Validation of a bioinformatics workflow for routine analysis of whole-genome sequencing data and related challenges for pathogen typing in a european national reference center: Neisseria meningitidis as a proof-of-concept.","volume":"10","author":"Bogaerts","year":"2019","journal-title":"Front. Microbiol."},{"key":"B8","doi-asserted-by":"publisher","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":"Bioinforma. Oxf. Engl."},{"key":"B9","doi-asserted-by":"publisher","first-page":"2443","DOI":"10.1093\/bioinformatics\/btv171","article-title":"MeDuSa: a multi-draft based scaffolder.","volume":"31","author":"Bosi","year":"2015","journal-title":"Bioinformatics"},{"key":"B10","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications.","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-3","article-title":"Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf.","volume":"14","author":"Cardona","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"B12","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.idairyj.2014.10.009","article-title":"Enterotoxin genes, enterotoxin production, and methicillin resistance in Staphylococcus aureus isolated from milk and dairy products in Central Italy.","volume":"42","author":"Carfora","year":"2015","journal-title":"Int. Dairy J."},{"key":"B13","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.","volume":"17","author":"Castresana","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/j.ijfoodmicro.2015.07.018","article-title":"Prevalence and diversity of enterotoxin genes with genetic background of Staphylococcus aureus isolates from different origins in China.","volume":"211","author":"Chao","year":"2015","journal-title":"Int. J. Food Microbiol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: hierarchical and refined dataset for big data analysis\u201410 years on.","volume":"44","author":"Chen","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B16","doi-asserted-by":"publisher","first-page":"997","DOI":"10.1093\/sysbio\/syw037","article-title":"Terrace aware data structure for phylogenomic inference from supermatrices.","volume":"65","author":"Chernomor","year":"2016","journal-title":"Syst. Biol."},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3390\/toxins9120407","article-title":"Food-borne outbreak investigation and molecular typing: high diversity of Staphylococcus aureus strains and importance of toxin detection.","volume":"9","author":"Denayer","year":"2017","journal-title":"Toxins"},{"key":"B18","doi-asserted-by":"publisher","first-page":"896","DOI":"10.1016\/j.fm.2009.06.007","article-title":"Differential temporal expression of the staphylococcal enterotoxins genes during cell growth.","volume":"26","author":"Derzelle","year":"2009","journal-title":"Food. Microbiol."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0130955","article-title":"Using whole genome analysis to examine recombination across diverse sequence types of Staphylococcus aureus.","volume":"10","author":"Driebe","year":"2015","journal-title":"PLoS ONE"},{"key":"B20","article-title":"The European Union One Health 2018 zoonoses report.","volume":"17","year":"2019","journal-title":"EFSA J."},{"key":"B21","doi-asserted-by":"publisher","first-page":"1008","DOI":"10.1128\/jcm.38.3.1008-1015.2000","article-title":"Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus.","volume":"38","author":"Enright","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"B22","author":"Felsenstein","year":"2013","journal-title":"PHYLIP (Phylogeny Inference Package) version 3.695"},{"key":"B23","doi-asserted-by":"publisher","first-page":"436","DOI":"10.3389\/fmicb.2018.00436","article-title":"Basis of virulence in enterotoxin-mediated staphylococcal food poisoning.","volume":"9","author":"Fisher","year":"2018","journal-title":"Front. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1016\/j.meegid.2013.03.013","article-title":"Staphylococcus aureus toxins \u2013 Their functions and genetics.","volume":"21","author":"Grumann","year":"2014","journal-title":"Infect. Genet. Evol."},{"key":"B25","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":"B26","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-015-1860-2","article-title":"ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data.","volume":"16","author":"Hawkey","year":"2015","journal-title":"BMC Genomics"},{"key":"B27","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1111\/j.1574-6976.2011.00311.x","article-title":"Staphylococcus aureus and its food poisoning toxins: characterization and outbreak investigation.","volume":"36","author":"Hennekinne","year":"2012","journal-title":"FEMS Microbiol. Rev."},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000131","article-title":"ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.","volume":"3","author":"Hunt","year":"2017","journal-title":"Microb. Genomics"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.166.1.669","article-title":"egc, a highly prevalent operon of enterotoxin gene, forms a putative nursery of superantigens in Staphylococcus aureus.","volume":"166","author":"Jarraud","year":"2001","journal-title":"J. Immunol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"B31","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/j.ijfoodmicro.2006.10.050","article-title":"Characterization of Staphylococcus aureus strains associated with food poisoning outbreaks in France.","volume":"115","author":"K\u00e9rouanton","year":"2007","journal-title":"Int. J. Food Microbiol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"3733","DOI":"10.1093\/bioinformatics\/btv465","article-title":"GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments.","volume":"31","author":"Kosugi","year":"2015","journal-title":"Bioinformatics"},{"key":"B33","first-page":"63","article-title":"Staphylococcus aureus and food poisoning.","volume":"2","author":"Le Loir","year":"2003","journal-title":"Genet. Mol. Res."},{"key":"B34","doi-asserted-by":"publisher","first-page":"283","DOI":"10.5001\/omj.2015.56","article-title":"Prevalence of enterotoxin genes and antibacterial susceptibility pattern of Staphylococcus aureus strains isolated from animal originated foods in west of iran.","volume":"30","author":"Mashouf","year":"2015","journal-title":"Oman Med. J."},{"key":"B35","doi-asserted-by":"publisher","first-page":"e1815","DOI":"10.1128\/JCM.01815-17","article-title":"Accuracy of different bioinformatics methods in detecting antibiotic resistance and virulence factors from Staphylococcus aureus whole-genome sequences.","volume":"56","author":"Mason","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.3390\/toxins10060247","article-title":"Staphylococcus aureus isolates from bovine mastitis in eight countries: genotypes, detection of genes encoding different toxins and other virulence genes.","volume":"10","author":"Monistero","year":"2018","journal-title":"Toxins"},{"key":"B37","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1099\/jmm.0.46183-0","article-title":"Enterotoxicity and genetic variation among clinical Staphylococcus aureus isolates in Jordan.","volume":"55","author":"Naffa","year":"2006","journal-title":"J. Med. Microbiol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"1441","DOI":"10.3201\/eid2309.170416","article-title":"Bioinformatic analyses of whole-genome sequence data in a public health laboratory.","volume":"23","author":"Oakeson","year":"2017","journal-title":"Emerg. Infect. Dis."},{"key":"B39","doi-asserted-by":"publisher","first-page":"3627","DOI":"10.1128\/IAI.00550-13","article-title":"Emetic potentials of newly identified staphylococcal enterotoxin-like toxins.","volume":"81","author":"Omoe","year":"2013","journal-title":"Infect. Immun."},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash.","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1111\/1348-0421.12460","article-title":"The emetic activity of Staphylococcal enterotoxins, SEK, SEL, SEM, SEN and SEO in a small emetic animal model, the house musk shrew.","volume":"61","author":"Ono","year":"2017","journal-title":"Microbiol. Immunol."},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00045-08","article-title":"Identification and characterization of two novel Staphylococcal enterotoxins, Types S and T.","volume":"76","author":"Ono","year":"2008","journal-title":"Infect. Immun."},{"key":"B43","doi-asserted-by":"publisher","first-page":"2117","DOI":"10.3390\/toxins2082117","article-title":"Multiple roles of Staphylococcus aureus enterotoxins: pathogenicity, superantigenic activity, and correlation to antibiotic resistance.","volume":"2","author":"Ortega","year":"2010","journal-title":"Toxins"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.2807\/ese.15.13.19528-en","article-title":"First evidence of a food poisoning outbreak due to staphylococcal enterotoxin type E, France, 2009.","volume":"15","author":"Ostyn","year":"2010","journal-title":"Eurosurveillance"},{"key":"B45","doi-asserted-by":"publisher","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":"B46","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.5261","article-title":"Staphylococcus aureus viewed from the perspective of 40,000+ genomes.","volume":"6","author":"Petit","year":"2018","journal-title":"PeerJ"},{"key":"B47","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1089\/fpd.2010.0679","article-title":"Characterization of Toxin genes and antimicrobial susceptibility of Staphylococcus aureus isolates from louisiana retail meats.","volume":"8","author":"Pu","year":"2010","journal-title":"Foodborne Pathog. Dis."},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00882","article-title":"Staphylococcus aureus strains associated with food poisoning outbreaks in France: comparison of different molecular typing methods, including MLVA.","volume":"6","author":"Roussel","year":"2015","journal-title":"Front. Microbiol."},{"key":"B49","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":"B50","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.","volume":"7","author":"Sievers","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1089\/fpd.2016.2162","article-title":"Molecular typing and virulence gene profiles of enterotoxin gene cluster (egc)-positive Staphylococcus aureus isolates obtained from various food and clinical specimens.","volume":"13","author":"Song","year":"2016","journal-title":"Foodborne Pathog. Dis."},{"key":"B52","doi-asserted-by":"publisher","first-page":"E10596","DOI":"10.1073\/pnas.1702472114","article-title":"Origin, evolution, and global transmission of community-acquired Staphylococcus aureus ST8.","volume":"114","author":"Strau\u00df","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B53","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1093\/bioinformatics\/btq228","article-title":"DendroPy: a Python library for phylogenetic computing.","volume":"26","author":"Sukumaran","year":"2010","journal-title":"Bioinformatics"},{"key":"B54","doi-asserted-by":"publisher","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge.","volume":"47","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B55","doi-asserted-by":"publisher","first-page":"6876","DOI":"10.3168\/jds.2018-16208","article-title":"Emergence of methicillin-resistant Staphylococcus aureus (MRSA) ST8 in raw milk and traditional dairy products in the Tizi Ouzou area of Algeria.","volume":"102","author":"Titouche","year":"2019","journal-title":"J. Dairy Sci."},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002271","article-title":"A Novel Core Genome-encoded superantigen contributes to lethality of community-associated MRSA necrotizing pneumonia.","volume":"7","author":"Wilson","year":"2011","journal-title":"PLoS Pathog."},{"key":"B57","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1016\/j.ijmm.2018.03.002","article-title":"Identification and characterization of two novel superantigens among Staphylococcus aureus complex.","volume":"308","author":"Zhang","year":"2018","journal-title":"Int. J. Med. Microbiol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2020.01483\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,30]],"date-time":"2020-06-30T05:39:21Z","timestamp":1593495561000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2020.01483\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,30]]},"references-count":57,"alternative-id":["10.3389\/fmicb.2020.01483"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2020.01483","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,30]]},"article-number":"1483"}}