{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,31]],"date-time":"2025-08-31T10:20:48Z","timestamp":1756635648061},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,2,2]],"date-time":"2019-02-02T00:00:00Z","timestamp":1549065600000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,1]]},"DOI":"10.1093\/gbe\/evz026","type":"journal-article","created":{"date-parts":[[2019,1,30]],"date-time":"2019-01-30T04:32:57Z","timestamp":1548822777000},"page":"776-785","source":"Crossref","is-referenced-by-count":9,"title":["Genome Analysis of<i>Shigella flexneri<\/i>Serotype 3b Strain SFL1520 Reveals Significant Horizontal Gene Acquisitions Including a Multidrug Resistance Cassette"],"prefix":"10.1093","volume":"11","author":[{"given":"Pawan","family":"Parajuli","sequence":"first","affiliation":[{"name":"Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lachlan P","family":"Deimel","sequence":"additional","affiliation":[{"name":"Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naresh K","family":"Verma","sequence":"additional","affiliation":[{"name":"Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,2,1]]},"reference":[{"issue":"9","key":"key\n\t\t\t\t2019031911471856600_evz026-B1","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1099\/0022-1317-50-9-780","article-title":"Distribution and structural variation of the she pathogenicity island in enteric bacterial pathogens","volume":"50","author":"Al-Hasani","year":"2001","journal-title":"J Med Microbiol"},{"issue":"1","key":"key\n\t\t\t\t2019031911471856600_evz026-B2","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/S0966-842X(99)01646-7","article-title":"Serotype-converting bacteriophages and O-antigen modification in Shigella flexneri","volume":"8","author":"Allison","year":"2000","journal-title":"Trends Microbiol"},{"key":"key\n\t\t\t\t2019031911471856600_evz026-B3","author":"Andrews","year":"2016"},{"issue":"W1","key":"key\n\t\t\t\t2019031911471856600_evz026-B4","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"},{"issue":"3","key":"key\n\t\t\t\t2019031911471856600_evz026-B5","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1111\/j.1365-2958.2006.05547.x","article-title":"Shigella chromosomal IpaH proteins are secreted via the type III secretion system and act as effectors","volume":"63","author":"Ashida","year":"2007","journal-title":"Mol Microbiol"},{"issue":"9955","key":"key\n\t\t\t\t2019031911471856600_evz026-B6","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1016\/S0140-6736(14)61789-X","article-title":"The extant World War 1 dysentery bacillus NCTC1: a genomic analysis","volume":"384","author":"Baker","year":"2014","journal-title":"Lancet"},{"issue":"W1","key":"key\n\t\t\t\t2019031911471856600_evz026-B7","doi-asserted-by":"crossref","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"15","key":"key\n\t\t\t\t2019031911471856600_evz026-B8","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":"key\n\t\t\t\t2019031911471856600_evz026-B9","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/978-1-4615-6369-3_3","volume-title":"Bacterial genomes: physical structure and analysis","author":"Campbell","year":"1998"},{"issue":"2","key":"key\n\t\t\t\t2019031911471856600_evz026-B10","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1128\/MMBR.67.2.238-276.2003","article-title":"Prophage genomics","volume":"67","author":"Canchaya","year":"2003","journal-title":"Microbiol Mol Biol Rev"},{"issue":"16","key":"key\n\t\t\t\t2019031911471856600_evz026-B11","doi-asserted-by":"crossref","first-page":"3422","DOI":"10.1093\/bioinformatics\/bti553","article-title":"ACT: the Artemis comparison tool","volume":"21","author":"Carver","year":"2005","journal-title":"Bioinformatics"},{"issue":"2","key":"key\n\t\t\t\t2019031911471856600_evz026-B12","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/j.jmb.2004.03.068","article-title":"The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging","volume":"339","author":"Casjens","year":"2004","journal-title":"J Mol Biol"},{"key":"key\n\t\t\t\t2019031911471856600_evz026-B13","first-page":"241","volume-title":"Manual of antimicrobial susceptibility testing","author":"Cavalieri","year":"2005"},{"issue":"10","key":"key\n\t\t\t\t2019031911471856600_evz026-B14","first-page":"739","article-title":"Estimating the burden of shigellosis in Thailand: 36-month population-based surveillance study","volume":"83","author":"Chompook","year":"2005","journal-title":"Bull World Health Organ"},{"issue":"7","key":"key\n\t\t\t\t2019031911471856600_evz026-B15","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res"},{"issue":"5","key":"key\n\t\t\t\t2019031911471856600_evz026-B16","doi-asserted-by":"crossref","DOI":"10.1093\/femspd\/ftw034","article-title":"Characterization of a multicomponent live, attenuated Shigella flexneri vaccine","volume":"74","author":"DeLaine","year":"2016","journal-title":"Pathog Dis"},{"issue":"2","key":"key\n\t\t\t\t2019031911471856600_evz026-B17","first-page":"145","article-title":"Recommended designations for the subserotypes of Shigella flexneri","volume":"16","author":"Ewing","year":"1966","journal-title":"Int J Syst Evol Microbiol"},{"key":"key\n\t\t\t\t2019031911471856600_evz026-B18","first-page":"113","volume-title":"Methods in microbiology","author":"Ewing","year":"1984"},{"issue":"4","key":"key\n\t\t\t\t2019031911471856600_evz026-B19","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1136\/gut.40.4.505","article-title":"Effect of Shigella enterotoxin 1 (ShET1) on rabbit intestine in vitro and in vivo","volume":"40","author":"Fasano","year":"1997","journal-title":"Gut"},{"issue":"9","key":"key\n\t\t\t\t2019031911471856600_evz026-B20","doi-asserted-by":"crossref","first-page":"e106085.","DOI":"10.1371\/journal.pone.0106085","article-title":"Shigella flexneri infection in Caenorhabditis elegans: cytopathological examination and identification of host responses","volume":"9","author":"George","year":"2014","journal-title":"PLoS One"},{"issue":"4","key":"key\n\t\t\t\t2019031911471856600_evz026-B21","doi-asserted-by":"crossref","first-page":"e94954.","DOI":"10.1371\/journal.pone.0094954","article-title":"The periplasmic enzyme, AnsB, of Shigella flexneri modulates bacterial adherence to host epithelial cells","volume":"9","author":"George","year":"2014","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t2019031911471856600_evz026-B22","doi-asserted-by":"crossref","first-page":"1817.","DOI":"10.3389\/fmicb.2017.01817","article-title":"Rapid gene turnover as a significant source of genetic variation in a recently seeded population of a healthcare-associated pathogen","volume":"8","author":"Grana-Miraglia","year":"2017","journal-title":"Front Microbiol"},{"issue":"Web Server","key":"key\n\t\t\t\t2019031911471856600_evz026-B23","doi-asserted-by":"crossref","first-page":"W181","DOI":"10.1093\/nar\/gkn179","article-title":"The CGView Server: a comparative genomics tool for circular genomes","volume":"36","author":"Grant","year":"2008","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"key\n\t\t\t\t2019031911471856600_evz026-B24","doi-asserted-by":"crossref","first-page":"5587","DOI":"10.1128\/IAI.67.11.5587-5596.1999","article-title":"Characterization of pic, a secreted protease of Shigella flexneri and enteroaggregative Escherichia coli","volume":"67","author":"Henderson","year":"1999","journal-title":"Infect Immun"},{"issue":"1","key":"key\n\t\t\t\t2019031911471856600_evz026-B25","first-page":"49","article-title":"Pathogenicity islands of Shigella","volume":"264","author":"Ingersoll","year":"2002","journal-title":"Curr Top Microbiol Immunol"},{"issue":"1","key":"key\n\t\t\t\t2019031911471856600_evz026-B26","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.femsre.2003.07.002","article-title":"Shigella flexneri infection: pathogenesis and vaccine development","volume":"28","author":"Jennison","year":"2004","journal-title":"FEMS Microbiol Rev"},{"issue":"6","key":"key\n\t\t\t\t2019031911471856600_evz026-B27","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"issue":"2","key":"key\n\t\t\t\t2019031911471856600_evz026-B28","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/S0008-6215(00)83357-1","article-title":"Basic structure of the oligosaccharide repeating-unit of the Shigella flexneri O-antigens","volume":"56","author":"Kenne","year":"1977","journal-title":"Carbohydr Res"},{"issue":"4","key":"key\n\t\t\t\t2019031911471856600_evz026-B29","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1007\/PL00006158","article-title":"Amelioration of bacterial genomes: rates of change and exchange","volume":"44","author":"Lawrence","year":"1997","journal-title":"J Mol Evol"},{"key":"key\n\t\t\t\t2019031911471856600_evz026-B30","doi-asserted-by":"crossref","first-page":"D57","DOI":"10.1093\/nar\/gkp938","article-title":"ACLAME: a CLAssification of Mobile genetic Elements, update 2010","volume":"38(Suppl 1)","author":"Leplae","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019031911471856600_evz026-B31","author":"Li","year":"2013"},{"issue":"16","key":"key\n\t\t\t\t2019031911471856600_evz026-B32","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"10","key":"key\n\t\t\t\t2019031911471856600_evz026-B33","doi-asserted-by":"crossref","first-page":"6012","DOI":"10.1128\/IAI.69.10.6012-6021.2001","article-title":"Ferric dicitrate transport system (Fec) of Shigella flexneri 2a YSH6000 is encoded on a novel pathogenicity island carrying multiple antibiotic resistance genes","volume":"69","author":"Luck","year":"2001","journal-title":"Infect Immun"},{"issue":"1","key":"key\n\t\t\t\t2019031911471856600_evz026-B34","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1046\/j.1365-2958.1999.01449.x","article-title":"The selC-associated SHI-2 pathogenicity island of Shigella flexneri","volume":"33","author":"Moss","year":"1999","journal-title":"Mol Microbiol"},{"issue":"1","key":"key\n\t\t\t\t2019031911471856600_evz026-B35","doi-asserted-by":"crossref","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":"key\n\t\t\t\t2019031911471856600_evz026-B36","doi-asserted-by":"crossref","first-page":"173.","DOI":"10.1186\/1471-2164-7-173","article-title":"Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a","volume":"7","author":"Nie","year":"2006","journal-title":"BMC Genomics"},{"issue":"2","key":"key\n\t\t\t\t2019031911471856600_evz026-B37","first-page":"133","article-title":"Shigellosis","volume":"43","author":"Niyogi","year":"2005","journal-title":"J Microbiol"},{"issue":"22","key":"key\n\t\t\t\t2019031911471856600_evz026-B38","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"},{"issue":"1","key":"key\n\t\t\t\t2019031911471856600_evz026-B39","doi-asserted-by":"crossref","first-page":"722.","DOI":"10.1186\/s12864-017-4109-4","article-title":"Bacteriophages are the major drivers of Shigella flexneri serotype 1c genome plasticity: a complete genome analysis","volume":"18","author":"Parajuli","year":"2017","journal-title":"BMC Genomics"},{"issue":"12","key":"key\n\t\t\t\t2019031911471856600_evz026-B40","doi-asserted-by":"crossref","first-page":"e0142927.","DOI":"10.1371\/journal.pone.0142927","article-title":"Aetiology-specific estimates of the global and regional incidence and mortality of diarrhoeal diseases commonly transmitted through food","volume":"10","author":"Pires","year":"2015","journal-title":"PLoS One"},{"issue":"12","key":"key\n\t\t\t\t2019031911471856600_evz026-B41","doi-asserted-by":"crossref","first-page":"4864","DOI":"10.1073\/pnas.0811058106","article-title":"A family of Salmonella virulence factors functions as a distinct class of autoregulated E3 ubiquitin ligases","volume":"106","author":"Quezada","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"11","key":"key\n\t\t\t\t2019031911471856600_evz026-B42","doi-asserted-by":"crossref","first-page":"4606","DOI":"10.1128\/IAI.65.11.4606-4614.1997","article-title":"Use of a novel approach, termed island probing, identifies the Shigella flexneri she pathogenicity island which encodes a homolog of the immunoglobulin A protease-like family of proteins","volume":"65","author":"Rajakumar","year":"1997","journal-title":"Infect Immun"},{"key":"key\n\t\t\t\t2019031911471856600_evz026-B43","author":"Rambaut","year":"2016"},{"issue":"2","key":"key\n\t\t\t\t2019031911471856600_evz026-B44","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.compbiolchem.2008.11.003","article-title":"Sequence assembly","volume":"33","author":"Scheibye-Alsing","year":"2009","journal-title":"Comput Biol Chem"},{"issue":"14","key":"key\n\t\t\t\t2019031911471856600_evz026-B45","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"issue":"1","key":"key\n\t\t\t\t2019031911471856600_evz026-B46","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1093\/glycob\/cwq136","article-title":"Effects of backbone substitutions on the conformational behavior of Shigella flexneri O-antigens: implications for vaccine strategy","volume":"21","author":"Theillet","year":"2011","journal-title":"Glycobiology"},{"issue":"2","key":"key\n\t\t\t\t2019031911471856600_evz026-B47","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsdottir","year":"2013","journal-title":"Brief Bioinform"},{"issue":"19","key":"key\n\t\t\t\t2019031911471856600_evz026-B48","doi-asserted-by":"crossref","first-page":"5535","DOI":"10.1128\/JB.183.19.5535-5543.2001","article-title":"Nested deletions of the SRL pathogenicity island of Shigella flexneri 2a","volume":"183","author":"Turner","year":"2001","journal-title":"J Bacteriol"},{"issue":"3","key":"key\n\t\t\t\t2019031911471856600_evz026-B49","doi-asserted-by":"crossref","first-page":"R30.","DOI":"10.1186\/gb-2011-12-3-r30","article-title":"ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes","volume":"12","author":"Varani","year":"2011","journal-title":"Genome Biol"},{"issue":"10","key":"key\n\t\t\t\t2019031911471856600_evz026-B50","doi-asserted-by":"crossref","first-page":"2435","DOI":"10.1111\/j.1365-2958.1991.tb02089.x","article-title":"Sequence variation in two ipaH genes of Shigella flexneri 5 and homology to the LRG-like family of proteins","volume":"5","author":"Venkatesan","year":"1991","journal-title":"Mol Microbiol"},{"issue":"1","key":"key\n\t\t\t\t2019031911471856600_evz026-B51","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1111\/j.1365-2958.1991.tb01827.x","article-title":"Molecular characterization of the O-acetyl transferase gene of converting bacteriophage SF6 that adds group antigen 6 to Shigella flexneri","volume":"5","author":"Verma","year":"1991","journal-title":"Mol Microbiol"},{"issue":"1","key":"key\n\t\t\t\t2019031911471856600_evz026-B52","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1046\/j.1365-2958.1999.01448.x","article-title":"The aerobactin iron transport system genes in Shigella flexneri are present within a pathogenicity island","volume":"33","author":"Vokes","year":"1999","journal-title":"Mol Microbiol"},{"issue":"11","key":"key\n\t\t\t\t2019031911471856600_evz026-B53","doi-asserted-by":"crossref","first-page":"e112963.","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"issue":"8","key":"key\n\t\t\t\t2019031911471856600_evz026-B54","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1016\/j.vaccine.2014.11.049","article-title":"An assessment of enterotoxigenic Escherichia coli and Shigella vaccine candidates for infants and children","volume":"33","author":"Walker","year":"2015","journal-title":"Vaccine"},{"issue":"5713","key":"key\n\t\t\t\t2019031911471856600_evz026-B55","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1126\/science.1108472","article-title":"Optimization of virulence functions through glucosylation of Shigella LPS","volume":"307","author":"West","year":"2005","journal-title":"Science"},{"issue":"2","key":"key\n\t\t\t\t2019031911471856600_evz026-B56","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.plasmid.2012.11.001","article-title":"The IncF plasmid pRSB225 isolated from a municipal wastewater treatment plant\u2019s on-site preflooder combining antibiotic resistance and putative virulence functions is highly related to virulence plasmids identified in pathogenic E. coli isolates","volume":"69","author":"Wibberg","year":"2013","journal-title":"Plasmid"},{"issue":"6","key":"key\n\t\t\t\t2019031911471856600_evz026-B57","doi-asserted-by":"crossref","first-page":"e1005595.","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput Biol"},{"issue":"2","key":"key\n\t\t\t\t2019031911471856600_evz026-B58","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1128\/JCM.00614-09","article-title":"Emergence of a new multidrug-resistant serotype X variant in an epidemic clone of Shigella flexneri","volume":"48","author":"Ye","year":"2010","journal-title":"J Clin Microbiol"}],"container-title":["Genome Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/gbe\/article-pdf\/11\/3\/776\/28122432\/evz026.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,25]],"date-time":"2020-11-25T06:35:13Z","timestamp":1606286113000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gbe\/article\/11\/3\/776\/5305889"}},"subtitle":[],"editor":[{"given":"Esperanza","family":"Martinez-Romero","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,2,1]]},"references-count":58,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2019,2,1]]},"published-print":{"date-parts":[[2019,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/gbe\/evz026","relation":{},"ISSN":["1759-6653"],"issn-type":[{"value":"1759-6653","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,3]]},"published":{"date-parts":[[2019,2,1]]}}}