{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T06:04:32Z","timestamp":1771913072329,"version":"3.50.1"},"reference-count":39,"publisher":"The Royal Society","issue":"12","license":[{"start":{"date-parts":[[2017,12,1]],"date-time":"2017-12-01T00:00:00Z","timestamp":1512086400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/royalsociety.org\/journals\/ethics-policies\/data-sharing-mining\/"}],"funder":[{"DOI":"10.13039\/100008973","name":"University of North Texas","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100008973","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["royalsocietypublishing.org"],"crossmark-restriction":true},"short-container-title":["Open Biol."],"published-print":{"date-parts":[[2017,12]]},"abstract":"<jats:p><jats:italic>Staphylococcus aureus<\/jats:italic>is a versatile pathogen that is capable of causing infections in both humans and animals. It can cause furuncles, septicaemia, pneumonia and endocarditis. Adaptation of<jats:italic>S. aureus<\/jats:italic>to the modern hospital environment has been facilitated, in part, by the horizontal acquisition of drug resistance genes, such as<jats:italic>mecA<\/jats:italic>gene that imparts resistance to methicillin. Horizontal acquisitions of islands of genes harbouring virulence and antibiotic resistance genes have made<jats:italic>S. aureus<\/jats:italic>resistant to commonly used antibiotics. To decipher genomic islands (GIs) in 22 hospital- and 9 community-associated methicillin-resistant<jats:italic>S. aureus<\/jats:italic>strains and classify a subset of GIs carrying virulence and resistance genes as pathogenicity and resistance islands respectively, we applied a host of methods for localizing genomic islands in prokaryotic genomes. Surprisingly,<jats:italic>none<\/jats:italic>of the frequently used GI prediction methods could perform well in delineating the resistance islands in the<jats:italic>S. aureus<\/jats:italic>genomes. Rather, a gene clustering procedure exploiting biases in codon usage for identifying horizontally transferred genes outperformed the current methods for GI detection, in particular in identifying the known islands in<jats:italic>S. aureus<\/jats:italic>including the SCC<jats:italic>mec<\/jats:italic>island that harbours the<jats:italic>mecA<\/jats:italic>resistance gene. The gene clustering approach also identified novel, as yet unreported islands, with many of these found to harbour virulence and\/or resistance genes. These as yet unexplored islands may provide valuable information on the evolution of drug resistance in<jats:italic>S. aureus<\/jats:italic>.<\/jats:p>","DOI":"10.1098\/rsob.170094","type":"journal-article","created":{"date-parts":[[2017,12,20]],"date-time":"2017-12-20T10:09:41Z","timestamp":1513764581000},"page":"170094","update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":25,"title":["Deciphering pathogenicity and antibiotic resistance islands in methicillin-resistant<i>Staphylococcus aureus<\/i>genomes"],"prefix":"10.1098","volume":"7","author":[{"given":"Mehul","family":"Jani","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Soham","family":"Sengupta","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kelsey","family":"Hu","sequence":"additional","affiliation":[{"name":"Texas Academy of Mathematics and Science, University of North Texas, Denton, TX 76203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6874-6146","authenticated-orcid":false,"given":"Rajeev K.","family":"Azad","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA"},{"name":"Department of Mathematics, University of North Texas, Denton, TX 76203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"175","published-online":{"date-parts":[[2017,12,20]]},"reference":[{"key":"e_1_3_6_2_2","doi-asserted-by":"publisher","DOI":"10.1001\/jama.279.8.593"},{"key":"e_1_3_6_3_2","doi-asserted-by":"publisher","DOI":"10.1086\/342576"},{"key":"e_1_3_6_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0402521101"},{"key":"e_1_3_6_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(02)08713-5"},{"key":"e_1_3_6_6_2","doi-asserted-by":"publisher","DOI":"10.3947\/ic.2013.45.2.117"},{"key":"e_1_3_6_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01255-09"},{"key":"e_1_3_6_8_2","first-page":"707","article-title":"Four pediatric deaths from community-acquired methicillin-resistant Staphylococcus aureus\u2014Minnesota and North Dakota, 1997\u20131999","volume":"48","author":"Centers for Disease Control and Prevention","year":"1999","journal-title":"MMWR Morb. Mortal. Wkly Rep."},{"key":"e_1_3_6_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(01)00091-3"},{"key":"e_1_3_6_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0966-842X(00)01791-1"},{"key":"e_1_3_6_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms4956"},{"key":"e_1_3_6_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00254-06"},{"key":"e_1_3_6_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm204"},{"key":"e_1_3_6_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(06)68231-7"},{"key":"e_1_3_6_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.187.7.2426-2438.2005"},{"key":"e_1_3_6_16_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl369"},{"key":"e_1_3_6_17_2","doi-asserted-by":"crossref","first-page":"223","DOI":"10.3233\/ISB-00352","article-title":"PredictBias: a server for the identification of genomic and pathogenicity islands in prokaryotes","volume":"8","author":"Pundhir S","year":"2008","journal-title":"In Silico Biol."},{"key":"e_1_3_6_18_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-333"},{"key":"e_1_3_6_19_2","first-page":"357","article-title":"Zisland explorer: detect genomic islands by combining homogeneity and heterogeneity properties","volume":"18","author":"Wei W","year":"2016","journal-title":"Brief. Bioinform."},{"key":"e_1_3_6_20_2","first-page":"214","article-title":"An accurate genomic island prediction method for sequenced bacterial and archaeal genomes","volume":"7","author":"Che D","year":"2014","journal-title":"J. Proteomics Bioinform."},{"key":"e_1_3_6_21_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0146352"},{"key":"e_1_3_6_22_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.01210"},{"key":"e_1_3_6_23_2","doi-asserted-by":"publisher","DOI":"10.1109\/18.61115"},{"key":"e_1_3_6_24_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.65.041905"},{"key":"e_1_3_6_25_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp030"},{"key":"e_1_3_6_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv401"},{"key":"e_1_3_6_27_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-7-142"},{"key":"e_1_3_6_28_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti054"},{"key":"e_1_3_6_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0966-842X(01)02175-8"},{"key":"e_1_3_6_30_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(00)04403-2"},{"key":"e_1_3_6_31_2","doi-asserted-by":"publisher","DOI":"10.1007\/PL00006158"},{"key":"e_1_3_6_32_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1289"},{"key":"e_1_3_6_33_2","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1128\/IAI.49.3.765-769.1985","article-title":"Virulence of Staphylococcus aureus in a mouse mastitis model: studies of alpha hemolysin, coagulase, and protein A as possible virulence determinants with protoplast fusion and gene cloning","volume":"49","author":"Jonsson P","year":"1985","journal-title":"Infect. Immun."},{"key":"e_1_3_6_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0966-842X(98)01400-0"},{"key":"e_1_3_6_35_2","doi-asserted-by":"crossref","first-page":"2358","DOI":"10.1128\/IAI.57.8.2358-2363.1989","article-title":"Fibrinogen-binding protein\/clumping factor from Staphylococcus aureus","volume":"57","author":"Boden MK","year":"1989","journal-title":"Infect. Immun."},{"key":"e_1_3_6_36_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.1996.tb02548.x"},{"key":"e_1_3_6_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_3_6_38_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq003"},{"key":"e_1_3_6_39_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00579-09"},{"key":"e_1_3_6_40_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.9.2711-2722.2003"}],"container-title":["Open Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/royalsocietypublishing.org\/doi\/pdf\/10.1098\/rsob.170094","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/royalsocietypublishing.org\/doi\/full-xml\/10.1098\/rsob.170094","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/royalsocietypublishing.org\/doi\/pdf\/10.1098\/rsob.170094","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,29]],"date-time":"2025-06-29T02:13:48Z","timestamp":1751163228000},"score":1,"resource":{"primary":{"URL":"https:\/\/royalsocietypublishing.org\/doi\/10.1098\/rsob.170094"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,12]]},"references-count":39,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["10.1098\/rsob.170094"],"URL":"https:\/\/doi.org\/10.1098\/rsob.170094","relation":{},"ISSN":["2046-2441"],"issn-type":[{"value":"2046-2441","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,12]]},"assertion":[{"value":"2017-04-15","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-11-16","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-12-20","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}