{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T13:16:20Z","timestamp":1789564580747,"version":"build-2803163510"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2019,10,7]],"date-time":"2019-10-07T00:00:00Z","timestamp":1570406400000},"content-version":"vor","delay-in-days":6,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Department of Science & Technology, Government of India","award":["DST\/INSPIRE\/04\/2015\/002935"],"award-info":[{"award-number":["DST\/INSPIRE\/04\/2015\/002935"]}]},{"DOI":"10.13039\/501100006144","name":"Kerala State Council for Science, Technology and Environment","doi-asserted-by":"crossref","award":["043\/YIPB\/KBC\/2017\/KSCSTE"],"award-info":[{"award-number":["043\/YIPB\/KBC\/2017\/KSCSTE"]}],"id":[{"id":"10.13039\/501100006144","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Department of Science & Technology Early Career Award","award":["ECR\/2017\/002980"],"award-info":[{"award-number":["ECR\/2017\/002980"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Multidrug-resistant Staphylococcus aureus is a leading concern worldwide. Coagulase-Negative Staphylococci are claimed to be the reservoir and source of important resistant elements in S.\u00a0aureus. However, the origin and evolutionary route of resistant genes in S.\u00a0aureus are still remaining unknown. Here, we performed a detailed phylogenomic analysis of 152 completely sequenced S.\u00a0aureus strains in comparison with 7,529 non-Staphylococcus aureus reference bacterial genomes. Our results reveal that S.\u00a0aureus has a large open pan-genome where 97 (55%) of its known resistant-related genes belonging to its accessory genome. Among these genes, 47 (27%) were located within the Staphylococcal Cassette Chromosome mec (SCCmec), a transposable element responsible for resistance against major classes of antibiotics including beta-lactams, macrolides, and aminoglycosides. However, the physically linked mec-box genes (MecA\u2013MecR\u2013MecI) that are responsible for the maintenance of SCCmec elements is not unique to S.\u00a0aureus, instead it is widely distributed within Staphylococcaceae family. The phyletic patterns of SCCmec-encoded resistant genes in Staphylococcus species are significantly different from that of its core genes indicating frequent exchange of these genes between Staphylococcus species. Our in-depth analysis of SCCmec-resistant gene phylogenies reveals that genes such as blaZ, ble, kmA, and tetK that are responsible for beta-lactam, bleomycin, kanamycin, and tetracycline resistance in S.\u00a0aureus were laterally transferred from non-Staphylococcus sources. In addition, at least 11 non-SCCmec-encoded resistant genes in S.\u00a0aureus, were laterally acquired from distantly related species. Our study evidently shows that gene transfers played a crucial role in shaping the evolution of antibiotic resistance in S.\u00a0aureus.<\/jats:p>","DOI":"10.1093\/gbe\/evz213","type":"journal-article","created":{"date-parts":[[2019,9,30]],"date-time":"2019-09-30T23:57:04Z","timestamp":1569887824000},"page":"2917-2926","source":"Crossref","is-referenced-by-count":34,"title":["Phylogenomic Analysis Reveals the Evolutionary Route of Resistant Genes in Staphylococcus aureus"],"prefix":"10.1093","volume":"11","author":[{"given":"Jiffy","family":"John","sequence":"first","affiliation":[{"name":"Computational Biology Laboratory, Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India"},{"name":"Manipal Academy of Higher Education (MAHE), Manipal, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sinumol","family":"George","sequence":"additional","affiliation":[{"name":"Computational Biology Laboratory, Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sai Ravi Chandra","family":"Nori","sequence":"additional","affiliation":[{"name":"Computational Biology Laboratory, Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shijulal","family":"Nelson-Sathi","sequence":"additional","affiliation":[{"name":"Computational Biology Laboratory, Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,10,3]]},"reference":[{"issue":"8","key":"2019102310391091900_evz213-B1","doi-asserted-by":"crossref","first-page":"5005","DOI":"10.1007\/s11033-014-3367-3","article-title":"Staphylococcus aureus mobile genetic 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