{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T05:47:22Z","timestamp":1779083242410,"version":"3.51.4"},"reference-count":30,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2023,10,1]],"date-time":"2023-10-01T00:00:00Z","timestamp":1696118400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,10,1]],"date-time":"2023-10-01T00:00:00Z","timestamp":1696118400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,6,23]],"date-time":"2023-06-23T00:00:00Z","timestamp":1687478400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["LA\/P\/0059\/2020"],"award-info":[{"award-number":["LA\/P\/0059\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["PTDC\/CTA-AMB\/28196\/2017"],"award-info":[{"award-number":["PTDC\/CTA-AMB\/28196\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDB\/50016\/2020"],"award-info":[{"award-number":["UIDB\/50016\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDB\/CVT\/00772\/2020"],"award-info":[{"award-number":["UIDB\/CVT\/00772\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["2020"],"award-info":[{"award-number":["2020"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100015321","name":"Universidade de Tr\u00e1s-os-Montes e Alto Douro","doi-asserted-by":"publisher","award":["PTDC\/SAUINF\/30101\/2017"],"award-info":[{"award-number":["PTDC\/SAUINF\/30101\/2017"]}],"id":[{"id":"10.13039\/501100015321","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Science of The Total Environment"],"published-print":{"date-parts":[[2023,10]]},"DOI":"10.1016\/j.scitotenv.2023.165078","type":"journal-article","created":{"date-parts":[[2023,6,24]],"date-time":"2023-06-24T12:09:26Z","timestamp":1687608566000},"page":"165078","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"special_numbering":"C","title":["Searching for links between environmental and clinical mecA Staphylococcus aureus: A comparative genomics study"],"prefix":"10.1016","volume":"895","author":[{"given":"Jaqueline","family":"Rocha","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vanessa","family":"Silva","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patr\u00edcia","family":"Poeta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jo\u00e3o","family":"Botelho","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C\u00e9lia M.","family":"Manaia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.scitotenv.2023.165078_bb0005","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.scitotenv.2023.165078_bb0010","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1007\/s10123-021-00184-y","article-title":"Threats of antibiotic resistance: an obliged reappraisal","volume":"24","author":"Baquero","year":"2021","journal-title":"Int. Microbiol."},{"issue":"1","key":"10.1016\/j.scitotenv.2023.165078_bb0015","first-page":"1","article-title":"Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary","volume":"17","author":"Brynildsrud","year":"2016","journal-title":"Genome Biol."},{"issue":"6","key":"10.1016\/j.scitotenv.2023.165078_bb0020","doi-asserted-by":"crossref","first-page":"e0083122","DOI":"10.1128\/msystems.00831-22","article-title":"Phenotypic and genomic comparison of Staphylococcus aureus highlight virulence and host adaptation favoring the success of epidemic clones","volume":"7","author":"Chen","year":"2022","journal-title":"mSystems"},{"issue":"issue 1","key":"10.1016\/j.scitotenv.2023.165078_bb0025","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1007\/s00239-019-09914-3","article-title":"Antimicrobial resistance in bacteria: mechanisms, evolution, and persistence","volume":"Vol. 88","author":"Christaki","year":"2020","journal-title":"J. Mol. Evol."},{"issue":"5","key":"10.1016\/j.scitotenv.2023.165078_bb0030","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1099\/jmm.0.47074-0","article-title":"Rapid determination of hospital-acquired meticillin-resistant Staphylococcus aureus lineages","volume":"56","author":"Cockfield","year":"2007","journal-title":"J. Med. Microbiol."},{"issue":"issue 3","key":"10.1016\/j.scitotenv.2023.165078_bb0035","article-title":"Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus","volume":"Vol. 38","author":"Enright","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.scitotenv.2023.165078_bb0040","series-title":"Antimicrobial Resistance Surveillance in Europe 2022\u20132020","author":"European Centre for Disease Prevention and Control","year":"2022"},{"key":"10.1016\/j.scitotenv.2023.165078_bb0045","author":"Francisco"},{"issue":"12","key":"10.1016\/j.scitotenv.2023.165078_bb0050","doi-asserted-by":"crossref","first-page":"5442","DOI":"10.1128\/JCM.41.12.5442-5448.2003","article-title":"Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management","volume":"41","author":"Harmsen","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.scitotenv.2023.165078_bb0055","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1038\/s41564-019-0503-9","article-title":"Defining and combating antibiotic resistance from one health and global health perspectives","volume":"4","author":"Hernando-Amado","year":"2019","journal-title":"Nat. Microbiol."},{"issue":"5","key":"10.1016\/j.scitotenv.2023.165078_bb0060","doi-asserted-by":"crossref","first-page":"1947","DOI":"10.1128\/JCM.42.5.1947-1955.2004","article-title":"mecA locus diversity in methicillin-resistant Staphylococcus aureus isolates in Brisbane, Australia, and the development of a novel diagnostic procedure for the western samoan phage pattern clone","volume":"42","author":"Huygens","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.scitotenv.2023.165078_bb0065","series-title":"A New Class of Genetic Element, Staphylococcus Cassette Chromosome Mec, Encodes Methicillin Resistance in Staphylococcus aureus","volume":"Vol. 44","author":"Katayama","year":"2000"},{"issue":"7","key":"10.1016\/j.scitotenv.2023.165078_bb0070","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."},{"issue":"issues 2\u20133","key":"10.1016\/j.scitotenv.2023.165078_bb0075","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.ijmm.2009.08.013","article-title":"Genomic variation and evolution of Staphylococcus aureus","volume":"Vol. 300","author":"Lindsay","year":"2010","journal-title":"Int. J. Med. Microbiol."},{"issue":"8","key":"10.1016\/j.scitotenv.2023.165078_bb0080","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1016\/j.tim.2004.06.004","article-title":"Staphylococcus aureus: superbug, super genome?","volume":"12","author":"Lindsay","year":"2004","journal-title":"Trends Microbiol."},{"issue":"6","key":"10.1016\/j.scitotenv.2023.165078_bb0085","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.03117-22","article-title":"Pan-genome analysis of Staphylococcus aureus reveals key factors influencing genomic plasticity","volume":"10","author":"Liu","year":"2022","journal-title":"Microbiol. Spectr."},{"issue":"Issue 18","key":"10.1016\/j.scitotenv.2023.165078_bb0090","doi-asserted-by":"crossref","first-page":"3057","DOI":"10.1007\/s00018-010-0389-4","article-title":"Mobile genetic elements of Staphylococcus aureus","volume":"Vol. 67","author":"Malachowa","year":"2010","journal-title":"Cell. Mol. Life Sci."},{"issue":"22","key":"10.1016\/j.scitotenv.2023.165078_bb0095","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":"2","key":"10.1016\/j.scitotenv.2023.165078_bb0100","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/j.tim.2016.09.009","article-title":"Architecture of a species: phylogenomics of Staphylococcus aureus","volume":"25","author":"Planet","year":"2017","journal-title":"Trends Microbiol."},{"issue":"1","key":"10.1016\/j.scitotenv.2023.165078_bb0105","doi-asserted-by":"crossref","DOI":"10.1186\/s12864-021-08279-6","article-title":"Third generation cephalosporin-resistant Klebsiella pneumoniae thriving in patients and in wastewater: what do they have in common?","volume":"23","author":"Rocha","year":"2022","journal-title":"BMC Genomics"},{"issue":"1","key":"10.1016\/j.scitotenv.2023.165078_bb0110","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-022-14547-6","article-title":"Common and distinctive genomic features of Klebsiella pneumoniae thriving in the natural environment or in clinical settings","volume":"12","author":"Rocha","year":"2022","journal-title":"Sci. Rep."},{"issue":"6","key":"10.1016\/j.scitotenv.2023.165078_bb0115","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1016\/j.cmi.2016.01.024","article-title":"Pan-genome multilocus sequence typing and outbreak-specific reference-based single nucleotide polymorphism analysis to resolve two concurrent Staphylococcus aureus outbreaks in neonatal services","volume":"22","author":"Roisin","year":"2016","journal-title":"Clin. Microbiol. Infect."},{"issue":"14","key":"10.1016\/j.scitotenv.2023.165078_bb0120","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":"3","key":"10.1016\/j.scitotenv.2023.165078_bb0125","article-title":"chewBBACA: a complete suite for gene-by-gene schema creation and strain identification","volume":"4","author":"Silva","year":"2018","journal-title":"Microb. Genom."},{"issue":"1","key":"10.1016\/j.scitotenv.2023.165078_bb0130","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1128\/JCM.44.1.108-118.2006","article-title":"Characterization of a strain of community-associated methicillin-resistant Staphylococcus aureus widely disseminated in the United States","volume":"44","author":"Tenover","year":"2006","journal-title":"J. Clin. Microbiol."},{"issue":"5","key":"10.1016\/j.scitotenv.2023.165078_bb0135","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0037212","article-title":"Panton-valentine leukocidin is not the primary determinant of outcome for Staphylococcus aureus skin infections: evaluation from the canvas studies","volume":"7","author":"Tong","year":"2012","journal-title":"PLoS One"},{"issue":"3","key":"10.1016\/j.scitotenv.2023.165078_bb0140","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1128\/CMR.00134-14","article-title":"Staphylococcus aureus infections: epidemiology, pathophysiology, clinical manifestations, and management","volume":"28","author":"Tong","year":"2015","journal-title":"Clin. Microbiol. Rev."},{"issue":"Issue 4","key":"10.1016\/j.scitotenv.2023.165078_bb0145","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/s41579-018-0147-4","article-title":"Methicillin-resistant Staphylococcus aureus: an overview of basic and clinical research","volume":"Vol. 17","author":"Turner","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.scitotenv.2023.165078_bb0150","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.mib.2019.06.005","article-title":"Environmental and clinical antibiotic resistomes, same only different","volume":"Vol. 51","author":"Wright","year":"2019","journal-title":"Curr. Opin. Microbiol."}],"container-title":["Science of The Total Environment"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0048969723037014?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0048969723037014?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T15:59:59Z","timestamp":1758729599000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0048969723037014"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10]]},"references-count":30,"alternative-id":["S0048969723037014"],"URL":"https:\/\/doi.org\/10.1016\/j.scitotenv.2023.165078","relation":{},"ISSN":["0048-9697"],"issn-type":[{"value":"0048-9697","type":"print"}],"subject":[],"published":{"date-parts":[[2023,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Searching for links between environmental and clinical mecA+ Staphylococcus aureus: A comparative genomics study","name":"articletitle","label":"Article Title"},{"value":"Science of The Total Environment","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.scitotenv.2023.165078","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Authors. Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"165078"}}