{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T21:51:02Z","timestamp":1791323462289,"version":"4.3.1"},"reference-count":70,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2022,11,16]],"date-time":"2022-11-16T00:00:00Z","timestamp":1668556800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Staphylococcus aureus is a pathogen that can cause severe illness and express resistance to multiple antimicrobial agents. It is part of the ESKAPE organisms and it has been included by the Centers for Disease Control and Prevention (CDC) of USA in the list of serious threats to humans. Many antimicrobial mechanisms have been identified, and, in particular, antimicrobial resistance genes (ARGs) can be determined by whole genome sequencing. Mobile genetic elements (MGEs) can determine the spread of these ARGs between strains and species and can be identified with bioinformatic analyses. The scope of this work was to analyse publicly available genomes of S. aureus to characterise the occurrence of ARGs present in chromosomes and plasmids in relation to their geographical distribution, isolation sources, clonal complexes, and changes over time. The results showed that from a total of 29,679 S. aureus genomes, 24,765 chromosomes containing 73 different ARGs, and 21,006 plasmidic contigs containing 47 different ARGs were identified. The most abundant ARG in chromosomes was mecA (84%), while blaZ was the most abundant in plasmidic contigs (30%), although it was also abundant in chromosomes (42%). A total of 13 clonal complexes were assigned and differences in ARGs and CC distribution were highlighted among continents. Temporal changes during the past 20 years (from 2001 to 2020) showed that, in plasmids, MRSA and macrolide resistance occurrence decreased, while the occurrence of ARGs associated with aminoglycosides resistance increased. Despite the lack of metadata information in around half of the genomes analysed, the results obtained enable an in-depth analysis of the distribution of ARGs and MGEs throughout different categories to be undertaken through the design and implementation of a relatively simple pipeline, which can be also applied in future works with other pathogens, for surveillance and screening purposes.<\/jats:p>","DOI":"10.3390\/antibiotics11111632","type":"journal-article","created":{"date-parts":[[2022,11,16]],"date-time":"2022-11-16T02:27:34Z","timestamp":1668565654000},"page":"1632","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Antimicrobial Resistance Genes Analysis of Publicly Available Staphylococcus aureus Genomes"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8752-3231","authenticated-orcid":false,"given":"Vincenzo","family":"Pennone","sequence":"first","affiliation":[{"name":"Department of Food and Drug, Universit\u00e0 degli Studi di Parma, 43121 Parma, Italy"},{"name":"Department of Food Hygiene and Technology, Universidad de Le\u00f3n, 24071 Le\u00f3n, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9202-3856","authenticated-orcid":false,"given":"Miguel","family":"Prieto","sequence":"additional","affiliation":[{"name":"Department of Food Hygiene and Technology, Universidad de Le\u00f3n, 24071 Le\u00f3n, Spain"},{"name":"Institute of Food Science and Technology, Universidad de Le\u00f3n, 24071 Le\u00f3n, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Avelino","family":"\u00c1lvarez-Ord\u00f3\u00f1ez","sequence":"additional","affiliation":[{"name":"Department of Food Hygiene and Technology, Universidad de Le\u00f3n, 24071 Le\u00f3n, Spain"},{"name":"Institute of Food Science and Technology, Universidad de Le\u00f3n, 24071 Le\u00f3n, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0898-2358","authenticated-orcid":false,"given":"Jos\u00e9 F.","family":"Cobo-Diaz","sequence":"additional","affiliation":[{"name":"Department of Food Hygiene and Technology, Universidad de Le\u00f3n, 24071 Le\u00f3n, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,11,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Gajd\u00e1cs, M. (2019). The Continuing Threat of Methicillin-Resistant Staphylococcus aureus. Antibiotics, 8.","DOI":"10.3390\/antibiotics8020052"},{"key":"ref_2","first-page":"188","article-title":"Staphylococcus aureus enterotoxins: A review","volume":"1","author":"Bhatia","year":"2007","journal-title":"J. Clin. Diagn. Res."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Haag, A.F., Fitzgerald, J.R., and Penad\u00e9s, J.R. (2019). Staphylococcus aureus in Animals. Microbiol. Spectr., 7.","DOI":"10.1128\/microbiolspec.GPP3-0060-2019"},{"key":"ref_4","unstructured":"CDC (2021, November 12). 2019 AR Threats Report, Available online: https:\/\/www.cdc.gov\/drugresistance\/biggest-threats.html?CDC_AA_refVal=https%3A%2F%2Fwww.cdc.gov%2Fdrugresistance%2Fbiggest_threats.html."},{"key":"ref_5","unstructured":"WHO (2022, March 08). Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics. Available online: https:\/\/www.who.int\/medicines\/publications\/WHO-PPL-Short_Summary_25Feb-ET_NM_WHO.pdf."},{"key":"ref_6","unstructured":"WHO (2021, November 12). Antimicrobial Resistance 2020. Available online: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/antimicrobial-resistance."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1186\/s13059-017-1252-9","article-title":"Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice","volume":"18","author":"Harkins","year":"2017","journal-title":"Genome Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1086\/595011","article-title":"Bad Bugs, No Drugs: No ESKAPE! An Update from the Infectious Diseases Society of America","volume":"48","author":"Boucher","year":"2009","journal-title":"Clin. Infect. Dis."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"511","DOI":"10.3389\/fmicb.2018.00511","article-title":"Routine Whole-Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a National Reference Center","volume":"9","author":"Durand","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"\u00c1lvarez-Molina, A., de Toro, M., Alexa, E.A., and \u00c1lvarez-Ord\u00f3\u00f1ez, A. (2020). 1.12\u2014Applying Genomics to Track Antimicrobial Resistance in the Food Chain. Comprehensive Foodomics, Elsevier.","DOI":"10.1016\/B978-0-08-100596-5.22700-5"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"607842","DOI":"10.3389\/fmicb.2020.607842","article-title":"Integrative Analysis of Whole Genome Sequencing and Phenotypic Resistance Toward Prediction of Trimethoprim-Sulfamethoxazole Resistance in Staphylococcus aureus","volume":"11","author":"Nurjadi","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e00138-20","DOI":"10.1128\/JCM.00138-20","article-title":"The Genotype-to-Phenotype Dilemma: How Should Laboratories Approach Discordant Susceptibility Results?","volume":"59","author":"Yee","year":"2021","journal-title":"J. Clin. Microbiol."},{"key":"ref_13","first-page":"e05898","article-title":"Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms","volume":"17","author":"Koutsoumanis","year":"2019","journal-title":"EFSA J."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1901","DOI":"10.3389\/fmicb.2018.01901","article-title":"Phylogenomic Classification and the Evolution of Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere","volume":"9","author":"Challagundla","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_15","first-page":"e000058","article-title":"Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic","volume":"2","author":"Jamrozy","year":"2016","journal-title":"Microb. Genom."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1111\/j.1469-0691.2006.01573.x","article-title":"The molecular evolution of methicillin-resistant Staphylococcus aureus","volume":"13","author":"Deurenberg","year":"2007","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e00088-17","DOI":"10.1128\/CMR.00088-17","article-title":"Mobile Genetic Elements Associated with Antimicrobial Resistance","volume":"31","author":"Partridge","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.drup.2010.08.003","article-title":"Aminoglycoside modifying enzymes","volume":"13","author":"Ramirez","year":"2010","journal-title":"Drug Resist. Updates"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.ijmm.2017.05.003","article-title":"High virulence of methicillin resistant Staphylococcus aureus ST30-SCCmecIVc-spat019, the dominant community-associated clone in Argentina","volume":"307","author":"Fernandez","year":"2017","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Mairi, A., Touati, A., and Lavigne, J.-P. (2020). Methicillin-Resistant Staphylococcus aureus ST80 Clone: A Systematic Review. Toxins, 12.","DOI":"10.3390\/toxins12020119"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"629681","DOI":"10.3389\/fcell.2021.629681","article-title":"Identification of Methicillin-Resistant Staphylococcus Aureus from Methicillin-Sensitive Staphylococcus aureus and Molecular Characterization in Quanzhou, China","volume":"9","author":"Bai","year":"2021","journal-title":"Front. Cell Dev. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Li, J., Wang, L., Ip, M., Sun, M., Sun, J., Huang, G., Wang, C., Deng, L., Zheng, Y., and Fu, Z. (2013). Molecular and Clinical Characteristics of Clonal Complex 59 Methicillin-Resistant Staphylococcus aureus Infections in Mainland China. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0070602"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1436","DOI":"10.3389\/fmicb.2021.652276","article-title":"Molecular Characteristics of Staphylococcus aureus from Food Samples and Food Poisoning Outbreaks in Shijiazhuang, China","volume":"12","author":"Lv","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_24","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":"17","author":"Turner","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1093\/jac\/dkr024","article-title":"Spread of methicillin-resistant Staphylococcus aureus between the community and the hospitals in Asian countries: An ANSORP study","volume":"66","author":"Song","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1007\/s00203-012-0797-y","article-title":"Characteristics and distribution of plasmids in a clonally diverse set of methicillin-resistant Staphylococcus aureus strains","volume":"194","year":"2012","journal-title":"Arch. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"McCarthy, A.J., and Lindsay, J.A. (2012). The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated. BMC Microbiol., 12, Available online: http:\/\/www.biomedcentral.com\/1471-2180\/12\/104.","DOI":"10.1186\/1471-2180-12-104"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1592","DOI":"10.3389\/fmicb.2019.01592","article-title":"Novel Methicillin-Resistant Staphylococcus aureus CC8 Clone Identified in a Hospital Setting in Armenia","volume":"10","author":"Jamrozy","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"3804","DOI":"10.1128\/AAC.00351-10","article-title":"Emergence of Resistance among USA300 Methicillin-Resistant Staphylococcus aureus Isolates Causing Invasive Disease in the United States","volume":"54","author":"McDougal","year":"2010","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1093\/jac\/dkt413","article-title":"Evolution of methicillin-resistant Staphylococcus aureus towards increasing resistance","volume":"69","author":"Strommenger","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2063","DOI":"10.3389\/fmicb.2018.02063","article-title":"Small Antimicrobial Resistance Plasmids in Livestock-Associated Methicillin-Resistant Staphylococcus aureus CC398","volume":"9","author":"Kadlec","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Jamrozy, D., Coll, F., Mather, A.E., Harris, S.R., Harrison, E.M., MacGowan, A., Karas, A., Elston, T., T\u00f6r\u00f6k, M.E., and Parkhill, J. (2017). Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: Temporal changes correlated with frequent loss and gain events. BMC Genom., 18.","DOI":"10.1186\/s12864-017-4065-z"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"5948","DOI":"10.1128\/AEM.00870-12","article-title":"Expansion of a Plasmid Classification System for Gram-Positive Bacteria and Determination of the Diversity of Plasmids in Staphylococcus aureus Strains of Human, Animal, and Food Origins","volume":"78","author":"Lozano","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"447","DOI":"10.2147\/IDR.S192611","article-title":"Antimicrobial resistance, virulence genes profiling and molecular relatedness of methicillin-resistant Staphylococcus aureus strains isolated from hospitalized patients in Guangdong Province, China","volume":"12","author":"Liang","year":"2019","journal-title":"Infect. Drug Resist."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1016\/j.ijmm.2014.09.004","article-title":"Characterization of tetracycline and methicillin resistant Staphylococcus aureus strains in a Spanish hospital: Is livestock-contact a risk factor in infections caused by MRSA CC398?","volume":"304","author":"Benito","year":"2014","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1093\/jac\/dkr497","article-title":"High prevalence of spa types associated with the clonal lineage CC398 among tetracycline-resistant methicillin-resistant Staphylococcus aureus strains in a Spanish hospital","volume":"67","author":"Lozano","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.1093\/jac\/dku174","article-title":"Emergence of trimethoprim resistance gene dfrG in Staphylococcus aureus causing human infection and colonization in sub-Saharan Africa and its import to Europe","volume":"69","author":"Nurjadi","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_38","unstructured":"(2021, November 15). Resistancemap 2021. Available online: https:\/\/resistancemap.cddep.org\/."},{"key":"ref_39","unstructured":"(2021, November 15). Resistancemap\u2014Antibiotic Use 2021. Available online: https:\/\/resistancemap.cddep.org\/AntibioticUse.php."},{"key":"ref_40","unstructured":"(2021, November 15). Resistancemap\u2014Methodology 2021. Available online: https:\/\/resistancemap.cddep.org\/MethodologyAU.php."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.ijmm.2014.11.007","article-title":"Are cases of Methicillin-resistant Staphylococcus aureus clonal complex (CC) 398 among humans still livestock-associated?","volume":"305","author":"Deiters","year":"2015","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"125","DOI":"10.35943\/mvmj.2020.21.322","article-title":"Genomic Overview into the Evolving Epidemiology of Methicillin-Resistant Staphylococcus aureus","volume":"21","author":"Mouftah","year":"2020","journal-title":"Mansoura Vet. Med. J."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1111\/1469-0691.12705","article-title":"New epidemiology of Staphylococcus aureus infection in Asia","volume":"20","author":"Chen","year":"2014","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Park, K.-H., Greenwood-Quaintance, K.E., Uhl, J.R., Cunningham, S.A., Chia, N., Jeraldo, P., Sampathkumar, P., Nelson, H., and Patel, R. (2017). Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0179003"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"2681","DOI":"10.3389\/fmicb.2019.02681","article-title":"Antimicrobial Resistance and Virulence Gene Profiles of Methicillin-Resistant and -Susceptible Staphylococcus aureus from Food Products in Denmark","volume":"10","author":"Li","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Monecke, S., Coombs, G., Shore, A.C., Coleman, D.C., Akpaka, P., Borg, M., Chow, H., Ip, M., Jatzwauk, L., and Jonas, D. (2011). A Field Guide to Pandemic, Epidemic and Sporadic Clones of Methicillin-Resistant Staphylococcus aureus. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0017936"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e01160-17","DOI":"10.1128\/JCM.01160-17","article-title":"Trends in Antibiotic Susceptibility in Staphylococcus aureus in Boston, Massachusetts, from 2000 to 2014","volume":"56","author":"Kanjilal","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"220","DOI":"10.15585\/mmwr.mm6809e2","article-title":"Vital Signs: Trends in Staphylococcus aureus infections in veterans affairs medical centers\u2014United States, 2005\u20132017","volume":"68","author":"Jones","year":"2019","journal-title":"Morb. Mortal. Wkly. Rep."},{"key":"ref_49","unstructured":"CDC (2019). Antibiotic Resistance Threats in the United States, 2019."},{"key":"ref_50","unstructured":"CDDEP (2021, November 15). Infectious Diseases in the South-East Asia Region. Available online: https:\/\/cddep.org\/wp-content\/uploads\/2021\/02\/Infectious-diseases-in-the-south-east-asia-region.pdf."},{"key":"ref_51","unstructured":"Ministry of Health Malaysia (2021, November 15). Malaysian Action Plan on Antimicrobial Resistance (MyAP-AMR) 2017\u20132021, Available online: https:\/\/www.moh.gov.my\/moh\/resources\/Penerbitan\/Garis%20Panduan\/Garis%20panduan%20Umum%20(Awam)\/National_Action_Plan_-_FINAL_29_june.pdf."},{"key":"ref_52","unstructured":"Norwegian Ministeries (2021, November 15). National Strategy against Antibiotic Resistance 2015\u20132020. Available online: https:\/\/www.regjeringen.no\/contentassets\/5eaf66ac392143b3b2054aed90b85210\/antibiotic-resistance-engelsk-lavopploslig-versjon-for-nett-10-09-15.pdf."},{"key":"ref_53","unstructured":"Swedish Institute for Infectious Disease Control (2021, November 15). SWEDRES 2001 a Report on Swedish Antibiotic Utilisation and Resistance in Human Medicine. Available online: https:\/\/www.folkhalsomyndigheten.se\/contentassets\/a21b86df576844cab59537f4d793ed87\/swedres-2001.pdf."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Tadesse, B.T., Ashley, E.A., Ongarello, S., Havumaki, J., Wijegoonewardena, M., Gonz\u00e1lez, I.J., and Dittrich, S. (2017). Antimicrobial resistance in Africa: A systematic review. BMC Infect. Dis., 17.","DOI":"10.1186\/s12879-017-2713-1"},{"key":"ref_55","unstructured":"Thailand Ministry of Public Health (2021, November 15). Thailand\u2019s National Strategic Plan on Antimicrobial Resistance 2017\u20132021, Available online: https:\/\/rr-asia.oie.int\/wp-content\/uploads\/2020\/03\/thailand_thailands-national-strategic-plan-on-amr-2017-2021.pdf."},{"key":"ref_56","unstructured":"The Government of Japan (2021, November 15). National Action Plan on Antimicrobial Resistance (AMR), Available online: https:\/\/www.mhlw.go.jp\/file\/06-Seisakujouhou-10900000-Kenkoukyoku\/0000138942.pdf."},{"key":"ref_57","unstructured":"WHO (2021, November 15). WHO Report on Surveillance of Antibiotic Consumption. Available online: https:\/\/www.who.int\/medicines\/areas\/rational_use\/who-amr-amc-report-20181109.pdf."},{"key":"ref_58","unstructured":"NCBI (2021, November 12). NCBI 2021, Available online: https:\/\/ftp.ncbi.nlm.nih.gov\/genomes\/GENOMES_REPORTS\/."},{"key":"ref_59","unstructured":"PATRIC (2021, November 12). PATRIC 2021. Available online: https:\/\/ftp.patricbrc.org\/."},{"key":"ref_60","unstructured":"PUBMLST (2021, November 12). PUBMLST 2021. Available online: https:\/\/pubmlst.org."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"662144","DOI":"10.3389\/fmicb.2021.662144","article-title":"Whole Resistome Analysis in Campylobacter jejuni and C. coli Genomes Available in Public Repositories","volume":"12","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_62","unstructured":"StarAMR (2021, November 12). Staramr 2021. Available online: https:\/\/github.com\/phac-nml\/staramr."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref_65","unstructured":"(2021, December 17). PubMLST S. aureus Scheme. Available online: https:\/\/github.com\/tseemann\/mlst\/blob\/master\/db\/pubmlst\/saureus\/saureus.txt."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Bouiller, K., Bertrand, X., Hocquet, D., and Chirouze, C. (2020). Human Infection of Methicillin-Susceptible Staphylococcus aureus CC398: A Review. Microorganisms, 8.","DOI":"10.3390\/microorganisms8111737"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"655994","DOI":"10.3389\/fmicb.2021.655994","article-title":"Genomic Analysis of Staphylococcus aureus of the Lineage CC130, Including mecC-Carrying MRSA and MSSA Isolates Recovered of Animal, Human, and Environmental Origins","volume":"12","author":"Gharsa","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"422","DOI":"10.3389\/fmicb.2020.00422","article-title":"The Genomic Context for the Evolution and Transmission of Community-Associated Staphylococcus aureus ST59 through the Food Chain","volume":"11","author":"Pang","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1093\/jac\/dkz232","article-title":"High prevalence of a globally disseminated hypervirulent clone, Staphylococcus aureus CC121, with reduced vancomycin susceptibility in community settings in China","volume":"74","author":"Shen","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"e35","DOI":"10.1093\/nar\/gkx1321","article-title":"PlasFlow: Predicting plasmid sequences in metagenomic data using genome signatures","volume":"46","author":"Krawczyk","year":"2018","journal-title":"Nucleic Acids Res."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/11\/11\/1632\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:19:07Z","timestamp":1760145547000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/11\/11\/1632"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,16]]},"references-count":70,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11]]}},"alternative-id":["antibiotics11111632"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics11111632","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,16]]}}}