{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T01:18:29Z","timestamp":1776820709173,"version":"3.51.2"},"reference-count":71,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2023,12,16]],"date-time":"2023-12-16T00:00:00Z","timestamp":1702684800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"crossref","award":["JP23wm0125008"],"award-info":[{"award-number":["JP23wm0125008"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"crossref","award":["JP233fa627005"],"award-info":[{"award-number":["JP233fa627005"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.mdpi.com"],"crossmark-restriction":true},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has been widespread globally in pigs and humans for decades. Nasal colonization of LA-MRSA is regarded as an occupational hazard to people who are regularly involved in livestock production. Our previous study suggested pig-to-human transmission caused by LA-MRSA clonal complex (CC) 398, using traditional molecular typing methods. Instead, this study aimed to investigate the zoonotic transmission of LA-MRSA CC398 using whole genome sequencing (WGS) technologies. A total of 63 LA-MRSA isolates were identified and characterized in Thailand. Further, the 16 representatives of LA-MRSA CC9 and CC398, including porcine and worker isolates, were subjected to WGS on the Illumina Miseq platform. Core-genome single nucleotide polymorphism (SNP)-based analyses verify the zoonotic transmission caused by LA-MRSA CC398 in two farms. WGS-based characterization suggests the emergence of a novel staphylococcal cassette chromosome (SCC) mec type, consisting of multiple cassette chromosome recombinase (ccr) gene complexes via genetic recombination. Additionally, the WGS analyses revealed putative multi-resistant plasmids and several cross-resistance genes, conferring resistance against drugs of last resort used in humans such as quinupristin\/dalfopristin and linezolid. Significantly, LA-MRSA isolates, in this study, harbored multiple virulence genes that may become a serious threat to an immunosuppressive population, particularly for persons who are in close contact with LA-MRSA carriers.<\/jats:p>","DOI":"10.3390\/antibiotics12121745","type":"journal-article","created":{"date-parts":[[2023,12,18]],"date-time":"2023-12-18T03:59:24Z","timestamp":1702871964000},"page":"1745","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Whole-Genome Investigation of Zoonotic Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complex 398 Isolated from Pigs and Humans in Thailand"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-3946-4760","authenticated-orcid":false,"given":"Pawarut","family":"Narongpun","sequence":"first","affiliation":[{"name":"Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8979-2440","authenticated-orcid":false,"given":"Pattrarat","family":"Chanchaithong","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8385-5359","authenticated-orcid":false,"given":"Junya","family":"Yamagishi","sequence":"additional","affiliation":[{"name":"Division of Collaboration and Education, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3447-6483","authenticated-orcid":false,"given":"Jeewan","family":"Thapa","sequence":"additional","affiliation":[{"name":"Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chie","family":"Nakajima","sequence":"additional","affiliation":[{"name":"Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan"},{"name":"International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1313-1494","authenticated-orcid":false,"given":"Yasuhiko","family":"Suzuki","sequence":"additional","affiliation":[{"name":"Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan"},{"name":"International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo 001-0020, Japan"},{"name":"Institute for Vaccine Research and Development, Hokkaido University, Sapporo 001-0020, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,12,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"529","DOI":"10.4142\/jvs.2014.15.4.529","article-title":"Occurrence and Characterization of Livestock-Associated Methicillin-Resistant Staphylococcus aureus in Pig Industries of Northern Thailand","volume":"15","author":"Patchanee","year":"2014","journal-title":"J. Vet. Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1382","DOI":"10.1089\/mdr.2019.0011","article-title":"Molecular Characterization and Antimicrobial Resistance of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates from Pigs and Swine Workers in Central Thailand","volume":"25","author":"Chanchaithong","year":"2019","journal-title":"Microbial. Drug Resist."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1136\/oemed-2020-106418","article-title":"Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) Colonisation and Infection among Livestock Workers and Veterinarians: A Systematic Review and Meta-Analysis","volume":"78","author":"Chen","year":"2021","journal-title":"Occup. Environ. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.3201\/eid1112.050428","article-title":"Methicillin-Resistant Staphylococcus aureus in Pig Farming","volume":"11","author":"Voss","year":"2005","journal-title":"Emerg. Infect. Dis. J."},{"key":"ref_5","unstructured":"The Danish Health Authority (2016). Guidance on Preventing the Spread of MRSA."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"18033","DOI":"10.1038\/nrdp.2018.33","article-title":"Methicillin-Resistant Staphylococcus aureus","volume":"4","author":"Lee","year":"2018","journal-title":"Nat. Rev. Dis. Primers"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1128\/AEM.02803-14","article-title":"Transmission and Persistence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus among Veterinarians and Their Household Members","volume":"81","author":"Bosch","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.diagmicrobio.2016.08.016","article-title":"Comparison of Livestock-Associated and Health Care\u2013Associated MRSA\u2014Genes, Virulence, and Resistance","volume":"86","author":"Mutters","year":"2016","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13620-021-00200-7","article-title":"Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) Prevalence in Humans in Close Contact with Animals and Measures to Reduce on-Farm Colonisation","volume":"74","author":"Lawlor","year":"2021","journal-title":"Ir. Vet. J."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.vetmic.2016.01.021","article-title":"In the Centre of an Epidemic: Fifteen Years of LA-MRSA CC398 at the University Hospital M\u00fcnster","volume":"200","author":"Ballhausen","year":"2017","journal-title":"Vet. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/cid\/cix504","article-title":"Emergence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Bloodstream Infections in Denmark","volume":"65","author":"Larsen","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"European Food Safety Authority (EFSA) (2009). Assessment of the Public Health Significance of Meticillin Resistant Staphylococcus aureus (MRSA) in Animals and Foods. EFSA J., 7, 993.","DOI":"10.2903\/j.efsa.2009.993"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e00020-18","DOI":"10.1128\/CMR.00020-18","article-title":"Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology","volume":"31","author":"Sahreena","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Cui, M., Ali, T., Li, J., Song, L., Shen, S., Li, T., Zhang, C., Cheng, M., Zhao, Q., and Wang, H. (2022). New Clues about the Global MRSA ST398: Emergence of MRSA ST398 from Pigs in Qinghai, China. Int. J. Food Microbiol., 378.","DOI":"10.1016\/j.ijfoodmicro.2022.109820"},{"key":"ref_15","unstructured":"Hemeg, H., Ozbak, H., and Afrin, F. (2018). Resistance of Staphylococci to Macrolides-Lincosamides-Streptogramins B (MLSB): Epidemiology and Mechanisms of Re-sistance. Staphylococcus Aureus, IntechOpen."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.plasmid.2018.06.002","article-title":"Mobile Lincosamide Resistance Genes in Staphylococci","volume":"99","author":"Wang","year":"2018","journal-title":"Plasmid"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.pisc.2014.12.004","article-title":"Diversity in Fosfomycin Resistance Proteins","volume":"4","author":"Thompson","year":"2015","journal-title":"Perspect. Sci."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Fu, Z., Ma, Y., Chen, C., Guo, Y., Hu, F., Liu, Y., Xu, X., and Wang, M. (2016). Prevalence of Fosfomycin Resistance and Mutations in MurA, GlpT, and UhpT in Methicillin-Resistant Staphylococcus aureus Strains Isolated from Blood and Cerebrospinal Fluid Samples. Front. Microbiol., 6.","DOI":"10.3389\/fmicb.2015.01544"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"00098-18","DOI":"10.1128\/mSystems.00098-18","article-title":"Comprehensive Virulence Gene Profiling of Bovine Non-Aureus Staphylococci Based on Whole-Genome Sequencing Data","volume":"4","author":"Naushad","year":"2019","journal-title":"mSystems"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.ijantimicag.2011.02.018","article-title":"Meticillin-Resistant Staphylococcus aureus in Pigs from Thailand","volume":"38","author":"Anukool","year":"2011","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1099\/jmm.0.000119","article-title":"SCCmec IX in Meticillin-Resistant Staphylococcus aureus and Meticillin-Resistant Coagulase-Negative Staphylococci from Pigs and Workers at Pig Farms in Khon Kaen, Thailand","volume":"64","author":"Sinlapasorn","year":"2015","journal-title":"J. Med. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.jgar.2018.03.012","article-title":"A Japanese Trial to Monitor Methicillin-Resistant Staphylococcus aureus (MRSA) in Imported Swine during the Quarantine Period","volume":"14","author":"Furuno","year":"2018","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.vetmic.2011.08.011","article-title":"The First Detection of Methicillin-Resistant Staphylococcus aureus ST398 in Pigs in Korea","volume":"155","author":"Lim","year":"2012","journal-title":"Vet. Microbiol."},{"key":"ref_24","unstructured":"Tanomsridachchai, W. (2023). Genetic Characterization of Methicillin-Resistant Staphylococcus aureus Isolated from Pigs and Pork Meat in Thailand. [Ph.D. Thesis, Hokkaido University]. Volume 14717."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Zong, Z., Peng, C., and L\u00fc, X. (2011). Diversity of SCCmec Elements in Methicillin-Resistant Coagulase-Negative Staphylococci Clinical Isolates. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0020191"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1871","DOI":"10.1093\/jac\/dkad174","article-title":"Exploring the Third-Generation Tetracycline Resistance of Multidrug-Resistant Livestock-Associated Methicillin-Resistant Staphylococcus aureus ST9 across Healthcare Settings in China","volume":"78","author":"Chen","year":"2023","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Chen, X.-P., Li, W.-G., Zheng, H., Du, H.-Y., Zhang, L., Zhang, L., Che, J., Wu, Y., Liu, S.-M., and Lu, J.-X. (2017). Extreme Diversity and Multiple SCCmec Elements in Coagulase-Negative Staphylococcus Found in the Clinic and Community in Beijing, China. Ann. Clin. Microbiol. Antimicrob., 16.","DOI":"10.1186\/s12941-017-0231-z"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1002\/emmm.201202413","article-title":"Whole Genome Sequencing Identifies Zoonotic Transmission of MRSA Isolates with the Novel MecA Homologue MecC","volume":"5","author":"Harrison","year":"2013","journal-title":"EMBO Mol. Med."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Tanomsridachchai, W., Changkaew, K., Changkwanyeun, R., Prapasawat, W., Intarapuk, A., Fukushima, Y., Yamasamit, N., Flav Kapalamula, T., Nakajima, C., and Suthienkul, O. (2021). Antimicrobial Resistance and Molecular Characterization of Methicillin-Resistant Staphylococcus aureus Isolated from Slaughtered Pigs and Pork in the Central Region of Thailand. Antibiotics, 10.","DOI":"10.3390\/antibiotics10020206"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"5406","DOI":"10.1128\/AAC.00580-10","article-title":"LmrS Is a Multidrug Efflux Pump of the Major Facilitator Superfamily from Staphylococcus aureus","volume":"54","author":"Floyd","year":"2010","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.vetmic.2015.02.031","article-title":"Prevalence of the Immune Evasion Gene Cluster in Staphylococcus aureus CC398","volume":"177","author":"Cuny","year":"2015","journal-title":"Vet. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1128\/JCM.44.3.847-853.2006","article-title":"Detection of New Methicillin-Resistant Staphylococcus aureus Clones Containing the Toxic Shock Syndrome Toxin 1 Gene Responsible for Hospital- and Community-Acquired Infections in France","volume":"44","author":"Durand","year":"2006","journal-title":"J. Clin. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.1128\/JB.188.4.1310-1315.2006","article-title":"The Innate Immune Modulators Staphylococcal Complement Inhibitor and Chemotaxis Inhibitory Protein of Staphylococcus aureus Are Located on \u03b2-Hemolysin-Converting Bacteriophages","volume":"188","author":"Rooijakkers","year":"2006","journal-title":"J. Bacteriol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"00305-11","DOI":"10.1128\/mBio.00305-11","article-title":"Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock","volume":"3","author":"Price","year":"2012","journal-title":"mBio"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2145","DOI":"10.1128\/IAI.74.4.2145-2153.2006","article-title":"Immunization with Staphylococcus aureus Clumping Factor B, a Major Determinant in Nasal Carriage, Reduces Nasal Colonization in a Murine Model","volume":"74","author":"Schaffer","year":"2006","journal-title":"Infect. Immun."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Mulcahy, M.E., Geoghegan, J.A., Monk, I.R., O\u2019Keeffe, K.M., Walsh, E.J., Foster, T.J., and McLoughlin, R.M. (2012). Nasal Colonisation by Staphylococcus aureus Depends upon Clumping Factor B Binding to the Squamous Epithelial Cell Envelope Protein Loricrin. PLoS Pathog., 8.","DOI":"10.1371\/journal.ppat.1003092"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Wertheim, H.F.L., Walsh, E., Choudhurry, R., Melles, D.C., Boelens, H.A.M., Miajlovic, H., Verbrugh, H.A., Foster, T., and van Belkum, A. (2008). Key Role for Clumping Factor B in Staphylococcus aureus Nasal Colonization of Humans. PLoS Med., 5.","DOI":"10.1371\/journal.pmed.0050017"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Sakr, A., Br\u00e9geon, F., M\u00e8ge, J.-L., Rolain, J.-M., and Blin, O. (2018). Staphylococcus aureus Nasal Colonization: An Update on Mechanisms, Epidemiology, Risk Factors, and Subsequent Infections. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.02419"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Lacey, K.A., Mulcahy, M.E., Towell, A.M., Geoghegan, J.A., and McLoughlin, R.M. (2019). Clumping Factor B Is an Important Virulence Factor during Staphylococcus aureus Skin Infection and a Promising Vaccine Target. PLoS Pathog., 15.","DOI":"10.1371\/journal.ppat.1007713"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/S8756-3282(01)00632-9","article-title":"Staphylococcus aureus Collagen Adhesin Contributes to the Pathogenesis of Osteomyelitis","volume":"30","author":"Elasri","year":"2002","journal-title":"Bone"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/iai.62.1.152-161.1994","article-title":"The Staphylococcus aureus Collagen Adhesin Is a Virulence Determinant in Experimental Septic Arthritis","volume":"62","author":"Patti","year":"1994","journal-title":"Infect. Immun."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"3776","DOI":"10.1128\/IAI.68.6.3776-3779.2000","article-title":"The Collagen-Binding Adhesin Is a Virulence Factor in Staphylococcus aureus Keratitis","volume":"68","author":"Rhem","year":"2000","journal-title":"Infect. Immun."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1093\/infdis\/174.1.83","article-title":"Collagen Binding of Staphylococcus aureus Is a Virulence Factor in Experimental Endocarditis","volume":"174","author":"Hienz","year":"1996","journal-title":"J. Infect. Dis."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Lister, J.L., and Horswill, A.R. (2014). Staphylococcus aureus Biofilms: Recent Developments in Biofilm Dispersal. Front. Cell Infect. Microbiol., 4.","DOI":"10.3389\/fcimb.2014.00178"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"3324","DOI":"10.1016\/j.csbj.2020.10.027","article-title":"The Staphylococcal Exopolysaccharide PIA\u2014Biosynthesis and Role in Biofilm Formation, Colonization, and Infection","volume":"18","author":"Nguyen","year":"2020","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1016\/j.tim.2016.06.012","article-title":"Host\u2013Bacterial Crosstalk Determines Staphylococcus aureus Nasal Colonization","volume":"24","author":"Mulcahy","year":"2016","journal-title":"Trends Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1128\/microbiolspec.VMBF-0022-2015","article-title":"The Staphylococcal Biofilm: Adhesins, Regulation, and Host Response","volume":"4","author":"Paharik","year":"2016","journal-title":"Microbiol. Spectr."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Zhang, F., Wu, S., Lei, T., Wu, Q., Zhang, J., Huang, J., Dai, J., Chen, M., Ding, Y., and Wang, J. (2022). Presence and Characterization of Methicillin-Resistant Staphylococcus aureus Co-Carrying the Multidrug Resistance Genes Cfr and Lsa(E) in Retail Food in China. Int. J. Food Microbiol., 363.","DOI":"10.1016\/j.ijfoodmicro.2021.109512"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1016\/j.vetmic.2013.07.017","article-title":"Complete Sequence of the Multi-Resistance Plasmid PV7037 from a Porcine Methicillin-Resistant Staphylococcus aureus","volume":"166","author":"Wendlandt","year":"2013","journal-title":"Vet. Microbiol."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements (IWG-SCC) (2009). Classification of Staphylococcal Cassette Chromosome Mec (SCCMec): Guidelines for Reporting Novel SCCMec Elements. Antimicrob. Agents Chemother., 53, 4961\u20134967.","DOI":"10.1128\/AAC.00579-09"},{"key":"ref_51","unstructured":"Andrews, S. (2022, March 31). FASTQC. A Quality Control Tool for High Throughput Sequence Data. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"bar011","DOI":"10.1093\/database\/bar011","article-title":"Integrating Diverse Databases into an Unified Analysis Framework: A Galaxy Approach","volume":"2011","author":"Blankenberg","year":"2011","journal-title":"Database"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality Assessment Tool for Genome Assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Wei, W., Michelle, B., Yue, H., Jin, X., Dajin, Y., Alexandre, M.-G., Ning, X., Hui, L., Shaofei, Y., and Menghan, L. (2021). Whole-Genome Sequencing and Machine Learning Analysis of Staphylococcus aureus from Multiple Heterogeneous Sources in China Reveals Common Genetic Traits of Antimicrobial Resistance. mSystems, 6.","DOI":"10.1128\/mSystems.01185-20"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Kaya, H., Hasman, H., Larsen, J., Stegger, M., Johannesen, T.B., Alles\u00f8e, R.L., Lemvigh, C.K., Aarestrup, F.M., Lund, O., and Larsen, A.R. (2018). SCCMecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome Mec in Staphylococcus aureus Using Whole-Genome Sequence Data. mSphere, 3.","DOI":"10.1128\/mSphere.00612-17"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"4305","DOI":"10.1128\/JCM.01979-14","article-title":"Comparing Whole-Genome Sequencing with Sanger Sequencing for Spa Typing of Methicillin-Resistant Staphylococcus aureus","volume":"52","author":"Bartels","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Feldgarden, M., Brover, V., Haft, D.H., Prasad, A.B., Slotta, D.J., Tolstoy, I., Tyson, G.H., Zhao, S., Hsu, C.-H., and McDermott, P.F. (2019). Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates. Antimicrob. Agents Chemother., 63.","DOI":"10.1128\/AAC.00483-19"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: A Reference Database for Bacterial Virulence Factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"D678","DOI":"10.1093\/nar\/gkac1003","article-title":"Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): A Resource Combining PATRIC, IRD and ViPR","volume":"51","author":"Olson","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_62","unstructured":"Seemann, T. (2022, November 16). Snippy: Fast Bacterial Variant Calling from NGS Reads. Available online: https:\/\/github.com\/tseemann\/snippy."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid Phylogenetic Analysis of Large Samples of Recombinant Bacterial Whole Genome Sequences Using Gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_64","unstructured":"Seemann, T., Klotzl, F., and Page, A.J. (2022, November 16). Snp-Dists. Pairwise SNP Distance Matrix from a FASTA Sequence Alignment. Available online: https:\/\/github.com\/tseemann\/snp-dists."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular Evolutionary Genetics Analysis Version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1007\/BF01731581","article-title":"A Simple Method for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide Sequences","volume":"16","author":"Kimura","year":"1980","journal-title":"J. Mol. Evol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"W256","DOI":"10.1093\/nar\/gkz239","article-title":"Interactive Tree Of Life (ITOL) v4: Recent Updates and New Developments","volume":"47","author":"Letunic","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Wickham, H. (2016). Ggplot2: Elegant Graphics for Data Analysis, Springer-Verlag. Available online: https:\/\/ggplot2.tidyverse.org.","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"ref_69","unstructured":"Hijmans, R. (2023, July 30). Raster: Geographic Data Analysis and Modeling. Available online: https:\/\/rspatial.org\/raster."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"439","DOI":"10.32614\/RJ-2018-009","article-title":"Simple Features for R: Standardized Support for Spatial Vector Data","volume":"10","author":"Pebesma","year":"2018","journal-title":"R J."},{"key":"ref_71","unstructured":"Wickham, H. (2023, July 30). Tidyverse: Easily Install and Load the \u201cTidyverse.\u201d. Available online: https:\/\/CRAN.R-project.org\/package=tidyverse."}],"updated-by":[{"DOI":"10.3390\/antibiotics13080681","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2023,12,16]],"date-time":"2023-12-16T00:00:00Z","timestamp":1702684800000}}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/12\/12\/1745\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,3]],"date-time":"2025-08-03T15:07:13Z","timestamp":1754233633000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/12\/12\/1745"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,16]]},"references-count":71,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["antibiotics12121745"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics12121745","relation":{"correction":[{"id-type":"doi","id":"10.3390\/antibiotics13080681","asserted-by":"object"}]},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,16]]}}}