{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,19]],"date-time":"2026-07-19T01:19:36Z","timestamp":1784423976579,"version":"3.55.0"},"reference-count":76,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2022,8,6]],"date-time":"2022-08-06T00:00:00Z","timestamp":1659744000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004281","name":"National Science Centre, Poland","doi-asserted-by":"publisher","award":["2019\/03\/X\/NZ6\/02096"],"award-info":[{"award-number":["2019\/03\/X\/NZ6\/02096"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>We report the first Polish representative of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA), lukS\/F-PV-positive, encoding the ermB gene, as a genetic determinant of constitutive resistance to macrolides, lincosamides, and streptogramin B antibiotics, cMLS-B. This is the first detection of the CA-MRSA strain responsible for nosocomial infection in the Warsaw Clinical Hospital. Resistance to \u03b2-lactams associates with a composite genetic element, SCCmec cassette type VT (5C2&amp;5). We assigned the strain to sequence type ST338 (single-locus variant of ST59), clonal complex CC59, spa-type t437, and agr-type I. Genomic-based comparison was designated SO574\/12 as an international Taiwan clone, which has been so far described mainly in the Asia-Pacific region. The ermB gene locates on the chromosome within the 14,690 bp mobile element structure, i.e., the MESPM1-like structure, which also encodes aminoglycoside- and streptothricin-resistance genes. The MESPM1-like structure is a composite transposon containing Tn551, flanked by direct repeats of IS1216V insertion sequences, which probably originates from Enterococcus. The ermB is preceded by the 273 bp regulatory region that contains the regulatory 84 bp ermBL ORF, encoding the 27 amino acid leader peptides. The latest research suggests that a new leader peptide, ermBL2, also exists in the ermB regulatory region. Therefore, the detailed function of ermBL2 requires further investigations.<\/jats:p>","DOI":"10.3390\/ijms23158755","type":"journal-article","created":{"date-parts":[[2022,8,7]],"date-time":"2022-08-07T22:51:46Z","timestamp":1659912706000},"page":"8755","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Genomic Insights of First ermB-Positive ST338-SCCmecVT\/CC59 Taiwan Clone of Community-Associated Methicillin-Resistant Staphylococcus aureus in Poland"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4314-3522","authenticated-orcid":false,"given":"Ksenia","family":"Szymanek-Majchrzak","sequence":"first","affiliation":[{"name":"Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004 Warsaw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gra\u017cyna","family":"M\u0142ynarczyk","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004 Warsaw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,6]]},"reference":[{"key":"ref_1","first-page":"229","article-title":"Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) in Poland: Further evidence for the changing epidemiology of MRSA","volume":"31","author":"Bogut","year":"2008","journal-title":"New Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/j.ijmm.2013.02.007","article-title":"Community-associated MRSA: What makes them special?","volume":"303","author":"Otto","year":"2013","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.ijid.2014.02.025","article-title":"Community-acquired necrotizing pneumonia caused by methicillin-resistant Staphylococcus aureus producing Panton-Valentine leukocidin in a Chinese teenager: Case report and literature review","volume":"26","author":"Chen","year":"2014","journal-title":"Int. J. Infect. Dis."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Rolo, J., Miragaia, M., Turlej-Rogacka, A., Empel, J., Bouchami, O., Faria, N.A., Tavares, A., Hryniewicz, W., Fluit, A.C., and de Lencastre, H. (2012). High genetic diversity among community-associated Staphylococcus aureus in Europe: Results from a multicenter study. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0034768"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1080\/14787210.2016.1236684","article-title":"Changing epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the Asia-Pacific region","volume":"14","author":"Huh","year":"2016","journal-title":"Expert Rev. Anti-Infect. Ther."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.3389\/fmicb.2019.02763","article-title":"Antibiotic Susceptibility, Virulence Pattern, and Typing of Staphylococcus aureus Strains Isolated from Variety of Infections in India","volume":"10","author":"Aggarwal","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_7","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":"Lakhundi","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"4719","DOI":"10.1128\/JCM.43.9.4719-4730.2005","article-title":"Successful multiresistant community-associated methicillin-resistant Staphylococcus aureus lineage from Taipei, Taiwan, that carries either the novel staphylococcal chromosome cassette mec (SCCmec) type VT or SCCmec type IV","volume":"43","author":"Ereshefsky","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1128\/AAC.48.7.2637-2651.2004","article-title":"Novel type V staphylococcal cassette chromosome mec driven by a novel cassette chromosome recombinase, ccrC","volume":"48","author":"Ito","year":"2004","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1128\/AAC.01001-07","article-title":"Novel characteristics of community-acquired methicillin-resistant Staphylococcus aureus strains belonging to multilocus sequence type 59 in Taiwan","volume":"52","author":"Takano","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1016\/S0140-6736(01)24468-7","article-title":"Staphylococcal toxin","volume":"219","author":"Panton","year":"1932","journal-title":"Lancet"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/labinvest.3700501","article-title":"Community-acquired methicillin-resistant Staphylococcus aureus: The role of Panton-Valentine leukocidin","volume":"87","author":"Daum","year":"2007","journal-title":"Lab. Investig."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"611","DOI":"10.3389\/fmicb.2020.00611","article-title":"Studying Staphylococcal Leukocidins: A Challenging Endeavor","volume":"11","author":"Tromp","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"631845","DOI":"10.3389\/fmicb.2021.631845","article-title":"Staphylococcus aureus ST59: Concurrent but Separate Evolution of North American and East Asian Lineages","volume":"12","author":"McClure","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"725340","DOI":"10.3389\/fmicb.2021.725340","article-title":"Evolution and Population Structures of Prevalent Methicillin-Resistant Staphylococcus aureus in Taiwan","volume":"12","author":"Chen","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1128\/AAC.46.4.1147-1152.2002","article-title":"Novel type of staphylococcal cassette chromosome mec identified in community-acquired methicillin resistant Staphylococcus aureus strains","volume":"46","author":"Ma","year":"2002","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Hung, W.C., Takano, T., Higuchi, W., Iwao, Y., Khokhlova, O., Teng, L.J., and Yamamoto, T. (2012). Comparative genomics of community-acquired ST59 methicillin-resistant Staphylococcus aureus in Taiwan: Novel mobile resistance structures with IS1216V. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0046987"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"106047","DOI":"10.1016\/j.ijantimicag.2020.106047","article-title":"Tracking the evolution of the two successful CC59 methicillin-resistant Staphylococcus aureus clones in Taiwan: The divergence time of the two clades is estimated to be the 1980s","volume":"56","author":"Su","year":"2020","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1016\/j.tibs.2018.06.011","article-title":"How Macrolide Antibiotics Work","volume":"43","author":"Mankin","year":"2018","journal-title":"Trends Biochem. Sci."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Mlynarczyk-Bonikowska, B., Kowalewski, C., Krolak-Ulinska, A., and Marusza, W. (2022). Molecular Mechanisms of Drug Resistance in Staphylococcus aureus. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23158088"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2579","DOI":"10.1016\/j.transproceed.2014.08.026","article-title":"Molecular and phenotypic characteristics of methicillin-resistant Staphylococcus aureus strains isolated from hospitalized patients in transplantation wards","volume":"46","author":"Mlynarczyk","year":"2014","journal-title":"Transplant. Proc."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1128\/jb.164.2.782-796.1985","article-title":"Complete nucleotide sequence of macrolide-lincosamide-streptogramin B-resistance transposon Tn917 in Streptococcus faecalis","volume":"164","author":"Shaw","year":"1985","journal-title":"J. Bacteriol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/S0934-8840(98)80165-5","article-title":"The genome of Staphylococcus aureus: A review","volume":"287","author":"Jeljaszewicz","year":"1998","journal-title":"Zentralbl. Bakteriol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1089\/mdr.1999.5.1","article-title":"The Staphylococcus aureus transposon Tn551: Complete nucleotide sequence and transcriptional analysis of the expression of the erythromycin resistance gene","volume":"5","author":"Wu","year":"1999","journal-title":"Microb. Drug Resist."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1414","DOI":"10.1016\/j.transproceed.2016.03.015","article-title":"Epidemiological and drug-resistance types of methicillin-resistant Staphylococcus aureus strains isolated from surgical and transplantation ward patients during 2010 to 2011","volume":"48","author":"Mlynarczyk","year":"2016","journal-title":"Transplant. Proc."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2930","DOI":"10.1128\/JCM.00869-08","article-title":"Countrywide molecular survey of methicillin-resistant Staphylococcus aureus strains in Poland","volume":"46","author":"Sulikowska","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1159\/000501788","article-title":"Antimicrobial Resistance Patterns in Methicillin-Resistant Staphylococcus aureus from Patients Hospitalized during 2015\u20132017 in Hospitals in Poland","volume":"29","author":"Kot","year":"2020","journal-title":"Med. Princ. Pract."},{"key":"ref_28","unstructured":"(2022, January 01). European Committee on Antimicrobial Susceptibility Testing, EUCAST Recommendations (2022b). Available online: https:\/\/www.eucast.org\/fileadmin\/src\/media\/PDFs\/EUCAST_files\/Breakpoint_tables\/v_12.0_Breakpoint_Tables.pdf."},{"key":"ref_29","first-page":"7","article-title":"Regulatory systems of gene expression in Staphylococcus aureus","volume":"48","author":"Szymanek","year":"2009","journal-title":"Post. Mikrobiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.ijid.2019.10.034","article-title":"Characterization of a community-acquired methicillin-resistant sequence type 338 Staphylococcus aureus strain containing a staphylococcal cassette chromosome mec type VT","volume":"90","author":"Chen","year":"2020","journal-title":"Int. J. Infect. Dis."},{"key":"ref_31","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_32","doi-asserted-by":"crossref","first-page":"2790","DOI":"10.3389\/fmicb.2018.02790","article-title":"Prevalence and Characterization of Staphylococcus aureus Isolated from Women and Children in Guangzhou, China","volume":"9","author":"Liang","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Grundmann, H., Aanensen, D.M., van den Wijngaard, C.C., Spratt, B.G., Harmsen, D., and Friedrich, A.W. (2010). Geographic Distribution of Staphylococcus aureus Causing Invasive Infections in Europe: A Molecular-Epidemiological Analysis. PLoS Med., 7.","DOI":"10.1371\/journal.pmed.1000215"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"20987","DOI":"10.2807\/1560-7917.ES2014.19.49.20987","article-title":"The dynamic changes of dominant clones of Staphylococcus aureus causing bloodstream infections in the European region: Results of a second structured survey","volume":"19","author":"Grundmann","year":"2014","journal-title":"Euro Surveill."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"347.e1","DOI":"10.1016\/j.cmi.2014.11.005","article-title":"Ensuring backwards compatibility: Traditional genotyping efforts in the era of whole genome sequencing","volume":"21","author":"Bletz","year":"2015","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"163.e1","DOI":"10.1016\/j.cmi.2014.09.010","article-title":"Staphylococcus aureus spa type t437: Identification of the most dominant community-associated clone from Asia across Europe","volume":"21","author":"Glasner","year":"2015","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1080\/22221751.2021.1914516","article-title":"The genetic feature and virulence determinant of Highly Virulent Community-Associated MRSA ST338-SCCmec Vb in China","volume":"7","author":"Jin","year":"2021","journal-title":"Emerg. Microbes Infect."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1042\/EBC20160057","article-title":"Fitness costs associated with the acquisition of antibiotic resistance","volume":"61","author":"Blanco","year":"2017","journal-title":"Essays Biochem."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1089\/mdr.2020.0426","article-title":"Fitness Cost of Antibiotic Resistance in Staphylococcus aureus: A Systematic Review","volume":"27","author":"Touati","year":"2021","journal-title":"Microb. Drug Resist."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.2174\/138955709790361557","article-title":"Mechanisms of the resistance and tolerance to beta-lactam and glycopeptide antibiotics in pathogenic Gram-positive cocci","volume":"9","author":"Mlynarczyk","year":"2009","journal-title":"Mini Rev. Med. Chem."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1782","DOI":"10.1128\/AAC.01376-07","article-title":"Translational attenuation and mRNA stabilization as mechanisms of erm(B) induction by erythromycin","volume":"52","author":"Min","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"3501","DOI":"10.1038\/ncomms4501","article-title":"Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide","volume":"5","author":"Arenz","year":"2014","journal-title":"Nat. Commun."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Lin, Y.T., Tseng, S.P., Hung, W.W., Chang, C.C., Chen, Y.H., Jao, Y.T., Chen, Y.H., Teng, L.J., and Hung, W.C. (2020). A Possible Role of Insertion Sequence IS1216V in Dissemination of Multidrug-Resistant Elements MESPM1 and MES6272-2 between Enterococcus and ST59 Staphylococcus aureus. Microorganisms, 8.","DOI":"10.3390\/microorganisms8121905"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/S0378-1135(00)00347-3","article-title":"Molecular epidemiology and genetic linkage of macrolide and aminoglycoside resistance in Staphylococcus intermedius of canine origin","volume":"79","author":"Boerlin","year":"2001","journal-title":"Vet. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"5788","DOI":"10.1128\/JB.180.21.5788-5791.1998","article-title":"Induction of ermAMR from a clinical strain of Enterococcus faecalis by 16-membered-ring macrolide antibiotics","volume":"180","author":"Oh","year":"1998","journal-title":"J. Bacteriol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/j.molcel.2013.10.013","article-title":"Regulation of gene expression by macrolide-induced ribosomal frameshifting","volume":"52","author":"Gupta","year":"2013","journal-title":"Mol. Cell"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"7178","DOI":"10.1128\/AAC.01806-16","article-title":"The Expression of Antibiotic Resistance Methyltransferase Correlates with mRNA Stability Independently of Ribosome Stalling","volume":"60","author":"Dzyubak","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"690744","DOI":"10.3389\/fmicb.2021.690744","article-title":"Translational Attenuation Mechanism of ErmB Induction by Erythromycin Is Dependent on Two Leader Peptides","volume":"12","author":"Wang","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1089\/mdr.2017.0279","article-title":"Resistance in In Vitro Selected Tigecycline-Resistant Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Is Driven by Mutations in mepR and mepA Genes","volume":"24","author":"Dabul","year":"2018","journal-title":"Microb. Drug Resist."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1016\/j.biopha.2018.10.131","article-title":"A review on mechanism of action, resistance, synergism, and clinical implications of mupirocin against Staphylococcus aureus","volume":"109","author":"Khoshnood","year":"2019","journal-title":"Biomed. Pharmacother."},{"key":"ref_51","unstructured":"(2022, January 01). European Committee on Antimicrobial Susceptibility Testing, EUCAST Recommendations (2022a). Available online: https:\/\/www.eucast.org\/ast_of_bacteria\/."},{"key":"ref_52","first-page":"39","article-title":"Prevalence of methicillin-resistant and mupirocin resistant Staphylococcus aureus strains among medical students of Medical University of Warsaw","volume":"73","year":"2019","journal-title":"Epidemiol. Rev."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1186\/s13756-018-0397-y","article-title":"Characteristics of glycopeptide-resistant Staphylococcus aureus strains isolated from inpatients of three teaching hospitals in Warsaw, Poland","volume":"7","author":"Mlynarczyk","year":"2018","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"4289","DOI":"10.1128\/JCM.40.11.4289-4294.2002","article-title":"Dissemination of new methicillin resistant Staphylococcus aureus clones in the community","volume":"40","author":"Okuma","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"2155","DOI":"10.1128\/AAC.46.7.2155-2161.2002","article-title":"Multiplex PCR strategy for rapid identification of structural types and variants of the mec element in methicillin-resistant Staphylococcus aureus","volume":"46","author":"Oliveira","year":"2002","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1128\/JCM.38.3.1008-1015.2000","article-title":"Multilocus sequence typing for characterization of methicillin-resistant and methicillin susceptible clones of Staphylococcus aureus","volume":"38","author":"Enright","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"ref_57","unstructured":"Andrew, S. (2021, August 21). A Quality Control Tool for High Throughput Sequence Data. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_59","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_60","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_61","doi-asserted-by":"crossref","unstructured":"Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., and Young, S.K. (2014). Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0112963"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","article-title":"Bandage: Interactive visualization of de novo genome assemblies","volume":"31","author":"Wick","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"8365","DOI":"10.1038\/srep08365","article-title":"RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes","volume":"5","author":"Brettin","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1007\/978-1-4939-7463-4_4","article-title":"Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center","volume":"1704","author":"Wattam","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1128\/AAC.00165-06","article-title":"Combination of multiplex PCRs for staphylococcal cassette chromosome mec type assignment: Rapid identification system for mec, ccr and major difference in junkyard regions","volume":"51","author":"Kondo","year":"2007","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_66","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., 56, 4961\u20134967."},{"key":"ref_67","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_68","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. Micobiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"2764","DOI":"10.1093\/jac\/dkx217","article-title":"PointFinder: A novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens","volume":"72","author":"Zankari","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Clausen, P.T.L.C., Aarestrup, F.M., and Lund, O. (2018). Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinform., 19.","DOI":"10.1186\/s12859-018-2336-6"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"PlasmidFinder and pMLST: In Silico detection and typing of plasmids","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1093\/jac\/dkaa390","article-title":"Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder","volume":"76","author":"Johansson","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"W181","DOI":"10.1093\/nar\/gkn179","article-title":"The CGView server: A comparative genomics tool for circular genomes","volume":"36","author":"Grant","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Darling, A.E., Mau, B., and Perna, N.T. (2010). progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0011147"},{"key":"ref_76","first-page":"D606","article-title":"The PATRIC Bioinformatics Resource Center: Expanding data and analysis capabilities","volume":"8","author":"Davis","year":"2020","journal-title":"Nucleic Acids Res."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/15\/8755\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:05:09Z","timestamp":1760141109000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/15\/8755"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8,6]]},"references-count":76,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2022,8]]}},"alternative-id":["ijms23158755"],"URL":"https:\/\/doi.org\/10.3390\/ijms23158755","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,8,6]]}}}