Comparative Pan-Genomic Analysis Revealed an Improved Multi-Locus Sequence Typing Scheme for Staphylococcus aureus

dc.contributor.authorJalil, Mairaen
dc.contributor.authorQuddos, Fatimaen
dc.contributor.authorAnwer, Farhaen
dc.contributor.authorNasir, Samavien
dc.contributor.authorRahman, Abduren
dc.contributor.authorAlharbi, Metaben
dc.contributor.authorAlshammari, Abdulrahmanen
dc.contributor.authorAlshammari, Huda Kamelen
dc.contributor.authorAli, Amjaden
dc.date.accessioned2022-11-29T13:17:52Zen
dc.date.available2022-11-29T13:17:52Zen
dc.date.issued2022-11-19en
dc.date.updated2022-11-24T14:43:25Zen
dc.description.abstractThe growing prevalence of antibiotic-resistant <i>Staphylococcus aureus</i> strains mandates selective susceptibility testing and epidemiological investigations. It also draws attention to an efficient typing strategy. Whole genome sequencing helps in genetic comparison, strain differentiation, and typing; however, it is not that cost-effective. In comparison, Multi-Locus Sequence Typing (MLST) is an efficient typing method employed for bacterial strain typing and characterizations. In this paper, a comprehensive pangenome and phylogenetic analysis of 502/1279 <i>S. aureus</i> genomes is carried out to understand the species divergence. Additionally, the current Multi-Locus Sequence Typing (MLST) scheme was evaluated, and genes were excluded or substituted by alternative genes based on reported shortcomings, genomic data, and statistical scores calculated. The data generated were helpful in devising a new Multi-Locus Sequence Typing (MLST) scheme for the efficient typing of <i>S. aureus</i> strains. The revised scheme is now a blend of previously used genes and new candidate genes. The genes <i>yQil</i>, <i>aroE</i>, and <i>gmk</i> are replaced with better gene candidates, <i>opuCC</i>, <i>aspS</i>, and <i>rpiB</i>, based on their genome localization, representation, and statistical scores. Therefore, the proposed Multi-Locus Sequence Typing (MLST) method offers a greater resolution with 58 sequence types (STs) in comparison to the prior scheme&rsquo;s 42 STs.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationJalil, M.; Quddos, F.; Anwer, F.; Nasir, S.; Rahman, A.; Alharbi, M.; Alshammari, A.; Alshammari, H.K.; Ali, A. Comparative Pan-Genomic Analysis Revealed an Improved Multi-Locus Sequence Typing Scheme for Staphylococcus aureus. Genes 2022, 13, 2160.en
dc.identifier.doihttps://doi.org/10.3390/genes13112160en
dc.identifier.urihttp://hdl.handle.net/10919/112723en
dc.language.isoenen
dc.publisherMDPIen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectmulti-locus sequence typing (MLST)en
dc.subjectStaphylococcus aureusen
dc.subjectmethicillin-resistance Staphylococcus aureus (MRSA)en
dc.subjectpangenomeen
dc.subjectcomparative genome analysisen
dc.titleComparative Pan-Genomic Analysis Revealed an Improved Multi-Locus Sequence Typing Scheme for Staphylococcus aureusen
dc.title.serialGenesen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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