Jalil, MairaQuddos, FatimaAnwer, FarhaNasir, SamaviRahman, AbdurAlharbi, MetabAlshammari, AbdulrahmanAlshammari, Huda KamelAli, Amjad2022-11-292022-11-292022-11-19Jalil, 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.http://hdl.handle.net/10919/112723The 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.application/pdfenCreative Commons Attribution 4.0 InternationalArticle - Refereed2022-11-24https://doi.org/10.3390/genes13112160