A new approach for establishing multilocus sequence typing scheme: Staphylococcus capitis as an example

Reliable and efficient typing methods for Staphylococcus capitis, an opportunistic pathogen of growing clinical and epidemiological concern, are urgently needed to support microbial epidemiological studies. In the study, we present a novel workflow for developing a multilocus sequence typing (MLST) scheme tailored to S. capitis. Core genome analysis of 603 high-quality S. capitis genomes revealed 2, 065 core genes. A hierarchical filtering strategy, including gene, fragment, and combination filters, was applied to select loci that balance discriminatory power and cluster specificity. The final MLST scheme comprised fragments from seven genes: mntC, phoA, atpB₂, hisS, rluB, carB, and clpP. Using this approach, we assigned 39 sequence types (STs) and defined five clonal complexes. The MLST typing results were highly concordant with phylogenetic analysis and demonstrated considerable discriminatory power. Notably, the globally prevalent NRCS-A clone and the linezolid-resistant L clone were designated as ST1 and ST6, respectively. Overall, we developed a reliable, high-resolution MLST scheme for S. capitis that enables accurate characterization of its population structure and facilitates monitoring of multidrug-resistant lineages.