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

Abstract

The growing prevalence of antibiotic-resistant Staphylococcus aureus 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 S. aureus 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 S. aureus strains. The revised scheme is now a blend of previously used genes and new candidate genes. The genes yQil, aroE, and gmk are replaced with better gene candidates, opuCC, aspS, and rpiB, 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’s 42 STs.

Antibiotic Susceptibility Profiling of Human Pathogenic Staphylococcus aureus Strains Using Whole Genome Sequencing and Genome-Scale Annotation Approaches

“…Analysis of the staphylococcal pan-, core-, and accessory genomes revealed the presence of a total of 3837 genes, from which 2027 genes represent the core genes that are shared in >99% of all isolates, indicating their high similarity, ribosomes, and proteins associated with biogenesis [ 66 , 67 ]. A total of 992 genes were identified as shell genes present in >15% of the isolates; cloud genes represented 0–15% (818 genes), and soft-core genes were not identified in our studied isolates ( Table 8 ).…”

Lentzea sokolovensis sp. nov., Lentzea kristufekii sp. nov. and Lentzea miocenica sp. nov., rare actinobacteria from Miocene lacustrine sediment of the Sokolov Coal Basin, Czech Republic

“…We performed core genome multi-locus sequence typing based on 100 single-copy genes from the core genome of our Lentzea dataset. cgMLST aims to take advantage of the discriminatory power from extensive genetic data derived from whole genome sequencing hence providing maximum-resolution phylogenomic analyses (up to strain level) and has been used in clinical microbiology to type clonal outbreaks [38][39][40][41][42][43][44]. The core genome was identified by Up-to-date Bacterial Core Genes 2 pipeline [45] and re-annotated with InterPro [46].…”