ArticleMicrobiology spectrum2022
Pan-Genome Analysis of Staphylococcus aureus Reveals Key Factors Influencing Genomic Plasticity.
Article in Microbiology spectrum, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 20 citations in OpenAlex.
- Integrated Genome-Wide Association Study and Machine Learning Approach for Characterizing the Determinants of Biofilm Formation in Staphylococcus aureus.Interdisciplinary sciences, computational life sciences · 2026Article
- Molecular epidemiological analysis of Staphylococcus aureus from hospital and food in Huai'an, Jiangsu, China, based on whole genome sequencing.Scientific reports · 2026Article
- Molecular epidemiology of clinicalFrontiers in microbiology · 2026Article
- Multi-scale ecological drivers shape the genome flexibility of soil-dwellingISME communications · 2026Article
- Network analysis of antimicrobial resistance inNAR genomics and bioinformatics · 2025Article
- Study on Genomic Diversity, Prophage Distribution of Bovine-DerivedMicroorganisms · 2025Article
- Genomic Characterization of Potential Opportunistic ZoonoticPathogens (Basel, Switzerland) · 2025Article
- Variation and spread of resistomes in swine manure, manure slurries, and long-term manure-fertilized soils.Frontiers in microbiology · 2025Article
- Epigenetic background of lineage-specific gene expression landscapes of four Staphylococcus aureus hospital isolates.PloS one · 2025Article
- Combined transcriptomic and pangenomic analyses guide metabolic amelioration to enhance tiancimycins production.Applied microbiology and biotechnology · 2024Article
- Genomic Comparisons Revealed the Key Genotypes ofBioengineering (Basel, Switzerland) · 2024Article
- Average Nucleotide Identity basedbioRxiv : the preprint server for biology · 2024Article
- Chromosomal gene order defines several structural classes of Staphylococcus epidermidis genomes.PloS one · 2024Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The massive quantities of bacterial genomic data being generated have facilitated in-depth analyses of bacteria for pan-genomic studies. However, the pan-genome compositions of one species differed significantly between different studies, so we used Staphylococcus aureus as a model organism to explore the influences driving bacterial pan-genome composition. We selected a series of diverse strains for pan-genomic analysis to explore the pan-genomic composition of S. aureus at the species level and the actual contribution of influencing factors (sequence type [ST], source of isolation, country of isolation, and date of collection) to pan-genome composition. We found that the distribution of core genes in bacterial populations restrained under different conditions differed significantly and showed "local core gene regions" in the same ST. Therefore, we propose that ST may be a key factor driving the dynamic distribution of bacterial genomes and that phylogenetic analyses using whole-genome alignment are no longer appropriate in populations containing multiple ST strains. Pan-genomic analysis showed that some of the housekeeping genes of multilocus sequence typing (MLST) are carried at less than 60% in S. aureus strains. Consequently, we propose a new set of marker genes for the classification of S. aureus, which provides a reference for finding a new set of housekeeping genes to apply to MLST. In this study, we explored the role of driving factors influencing pan-genome composition, providing new insights into the study of bacterial pan-genomes.
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