ArticlePloS one2015
Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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Who cites it
29 citing papers in PubMed.
- Mammaliicoccus sciuri as a sentinel for antimicrobial resistance and virulence: genomic epidemiology, transmission dynamics, and control in the one health era.Veterinary research communications · 2026Review
- Lineage-specific variation in frequency and hotspots of recombination in invasive Escherichia coli.BMC genomics · 2025Article
- Epidemiological characterization of clinical isolates of meticillin resistant Staphylococcus aureus through multilocus sequence typing and staphylococcal cassette chromosome mec typing in Northwest Iran.Molecular biology reports · 2024Article
- Article
- Recombination-mediated dissemination of Methicillin-resistant S. aureus clonal complex 1 in the Egyptian health care settings.Annals of clinical microbiology and antimicrobials · 2023Article
- Leaky barriers to gene sharing between locally co-existing coagulase-negative Staphylococcus species.Communications biology · 2023Article
- Biofilm forming multidrug resistantIranian journal of veterinary research · 2023Article
- Antimicrobial Resistance and Molecular Epidemiology ofPathogens (Basel, Switzerland) · 2022Article
- Pathogenomes and variations in Shiga toxin production among geographically distinct clones ofMicrobial genomics · 2022Article
- Extensive Horizontal Gene Transfer within and between Species of Coagulase-Negative Staphylococcus.Genome biology and evolution · 2021Article
- Genomic epidemiology of methicillin-resistant and -susceptible Staphylococcus aureus from bloodstream infections.BMC infectious diseases · 2021Article
- Genome Sequencing of a Historic Staphylococcus aureus Collection Reveals New Enterotoxin Genes and Sheds Light on the Evolution and Genomic Organization of This Key Virulence Gene Family.Journal of bacteriology · 2021Article
- Molecular investigations on a chimeric strain of Staphylococcus aureus sequence type 80.PloS one · 2020Article
- NAuRA: Genomic Tool to Identify Staphylococcal Enterotoxins inFrontiers in microbiology · 2020Article
- Phenotypic and genotypic characterization of clinical Staphylococcus aureus isolates from Kenya.BMC microbiology · 2019Article
- Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.Nature genetics · 2019Article
- Long-Term Intrahost Evolution of Methicillin ResistantFrontiers in genetics · 2019Article
- A statistical method to identify recombination in bacterial genomes based on SNP incompatibility.BMC bioinformatics · 2018Article
- Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity.Microbial genomics · 2018Article
- Evidence of latent molecular diversity determining the virulence of community-associated MRSA USA300 clones in mice.Immunity, inflammation and disease · 2018Article
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Staphylococcus aureus is an important clinical pathogen worldwide and understanding this organism's phylogeny and, in particular, the role of recombination, is important both to understand the overall spread of virulent lineages and to characterize outbreaks. To further elucidate the phylogeny of S. aureus, 35 diverse strains were sequenced using whole genome sequencing. In addition, 29 publicly available whole genome sequences were included to create a single nucleotide polymorphism (SNP)-based phylogenetic tree encompassing 11 distinct lineages. All strains of a particular sequence type fell into the same clade with clear groupings of the major clonal complexes of CC8, CC5, CC30, CC45 and CC1. Using a novel analysis method, we plotted the homoplasy density and SNP density across the whole genome and found evidence of recombination throughout the entire chromosome, but when we examined individual clonal lineages we found very little recombination. However, when we analyzed three branches of multiple lineages, we saw intermediate and differing levels of recombination between them. These data demonstrate that in S. aureus, recombination occurs across major lineages that subsequently expand in a clonal manner. Estimated mutation rates for the CC8 and CC5 lineages were different from each other. While the CC8 lineage rate was similar to previous studies, the CC5 lineage was 100-fold greater. Fifty known virulence genes were screened in all genomes in silico to determine their distribution across major clades. Thirty-three genes were present variably across clades, most of which were not constrained by ancestry, indicating horizontal gene transfer or gene loss.
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