The mutational landscape of Staphylococcus aureus during colonisation

This GitHub project contains the data and code necessary to reproduce the findings of the study 'The mutational landscape of Staphylococcus aureus during colonisation', and includes the following directories:

• adaptive_mutations_analysis: contains multiple directories with scripts executing genomic analyses:
  • applied to all isolates:
    • amrfinder: Files and scripts used to run AMRFinderPlus from S. aureus assemblies.
    • assembly: Files and script to run de novo assembly from Illumina short reads.
    • mapping_ref: scripts used to map Illumina short reads to S. aureus reference genomes.
    • mlst: scripts to run in silico MLST typing.
  • applied to multiple isolates per CC
    • pairwise_snp_distances: scripts to create pairwise SNP matrix for all isolates (across CCs)
    • phylogeny_per_cc: scripts to generate core-genome phylogenetic per clonal complex.
  • applied to isolates of the same host
    • identify_ancestral: pipeline to re-construct the MRCA sequence of each host clonal strain.
    • mapping_mrca: pipeline used to identify de novo mutations arising in each host clonal strain.
  • applied to all hosts
    • association_mrca: R scripts used to filter de novo mutations per host clonal strain and to identify functional units with an excess of protein-altering mutations.
• agr_mutants: R script is used to calculate agr-mutant frequencies in different subsets of patients and to test the effect of several variables on the emergence of agr mutants.
• data: directory with input data files used by scripts in this GitHub project.
• genetic_diversity: scripts to summarise within-host genetic diversity.
• growth_curves: growth curves data of knockout strains and natural mutants grown under sub-inhibitory concentrations of daptomycin, and R script used to analyse this data.
• growth_curves_nitrogen: growth curves data of transposon knockout strains and natural mutants grown under multiple nitrogen sources in Biolog PM3 plates, and R script used to analyse this data.

Citation

Coll F, Blane B, Bellis KL, et al. The mutational landscape of Staphylococcus aureus during colonisation. Nature Communications. 2025;16(1):302. doi:10.1038/s41467-024-55186-x