Identity
Canonical name: Staphylococcus aureus.1
Known aliases: None specified in the source.1
Stable external identifier: Not reported in the source.1
Staphylococcus aureus is an organism analyzed in the environmental resistome study and compared with klebsiella-pneumoniae, salmonella-enterica, streptococcus-pneumoniae, and mycobacterium-tuberculosis.1
AMR findings
The environmental-resistome dataset included 13,274 Staphylococcus aureus genomes and 642 AMR gene clusters.1 Of these clusters, 9 were core and 633 were accessory, corresponding to 99% accessory AMR.1 The species was clinical-dominant, with 85% of its genomes classified as originating from clinical sources.1
These results contribute to environmental-resistome, which synthesizes environment-associated AMR diversity and core/accessory composition at pangenome scale. The broader within-species analysis supports the clinical-association finding: human-clinical isolates had the highest AMR burden in comparisons of host-associated, terrestrial, and aquatic species, although the collection is biased toward clinical and human-associated genomes.2 The analysis also used S. aureus as a case study in which UMAP—nonlinear dimensionality reduction—plots showed visible environmental structuring, but sparse metadata and underpowered tests mean this does not establish a general environment–ecotype association.2
The AMR clusters were identified using amrfinderplus-focused annotation and the kbase-ke-pangenome collection.1
Integration with the pan-bacterial atlas
The pan-bacterial atlas refines the species-level findings with a family-level comparison: Staphylococcaceae was among the AMR hotspot families, averaging 37.3 AMR clusters per species.3 This broader result supports the existing interpretation that the strongly clinical-associated profile is coupled to substantial, predominantly accessory AMR, while not replacing the species-specific counts above.3
Source
See the full project summaries: Environmental Resistome at Pangenome Scale, Pan-Bacterial AMR Gene Landscape, and Within-Species AMR Strain Variation.1,3,2