What this entity is
Canonical name: Salmonella enterica. 1
Known aliases: No aliases were reported in the source document. 1
Stable external identifier: None was provided in the source document. 1
Key facts
Salmonella enterica was one of the deeply sampled species case studies in the environmental resistome analysis. 1 That dataset contained 10,097 Salmonella enterica genomes and 836 AMR gene clusters; 11 were classified as core and 825 as accessory, corresponding to 98% accessory AMR. 1 Salmonella enterica was host-associated-dominant, with host-associated genomes representing 31% of its environmental classification. 1 This case study illustrated extensive accessory AMR variation in a deeply sampled species. 1
A separate metabolic-capability analysis used 11,396 Salmonella enterica genomes and identified six metabolic clusters with a silhouette score of 0.894, the strongest clustering reported among its 10 target species. 2 This supports strain-level heterogeneity within the species, while the different genome counts and measurements mean that metabolic clustering should not be treated as a direct description of the AMR dataset. 2 Metabolic cluster membership was significantly associated with isolation environment (χ²=1570.2, df=25, p<0.0001), consistent with differentiation across clinical, food, and environmental sources; this interpretation is observational and does not establish causality. 2 Because explicit phylogenetic correction was not performed, the environment association may be confounded by phylogenetic structure. 2
The within-species strain-variation analysis included Salmonella enterica among its case-study UMAP plots, which showed visible environmental structuring; because the environmental tests were underpowered, this refines rather than establishes the general claim that environment determines AMR ecotypes. 3 The metabolic-cluster result supports investigating environmental structure in both metabolic and accessory AMR repertoires, but its stronger statistical association does not resolve the AMR-specific metadata and power limitations. 2
Integration with the pan-bacterial atlas
The pan-bacterial atlas reports Salmonella as the second-highest genus for AMR density, with 198 AMR clusters per species. 4 This supports the existing case-study interpretation of extensive AMR variation, while the two reports use different aggregation levels and should not be treated as directly equivalent counts. 4
Together, these results support environmental-resistome by showing that a host-associated-dominant species can contain many AMR clusters while retaining very few core clusters. 1 They also contribute to pangenome-integration, where core/accessory AMR composition is analyzed across species and ecological environments. 1 The metabolic findings additionally refine this picture by showing that environment-linked within-species structure can be detected in pathway profiles, although the ecological interpretation remains non-causal and potentially confounded. 2