Comparative genomics of Staphylococcus coagulans and Staphylococcus pseudintermedius reveals contrasting population structure and gene repertoire diversity, with insights from Peruvian isolates

Background Staphylococcus coagulans and Staphylococcus pseudintermedius occupy overlapping canine skin and mucosal niches, yet their population-genomic architectures have rarely been compared using harmonized analytical criteria. We compared core- and accessory-genome structure, functional profiles, clinically relevant determinants, predicted proviruses, and antiviral defense systems, while contextualizing newly sequenced Peruvian isolates within broader global species diversity. Results The analysis comprised 102 S. coagulans and 340 S. pseudintermedius genomes, including 15 and 17 Peruvian isolates, respectively. Both collections exhibited open pangenomes. S. pseudintermedius had a slightly higher pangenome-growth exponent than S. coagulans (Heaps’ law γ = 0.134 versus 0.119) and a larger accessory fraction (52.5%), whereas S. coagulans had a larger proportional core (54.0%). COG functional profiles of the core fractions were broadly similar between species, while greater functional differentiation occurred in the accessory and unique fractions. S. coagulans comprised four operational phylogenetic groups, with 12 of the 15 Peruvian genomes assigned to C2b. Computational SCC mec assignments showed lineage-associated patterns: type V predominated in C2a, types V and XIV occurred in C2b, and all 12 Peruvian C2b genomes carried mecA and were assigned to type XIV. S. pseudintermedius showed a more heterogeneous population structure. Its 17 Peruvian genomes represented 16 sequence types; three clustered within the ST551-associated clade and none belonged to the ST71-associated lineage. Accessory-gene composition was associated with the independently defined phylogenetic groupings, although differences in multivariate dispersion limited a centroid-only interpretation. S. pseudintermedius carried more AMR and virulence-associated determinants per genome, more predicted proviruses and a broader diversity of antiviral defense-system types. Conversely, S. coagulans carried more stress-response determinants and predicted CRISPR–Cas systems per genome. Conclusions Both species shared broadly similar conserved functional profiles but differed markedly in population structure and in the distribution of non-core, clinically relevant and antiviral defense-associated features. The inclusion of Peruvian genomes expands South American genomic representation and supports lineage-aware surveillance of both species. Broader prospective sampling and experimental validation are needed to establish the epidemiological and clinical relevance of these genomic patterns.