Abstract

Objective: Cutibacterium acnes (C. acnes) has been detected in culture and molecular studies of endodontic microbiota, indicating its potential as a neglected pathogen in endodontic infections. This study aimed to conduct a complete genomic analysis of three Cutibacterium spp. isolates obtained from persistent endodontic infections in patients from Chile. Design: Whole genome sequencing and comprehensive genomic analysis using diverse bioinformatics platforms and databases were carried out. Results: In-silico analysis confirmed that strains A1 and E3 correspond to C. acnes species, while strain B1 corresponds to C. namnetense. Additionally, C. acnes strain A1 belongs to the phylotype IA1, sequence type (ST) 4 and belongs to the clonal complex (CC) 4, whereas C. acnes strain E3 belongs to a novel ST. No antibiotic resistance, however, a variable distribution and identity of the VF was found. Conclusions: Detailed analysis of genes associated with virulence factors shed light on the intrinsic pathogenic capacity of these strains, which may indicate differential adaptation to their specific niches or diversity in pathogenicity within the species. © 2025 Elsevier Ltd