Enterococcus faecalis is a microorganism frequently implicated in endodontic infections, capable of colonising both biological tissues and inert surfaces. However, the relationship between its chromosomal and plasmid gene repertoires and the type of endodontic environment it inhabits remains poorly elucidated. To analyse the distribution of E. faecalis virulence genes and their association with the ecological origin of biotic and abiotic isolates. Seventy-five E. faecalis isolates obtained from biotic and abiotic samples collected between 2018 and 2022 were analysed. Taxonomic identification was performed using a MALDI-TOF MS system, and virulence genes were detected by conventional PCR. Gene profiles and their association with the ecological origin of the isolates were evaluated using Factor Analysis of Mixed Data (FAMD), followed by Ward’s hierarchical clustering and K-means optimisation. Three genetic clusters of E. faecalis were identified and differentiated by their gene repertoires: chromosomal (ace, efaA, gelE), plasmid (asa, asa373, cylA), and mixed (esp). Chromosomal repertoires predominated in biotic isolates, whereas plasmid repertoires were more frequent in abiotic isolates, indicating a significant genetic structure according to ecological origin (p < 0.05). The gene repertoires of E. faecalis tend to cluster according to their chromosomal or plasmid nature, reflecting distinct patterns of ecological adaptation between biotic and abiotic endodontic environments.
