Uncovering Antibiotic Resistance Signatures in Endodontic Enterococcus faecalis

Due to its resilience and resistance to common intracanal disinfectants and medicines, Enterococcus faecalis, also known as E. faecalis, is a notorious pathogen in endodontics that is frequently isolated from persistent and secondary root canal infections. Its growing resistance to antibiotics that target the cell wall is concerning, and its clinical impact on endodontic failure is widely acknowledged. Yet, there remains a lack of comprehensive understanding of the global transcriptional responses that E. faecalis employs to survive exposure to widely used β-lactams and glycopeptides.

The Affymetrix E. faecalis OG1RF array microarray dataset, GSE45306, which comprised 15 samples, was examined, and the untreated controls and cultures were exposed to 10× MIC of Ampicillin, Bacitracin, Cephalothin, and Vancomycin for 30 minutes. Gene expression omnibus 2R (GEO2R)/limma was referred to identify differentially expressed genes (DEGs) after quality control and robust multi-array average (RMA) normalization, using an adjusted p < 0.05 and |log₂ fold change| > 1.5. Heatmaps, Venn diagrams, and volcano plots were used to visualize both treatment-specific and shared transcriptional responses.

With 552 distinct DEGs, Vancomycin caused the biggest transcriptional shift, whereas Cephalothin and Bacitracin affected 77 and 10 genes, respectively. A core set of 55 stress-responsive genes, many of which code for proteins with unclear or poorly understood activities, was shown to be consistently changed across all antibiotic treatments. Common themes revealed by pathway, and expression analysis included increased expression of efflux transporters, metabolic changes, especially involving Adenosine triphosphate (ATP) synthase and pyruvate dehydrogenase, and cell wall remodeling. Furthermore, a number of regulators particular to antibiotics, such as membrane-associated sensors and members of the cell envelope-associated transcriptional attenuator LytR-CpsA-Psr family, indicated specific adaptation mechanisms.

Enterococcus faecalis has a sophisticated, adaptable transcriptional response to antibiotic stress, as well as drug-specific and transparently preserved survival strategies.

During endodontic treatment, the antibiotic-specific transcriptional regulators, such as E. faecalis-membrane-associated sensors and members of the LytR-CpsA-Psr family, undergo adaptive responses. Thus, to enhance root canal disinfection and fight antibiotic resistance, these molecular targets are considered the most promising aspects of acumen. How to cite this article: Boreak N, Faqehi W, Ageeli RE, et al. Uncovering Antibiotic Resistance Signatures in Endodontic Enterococcus faecalis. J Contemp Dent Pract 2026;27(2):130-140.