Heteroresistance in Enterococcus faecalis is prevalent for key antibiotics and mainly caused by mutations

Heteroresistance (HR), the coexistence of a rare resistant subpopulation within a predominantly susceptible bacterial population, is a clinically relevant problem. The resistant subpopulation often escapes detection by standard susceptibility testing, which can lead to treatment failure. To investigate HR in Enterococcus faecalis, we performed population analysis profiling (PAP) on 40 clinical isolates against five clinically important antibiotics and whole-genome sequenced (WGS) the resistant subpopulations. HR was identified for daptomycin (20.0%), gentamicin (13.2%), and tigecycline (35.9%), but not for linezolid, and vancomycin. Genomic analysis revealed that daptomycin resistance was primarily caused by mutations affecting cell envelope integrity and stress-response pathways. Gentamicin resistance was linked to alterations in efflux regulation, ribosomal proteins synthesis, and transcriptional control. Tigecycline resistance involved deletions in the tet(M) leader peptide, resulting in a 25-fold increased tet(M) expression, as well as transposition of the transposon Tn916 carrying tet(M) to multiple chromosomal sites, causing an increased gene dosage of tet(M). These findings highlight the role of chromosomal mutations and mobile genetic elements in causing HR in E. faecalis Author SummaryAntibiotic resistance is one of the most critical challenges in modern medicine, undermining the efficacy of antimicrobial therapies and compromising patient safety. Bacterial strains that are heteroresistant (HR), show a minor subpopulation of resistant bacteria within a main susceptible bacterial population. HR strains are mostly classified as susceptible strains since the subpopulation are usually too small to be detected with standard susceptibility testing. Treatment with antibiotics will lead to survival and increase of the resistant subpopulation that can lead to treatment failure. In this study, we observed a high frequency of HR among clinical Enterococcus faecalis strains against gentamicin, daptomycin and tigecycline, three commonly used antibiotics for treatment of E. faecalis infections. Chromosomal mutations and changes in gene expression were the genetic mechanisms generating the resistant subpopulations.