Functional Genomics of Antibiotic Susceptibility in Enterococcus faecalis From Infective Endocarditis

Abstract

Abstract Enterococcus faecalis is an opportunistic pathogen that causes infective endocarditis. Despite in vitro synergy of the recommended combination ampicillin-ceftriaxone (AC), E faecalis infective endocarditis (EFIE) mortality remains high. We characterized 119 isolates from patients with EFIE in our health system from 2018 to 2023 genomically and phenotypically. Three genetic lineages (ST6, ST40, and ST179) accounted for 41% of all infections. ST6 isolates were less susceptible to ceftriaxone and AC in dual-antibiotic checkerboard assays, but also exhibited decreased survival in dual-antibiotic killing assays using humanized AC exposures. ST6 isolates encoded a known genetic disruption affecting pbp4 as well as mutation of a putative hydrolase called phnP. Functional studies confirmed that both alterations contributed to altered AC susceptibility. Finally, we found that ampicillin plus daptomycin showed robust growth inhibition and killing against EFIE isolates with decreased AC susceptibility. These findings enhance our understanding of EFIE and may guide better therapeutic strategies.