Genomic and Transcriptomic Analysis of Enterococcus Faecalis Responses to Cationic Antimicrobials




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Over the last decade, antibiotic-resistant bacterial infections have been occurring at an alarming rate and are an increasing risk to public health. Unfortunately, the pace of discovery and approval of new antibiotics is too slow to effectively combat the threat from antibiotic-resistant microbes. The seriousness of antibiotic resistance stems from the fact that these bacterial strains are not only resistant to commonly available antibacterials but also may have acquired traits that enhance damage to the host. Therefore, an understanding of antibiotic resistance mechanisms is of crucial importance to counter the spread of multidrug-resistant pathogens and to develop new drugs. In my dissertation work, I studied the Gram-positive bacterium and opportunistic pathogen, Enterococcus faecalis. E. faecalis is among the leading causes of antibiotic-resistant hospital-acquired infections. I performed transcriptomic analysis to identify genes that are differentially regulated when E. faecalis V583 is exposed to the antiseptic chlorhexidine. Chlorhexidine is a cationic antimicrobial that is commonly used for infection control in hospitals. The genes efrE (EF2226) and efrF (EF2227), encoding a heterodimeric ABC transport system, are the most highly up-regulated genes. Deletion of efrEF increased E. faecalis V583 susceptibility to CHG. I identified a transcriptional regulator of efrEF, which I have named ChlR. ChlR, a MerR-like regulator encoded upstream of efrEF, mediates the chlorhexidine-dependent up-regulation of efrEF, and deletion of chlR also increases chlorhexidine susceptibility. In addition, to investigate the hypothesis that E. faecalis adapts to frequent chlorhexidine exposure, I designed a controlled serial passage (in vitro evolution) experiment for E. faecalis V583 with chlorhexidine. After 20 days passage, I discovered that E. faecalis V583 evolved increased tolerance of chlorhexidine. Moreover, ΔefrEF and ΔchlR similarly adapted to chlorhexidine, indicating that E. faecalis encodes additional chlorhexidine tolerance mechanisms. In light of the rise of nosocomial E. faecalis infections and decreased susceptibility to chlorhexidine, it is crucially important to understand the mechanisms of how E. faecalis, especially multidrug-resistant E. faecalis, tolerate chlorhexidine. In other dissertation work, I used genomics to identify mutations associated with reduced susceptibility to the lipopeptide antibiotic surotomycin in C. difficile and E. faecalis. In summary, my dissertation research uncovered and characterized coordinated and specific genes in E. faecalis V583 that are differentially expressed in response to chlorhexidine exposure, which contributes to our understanding of E. faecalis antimicrobial tolerance mechanisms and provides opportunities for exploring new avenues for drug targets.



Enterococcus faecalis, Chlorhexidine, Drug resistance in microorganisms, Microbial genomics


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