Palmer, Kelli L.
Permanent URI for this collectionhttps://hdl.handle.net/10735.1/4295
Kelli Palmer is an Assistant Professor in the Department of Molecular and Cell Biology. Dr. Palmer uses genomic, transcriptomic, and biochemical approaches to study antibiotic resistance in pathogenic bacteria. Her research focuses on microorganisms contributing to significant mortality and cost burdens in the health care industry.
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Browsing Palmer, Kelli L. by Subject "Bacteriophages"
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Item An Attenuated CRISPR-Cas System In Enterococcus faecalis Permits DNA Acquisition(Amer Soc Microbiology) Hullahalli, Karthik; Rodrigues, Marinelle; Uyen Thy Nguyen; Palmer, Kelli L.; 0000-0002-7343-9271 (Palmer, KL); Hullahalli, Karthik; Rodrigues, Marinelle; Uyen Thy Nguyen; Palmer, Kelli L.Antibiotic-resistant bacteria are critical public health concerns. Among the prime causative factors for the spread of antibiotic resistance is horizontal gene transfer (HGT). A useful model organism for investigating the relationship between HGT and antibiotic resistance is the opportunistic pathogen Fnterococcus faecolis, since the species possesses highly conjugative plasmids that readily disseminate antibiotic resistance genes and virulence factors in nature. Unlike many commensal E. faecalis strains, the genomes of multidrug-resistant (MDR) E. faecalis clinical isolates are enriched for mobile genetic elements (MGEs) and lack clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) genome defense systems. CRISPRCas systems cleave foreign DNA in a programmable, sequence-specific manner and are disadvantageous for MGE-derived genome expansion. An unexplored facet of CRISPR biology in F. faecolis is that MGEs that are targeted by native CRISPR-Cas systems can be maintained transiently. Here, we investigate the basis for this "CRISPR tolerance." We observe that E. faecalis can maintain self-targeting constructs that direct Cas9 to cleave the chromosome, but at a fitness cost. Interestingly. DNA repair genes were not upregulated during self-targeting, but integrated prophages were strongly induced. We determined that low cas9 expression contributes to this transient nonlethality and used this knowledge to develop a robust CRISPR- assisted genome-editing scheme. Our results suggest that E. faecatis has maximized the potential for DNA acquisition by attenuating its CRISPR machinery, thereby facilitating the acquisition of potentially beneficial MGEs that may otherwise be restricted by genome defense. IMPORTANCE CRISPR-Cas has provided a powerful toolkit to manipulate bacteria, resulting in improved genetic manipulations and novel antimicrobials. These powerful applications rely on the premise that CRISPR-Cas chromosome targeting, which leads to double-stranded DNA breaks, is lethal. In this study, we show that chromosomal CRISPR targeting in Enterococcus faecalis is transiently nonlethal. We uncover novel phenotypes associated with this "CRISPR tolerance" and, after determining its genetic basis, develop a genome-editing platform in E. faecafis with negligible off target effects. Our findings reveal a novel strategy exploited by a bacterial pathogen to cope with CRISPR- induced conflicts to more readily accept DNA, and our robust CRISPR editing platform will help simplify genetic modifications in this organism.Item Bacteriophage Resistance Alters Antibiotic-Mediated Intestinal Expansion of Enterococci(American Society for Microbiology, 2019-05-21) Chatterjee, A.; Johnson, C. N.; Luong, P.; Hullahalli, Karthik; McBride, S. W.; Schubert, A. M.; Palmer, Kelli L.; Carlson, P. E.; Duerkop, B. A.; 0000-0002-7343-9271 (Palmer, KL); Hullahalli, Karthik; Palmer, Kelli L.Enterococcus faecalis is a human intestinal pathobiont with intrinsic and acquired resistance to many antibiotics, including vancomycin. Nature provides a diverse and virtually untapped repertoire of bacterial viruses, or bacteriophages (phages), that could be harnessed to combat multidrug-resistant enterococcal infections. Bacterial phage resistance represents a potential barrier to the implementation of phage therapy, emphasizing the importance of investigating the molecular mechanisms underlying the emergence of phage resistance. Using a cohort of 19 environmental lytic phages with tropism against E. faecalis, we found that these phages require the enterococcal polysaccharide antigen (Epa) for productive infection. Epa is a surface-exposed heteroglycan synthesized by enzymes encoded by both conserved and strain-specific genes. We discovered that exposure to phage selective pressure favors mutation in nonconserved epa genes both in culture and in a mouse model of intestinal colonization. Despite gaining phage resistance, epa mutant strains exhibited a loss of resistance to cell wall-targeting antibiotics. Finally, we show that an E. faecalis epa mutant strain is deficient in intestinal colonization, cannot expand its population upon antibiotic-driven intestinal dysbiosis, and fails to be efficiently transmitted to juvenile mice following birth. This study demonstrates that phage therapy could be used in combination with antibiotics to target enterococci within a dysbiotic microbiota. Enterococci that evade phage therapy by developing resistance may be less fit at colonizing the intestine and sensitized to vancomycin, preventing their overgrowth during antibiotic treatment. Copyright © 2019 American Society for Microbiology. All Rights Reserved.