Antibiotic resistance among bacterial pathogens remains one of the great challenges confronting public health in the world today. Despite the remarkable success of antibiotics, bacterial infections remain one of the leading causes for mortality. Increasingly, sustained and broad use of antibiotics has selected for multi-drug resistant bacteria that adapt rapidly to newer generation antibiotics and shorten their clinical efficacy. We have developed a scalable and holistic approach that we call 'Quantitative Evolutionary Dynamics'(QED) to study daptomycin and tigecycline resistance in clinical isolates of vancomycin-resistant enterococci (VRE) and to tigecycline resistance in Acinetobacter baumannii. QED can be applied across many organisms and antibiotics to provide: 1) conceptual and mechanistic insights, 2) new targets for drug design, and 3) reveal the underlying biophysical basis for changes in cellular fitness leading to greater resistance during selection. To conduct QED, we use a combination of experimental evolution in turbidostats (fermentors that maintain bacterial populations at their fastest growth rate), genomic sequencing, DNA bar-coding to measure allelic frequencies (FREQ-SEQ), RNA-Seq and physicochemical characterization, including X-ray crystallography, to provide an integrative approach to the identification and characterization of drug resistance targets and mechanisms. QED uses experimental evolution to identify the intermediates of adaptation to reconstruct the adaptive networks responsible for resistance. We use principles from evolutionary biology to rank the likely importance of such changes within the population and prioritize the most important targets for the more time consuming physical studies. QED shows excellent correspondence to in vivo clinical observations of antibiotic resistance. We produce insights not just into the clinically relevant strategies for resistance, but also the specific biochemical mechanisms of resistance, the specific candidate genes responsible for those biochemical changes, and the basis for developing a quantitative link between those changes and the fitness (e.g. resistance) of the pathogen towards a specific drug. QED is a powerful and novel approach that can complement in vivo and clinical studies as well as reveal the evolutionary dynamics of antibiotic resistance.

Public Health Relevance

In this proposal we will identify the molecular mechanisms of daptomycin and tigecycline resistance in vancomycin-resistant enterococci (VRE) and to tigecycline resistance in Acinetobacter baumannii. We use a combination of experimental evolution and biophysics to explore how changes in the genome give rise to resistance and how these changes are brought about at the molecular level. We use that information to understand how adaptation to antibiotics happens and how we might develop drugs to limit adaptation and thereby increase the effectiveness of current and future antibiotics.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
Project #
Application #
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
Huntley, Clayton C
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Rice University
Schools of Arts and Sciences
United States
Zip Code
Diaz, Lorena; Tran, Truc T; Munita, Jose M et al. (2014) Whole-genome analyses of Enterococcus faecium isolates with diverse daptomycin MICs. Antimicrob Agents Chemother 58:4527-34
Davlieva, Milya; Donarski, James; Wang, Jiachen et al. (2014) Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis. Nucleic Acids Res 42:10795-808
Davlieva, Milya; Zhang, Wanna; Arias, Cesar A et al. (2013) Biochemical characterization of cardiolipin synthase mutations associated with daptomycin resistance in enterococci. Antimicrob Agents Chemother 57:289-96
Tran, Truc T; Panesso, Diana; Gao, Hongyu et al. (2013) Whole-genome analysis of a daptomycin-susceptible enterococcus faecium strain and its daptomycin-resistant variant arising during therapy. Antimicrob Agents Chemother 57:261-8
Tran, Truc T; Panesso, Diana; Mishra, Nagendra N et al. (2013) Daptomycin-resistant Enterococcus faecalis diverts the antibiotic molecule from the division septum and remodels cell membrane phospholipids. MBio 4:
Miller, Corwin; Kong, Jiayi; Tran, Truc T et al. (2013) Adaptation of Enterococcus faecalis to daptomycin reveals an ordered progression to resistance. Antimicrob Agents Chemother 57:5373-83
Agrawal, Aditya; Chipara, Alin C; Shamoo, Yousif et al. (2013) Dynamic self-stiffening in liquid crystal elastomers. Nat Commun 4:1739
Walkiewicz, Katarzyna; Davlieva, Milya; Wu, Gang et al. (2011) Crystal structure of Bacteroides thetaiotaomicron TetX2: a tetracycline degrading monooxygenase at 2.8 A resolution. Proteins 79:2335-40
Arias, Cesar A; Panesso, Diana; McGrath, Danielle M et al. (2011) Genetic basis for in vivo daptomycin resistance in enterococci. N Engl J Med 365:892-900
Pena, Matthew I; Van Itallie, Elizabeth; Bennett, Matthew R et al. (2010) Evolution of a single gene highlights the complexity underlying molecular descriptions of fitness. Chaos 20:026107