The Origins of Antibiotic Resistance

Abstract

The emergence of bacterial antibiotic resistance is a growing problem. Many antibiotic drugs fail because resistant mutants evolve and populate again, as seen by the global spread of the infectious pathogens that cause diseases like tuberculosis. In the course of evolution in human body, bacteria encounter heterogeneous environment full of transient chemical and nutrient gradients. Antibiotic gradients can arise when a patient begins and ends therapies, or forgets doses. Bacteria have successfully adapted to a wide variety of physical/chemical conditions, suggesting that spatial heterogeneity must play an important role in evolution. However, the space dimension was under-appreciated by previous laboratory models of microbial evolution.

Such observations motivate us to design a novel reactor that mimics naturally occurring heterogeneous ecology. Chapter 2 shows the reactor &ldquo Death Galaxy &rdquo that we make by microfabrication and microfluidic techniques. We find that the resistance of model bacterial <italic> Escherichia coli </italic> to the broad-spectrum antibiotic ciprofloxacin develops within 10 hours. Resistance emerges with as few as 100 bacteria in the initial inoculation. Whole-genome sequencing of the resistant organisms reveals that four functional single-nucleotide polymorphisms attain fixation. We further investigate how each factor involved in &ldquo Death Galaxy &rdquo - antibiotic gradient, motility, metapopulations - affects the rate of evolution, with both numerical simulations and experiments.

The major role of heterogeneous environment is to increase the fixation rate of the resistant mutant. But how can the mutant emerge quickly when a sensitive population encounters antibiotics? In chapter 3, we zoom in to the single cell level and search for the origin of mutants. We find that the <italic> Escherichia coli </italic> is able to develop single cell mesoscopic ecological niches as a response to external antibiotics, where chromosomal replication can proceed to generate mutants. We then show that such strategy is implemented by the present order of genes placed on the chromosome with respect to the origin of replication.

Finally, in chapter 4, we explore how interactions between individual genome affect the rate of evolution. We propose an evolutionary game theory model to calculate the conditions for horizontal gene transfer to be stable strategy. We further suggest horizontal gene transfer could play crucial role in microbial speciation through analyzing the genomic structure of closed bacterial species.