The Influence of Escherichia coli Metabolism on Antibiotic Resistance

Abstract

Antibiotics are important tools to fight bacteria in complement to vaccines and public hygiene regulation. Antibiotics are molecules that interfere with key bacterial processes, ranging from translation and transcription to cell wall synthesis. This results in arrest of bacterial proliferation. Because of the selective pressure antibiotics impose on microbes, they are challenged by the formidable capacities of evolution. Indeed, bacteria have been shown to counteract antibiotics through multiple strategies, either at population or clonal levels. This is notably the case for ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter braumannii, Pseudomonas aeruginosa and species of the genus Enterobacter). These bacterial species quickly evolve escape mechanisms to currently used antibiotics as well as new-to-market antibiotics. Two main routes of antibiotic escape are resistance and tolerance. Antibiotic tolerance permits to withstand antibiotic treatment for a longer period of time while antibiotic resistance allows to grow in the presence of the antibiotic at normally non-permissive concentrations. Resistant or tolerant pathogens often require the use of last-resort antibiotics or longer and heavier treatments to be eradicated. However, these alternatives are also met with evolutionary escape while the development of new antibiotics takes a substantial time. This leads to a sharp decrease of new antibiotic development and ever-increasing pressure on health authorities. Therefore, it is pressing to understand evolutionary strategies employed by bacterial pathogens to escape antibiotic treatment in order to anticipate and counter them. One key evolutionary weapon is the acquisition of genomic mutations that confer antibiotic resistance or tolerance. Some of these mutations have relatively trivial effects. Mutations in the direct target of an antibiotic alter binding interactions and nullify antibiotic effects. Efflux pumps regulators can also be mutated to affect antibiotic import or export towards their targets. More recently, mutations in core metabolic genes have been shown to affect antibiotic treatments. However, how these mutations affect metabolism and lead to antibiotic treatment failure remains poorly understood. It is generally assumed that antibiotic treatments could be globally affected by a general “metabolic state”, or metabolic-dependent phenomenon such as growth rate. However, these observations were made while studying antibiotic tolerance and not antibiotic resistance. Whether a general “metabolic state” could confer resistance to multiple antibiotics remains unknown. Here is presented a body of work that investigates the link between metabolism and antibiotic treatment in the ESKAPE pathogen Escherichia coli with a focus on antibiotic resistance. The following question is formulated for this thesis: Do mutations in metabolic genes of E. coli have a general impact on antibiotic resistance? This thesis will first present a general introduction of its scientific framework. Chapter 1 discusses the elaboration of the main tool used in the thesis: a library of E. coli strains each with a genomic mutation in an essential gene. Chapter 2 covers the main body of work done in this thesis and present its most important findings. Chapter 3 further discusses findings made in Chapter 2 and provides additional experiments and hypothesis.