Developing photonic, microfluidic and electrical systems to study the antibiotic susceptibility of individual Escherichia coli

Antimicrobial Resistance (AMR) is an important societal and medical burden being faced by every healthcare system in the world. The large overuse of antibiotics favours bacterial resistance, thereby causing drugs to become ineffective. While traditional susceptibility tests are well established, they are slow at informing prescriptions, which means that many antibiotics are prescribed without proper diagnostics. This inefficacy stems from the detection of bacterial growth at the bulk colony level. In addition, averaging over bulk colonies masks any cell-to-cell difference even though it is well known that bacterial populations and their response to antibiotics are heterogenous. These differences need to be considered to correctly assess the efficacy of any microbial agent in a timely manner. This thesis presents a multiparameter approach for profiling the susceptibility of individual bacteria to antibiotics. Hydrodynamic trapping provides the mechanism for retaining and examining hundreds of single E. coli in a microfluidic channel. The multiparameter aspect consists of the simultaneous assessment of bacterial motility and morphology upon exposure to antibiotics. This combined approach allows us to detect susceptibility and resistance of E. coli MG1655 in as little as 1 hour from spiking the culture. Standard microdilution assays and bacteria counts confirmed the validity of the classification. Additionally, the richness of single-cell data enables us to study the dynamics of population killing and the mode of action of the antibiotics. The methodological approach presented here has the potential to complement traditional susceptibility tests by providing a deeper understanding of the drugs’ action and a more rapid way of assessing the bacterial response to antimicrobial agents. More generally, the assay provides a platform for monitoring the behaviour of hundreds of single bacteria over time, while preserving the individuality of each microorganism.