In 2017, Tuberculosis (TB), the disease due to an infection by Mycobacterium tuberculosis (MTB), caused an estimated 1.6 million deaths, making TB one of the top deadliest infectious disease in the world. Drug-resistant TB continues to be a public health crisis. In 2017, around 600 000 people contracted an infection by a MTB that was resistant the most effective first-line drug (rifampicin), of these 82% had multidrug-resistant TB (MDR-TB), and of these MDR-TB, 8.5% had extensively drug-resistant TB (XDR-TB). Besides the global effort to fight against this disease, the World Health Organization reported in 2018 that the proportion of new TB cases with MDR increases over the years. Biofilms are structures composed of microorganisms embedded within a slimy extracellular matrix in which cells stick to each other and often also to a surface. It has been shown that the biofilm structure provides a shelter to bacteria which become resistant to harmful factors such as desiccation, antibiotics, and a host body's immune system. Besides the fact that MTB biofilms were observed in patient lungs, the selection of resistant MTB within these structures remain largely unknown. Are antibiotic concentrations comparable in biofilms and in patient tissues? Are mutations providing resistance the same in biofilms than in other media?

The goal of this project was to study the selection of MTB resistant to the antibiotics used to treat patients, when growing as a biofilm. To do so I developed a technique to grow MTB biofilms on nitrocellulose filters, placed on agar plates. This technique provides a convenient method to study biofilms on the long term, since the filter can easily be moved from an old plate to a fresh one.

To study the selection of resistant MTB in biofilms, the idea is to compare resistant mutants arising in biofilms placed on agar plates containing antibiotics, compared to MTB grown in liquid cultures containing the same antibiotic concentration than the agar plate. The frequency of selection could be estimated under both growing conditions, and mutants could be sampled, sequenced and studied in subsequent experiments.

Additionally to antibiotic concentrations, this biological system also allows to test other environmental factors. It has been shown that the acidity of the infected lung could vary over the course of the infection. Studying the impact of pH variation on antibiotic efficiency and the selection of mutants resistant to antibiotics could also improve our comprehension of the emergence of drug resistant MTB in biofilm structures.