Nouvelles méthodes de séquençage de génomes entiers à partir de cellules individuelles pour l'étude de la variabilité génétique chez les microorganismes.

Chercheurs boursiers - Junior 1 | Concours 2012-2013

Sébastien Rodrigue

Université de Sherbrooke


Domaine : Maladies infectieuses et immunitaires

Genome sequencing is an extremely powerful tool for understanding biology. However, this technique requires a relatively large amount of DNA that is traditionally obtained by growing a large clonal population of cells. This is difficult or simply impossible for the vast majority (>99%) of microorganisms -including bacterial pathogens- that resist cultivation attempts for studying cell to cell genome variability inside a same multicellular organism. I proposed to utilize a novel method for single-cell genomics, i.e. the sequencing of genomes from only one cell sampled directly from the environment without any need for cultivation, to understand genetic diversity and its impacts on infections by uncultured microbial pathogens. The proposed approach has the potential to become a very powerful tool for genomics and personalized medicine.

As a concrete demonstration of the approach, I will study the human obligate intracellular pathogen Chlamydia trachomatis, the aetiologic agent of chlamydia. Chlamydia is by far the most prevalent sexually transmissible infection in Québec. Although detection and treatment strategies are in place, chlamydia rates never declined and keep increasing since 1998. Even when treated with antibiotics such as Azithromycin, 10-15% of patients are still infected when retested after 1 to 3 months. Since Chlamydia trachomatis is an obligate intracellular bacterium that grows inside mammalian cells, it cannot be isolated and cultivated on conventional bacteriological medium, making this pathogen particularly difficult to study. I will first analyze and compare the composition of the Chlamydia trachomatis population during the initial infection and after treatment failure or persistent infection using clinical samples of a group of patients and the single-cell genomics pipeline mentioned above. Interesting single C. trachomatis cells will be selected for whole-genome sequencing with the objective of finding mutations that could explain the antibiotic resistance and/or persistence of infection.