A toolkit for genome-wide association studies in bacteria

Principal Investigator: Jesse Shapiro
Theme : Development of New Technologies
Competition : 2015 Bioinformatics and Computational Biology Competition
Status : Completed
Start : Oct. 1, 2016
End: Sept. 30, 2018
Budget : $250,000.00

There is a pressing need for better diagnosis of antibiotic-resistant infections. Diagnostics allow doctors and veterinarians to prescribe the right antibiotics in a timely fashion. In many cases, this is essential for minimizing morbidity and mortality from the infection and reducing the costs of antibiotic-resistant infections, currently estimated at $500 million/year. One of the most significant barriers is the length of time it takes to culture bacteria.


Molecular diagnostics offer the potential for faster, point-of-care tests, but require knowing which genes or mutations to look for, a challenge when the genes involved in antibiotic resistance are still unknown. Jesse Shapiro (Université de Montréal) and Luis Barreiro (CHU Sainte-Justine) are developing software to identify the bacterial genes or mutations associated with antibiotic resistance – or any other bacterial trait of interest – using genome-wide association studies. This software will provide the missing link between bacterial genome sequencing and reliable, rapid molecular diagnostics. Researchers, clinicians and veterinarians will be able to make informed decisions about treatment, reducing costly and unnecessary treatments and improving human and animal health.


Co-project leader:

Luis Barreiro CHU Sainte-Justine