Next-Generation Antimicrobial Diagnostics: Speed and Precision via Whole Genome Sequencing

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Bacterial infections cause millions of infections and take tens of thousands of lives every year,and without antibiotics the death toll would skyrocket. Unfortunately, antibiotics are rapidlybecoming less effective due to the evolution of resistance. On top of this, doctors often have adifficult time identifying what drugs will be most effective against infecting pathogens a timelymanner. For these reasons there is desperate need for new antimicrobial diagnostic methodsthat can rapidly provide physicians accurate information to guide their treatments. One verypromising new approach to this problem is to sequence the genomes of the infectingpathogens and use this information predict how they will respond to treatment. We propose toproduce genome sequence data and use sophisticated genome-wide association andpredictive modeling methods to develop a new antimicrobial diagnostic tool. We willspecifically focus on stopping a bacterial pathogen called Pseudomonas aeruginosa thatcauses a disproportionate number of hospital infections and deaths. We will work incollaboration with our partners at the Hospital for Sick Children in Toronto to generate thisstate-of-the-art diagnostic tool and then develop procedures to move it into the clinic. Thesuccess of this project will speed diagnosis, improve patient care, reduce healthcare costs,and enhance stewardship of antibiotics; thereby, preserving their efficacy for the future.