Laboratory Research

We ask questions about how communities of microorganisms that normally live within us (human microbiome) are involved in the development and maintenance of health. We focus on the intestinal microbiota. Our laboratory uses next generation sequencing and other technologies to learn about the function of the microbiota.

Current Projects

Intestinal microbiota and child health

Under-nutrition causes one-third of child mortality under the age of 5 years. We are working with our global partner ZVITAMBO and the SHINE Trial in Zimbabwe to understand how the intestinal microbiota may contribute to infant growth faltering and environmental enteric dysfunction.

Fecal microbiota transplantation (FMT) for decolonization of multidrug-resistant pathogenic Enterobacteriaceae

Bacterial infections are the most common type of infections following solid organ transplantation. Renal transplant patients are at special risk for chronic, recurrent, multidrug-resistant extraintestinal infections (urinary tract, kidney and bloodstream infections). We are testing whether FMT will decolonize and reconstitute the microbiota of renal transplant patients at-risk of developing a MDR, thereby preventing difficult to treat post-transplant infections.  We have promising results for our first few patients, and we are working to expand this clinical study.

Resistance gene carriage in children who are randomized to continue on cotrimoxazole prophylaxis or to stop cotrimoxazole prophylaxis (a sub-study of the ARROW Trial)

The WHO recommends cotrimoxazole prophylaxis, starting at 4-6 weeks of age of life, to reduce the incidence of opportunistic infections and mortality among HIV-exposed (but not infected) and HIV-infected infants and children. Long-term exposure to cotrimoxazole may increase the carriage of antibiotic resistance organisms by the gut microbiota, which may result in subsequent resistant infections. This study will test whether resistance gene carriage is increased in children who are randomized to continue on cotrimoxazole prophylaxis or to stop cotrimoxazole prophylaxis.  It is a sub-study of the ARROW Trial.

Food safety and extraintestinal (non-diarrheal) Escherichia coli

We are working with the Public Health Agency of Canada, Laboratory for Foodborne Zoonoses and the Canadian Integrated Program for Antimicrobial Resistance Surveillance to examine the relationship between the foodborne transmission of antimicrobial resistant Escherichia coli and the development of community-acquired extraintestinal infections (e.g., urinary tract and bloodstream infections).