Validation of whole genome sequencing analyses to replace phenotypic antimicrobial resistance surveillance of Streptococcus pyogenes and Streptococcus agalactiae

Funding period: 2023–2025
Leads: Alyssa Golden and Irene Martin
Total GRDI funding: $290,300

Invasive Streptococcus pyogenes (group A Streptococcus, group A strep) is responsible for a wide range of human diseases, the most serious of which include bacteraemia, streptococcal toxic shock syndrome, necrotizing fasciitis and endocarditis. This project aims to validate the methodology for routine prediction of group A strep and group B strep minimum inhibitory concentrations using whole genome sequencing, which will replace the existing phenotypic workflows.

Goals of the project:

• Perform quantitative antimicrobial susceptibility testing by E-test to obtain accurate and precise minimum inhibitory concentration values for group A strep and group B strep isolates
• Complete the corresponding whole genome sequencing for these isolates
• Use machine learning techniques to design, develop and validate the methodology to predict minimum inhibitory concentrations from whole genome sequencing data