Project Details

Diagnosing infection and antibiotic resistance using 3D-genome based genome assemblies

Aviva Aiden, MD, PhD

Summary

BACKGROUND: More than half of the 11 million children who will die this year will die of infections; we need to be able to quickly identify infectious agents and what will treat them. GAP: The current gold standard for diagnosis of infection and antibiotic susceptibility were developed in the 1950s - they are robust but have limitations. We have developed a method based on 3D genome sequencing whereby we can assemble the genome of an organism from scratch, affordably and quickly. HYPOTHESIS: I hypothesize that I can use 3D based assembly to diagnose infections and determine the antimicrobial susceptibility of the pathogens quickly and affordably. METHODS: I will develop our experimental methods to reliably identify infectious agents, specifically bacteria and fungus, in mixed samples. I will develop software tools to allow for multi-species genome assembly in an automated fashion. I will perform a clinical proof of principle test where we will complete our protocol to sequence the genomes (human and pathogen) in a clinical sample. RESULTS: Pending IMPACT: I anticipate that this new method will assist in rapid diagnosis of infectious in children, allowing for better and quicker targeted therapy.