Project Description
SBIR: An Integrated Pan Genome Resistome Platform for Nosocomial Pathogen Surveillance in Hospitals
Agency: Department of Health and Human Services
Branch: National Institutes of Health
Contract: 1R43AI129187-01
Nosocomial hospital infections are a significant public health concern as they severely harm patients, disrupt normal operations, and increase hospital costs. To reduce these risks and allow for preemptive responses there is a critical need for routine surveillance of nosocomial pathogens within a hospital environment patients staff ventilation equipment With the decreasing costs of sequencing whole genome sequencing is increasingly becoming viable as a diagnostic tool However translating its genomic information into a distinctive surveillance signature has been a significant challenge
Our approach will employ a unique Pan Genome that will translate the entire genome content of the unknown strain into a distinctive strain signature. Likewise, our resistome analysis will employ a Pan Resistome that will translate the resistome content of the unknown strain into a distinctive resistome signature. Taken together these strain and resistome signatures will provide a comprehensive set of genome markers that will be used to connect newly sequenced strains in the event of a new infection.
Our aims are to:
- Develop a screening framework that rapidly identifies unknown strains and assigns them to a node Aim
- Develop a strain analysis framework that analyzes the unknown strain and establishes a list of closely related strain clusters Aim
- Develop a resistome analysis framework that analyzes the unknown strain and establishes a list of closely related resistomes
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