Project Description

SBIR: A cloud-based WGS platform for routine surveillance of plasmid-borne carbapenem resistance

Agency: Department of Health and Human Services

Branch: National Institutes of Health

Contract: 1R43AI131944-01A1

Plasmid borne carbapenem resistance has become a serious global threat in hospital settings As hospitals face a dwindling number of treatment options there is a great urgency to track the movement of carbapenem-resistant plasmids and the associated resistant genes While whole-genome sequencing has great diagnostic potential plasmids pose a unique set of challenges as they lack a clear well-defined structure and contain a wide range of repetitive genetic elements ……. Our proposal aims are to

  • Develop a plasmid framework that quantifies plasmids with both global and transposon biomarker sequences 
  • Develop a plasmid strain alignment framework that will search new strains for plasmid biomarker sequences and then identify other strains that contain similar global biomarker sequences 
  • Develop a transposon alignment framework that will search new strains for KPC gene carrying transposon sequences and then identify other strains with similar biomarker sequences 

Our plasmid bioinformatics framework will allow hospitals to closely monitor their drug-resistant plasmids their association with various strains and the various points of entry within the hospital. Read full SBIR Abstract (link)