Sensitive treponema pallidum genome recovery through tiling amplicon sequencing
Ended Project Grant Awarded Last action
- Award ID
- R21AI185726
- Recipient
-
University Of Washington UEI HD1WMN6945W6
- Awarding agency
-
National Institute of Allergy and Infectious Diseases
National Institutes of Health, Department of Health and Human Services
- Obligated
- $485,375
Award facts
- Assistance listing
- 93.855 Allergy and Infectious Diseases Research
- Completion date
- Place of performance
- Seattle, WA 98109, USA
Award details come from USAspending.gov.
Description
- Abstract
- Sensitive treponema pallidum genome recovery through tiling amplicon sequencing genomic epidemiology is now a standard part of the public health response to outbreaks of bacterial pathogens. For most bacteria, genome recovery is performed via shotgun sequencing of clinical isolates. Genome recovery for treponema pallidum, the causative agent of syphilis, is more complicated due to the lack of routine culture for the organism in clinical labs. Expensive reagents and complicated protocols are required to perform hybridization capture, which is not standard in clinical or public health microbiology laboratories. Even then, the analytical sensitivity of hybridization capture does not meet the low levels of t. Pallidum DNA present in most clinical samples, leading to failure of complete genome recovery in over half of clinical specimens that test PCR positive for t. Pallidum DNA. Here, we propose to optimize methods to recover t. Pallidum genomes from diverse specimens to allow for greater analytical sensitivity and scale. Specifically, based on recent data from hundreds of newly sequenced t. Pallidum genomes, we will design a tiling amplicon sequencing approach for t. Pallidum genome recovery, using 2- 3KB sized PCR amplicons compatible with both long-read and short-read sequencing. We will then fully validate this tiling amplicon library generation approach using both cultured isolates and diverse clinical t. Pallidum specimens taken from across the world to determine its analytical sensitivity, specificity, precision, and accuracy. Finally, we will widely share our standard operation procedures and reagents for executing this work in research and public health laboratories across the world. The proposed work will extend the analytical sensitivity, ease of workflow, and cost-effectiveness for t. Pallidum genome recovery, enabling genomic epidemiology to inform outbreak response and prevention for syphilis.
Transactions
| Action | Obligated | Date |
|---|---|---|
| Amendment | $220,625 | |
| Original award | $264,750 |
Quick answers
Who received award R21AI185726?
R21AI185726 was awarded to University Of Washington by National Institute of Allergy and Infectious Diseases (National Institutes of Health) on August 5, 2024.
How much is award R21AI185726 worth?
$485,375 has been obligated on R21AI185726.
On GovTribe
See this award's full record
- Every transaction and subaward
- The recipient's other awards and teaming partners
- Similar grant awards
- Ask GovTribe AI about this award