# Sensitive Treponema pallidum genome recovery through tiling amplicon sequencing

> **NIH NIH R21** · UNIVERSITY OF WASHINGTON · 2024 · $264,750

## Abstract

Project Summary
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.

## Key facts

- **NIH application ID:** 10975482
- **Project number:** 1R21AI185726-01
- **Recipient organization:** UNIVERSITY OF WASHINGTON
- **Principal Investigator:** Alexander L Greninger
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $264,750
- **Award type:** 1
- **Project period:** 2024-08-05 → 2026-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10975482

## Citation

> US National Institutes of Health, RePORTER application 10975482, Sensitive Treponema pallidum genome recovery through tiling amplicon sequencing (1R21AI185726-01). Retrieved via AI Analytics 2026-06-12 from https://api.ai-analytics.org/grant/nih/10975482. Licensed CC0.

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