Diagnostics for yaws eradication: insights from direct next generation sequencing of cutaneous strains of Treponema pallidum

Abstract

Background

Yaws-like chronic ulcers can be caused by Treponema pallidum subsp. pertenue, Haemophilus ducreyi, or other still-undefined bacteria. To permit accurate evaluation of yaws elimination efforts programmatic use of molecular diagnostics is required. The accuracy and sensitivity of current tools remains unclear because our understanding of T. pallidum diversity is limited by the low number of sequenced genomes.

Methods

We tested samples from patients with suspected yaws collected in previous studies in the Solomon Islands and Ghana. All samples were from patients whose lesions had previously tested negative using the current CDC diagnostic assay in widespread use. However, some of these patients had positive serological assays for yaws on blood. We used direct whole genome sequencing to identify T.p subsp. pertenue strains missed by the current assay.

Results

From 45 Solomon Islands and 27 Ghanaian samples, 11 were positive for T. pallidum DNA using the species-wide qPCR, from which we obtained 6 previously undetected T. p. subsp. pertenue whole genome sequences. These sequences show that Solomon Islands sequences represent distinct T. p. subsp. pertenue clades. These isolates were invisible to the CDC diagnostic PCR assay in widespread current use, due to sequence variation in the primer binding site.

Conclusion

Our data double the number of published T. p. subsp. pertenue genomes. We show that Solomon Islands strains are undetectable by the PCR used in many studies and by health ministries. This assay is therefore not adequate for the eradication programme. Next-generation genome sequence data are essential for these efforts.