A genomic epidemiology investigation of yaws re-emergence and bacterial drug resistance selection

Abstract

Background: In a longitudinal study assessing the WHO strategy for yaws eradication using mass azithromycin treatment, we observed resurgence of yaws cases with dominance of a single JG8 sequence type and emergence of azithromycin-resistant Treponema pallidum. Here, we analyse genomic changes in the bacterial population using samples collected during the study. Methods: We performed whole bacterial genome sequencing directly on DNA extracted from 37 lesion swabs collected from patients on Lihir Island, Papua New Guinea, between 2013 and 2016. We produced phylogenies and correlated these with temporo-spatial information to investigate the source of new cases and the emergence of five macrolide-resistant cases. We used deep amplicon sequencing of surveillance samples to assess the presence of minority macrolide resistance populations. Findings: We recovered 20 whole Treponema genomes, and phylogenetic analysis showed that the re-emerging JG8 sequence type was composed of three bacterial sub-lineages characterised by distinct temporo-spatial patterns. Of five patients with resistant Treponema, all epidemiologically linked, we recovered genomes from three and found no variants. Deep sequencing showed that pre-treatment, the index patient harboured fixed macrolide-sensitive Treponema, while the post-treatment sample harboured a fixed resistant genotype, as did three of four contact cases. We also found no evidence of pre-existing minority Treponema drug-resistance variants in the general population. Interpretation: In this study, re-emergence of yaws cases was polyphyletic, indicating multiple epidemiological sources. However, given the genomic and epidemiological linkage of resistant cases and the rarity of resistance alleles in the general population, it is likely that azithromycin resistance evolved only once in this study, followed by onward dissemination.

Diagnostics to support the eradication of yaws – Development of Two Target Product Profiles

“…Two challenges faced are: the lack of molecular point of care tests and PCR testing facilities; and the emergence of azithromycin-resistant yaws. The availability of tests that can reliably identify a single case of yaws is critical in deciding when to start and stop mass drug administration (MDA) as is the availability of tools that can rapidly and effectively detect cases of azithromycin resistance post MDA will be useful in avoiding unnecessary treatment and ensuring resistant cases can be treated directly with benzathine penicillin (6). To date, clinical examination combined with serological tests for T. pallidum (i.e., not specific for T .…”

“…A major concern has been the identification of a small number of cases of yaws which have developed resistance to azithromycin (6). Two point mutations (A2059G and A2058G in the 23S ribosomal genes) are known to confer resistance to azithromycin in T .…”

Evaluating the yaws diagnostic gap: A survey to determine the capacity of and barriers to improving diagnostics in all yaws-endemic countries

“…Molecular tools are also the only available diagnostic tool for detecting azithromycin resistant TPE (20,21). This is important, as although only recently detected in TPE, drug resistance has the potential to derail eradication efforts (22,23). The latest WHO manual on yaws eradication for programme managers (24), highlights the importance of molecular tools both for declaring interruption of yaws transmission and for surveillance after eradication certification.…”