Yaws re-emergence and bacterial drug resistance selection after mass administration of azithromycin: a genomic epidemiology investigation

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 subspecies pertenue (T p pertenue). Here, we analyse genomic changes in the bacterial population using samples collected during the study. MethodsWe did whole bacterial genome sequencing directly on DNA extracted from 37 skin lesion swabs collected from patients on Lihir Island, Papua New Guinea, between April 1, 2013, and Nov 1, 2016. We produced phylogenies and correlated these with spatiotemporal 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-resistant populations.Findings We recovered 20 whole T p pertenue genomes, and phylogenetic analysis showed that the re-emerging JG8 sequence type was composed of three bacterial sublineages characterised by distinct spatiotemporal patterns. Of five patients with resistant T p pertenue, all epidemiologically linked, we recovered genomes from three and found no variants. Deep sequencing showed that before treatment, the index patient had fixed macrolide-sensitive T p pertenue, whereas the post-treatment sample had a fixed resistant genotype, as did three of four contact cases.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, azithromycin resistance is likely to have evolved only once in this study, followed by onward dissemination.Funding Wellcome and Provincial Deputation of Barcelona.

Epidemiologic and Genomic Reidentification of Yaws, Liberia

“…This finding suggests evolution and expansion of local TPE strains from a common ancestor subsequent to the benzathine penicillin-based eradication campaigns conducted until the 1960s, rather than recent importation from elsewhere. This information contrasts with a recent study on highly endemic Lihir Island, Papua New Guinea, where TPE was polyphyletic and exhibited > 3 distinct phylogenetic clades ( 15 ). These observations were made despite a smaller geographic area and population and may reflect both higher TPE transmission rates and mobility among island inhabitants.…”

“…From all TPE PCR-positive swabs in the study, we submitted samples with a qPCR threshold of <Cq 32 for whole-genome sequencing using the pooled sequence capture method described previously ( 14 , 22 ). We mapped Treponema -specific sequencing reads to the Samoa D reference genome (bwa mem version 0.7.15), as previously described ( 15 ), to infer a whole genome multiple sequence alignment (samtools version 1.6, bcftools version 1.6, http://www.htslib.org ), contextualized by 33 high-quality publicly available TPE genomes (and 1 T. pallidum subsp. endemicum as outgroup) from around the world.…”

“…We used Gubbins version 2.4.1 ( https://github.com/sanger-pathogens/gubbins ) to mask recombination and generated a maximum likelihood phylogeny (IQ-Tree version 1.6.10, http://www.iqtree.org ). Macrolide resistance-associated alleles were inferred as previously described ( 15 ). We inferred pairwise single nucleotide polymorphism distances between samples using pairsnp ( https://github.com/gtonkinhill/pairsnp ).…”

“…For T. pallidum subspecies pallidum , genetic epidemiology has informed understanding on global transmission patterns and macrolide resistance ( 14 , 15 ). Despite their close genetic relationship, few whole-genome sequences are currently available for TPE.…”

Contemporary syphilis is characterised by rapid global spread of pandemicTreponema pallidumlineages

“…500 ng pooled DNA was hybridised using 120-mer RNA baits (SureSelect Target enrichment system, Agilent technologies; Bait design ELID ID 0616571) 4,35 . Enriched libraries were sequenced on Illumina HiSeq 4000 to generate 150 bp paired end reads at the Wellcome Sanger Institute (Cambridgeshire, UK) as previously described 36 . For one rabbit passaged sample from Melbourne, Australia (TPA_AUSMELT-1) 29 , genomic DNA extracted from historically archived tissue lysate was sequenced on Illumina NextSeq 500 (150 bp paired end reads, Nextera DNA Flex libraries) without any prior enrichment to an estimated 1Gb/sample at the Doherty Institute (Melbourne, Australia).…”