Nurudeen Rahman
Switzerland
Nanopore-based analysis unravels the phylogenetic placement of human-infecting Trichuris species in Cote d’Ivoire, Laos Tanzania and Uganda
Nurudeen Rahman1, 2, Max Bär1,2, Julian Dommann1,2, Eveline Hürlimann1,2, Jean
Coulibaly1,2,3,4, Said Ali5, Somphou Sayasone1,2,6, Prudence Beinamaryo7, Jennifer Keiser1,2, Pierre HH Schneeberger1,2
1 Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health
Institute, Allschwil, Switzerland
2 University of Basel, Basel, Switzerland
3 Unité de Formation et de Recherche Biosciences, Université Felix Houphouët-Boigny,
Abidjan, Côte dIvoire
4 Centre Suisse de Recherches Scientifiques en Côte dIvoire, Abidjan, Côte dIvoire
5 Public Health Laboratory Ivo de Carneri, Chake Chake, Pemba, Zanzibar, Tanzania
6 Lao Tropical and Public Health Institute, Vientiane, Laos
7 Vector Borne and Neglected Tropical Diseases Division, Ministry of Health, Kampala,
Uganda
Abstract
Background
Soil-transmitted helminthiases (STH), including trichuriasis, pose a significant global burden, affecting numerous mammalian hosts. Traditional diagnostic methods have struggled to differentiate species within the Trichuris genus, prompting the use of molecular techniques to understand the diversity and zoonotic transmission of Trichuris spp. among humans and non-human primates (NHP), dogs, and pigs.
Methods
Four double-blinded, parallel-group, randomized controlled human clinical trials were recently conducted to assess the efficacy of albendazole-ivermectin combination therapy against Trichuris in Côte dIvoire, Uganda, Laos, and Tanzania. While high efficacy against Trichuris was observed in Lao PDR, Uganda, and Tanzania (ERR above 98%), the efficacy was much lower in Côte dIvoire (ERR below 70%). To explore whether this difference in combination treatment efficacy could be due to genetic differences in the parasite, we developed nanopore-based amplicon sequencing on 670 frozen and ethanol-preserved Trichuris PCR-positive faecal samples from patients from this clinical trial in the four regions using barcoded ITS2 loci.
Results
Nanopore-based full-length ITS2 rDNA sequencing genetically characterized and confirmed the phylogenetic placement of the newly identified human-infecting Trichuris incognita and the well-known Trichuris trichiura, revealing an extremely high level of genetic differentiation of the Cote dIvoire Trichuris population from those in Laos, Uganda, and Tanzania, as well as markedly lower genetic diversity at both of these loci. The majority of the Trichuris ITS-2 Amplicon Sequence Variants (ASVs) from the Cote d’Ivoire patients belong to a phylogenetic clade distinct from T. trichuria and much closer to reference sequences from the Trichuris suis. We found a varying prevalence of T. incognita and T. trichiura across the four countries and that these were also present in non-human primates.
Conclusions
Our findings demonstrated that ITS2 fragment length accurately differentiates both human-infecting Trichuris species and thus makes it a good diagnostic marker for future point-of-care applications in resource-constrained settings, hence aiding the WHO 2030 trichuriasis elimination goal. Future research should refine this diagnostic method and explore other genetic markers in conjunction with ITS2 fragment length to enhance diagnostic precision and provide deeper insights into the evolutionary relationships within the Trichuris genus.
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