Role of DNA-detection–based tools for monitoring the soil-transmitted helminth treatment response in drug-efficacy trials

Gandasegui, Javier; Martínez‐Valladares, María; Grau-Pujol, Berta; Krolewiecki, Alejandro; Balaña‐Fouce, Rafael; Gelaye, Woyneshet; Lieshout, Lisette van; Kepha, Stella; Mandomando, Inácio; Muñóz, José

doi:10.1371/journal.pntd.0007931

Cited by 14 publications

(10 citation statements)

References 24 publications

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“…suum , to date none of the BZ resistance associated SNPs have been described in the single β-tubulin gene that has been examined [ 42 ]. Consequently, for both species, the current evidence for these SNPs as a marker for BZ resistance is not yet well-defined [ 4 , 43 ]. Furthermore, because of the poor knowledge of the β-tubulin gene family composition in the Ascaris species, it is difficult to interpret the relevance of the absence of potential resistance conferring SNPs in a particular β-tubulin gene without knowledge of other β-tubulin loci that may be relevant.…”

Section: Introductionmentioning

confidence: 99%

Characterization of the β-tubulin gene family in Ascaris lumbricoides and Ascaris suum and its implication for the molecular detection of benzimidazole resistance

et al. 2021

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Background The treatment coverage of control programs providing benzimidazole (BZ) drugs to eliminate the morbidity caused by soil-transmitted helminths (STHs) is unprecedently high. This high drug pressure may result in the development of BZ resistance in STHs and so there is an urgent need for surveillance systems detecting molecular markers associated with BZ resistance. A critical prerequisite to develop such systems is an understanding of the gene family encoding β-tubulin proteins, the principal targets of BZ drugs. Methodology and principal findings First, the β-tubulin gene families of Ascaris lumbricoides and Ascaris suum were characterized through the analysis of published genomes. Second, RNA-seq and RT-PCR analyses on cDNA were applied to determine the transcription profiles of the different gene family members. The results revealed that Ascaris species have at least seven different β-tubulin genes of which two are highly expressed during the entire lifecycle. Third, deep amplicon sequencing was performed on these two genes in more than 200 adult A. lumbricoides (Ethiopia and Tanzania) and A. suum (Belgium) worms, to investigate the intra- and inter-species genetic diversity and the presence of single nucleotide polymorphisms (SNPs) that are associated with BZ resistance in other helminth species; F167Y (TTC>TAC or TTT>TAT), E198A (GAA>GCA or GAG>GCG), E198L (GAA>TTA) and F200Y (TTC>TAC or TTT>TAT). These particular SNPs were absent in the two investigated genes in all three Ascaris populations. Significance This study demonstrated the presence of at least seven β-tubulin genes in Ascaris worms. A new nomenclature was proposed and prioritization of genes for future BZ resistance research was discussed. This is the first comprehensive description of the β-tubulin gene family in Ascaris and provides a framework to investigate the prevalence and potential role of β-tubulin sequence polymorphisms in BZ resistance in a more systematic manner than previously possible.

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Section: Introductionmentioning

confidence: 99%

Characterization of the β-tubulin gene family in Ascaris lumbricoides and Ascaris suum and its implication for the molecular detection of benzimidazole resistance

et al. 2021

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“…There is substantial variation in the readings, resulting from uneven distribution of eggs within a single stool sample (within sample variation), day-to-day fluctuations of egg excretion (between sample variations) and ultimately results depend on the readers’ skills and experience [ 17 – 20 ]. Most importantly, the Kato-Katz method may particularly miss low-intensity infections leading to underestimation of the actual prevalence, but in the case of efficacy trials artificially inflate cure rates (CRs) from undetected residual low-egg count infections post-treatment [ 21 ]. Moreover, expertise in microscopy is increasingly rare [ 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

Performance of the Kato-Katz method and real time polymerase chain reaction for the diagnosis of soil-transmitted helminthiasis in the framework of a randomised controlled trial: treatment efficacy and day-to-day variation

et al. 2020

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Background Accurate, scalable and sensitive diagnostic tools are crucial in determining prevalence of soil-transmitted helminths (STH), assessing infection intensities and monitoring treatment efficacy. However, assessments on treatment efficacy comparing traditional microscopic to newly emerging molecular approaches such as quantitative Polymerase Chain Reaction (qPCR) are scarce and hampered partly by lack of an established diagnostic gold standard. Methods We compared the performance of the copromicroscopic Kato-Katz method to qPCR in the framework of a randomized controlled trial on Pemba Island, Tanzania, evaluating treatment efficacy based on cure rates of albendazole monotherapy versus ivermectin-albendazole against Trichuris trichiura and concomitant STH infections. Day-to-day variability of both diagnostic methods was assessed to elucidate reproducibility of test results by analysing two stool samples before and two stool samples after treatment of 160 T. trichiura Kato-Katz positive participants, partially co-infected with Ascaris lumbricoides and hookworm, per treatment arm (n = 320). As negative controls, two faecal samples of 180 Kato-Katz helminth negative participants were analysed. Results Fair to moderate correlation between microscopic egg count and DNA copy number for the different STH species was observed at baseline and follow-up. Results indicated higher sensitivity of qPCR for all three STH species across all time points; however, we found lower test result reproducibility compared to Kato-Katz. When assessed with two samples from consecutive days by qPCR, cure rates were significantly lower for T. trichiura (23.2 vs 46.8%), A. lumbricoides (75.3 vs 100%) and hookworm (52.4 vs 78.3%) in the ivermectin-albendazole treatment arm, when compared to Kato-Katz. Conclusions qPCR diagnosis showed lower reproducibility of test results compared to Kato-Katz, hence multiple samples per participant should be analysed to achieve a reliable diagnosis of STH infection. Our study confirms that cure rates are overestimated using Kato-Katz alone. Our findings emphasize that standardized and accurate molecular diagnostic tools are urgently needed for future monitoring within STH control and/or elimination programmes.

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“…Future studies exploiting genome-wide analyses on parasite populations that are phenotypically well-defined for drug response 43 are needed to define the genetic architecture of drug response in T. trichiura. It will be particularly important to disentangle known variation in the tolerance to benzimidazole drugs by T. trichiura 44,45 from the emergence of loss of efficacy due to high drug exposure 6 , especially if the promise of using molecular diagnostics to monitor the emergence of anthelmintic resistance is to be realised [46][47][48][49] .…”

Section: Discussionmentioning

confidence: 99%

Population genomics of ancient and modernTrichuris trichiura

Doyle

Søe

Nejsum

et al. 2021

Preprint

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The neglected tropical disease trichuriasis is caused by the whipworm Trichuris trichiura, a soil-transmitted helminth that has infected humans for millennia. Today, T. trichiura infects as many as 500 million people, predominantly in communities with poor sanitary infrastructure enabling sustained faecal-oral transmission. Using whole-genome sequencing of geographically distributed worms collected from human and other primate hosts, together with ancient samples preserved in archaeologically-defined latrines and deposits dated up to one thousand years old, we present the first population genomics study of T. trichiura. We describe the continent-scale genetic structure between whipworms infecting humans and baboons relative to those infecting other primates. Admixture and population demographic analyses support a stepwise distribution of genetic variation that is highest in Uganda, consistent with an African origin and subsequent translocation with human migration. Finally, genome-wide analyses between human samples and between human and non-human primate samples reveal local regions of genetic differentiation between geographically distinct populations. These data provide insight into zoonotic reservoirs of human-infective T. trichiura and will support future efforts toward the implementation of genomic epidemiology of this globally important helminth.

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Role of DNA-detection–based tools for monitoring the soil-transmitted helminth treatment response in drug-efficacy trials

Abstract: ¶ Membership of the Stopping Transmission Of intestinal Parasites (STOP) project consortium is provided in the Acknowledgments.

Cited by 14 publications

References 24 publications

Characterization of the β-tubulin gene family in Ascaris lumbricoides and Ascaris suum and its implication for the molecular detection of benzimidazole resistance

Characterization of the β-tubulin gene family in Ascaris lumbricoides and Ascaris suum and its implication for the molecular detection of benzimidazole resistance

Performance of the Kato-Katz method and real time polymerase chain reaction for the diagnosis of soil-transmitted helminthiasis in the framework of a randomised controlled trial: treatment efficacy and day-to-day variation

Population genomics of ancient and modernTrichuris trichiura

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