Validating Egg-based Diagnostics and Molecular Markers for the Spread of Anthelmintic Resistance (StarwormsWP1)

Validation of Both Automated Quality Assured Egg Counting System and Molecular Markers for Monitoring the Spread of Anthelmintic Resistance.

Soil-transmitted helminths (STHs) are a group of parasitic worms that infect millions of children in sub-tropical and tropical countries, resulting in malnutrition, growth stunting, intellectual retardation and cognitive deficits. To control the morbidity due to these worms, school-based deworming programs are implemented, in which anthelminthic drugs are administered to children without prior diagnosis. The continued fight against these worms is aided by the London declaration on neglected tropical diseases, which helps sustain and expand global drug donation program, resulting in an unprecedented growth of deworming programs. However, the high degree of drug pressure makes deworming programs vulnerable to the development of anthelmintic resistance because they only rely on one drug with sometimes suboptimal efficacy and there is no availability of alternative drugs. Moreover, at present, there is no surveillance system to monitor the emergence and spread of anthelmintic resistance. It remains unclear to what extent the efficacy of drugs may have dropped and whether anthelmintic resistance is already present. This project aims to strengthen the monitoring and surveillance of drug efficacy and anthelmintic resistance in STH programs. As such, it will support deworming programs in their quest to eliminate STHs as a public health problem. The specific objectives of the first work package are to validate diagnostic tools to monitor drug efficacy and the spread of anthelmintic resistance, and to validate molecular markers for benzimidazole resistance. This study will be conducted at four different sites (Ethiopia, Tanzania, Lao PDR and Brazil) and will focus on school-aged children (age 5-14). At baseline subjects will be asked to provide a recent stool sample which will be processed using 3 different microscopic techniques (KK, Mini-Flotac and FECPAKG2). All children will be treated with a single-oral dose of albendazole (ALB) 400 mg and 14-21 days after treatment, a second stool sample will be collected from all children to again determine the fecal egg counts. At each sampling, stool is stored in preservative. Stored stool will be shipped to Belgium for DNA extraction and quantitative PCR (qPCR) analysis. A subset of the samples will be analysed by pyrosequencing to evaluate the single nucleotide polymorphisms in the b-tubulin gene. Pooling of the stored samples will also be performed to compare with the values obtained from analysing individual samples.

Background Soil-transmitted helminths (STHs) are a group of parasitic worms that infect millions of children in sub-tropical and tropical countries, resulting in malnutrition, growth stunting, intellectual retardation and cognitive deficits. To control the morbidity due to these worms, school-based deworming programs are implemented, in which anthelminthic drugs are administered to children without prior diagnosis. The continued fight against these worms is aided by the London Declaration on Neglected Tropical Diseases, which helps sustain and expand global drug donation program, resulting in an unprecedented growth of deworming programs. to illustrate, in the last four years the coverage of mass drug administration (MDA) has doubled from 30 to 60%, and ongoing global efforts are made to ultimately reach the milestone of 75% by 2020. Threats While the laudable long-term aim is to eliminate STHs as a public health problem by 2020, and to eventually declare targeted geographical areas free from infections, this high degree of drug pressure makes deworming programs vulnerable to the development of anthelmintic resistance because the programs only rely on one drug with sometimes suboptimal efficacy and there is no availability of alternative drugs. Challenges At present, there is no surveillance system to monitor the emergence and spread of anthelmintic resistance. It remains unclear to what extent the efficacy of drugs may have dropped and whether anthelmintic resistance is already present. However, developing such a system is not straightforward. Deworming programs typically operate in resource-constrained settings, and program managers require some flexibility to minimize both financial and technical resources, while ensuring a reliable assessment of the drug efficacy. The most important obstacles to globally monitor patterns of changing drug efficacy and spread of anthelmintic resistance are the following: the shortage of diagnostic laboratories with experienced staff to perform the surveys and analyze and report the obtained data the absence of a quality assurance system that guarantees auditable results the lack of guidance in designing surveys as the programs progresses the lack of data supporting the validity of molecular markers to detect anthelmintic resistance in human STHs the lack of sensitive and point-of-care tools that allow the detection of low frequencies of anthelmintic resistance Main objective This project aims to strengthen the monitoring and surveillance of drug efficacy and anthelmintic resistance in STH programs. As such, it will support deworming programs in their quest to eliminate STHs as a public health problem by 2020. The specific objectives of the first part of the project are to validate diagnostic tools to monitor drug efficacy and the spread of anthelmintic resistance, and to validate molecular markers for benzimidazole resistance. Study protocol This study will conducted at four different sites at Africa (Ethiopia and Tanzania), Asia (Lao PDR) and Latin-America (Brazil). The selection of these sites is based on their experience in assessing drug efficacy and evaluating the performance of diagnostic tools, the availability of well-equipped diagnostic facilities and skilled personnel, and their national MDA history. The study will focus on school-aged children (age of 5 to 14 years). At baseline subjects will be asked to provide a recent (within 4 hours) stool sample of at least 9 grams. All stool samples will be processed using the FECPAKG2, a duplicate Kato-Katz thick smear (the most commonly applied fecal egg count (FEC) technique) and Mini-Flotac (a novel technique that has a sensitivity at least equal to that of Kato-Katz). All children providing a stool sample will be provided a single-oral dose of ALB 400 mg under supervision. Fourteen to 21 days after treatment, a second stool sample will be collected from all the children that proved positive for any STH species at baseline to determine the FECs. At each sampling, 2x 1 gram of stool is stored in preservative for downstream molecular analysis. Stored stool will be shipped to Belgium for DNA extraction and qPCR analysis. A subset of the samples will be analysed by Pyrosequencing to evaluate the single nucleotide polymorphisms in the b-tubulin gene. Pooling of the stored samples will also be performed to compare with the values obtained from analysing individual samples. Data handling Data will first be recorded on specific study record forms. These results will then be entered into the custom designed Excel-files by two different data entry clerks to minimize errors in data due to incorrect data entry. Study management Studies in the different sites will be organized and supported out of Ghent University. The project team members will travel to each individual trial site to train local personnel in the different coprological techniques and to get them acquainted with the trial protocol and documents.

parasitology, helminth infections, diagnosis, drug resistance, albendazole, benzimidazole drugs, Ascaris, Trichuris, hookworm, qPCR, microscopy

All participants that meet all inclusion criteria and none of the exclusion criteria will be enrolled in the study and receive a subject identifier (SubjectID). At baseline, all participants will receive a single treatment of albendazole 400mg and their stool will be examined for helminth eggs. Two to three weeks after treatment a follow-up examination of their stool is performed.

We will validate the performance of the FECPAKG2 as well as its ability to assess drug efficacy by means of egg reduction rates.

We will check the variation in egg counts obtained in repeated measurements and by different technicians and make a cost assessment.

This will be done through assessment of the polymorphisms at the b-tubulin gene using a pyrosequencing approach. We will compare results obtained from the 4 different study sites which have a varying MDA history as well as results obtained from responders, poor responders and non-responders within each different site.

Comparing the sensitivity of quantitative PCR with traditional diagnostic tools (Kato-Katz, Mini-FLOTAC and FECPAKG2) for the detection of soil-transmitted helminth infections.

It is commonly accepted that molecular tools are more sensitive to traditional diagnostic tools, however studies comparing qPCR with a wide range of traditional microscopic techniques are scarce. In this project we will evaluate the performance of qPCR in terms of sensitivity to detect infection compared to the results obtained by coprological analysis of samples by Kato-Katz, Mini-FLOTAC and FECPAKG2.

Comparing the use of individual and pooled stool samples to assess polymorphisms in the β-tubulin gene.

Pyrosequencing results for β-tubulin gene from individual samples will be compared to those from pooled samples. This will shed a light on whether or not pooling stool samples provides similar information regarding the presence of single nucleotide polymorphisms as when compared to evaluating individual samples. This is important because pooling samples would allow important cuts in both technical and financial resources to process the samples.

Inclusion Criteria: Subject, male or female, is 5-14 years of age Subject is otherwise in an healthy condition (medical history and physical examination) Parent(s)/guardians of subjects (or their legally-accepted representatives) signed an informed consent document indicating that they understand the purpose of and procedures required for the study and are willing to have their child participate in the study. Subject of ≥6 years has assented (agreed) to participate in the study. Subject of ≥12 has signed an informed consent document indicating that they understand the purpose of and procedures required for the study and are willing to participate in the study. The subject swallowed the entire drug (ALB 400 mg) under supervision Subject provides a stool sample of at least 9 grams Exclusion Criteria: Subject has active diarrhea (defined as the passage of 3 or more loose or liquid stools per day) at baseline or follow-up Subject has any acute medical condition or is experiencing a severe concurrent medical condition Subject has a known hypersensitivity to benzimidazole drugs Subject has received an anthelminthic treatment within 90 of the start of the treatment. Subject vomited within 4 hours after drug administration Subject is unable to provide a stool sample at follow-up

De-identified results will be shared online and with collaborating researchers for further extensive analysis.

A general overview of the project is already published on our project website. The specific study protocol for work-package 1 of the project is currently being submitted for publication. Once final data is collected, De-identified data will be available through the project website as well. No specific time-frame will be applied.

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Vlaminck J, Cools P, Albonico M, Ame S, Ayana M, Bethony J, Cringoli G, Dana D, Keiser J, Maurelli MP, Montresor A, Mekonnen Z, Mirams G, Correa-Oliveira R, Prichard R, Rashwan N, Rinaldi L, Sayasone S, Thomas E, Verweij JJ, Vercruysse J, Levecke B. Comprehensive evaluation of stool-based diagnostic methods and benzimidazole resistance markers to assess drug efficacy and detect the emergence of anthelmintic resistance: A Starworms study protocol. PLoS Negl Trop Dis. 2018 Nov 2;12(11):e0006912. doi: 10.1371/journal.pntd.0006912. eCollection 2018 Nov.