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Background Soil-transmitted helminths (STHs) are parasitic nematodes that inhabit the human intestine. They affect more than 1.5 billion people worldwide, causing physical and cognitive impairment in children. The global strategy to control STH infection includes periodic mass drug administration (MDA) based on the results of diagnostic testing among populations at risk, but the current microscopy method for detecting infection has diminished sensitivity as the intensity of infection decreases. Thus, improved diagnostic tools are needed to support decision-making for STH control programs. Methodology We developed a nucleic acid amplification test based on recombinase polymerase amplification (RPA) technology to detect STH in stool. We designed primers and probes for each of the four STH species, optimized the assay, and then verified its performance using clinical stool samples. Principal findings Each RPA assay was as sensitive as a real-time polymerase chain reaction (PCR) assay in detecting copies of cloned target DNA sequences. The RPA assay amplified the target in DNA extracted from human stool samples that were positive for STH based on the Kato-Katz method, with no cross-reactivity of the non-target genomic DNA. When tested with clinical stool samples from patients with infections of light, moderate, and heavy intensity, the RPA assays demonstrated performance comparable to that of real-time PCR, with better results than Kato-Katz. This new rapid, sensitive and field-deployable method for detecting STH infections can help STH control programs achieve their goals. Conclusions Semi-quantitation of target by RPA assay is possible and is comparable to real-time PCR. With proper instrumentation, RPA assays can provide robust, semi-quantification of STH DNA targets as an alternative field-deployable indicator to counts of helminth eggs for assessing infection intensity., Author summary More than 1.5 billion people are infected with parasitic intestinal worms called soil-transmitted helminths. Infection is transmitted by helminth eggs in human feces, which contaminate soil in areas with poor sanitation. Adverse health effects include physical and cognitive impairment in children. A key strategy to control infection is periodic mass drug administration for populations with a high prevalence of disease based on the results of diagnostic testing. The current microscopy method for detecting infection, however, has limited ability to detect disease as the intensity of infection decreases with repeated mass drug administration. To address limitations of current diagnostic methods, we developed a novel technique to diagnose infections, including those at very low levels of intensity, by detecting helminth DNA in stool samples. Our initial studies suggest that the new diagnostic technique reliably detects the presence of intestinal worms, even at low intensities of infection, and may be more useful than currently available diagnostic tools for guiding the use of periodic mass drug administration to eliminate disease in low-resource settings.

Background Soil-transmitted helminths (STHs) comprise a group of helminth parasites that are included in the list of Neglected Tropical Diseases and require a passage through the soil to become infective. Several studies have detected that infection with STHs are associated with certain socioeconomic, environmental and soil characteristics. In Argentina, the presence of these parasites has been detected through a few point studies conducted in localities from 11 of the 23 provinces that comprise the country. Methods/Principal findings The most important characteristics previously associated with the presence of STHs were identified and ranked through the use of an expert survey and the Analytical Hierarchy Process (AHP) in order to construct a risk map of STHs specific for Argentina. Prevalence data from previous studies was used to validate the generated risk map. The map shows that half of Argentina, from the Central provinces to the North, contains localities with the characteristics necessary for the development of these parasites. Conclusions/Significance The predicted map should serve as a useful tool for guiding the identification of survey areas for the generation of baseline data, detecting hotspots of infection, planning and prioritizing areas for control interventions, and eventually performing post-implementation surveillance activities., Author summary Given the lack of information on the prevalence of soil-transmitted helminths (STH) in Argentina, the aim of this study was to generate a national risk map to guide the implementation of surveys to determine baseline data. For this purpose, factors most associated with the presence of STHs from previous studies conducted in other countries were ranked by experts in the field through the use of an Analytical Hierarchy Process. These characteristics were grouped into categories: socioeconomic, environmental and soil characteristics. The resulting map was validated against point prevalence studies conducted in the country and it showed that the top half of the country, from the Central provinces to the North, have localities with conditions appropriate for the development of these parasites.

The World Health Organization (WHO) has defined moderate-to-heavy intensity (M&HI) infections with soil-transmitted helminths (Ascaris lumbricoides, Trichuris trichiura and the two hookworms, Ancylostoma duodenale and Necator americanus) based on specific values of eggs per gram of stool, as measured by the Kato-Katz method. There are a variety of novel microscopy and DNA-based methods but it remains unclear whether applying current WHO thresholds on to these methods allows for a reliable classification of M&HI infections. We evaluated both WHO and method-specific thresholds for classifying the M&HI infections for novel microscopic (FECPAKG2, McMaster and Mini-FLOTAC) and DNA-based (qPCR) diagnostic methods. For this, we determined method-specific thresholds that best classified M&HI infections (defined by Kato-Katz and WHO thresholds; reference method) in two multi-country drug efficacy studies. Subsequently, we verified whether applying these method-specific thresholds improved the agreement in classifying M&HI infections compared to the reference method. When we applied the WHO thresholds, the new microscopic methods mainly misclassified M&HI as low intensity, and to a lesser extent low intensity infection as M&HI. For FECPAKG2, applying the method-specific thresholds significantly improved the agreement for Ascaris (moderate → substantial), Trichuris and hookworms (fair → moderate). For Mini-FLOTAC, a significantly improved agreement was observed for hookworms only (fair → moderate). For the other STHs, the agreement was almost perfect and remained unchanged. For McMaster, the method-specific thresholds revealed a fair to a substantial agreement but did not significantly improve the agreement. For qPCR, the method-specific thresholds based on genome equivalents per ml of DNA moderately agreed with the reference method for hookworm and Trichuris infections. For Ascaris, there was a substantial agreement. We defined method-specific thresholds that improved the classification of M&HI infections. Validation studies are required before they can be recommended for general use in assessing M&HI infections in programmatic settings., Author summary The prevalence of moderate-to-heavy intensity (M&HI) infections is a key indicator for measuring the success of large-scale deworming programs for intestinal worms because they account for the majority of the worm-attributable morbidity. Currently, intestinal worm infections are classified as M&HI when the number of worm eggs that are microscopically detected in stool using a standard diagnostic method exceeds a threshold set by the World Health Organization. Over the years, a variety of new promising diagnostic methods have been introduced for the diagnosis of intestinal worms. Although they have some important advantages over the current standard method, it is not clear whether they can reliably classify M&HI infections. This is because their test results either systematically indicate lower egg counts or are expressed in a unit other than eggs per gram of stool (e.g, concentration of worm DNA), warranting the need for method-specific thresholds. We defined method-specific thresholds and verified whether they increased the correct classification of M&HI infections. Overall, our results indicate that method-specific thresholds improved the classification of M&HI infections, but that further validation is required before they can be recommended for evaluating the occurrence M&HI infections in large-scale deworming programs.

Prevalence is a common epidemiological measure for assessing soil-transmitted helminth burden and forms the basis for much public-health decision-making. Standard diagnostic techniques are based on egg detection in stool samples through microscopy and these techniques are known to have poor sensitivity for individuals with low infection intensity, leading to poor sensitivity in low prevalence populations. PCR diagnostic techniques offer very high sensitivities even at low prevalence, but at a greater cost for each diagnostic test in terms of equipment needed and technician time and training. Pooling of samples can allow prevalence to be estimated while minimizing the number of tests performed. We develop a model of the relative cost of pooling to estimate prevalence, compared to the direct approach of testing all samples individually. Analysis shows how expected relative cost depends on both the underlying prevalence in the population and the size of the pools constructed. A critical prevalence level (approx. 31%) above which pooling is never cost effective, independent of pool size. When no prevalence information is available, there is no basis on which to choose between pooling and testing all samples individually. We recast our model of relative cost in a Bayesian framework in order to investigate how prior information about prevalence in a given population can be used to inform the decision to choose either pooling or full testing. Results suggest that if prevalence is below 10%, a relatively small exploratory prevalence survey (10–15 samples) can be sufficient to give a high degree of certainty that pooling may be relatively cost effective., Author summary Current diagnostic methods for assessing prevalence of soil-transmitted helminths (STHs) largely rely on microscopic visualization of helminth eggs, an inexpensive but insensitive method of detection. However, growing interest in going beyond control to break transmission of STH through mass drug administration will require highly sensitive assays to detect the low intensity infections that occur when prevalence is low within a population. Molecular tools, such as real-time PCR, offer the required sensitivity, but depend on well-equipped laboratories and adequately trained technicians. In addition, current assays are relatively expensive to perform at the scale required for surveys. Sample pooling is a technique that can be used to estimate prevalence from a set of samples, while potentially employing fewer tests for a given sample size, reducing cost. The decision in favour of or against pooling will determine how samples are collected, properly stored and analysed, and that needs to be established early in the study or program design process. Our work identifies the key determinants on which this decision should be made, what information is needed to make the choice and how the decision can be made.

Morbidity induced by infection with the major soil transmitted infections (STH—Ascaris lumbricoides, Trichuris trichiura, and hookworms) results in an estimated 5.19 million disability-adjusted life years (DALYs) [1]. The World Health Organization’s (WHO) policy for control centres on three groups, preschool aged children (pre-SAC), school-aged children (SAC), and women of child bearing age, on the basis that heavy infection in these groups will have a detrimental impact on anaemia, child growth, and development. The current WHO guidelines focus on school-aged children, both for monitoring infection and as a target for treatment, although treatment of pre-SAC and women of childbearing age is also recommended where sustainable delivery mechanisms exist, especially in areas of intense transmission [2,3]. The guidelines recommend treating SAC annually where any STH prevalence falls between 20% and 50% and twice a year where it exceeds 50% [3].\ud \ud The London Declaration on Neglected Tropical Diseases in 2012 endorsed WHO goals to scale up mass drug administration (MDA) for STH, so that by 2020, 75% of the pre-SAC and SAC in need will be treated regularly [4]. Building on an existing roadmap, WHO announced an intention to meet the target [2,5,6]. Progress has been good in some areas, but less so in others. In 2012, global coverage of those in need was 37% for SAC and 29% for pre-SAC [5]. Data for the more recent years is as yet to be published by WHO [5], but a huge gain in coverage is not expected, despite increased drug donations from the pharmaceutical companies who manufacture the main anthelmintics. This is due in part to the logistical challenges in getting even donated drugs to these populations, who are often beyond “the end of the road.” At present, many countries with endemic STH infections are not availing themselves of the freely donated drugs to treat children.\ud \ud We are still a long way from the 2020 target of 75%. Even if this target is reached, will it be enough to eliminate transmission and the disease arising from heavy infections with STH? If not, how should the guidelines be changed to push towards morbidity control, and ideally, the eventual elimination of transmission?

Lymphatic filariasis (LF) and soil-transmitted-helminths (STH) are co-endemic in 58 countries which are mostly in Africa and Asia. Worldwide, 486 million school-age children are considered at risk of both diseases. In 2000, the World Health Organization (WHO) established the global programme to eliminate LF by 2020. Since then, the LF elimination programme has distributed ivermectin or diethylcarbamazine citrate (DEC) in combination with albendazole, thereby also treating STH. Consequently, many school-age children have been treated for STH through the LF programme. As treatment targets towards the 2020 LF elimination goal are achieved, many countries are implementing the transmission assessment survey (TAS) and, if the LF prevalence is estimated to be less than 1%, scaling down mass drug administration (MDA). We analysed the 2014 data on preventive chemotherapy (PC) reported from LF STH co-endemic countries and projected the year and location of TAS expected to be conducted between 2016 and 2020 to assess the impact of this scaling down on STH PC. Eighty percent of all co-endemic countries that have already stopped LF MDA nationally were able to establish STH PC through schools. It is estimated that 14% of the total number of children presently covered by the LF programme is at risk of not continuing to receive PC for STH. In order to achieve and maintain the WHO 2020 goal for STH control, there is an urgent need to establish and reinforce school-based deworming programmes in countries scaling-down national LF elimination programmes., Author Summary Lymphatic filariasis (LF) and soil-transmitted helminths (STH) (i.e. intestinal worms) are two tropical diseases that are found together in 58 countries in the world. School-age children are most affected by intestinal worms, albendazole, one of the two drugs used for LF, also treats STH. For this reason, large-scale delivery of LF drugs in the community has been used as a means to also treat school-age children for intestinal worm infections in many countries. In line with the WHO goal to eliminate LF by 2020, countries that have achieved that objective have started stopping community-based LF treatment. Therefore, we analysed treatment data from 2014 to quantify the effect of this reduction on treatment of school-age children for intestinal worms. The results show that 80% of countries that have already stopped LF treatment were able to administer deworming drugs for STH to school-age children within school-based treatment programmes. There is an urgent need to continue to establish and strengthen deworming through school health programmes in endemic countries in order to meet the WHO established goal to treat at least 75% of at risk school-age children for STH by 2020.

Background Soil-transmitted helminths (STH) – a class of parasites that affect billions of people – can be mitigated using mass drug administration, though reinfection following treatment occurs within a few months. Improvements to water, sanitation and hygiene (WASH) likely provide sustained benefit, but few rigorous studies have evaluated the specific WASH components most influential in reducing infection. There is a need for alternative analytic approaches to help identify, characterize and further refine the WASH components that are most important to STH reinfection. Traditional epidemiological approaches are not well-suited for assessing the complex and highly correlated relationships commonly seen in WASH. Methodology We introduce two recursive partitioning approaches: classification and regression trees (C&RT) and conditional inference trees (CIT), which can be used to identify complex interactions between WASH indicators and identify sub-populations that may be susceptible to STH reinfection. We illustrate the advantages and disadvantages of these approaches utilizing school- and household-level WASH indicators gathered as part of a school-based randomized control trial in Kenya that measured STH reinfection of pupils 10 months following deworming treatment. Principal Findings C&RT and CIT analyses resulted in strikingly different decision trees. C&RT may be the preferred approach if interest lies in using WASH indicators to classify individuals or communities as STH infected or uninfected, whereas CIT is most appropriate for identifying WASH indicators that may be causally associated with STH infection. Both tools are well-suited for identifying complex interactions among WASH indicators. Conclusions/Significance C&RT and CIT are two analytic approaches that may offer valuable insight regarding the identification, selection and refinement of WASH indicators and their interactions with regards to STH control programs; however, they represent solutions to two distinct research questions and careful consideration should be made before deciding which approach is most appropriate., Author Summary Soil-transmitted helminths (STH) are pervasive enteric parasites that lead to cognitive, nutritional and educational sequelae. Mass drug administration is employed to reduce morbidity, but reinfection occurs rapidly in the absence of changes to other environmental conditions, such as improvements to water, sanitation and hygiene (WASH). Since WASH behaviors and conditions are highly interrelated, typical epidemiological methods are limited. Few rigorous studies have assessed the impact of WASH components as they complement deworming and even fewer have sought to prioritize among the available indicators or identify complex interactions. In this paper we introduce two recursive partitioning approaches: classification and regression trees (C&RT) and conditional inference trees (CIT). We demonstrate these two tools using data from a school-based cluster-randomized trial conducted in Kenya. We discuss the advantages and disadvantages of each tool and give examples of how they may be used to improve STH control programs.

Background Implementation of control of parasitic diseases requires accurate, contemporary maps that provide intervention recommendations at policy-relevant spatial scales. To guide control of soil transmitted helminths (STHs), maps are required of the combined prevalence of infection, indicating where this prevalence exceeds an intervention threshold of 20%. Here we present a new approach for mapping the observed prevalence of STHs, using the example of Kenya in 2009. Methods and Findings Observed prevalence data for hookworm, Ascaris lumbricoides and Trichuris trichiura were assembled for 106,370 individuals from 945 cross-sectional surveys undertaken between 1974 and 2009. Ecological and climatic covariates were extracted from high-resolution satellite data and matched to survey locations. Bayesian space-time geostatistical models were developed for each species, and were used to interpolate the probability that infection prevalence exceeded the 20% threshold across the country for both 1989 and 2009. Maps for each species were integrated to estimate combined STH prevalence using the law of total probability and incorporating a correction factor to adjust for associations between species. Population census data were combined with risk models and projected to estimate the population at risk and requiring treatment in 2009. In most areas for 2009, there was high certainty that endemicity was below the 20% threshold, with areas of endemicity ≥20% located around the shores of Lake Victoria and on the coast. Comparison of the predicted distributions for 1989 and 2009 show how observed STH prevalence has gradually decreased over time. The model estimated that a total of 2.8 million school-age children live in districts which warrant mass treatment. Conclusions Bayesian space-time geostatistical models can be used to reliably estimate the combined observed prevalence of STH and suggest that a quarter of Kenya's school-aged children live in areas of high prevalence and warrant mass treatment. As control is successful in reducing infection levels, updated models can be used to refine decision making in helminth control., Author Summary Effective targeting of mass drug administration for the treatment of soil-transmitted helminths (STH) requires reliable, up-to-date maps that indicate where prevalence exceeds the 20% intervention threshold recommended by the World Health Organization. We present a new approach for mapping the prevalence of STH in Kenya, incorporating observed prevalence data from 945 cross-sectional surveys undertaken between 1974 and 2009. The distribution of each species was modelled using model-based geostatistics; models included information on environmental factors, the spatial distribution of existing surveys and when these surveys were conducted. Resulting risk maps were combined and linked with population data enabling estimation of the population at risk of any STH infection and requiring treatment in 2009. In most areas, there was high certainty that combined STH prevalence was below the 20% intervention threshold, with areas of high prevalence located around the shores of Lake Victoria and on the coast. Results also suggest that observed prevalence decreased over time and emphasise the importance of continued surveillance in areas where observed prevalence was historically high. We show how spatial modelling can be used to develop up-to-date maps of STH risk to help improve the precision of decision making in disease control.

Background In 2004 Niger established a large scale schistosomiasis and soil-transmitted helminths control programme targeting children aged 5–14 years and adults. In two years 4.3 million treatments were delivered in 40 districts using school based and community distribution. Method and Findings Four districts were surveyed in 2006 to estimate the economic cost per district, per treatment and per schistosomiasis infection averted. The study compares the costs of treatment at start up and in a subsequent year, identifies the allocation of costs by activity, input and organisation, and assesses the cost of treatment. The cost of delivery provided by teachers is compared to cost of delivery by community distributers (CDD). The total economic cost of the programme including programmatic, national and local government costs and international support in four study districts, over two years, was US$ 456,718; an economic cost/treatment of $0.58. The full economic delivery cost of school based treatment in 2005/06 was $0.76, and for community distribution was $0.46. Including only the programme costs the figures are $0.47 and $0.41 respectively. Differences at sub-district are more marked. This is partly explained by the fact that a CDD treats 5.8 people for every one treated in school. The range in cost effectiveness for both direct and direct and indirect treatments is quantified and the need to develop and refine such estimates is emphasised. Conclusions The relative cost effectiveness of school and community delivery differs by country according to the composition of the population treated, the numbers targeted and treated at school and in the community, the cost and frequency of training teachers and CDDs. Options analysis of technical and implementation alternatives including a financial analysis should form part of the programme design process., Author Summary Schistosomiasis and soil-transmitted helminth control programmes are important, relatively low cost means to improve the health of those affected, in particular rural school age children. It can also reduce schistosomiasis related morbidity in their later lives. The paper presents information on the implementation and costs of a large scale national programme in Niger. The total economic cost per treatment was $0.58. This includes programme, government and international costs. Two systems, school based and community delivery were used to treat children and targeted adults. Contrary to findings in some countries we find that school based delivery is less cost effective than community delivery. This is due to the low proportion of the population targeted and treated by the school based system. Treating adults as well as children increased the numbers treated and reduced the overall cost per treatment. Prevalence and infection is higher in children than adults and overall effectiveness in terms of infection averted is affected. The cost per infection averted is assessed for direct treatment and direct and indirect treatment effects. The study expands the evidence available for decision makers involved in programme planning and design, funding and implementation.

Background Standard diagnosis of human soil-transmitted helminth (STH) infections is based on the microscopic detection of helminth eggs in stool and supports programmatic decision making in control programs. However, the current standard diagnostic techniques still show a number of limitations. Recently, the FECPAKG2 method was developed to detect helminth infections and asses drug efficacy in sheep or cattle. It includes a device that takes digital images of helminth eggs that have been concentrated into one microscopic field of view and stores these images online for future evaluation. The goal of this study was to introduce a standard operating procedure (SOP) for the detection and quantification of human STH eggs using the FECPAKG2 and to optimize 2 crucial steps of the protocol, namely the sedimentation step (aimed at separating sinking eggs from floating debris) and the accumulation step (aimed at concentrating the eggs by flotation). Methodology/Principal findings A total of 55 stool samples from naturally infected children were used from 4 different geographical areas (Ethiopia, Laos, Tanzania and Brazil). The results showed that Trichuris eggs generally moved slower than eggs of the other two STH species during both sedimentation in water in the FECPAKG2 sedimenter as during accumulation in flotation solution in the FECPAKG2 cassettes. The highest number of eggs were present in the slurry of the sedimenter after overnight sedimentation (Ascaris: 95.7%, Trichuris: 89.8% and hookworm: 94.2% of the eggs). A minimum of 24 minutes were needed to ensure the accumulation of at least 80% of the eggs from all three STH species in the FECPAKG2 cassette (Ascaris: 96.1%; Trichuris: 88.2% and hookworm: 87.6%). Conclusions/Significance This study introduces for the first time a SOP for the FECPAKG2 method. Different aspects of the method for diagnosing human STH infections were optimized. Our study forms the basis for a thorough and objective evaluation of the system as a diagnostic tool that could be implemented in STH control programs.