Soil-transmitted helminths (STH) including the hookworms Necator americanus and Ancylostoma spp., Ascaris lumbricoides, and Trichuris trichiura affect over 1.5 billion people worldwide and are estimated to have caused 1.9 million disability-adjusted life years (DALYs). With the concerted effort in expanding and improving targeted mass drug administration (MDA) programs over the past decade, along with decreasing prevalence, infections in several endemic areas tend to be of low intensity. Conventional microscopy-based methods recommended for the detection of STH in parasitological surveys have been shown to be less sensitive in these low-intensity settings. As communities progress towards STH elimination through MDA and improved sanitation, there is a pressing need for highly sensitive techniques that detect the true prevalence of STH to evaluate the effectiveness of ongoing programs and interventions. Molecular methods that involve analysis of DNA rather than the morphology of the organism are highly sensitive and specific, allowing for both quantitation and species discrimination. The following review discusses different sample collection strategies, pre-processing steps, DNA extraction platforms, and nucleic acid detection methods available for diagnosis and surveillance of STH. We have contrasted the utility of these molecular tools against conventional microscopy-based methods currently used in most endemic settings. While the detection methods are primarily qPCR based, several newer technologies have also become available along with automation and increased throughput, making these molecular tools increasingly cost-effective and potentially amenable for use in low-resource settings.

The high burden of soil-transmitted helminth infections has been studied in India; however, little data exist on zoonotic helminths, and on animal-associated exposure to soil-transmitted helminths. Our study took place in the Jawadhu Hills, which is a tribal region in Tamil Nadu, India. Using a One Health approach, we included animal and environmental samples and human risk factors to answer questions about the associations among infected household soil, domestic animals, and human risk factors. Helminth eggs were identified by microscopy in animal and soil samples, and a survey about risk factors was administered to the head of the household. Contact with animals was reported in 71% of households. High levels of helminth infections were found across domestic animal species, especially in goats, chickens, and dogs. Helminth eggs were recorded in 44% of household soil (n = 43/97) and separately in 88% of soil near a water source (n = 28/32). Animal contact was associated with 4.05 higher odds of having helminth eggs in the household soil (P = 0.01), and also having a water source at the household was associated with a 0.33 lower odds of having helminth eggs in the household soil (P = 0.04). Soil moisture was a mediator of this association with a significant indirect effect (P < 0.001). The proportion mediated was 0.50. While our work does not examine transmission, these results support consideration of animal-associated exposure to STH and potentially zoonotic helminths in future interventions to reduce helminth burden. Our study provides support for further investigation of the effects of animals and animal fecal matter on human health.

One-fifth of the global population is infected with soil-transmitted helminths (STH). Mass drug administration (MDA) with deworming medication is widely implemented to control morbidity associated with STH infections. However, surveillance of human infection prevalence by collecting individual stool samples is time-consuming, costly, often stigmatized, and logistically challenging. Current methods of STH detection are poorly sensitive, particularly in low-intensity and low-prevalence populations. Here, we developed a sensitive and specific molecular method for detecting STH DNA in large volumes of soil by conducting laboratory and proof of concept studies across field sites in Kenya, Benin, and India. We collected human stool (n=669) and soil (n= 478) from 322 households across the three study sites. The overall prevalence of STH in soil was 31% for Ascaris lumbricoides , 3% for T. trichuris , and 24% for any hookworm species. Detection of an STH species in household soil was strongly associated with increased odds of a household member being infected with that species. Soil surveillance for STH has several benefits over stool-based surveillance, including lower cost and higher success rates for sample collection. Considering that delivery of MDA occurs at the community level, environmental surveillance using molecular methods could be a cost-effective alternate strategy for monitoring STH in these populations. Synopsis: Limited data exists on the prevalence and reliability of environmental soil-transmitted helminth (STH) DNA as a marker of human infections in endemic populations. We developed a new molecular detection method for STH DNA in large-volume soil samples and field-tested it across three countries.

: Soil-transmitted helminths (STHs) remain a major public health concern, especially in low- and middle-income countries. Although Ascaris lumbricoides , Trichuris trichiura , and hookworms ( Ancylostoma duodenale and Necator americanus ) are commonly identified in humans, emerging evidence using molecular diagnostics capable of differentiating morphologically similar ova suggests zoonotic drivers of transmission, particularly in areas with close human–animal interaction. This pilot study investigated human and animal STH infections across nine villages of Meghalaya in the northeastern region of India, using quantitative polymerase chain reaction with species-specific primers. The estimated STH prevalence was 23.3% (95% CI: 17.9–29.9%). Zoonotic potential was evident, with Ancylostoma ceylanicum detected in humans (2.8%), and Ascaris spp. and Necator americanus detected in pigs (64.5% and 3.2%, respectively) and goats (15.2% and 3.0%, respectively). To meet World Health Organization’s target of eliminating STH morbidity by 2030, endemic regions may need to adopt an integrated One Health approach.

Leishmaniasis is endemic in the Indian subcontinent with predominance of visceral leishmaniasis (VL) due to Leishmania donovani. Cutaneous leishmaniasis (CL) is uncommon, and mucocutaneous leishmaniasis (MCL) is rarely reported in this region. Recent reports reveal a changing epidemiology and atypical manifestations. A retrospective study of 52 suspected cases with cutaneous and mucosal involvement seen from January 2008 to December 2018 in a tertiary care setting in a non-endemic state in southern India is reported. Twelve patients were confirmed to have leishmaniasis; seven had MCL, two had CL, and three had post-kala-azar dermal leishmaniasis (PKDL). All cases were male, with a median age of 41.5 years (interquartile range, 30–55.5 years), and the median duration of the disease was 6 years (interquartile range, 1–9.5 years). Patients with MCL had mucosal involvement including destructive ulcero-proliferative lesions due to delayed diagnosis; none had a history of travel to countries endemic for MCL and all were attributable to L. donovani species. On the other hand, Leishmania major which was the causative species in both CL patients was associated with travel to the Middle East. Patients with PKDL presented with multiple plaques and hypopigmented patches; one had concomitant VL and all were from endemic areas. Hitherto uncommon MCL, caused by potentially atypical variants of L. donovani, has emerged as a new manifestation of leishmaniasis in this region. A high index of suspicion based on lesions seen and history of travel combined with PCR-based diagnostics are required to confirm diagnosis for the various skin manifestations of leishmaniasis.

Amoebic liver abscess (ALA) is the most common extra-intestinal complication of Entamoeba histolytica, accounting for 50,000 deaths annually, and is endemic in South Asia. Diagnosis based on microscopic examination is insensitive, and serological assays are not discerning of current infections in endemic settings with high exposure. For a rapid and confirmatory laboratory diagnosis of ALA, the performance of a polymerase chain reaction (PCR), quantitative real time PCR (qPCR), digital droplet PCR (ddPCR), and a loop-mediated isothermal amplification (LAMP) assay that detects E. histolytica DNA in liver abscess pus, and a lectin antigen detection ELISA were evaluated against clinical diagnosis (based on predefined criteria) as the gold standard. Owing to the lack of a laboratory gold standard, a Bayesian latent class analysis approach was also used to determine sensitivity and specificity of these assays. In the latent class analysis, qPCR and ddPCR showed the highest sensitivity (98% and 98.1%) and specificity (both 96.6%), and although clinical diagnosis had a comparable sensitivity to qPCR and ddPCR (95.2%), poorer specificity (64.3%) was seen. Kappa agreement analysis showed that qPCR and ddPCR had a perfect agreement of 1 followed by an agreement of 0.76 (95% CI: 0.64–0.88) with PCR. Considering the performance characteristics and relative ease of setting up qPCR as well as the wide availability of qPCR equipment needed, this would be the most optimal assay for rapid, confirmatory, molecular diagnosis of ALA in the tertiary care laboratory setting in India, whereas further optimization of LAMP or antibody-based detection is required for use at smaller or secondary hospitals.