Linked surveillance and genetic data uncovers programmatically relevant geographic scale of Guinea worm transmission in Chad

Background

Guinea worm (Dracunculus medinensis) was detected in Chad in 2010 after a supposed ten-year absence, posing a challenge to the global eradication effort. Initiation of a village-based surveillance system in 2012 revealed a substantial number of dogs infected with Guinea worm, raising questions about paratenic hosts and cross-species transmission.

Methodology/principal findings

We coupled genomic and surveillance case data from 2012-2018 to investigate the modes of transmission between dog and human hosts and the geographic connectivity of worms. Eighty-six variants across four genes in the mitochondrial genome identified 41 genetically distinct worm genotypes. Spatiotemporal modeling revealed worms with the same genotype (‘genetically identical’) were within a median range of 18.6 kilometers of each other, but largely within approximately 50 kilometers. Genetically identical worms varied in their degree of spatial clustering, suggesting there may be different factors that favor or constrain transmission. Each worm was surrounded by five to ten genetically distinct worms within a 50 kilometer radius. As expected, we observed a change in the genetic similarity distribution between pairs of worms using variants across the complete mitochondrial genome in an independent population.

Conclusions/significance

In the largest study linking genetic and surveillance data to date of Guinea worm cases in Chad, we show genetic identity and modeling can facilitate the understanding of local transmission. The co-occurrence of genetically non-identical worms in quantitatively identified transmission ranges highlights the necessity for genomic tools to link cases. The improved discrimination between pairs of worms from variants identified across the complete mitochondrial genome suggests that expanding the number of genomic markers could link cases at a finer scale. These results suggest that scaling up genomic surveillance for Guinea worm may provide additional value for programmatic decision-making critical for monitoring cases and intervention efficacy to achieve elimination.

The global eradication effort for Guinea worm disease has dramatically decreased the global burden of the disease and enabled 187 countries to be certified by the World Health Organization to be free of endemic transmission. Despite this progress, several countries continue to have endemic transmission. In Chad, a long absence of reported cases was interrupted with the identification of new Guinea worm cases, prompting a substantial scale up of surveillance and intervention efforts. Here, we study the value of increasing genomic surveillance as a tool for programmatic evaluation of surveillance and intervention efforts in Chad. Linking surveillance and genomic samples, parsimonious spatial models help reveal a consistent geographic clustering of similar genetic sequences across Chad. We also demonstrate that expanding the sequencing can offer better resolution for distinguishing Guinea worm samples. In this retrospective study, we found evidence that scaling up genomic surveillance can be an important monitoring and evaluation tool for the eradication program in Chad.

Spatial and temporal dynamics of space use by free-ranging domestic dogs Canis familiaris in rural Africa

Variation in the spatial ecology of animals influences the transmission of infections and so understanding host behavior can improve the control of diseases. Despite the global distribution of free-ranging domestic dogs Canis familiaris and their role as reservoirs for zoonotic diseases, little is known about the dynamics of their space use. We deployed GPS loggers on owned but free-ranging dogs from six villages in rural Chad, and tracked the movements of 174 individuals in the dry season and 151 in the wet season. We calculated 95% and core home ranges using auto-correlated kernel density estimates (AKDE₉₅ and AKDE_core ), determined the degree to which their movements were predictable, and identified correlates of movement patterns. The median AKDE₉₅ range in the dry season was 0.54 km² and in the wet season was 0.31 km² , while the median AKDE_core range in the dry season was 0.08 km² and in the wet season was 0.04 km² . Seasonal variation was, in part, related to owner activities; dogs from hunting households had ranges that were five times larger in the dry season. At least 70% of individuals were more predictably "at home" (<50 m from the household) throughout the day in the dry season, 80% of dogs demonstrated periodicity in activity levels (speed), and just over half the dogs exhibited periodicity in location (repeated space use). In the wet season, dogs mostly exhibited 24-h cycles in activity and location, with peaks at midday. In the dry season, dogs exhibited both 12- and 24-h cycles, with either a single peak at midday, or one peak between 06:00 and 12:00 and a second between 18:00 and 22:00. Strategies to control canine-mediated zoonoses can be improved by tailoring operations to the local spatial ecology of free-ranging dogs. Interventions using a door-to-door strategy in rural Chad would best conduct operations during the dry season, when access to dogs around their household more reliably exceeds 70% throughout the day. Given the importance of use in hunting for explaining variation in dog space-use, targeting approaches to disease control at the household level on the basis of owner activities offers potential to improve access to dogs.

Community-based Guinea worm surveillance in Chad: Evaluating a system at the intersection of human and animal disease

Background

Guinea worm is a debilitating parasitic infection targeted for eradication. Annual human cases have dropped from approximately 3,500,000 in 1986 to 54 in 2019. Recent identification of canine cases in Chad threatens progress, and therefore detection, prevention, and containment of canine cases is a priority. We investigated associations between disease knowledge, community engagement, and canine cases in Chad to identify opportunities to improve active surveillance.

Methods

We surveyed 627 respondents (villagers, local leaders, community volunteers, and supervisors) across 45 villages under active surveillance. Descriptive statistics were analyzed by respondent category. Logistic regression models were fitted to assess the effects of volunteer visit frequency on villager knowledge.

Results

Knowledge increased with respondents’ associations with the Guinea worm program. Household visit frequency by community volunteers was uneven: 53.0% of villagers reported visits at least twice weekly and 21.4% of villagers reported never being visited. Villagers visited by a volunteer at least twice weekly had better knowledge of Guinea worm symptoms (OR: 1.71; 95% CI: 1.04–2.79) and could name more prevention strategies (OR: 2.04; 95% CI: 1.32–3.15) than villagers visited less frequently. The primary motivation to report was to facilitate care-seeking for people with Guinea worm. Knowledge of animal “containment” to prevent contamination of water, knowledge of rewards for reporting animal cases, and ability to name any reasons to report Guinea worm were each positively correlated with village canine case counts.

Conclusions

Community volunteers play crucial roles in educating their neighbors about Guinea worm and facilitating surveillance. Additional training and more attentive management of volunteers and supervisors could increase visit frequency and further amplify their impact. Emphasizing links between animal and human cases, the importance of animal containment, and animal rewards might improve surveillance and canine case detection. The surveillance system should be evaluated routinely to expand generalizability of data and monitor changes over time.

Guinea worm eradication depends on detecting people and animals with the disease in order to prevent transmission. The situation in Chad is especially urgent because the number of domestic dogs with Guinea worm has been rapidly increasing in the past five years, and now represents the vast majority of Guinea worm cases globally. The global Guinea Worm Eradication Program, the Chad Guinea Worm Eradication Program, and the Chad Ministry of Public Health requested an investigation to evaluate the associations between Guinea worm knowledge, community engagement, and case detection and to investigate how the active surveillance system could be improved to more effectively detect and contain every Guinea worm case. We surveyed 627 people across 45 villages in Chad. We found that Chad’s system for monitoring Guinea worm operates unevenly, with some villagers receiving frequent visits by community volunteers and other villagers reporting never being visited. Villagers visited by a community volunteer at least twice per week had much better knowledge of Guinea worm symptoms and prevention, compared with villagers visited less frequently. Community volunteers are instrumental to Guinea worm eradication efforts in Chad because they transmit key educational messages that facilitate disease detection. More efforts should be made to increase volunteer accountability and to provide volunteers and their supervisors with targeted, high quality training.

Ecology of domestic dogs Canis familiaris as an emerging reservoir of Guinea worm Dracunculus medinensis infection

Global eradication of human Guinea worm disease (dracunculiasis) has been set back by the emergence of infections in animals, particularly domestic dogs Canis familiaris. The ecology and epidemiology of this reservoir is unknown. We tracked dogs using GPS, inferred diets using stable isotope analysis and analysed correlates of infection in Chad, where numbers of Guinea worm infections are greatest. Dogs had small ranges that varied markedly among villages. Diets consisted largely of human staples and human faeces. A minority of ponds, mostly <200 m from dog-owning households, accounted for most dog exposure to potentially unsafe water. The risk of a dog having had Guinea worm was reduced in dogs living in households providing water for animals but increased with increasing fish consumption by dogs. Provision of safe water might reduce dog exposure to unsafe water, while prioritisation of proactive temephos (Abate) application to the small number of ponds to which dogs have most access is recommended. Fish might have an additional role as transport hosts for Guinea worm, by concentrating copepods infected with worm larvae.

Guinea worm is a parasite that causes profoundly debilitating disease in humans. An eradication program has been successful in nearly eliminating the disease from people. However, the same worm has now been found in domestic dogs and the frequency of detecting Guinea worm in dogs has been increasing. This means that to eradicate Guinea worm, the infection must be eliminated in dogs as well as in people. However, not much is known about the disease in dogs. This study is the first to investigate dog ecology in relation to Guinea worm infection. We worked in the worst-affected country, Chad. We attached GPS collars to dogs to track their ranging and use of water bodies and analysed their diets using a forensic technique, based on analysing stable isotope compostion of their whiskers and potential food items. We showed that dogs living in households that provided water to their animals had a lower risk of having had Guinea worm and that dogs that ate more fish had an increased risk. These findings suggest there is a classical route for worm transmission in dogs, via drinking contaminated water, as well as a novel route, potentially by eating fish carrying a source of infection.

Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing

Whole-genome sequencing is being rapidly applied to the study of helminth genomes, including de novo genome assembly, population genetics, and diagnostic applications. Although late-stage juvenile and adult parasites typically produce sufficient DNA for molecular analyses, these parasitic stages are almost always inaccessible in the live host; immature life stages found in the environment for which samples can be collected non-invasively offer a potential alternative; however, these samples typically yield very low quantities of DNA, can be environmentally resistant, and are susceptible to contamination, often from bacterial or host DNA. Here, we have tested five low-input DNA extraction protocols together with a low-input sequencing library protocol to assess the feasibility of whole-genome sequencing of individual immature helminth samples. These approaches do not use whole-genome amplification, a common but costly approach to increase the yield of low-input samples. We first tested individual parasites from two species spotted onto FTA cards-egg and L1 stages of Haemonchus contortus and miracidia of Schistosoma mansoni-before further testing on an additional five species-Ancylostoma caninum, Ascaridia dissimilis, Dirofilaria immitis, Strongyloides stercoralis, and Trichuris muris-with an optimal protocol. A sixth species-Dracunculus medinensis-was included for comparison. Whole-genome sequencing followed by analyses to determine the proportion of on- and off-target mapping revealed successful sample preparations for six of the eight species tested with variation both between species and between different life stages from some species described. These results demonstrate the feasibility of whole-genome sequencing of individual parasites, and highlight a new avenue toward generating sensitive, specific, and information-rich data for the diagnosis and surveillance of helminths.

High-resolution contact networks of free-ranging domestic dogs Canis familiaris and implications for transmission of infection

Contact patterns strongly influence the dynamics of disease transmission in both human and non-human animal populations. Domestic dogs Canis familiaris are a social species and are a reservoir for several zoonotic infections, yet few studies have empirically determined contact patterns within dog populations. Using high-resolution proximity logging technology, we characterised the contact networks of free-ranging domestic dogs from two settlements (n = 108 dogs, covering >80% of the population in each settlement) in rural Chad. We used these data to simulate the transmission of an infection comparable to rabies and investigated the effects of including observed contact heterogeneities on epidemic outcomes. We found that dog contact networks displayed considerable heterogeneity, particularly in the duration of contacts and that the network had communities that were highly correlated with household membership. Simulations using observed contact networks had smaller epidemic sizes than those that assumed random mixing, demonstrating the unsuitability of homogenous mixing models in predicting epidemic outcomes. When contact heterogeneities were included in simulations, the network position of the individual initially infected had an important effect on epidemic outcomes. The risk of an epidemic occurring was best predicted by the initially infected individual's ranked degree, while epidemic size was best predicted by the individual's ranked eigenvector centrality. For dogs in one settlement, we found that ranked eigenvector centrality was correlated with range size. Our results demonstrate that observed heterogeneities in contacts are important for the prediction of epidemiological outcomes in free-ranging domestic dogs. We show that individuals presenting a higher risk for disease transmission can be identified by their network position and provide evidence that observable traits hold potential for informing targeted disease management strategies.

A search for tiny dragons (Dracunculus medinensis third-stage larvae) in aquatic animals in Chad, Africa

Dracunculus medinensis, or human Guinea worm (GW), causes a painful and debilitating infection. The global Guinea Worm Eradication Program (GWEP) has successfully reduced human GW cases from 3.5 million in 21 countries in 1986 to only 30 cases in three remaining countries in 2017. Since 2012, an increase in GW infections in domestic dogs, cats and baboons has been reported. Because these infections have not followed classical GW epidemiological patterns resulting from water-borne transmission, it has been hypothesized that transmission occurs via a paratenic host. Thus, we investigated the potential of aquatic animals to serve as paratenic hosts for D. medinensis in Chad, Africa. During three rainy and two dry season trips we detected no GW larvae in 234 fish, two reptiles and two turtles; however, seven GW larvae were recovered from 4 (1.4%) of 276 adult frogs. These data suggest GW infections may occur from ingestion of frogs but the importance of this route is unknown. Additional studies are needed, especially for other possible routes (e.g., ingestion of fish intestines that were recently shown to be a risk). Significantly, 150 years after the life cycle of D. medinensis was described, our data highlights important gaps in the knowledge of GW ecology.