Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

Prevalence of onchocerciasis and associated clinical manifestations in selected hypoendemic communities in Ghana following long-term administration of ivermectin

Background

Onchocerciasis is a neglected tropical disease which is still of immense major public health concern in several areas of Africa and the Americas. The disease manifests either as ocular or as dermal onchocerciasis with several symptoms including itching, nodules, skin thickening, visual impairment and blindness. Ivermectin has been an efficient microfilaricide against the causative agent of the disease (Onchocerca volvulus) but reports from some areas in Africa suggest the development of resistance to this drug. The aim of this study was to determine the prevalence of onchocerciasis and associated clinical conditions frequently associated with the disease in three endemic communities in Ghana which have been subjected to 18 to 20 rounds of mass drug administration of ivermectin. This was to help determine whether or not onchocerciasis persists in these communities.

Methods

A cross-sectional study design was adopted. Three communities (Tanfiano, Senya and Kokompe) in the Nkoranza North District of Ghana where mass drug administration of ivermectin had been ongoing for more than two decades were selected for the study. The population was randomly sampled and 114 participants recruited for the study based on the eligibility criteria. The study participants were examined for the presence of parasites and clinical manifestations of onchocerciasis following established protocols.

Results

The study showed that the prevalence of microfilaria in the Tanfiano, Senya, Kokompe communities were 13.2, 2.4, and 2.9%, with nodule prevalence being 5.3, 4.9 and 14.3% respectively. Females in the study communities had a higher prevalence of microfilaria carriers (5.17%) relative to males (2.44%), but this difference was not statistically significant (p = 0.2800, unpaired t test). The most frequent clinical manifestation observed in this study among all participants was dermatitis (25.4%), followed by visual impairment & nodules (7.9% each) and then by blindness (4.4%).

Conclusion

The study showed that despite several years of mass drug administration with ivermectin, infection with onchocerciasis and the commonly associated clinical manifestations of the disease still persist in the study communities. This calls for a greater urgency for research and development aimed at discovering new or repurposed anti-filarial agents which will augment ivermectin if global onchocerciasis eradication targets are to be achieved.

Ivermectin: From theory to clinical application

Approximately 250 million people have been using ivermectin (IVM) annually to combat many parasitic diseases including filariasis, onchocerciasis, strongyloidiasis, scabies and pediculosis. Many clinical studies have proven its efficacy against these diseases and have reported the optimum dose and duration of treatment. Moreover, its antiparasitic range has increased to cover more parasitic infections, but it still requires further exploration, e.g. for trichinosis and myiasis. Furthermore, IVM showed high efficacy in killing vectors of disease-causing parasites such as mosquitoes, sandflies and tsetse flies. The World Health Organization (WHO) has managed many control programmes involving the use of IVM to achieve elimination of onchocerciasis and lymphatic filariasis and to reduce malaria transmission. However, IVM is not exempt from the possibility of resistance and, certainly, its intensive use has led to the emergence of resistance in some parasites. Recent research is investigating the possibility of novel drug delivery systems for IVM that increase its potential to treat a new range of diseases and to overcome the possibility of drug resistance. This review highlights the most common human uses of IVM, with special reference to the new and promising properties of IVM.

Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus

BACKGROUND

Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use of anthelmintics has driven the evolution of resistance in a number of species that infect livestock and companion animals, and there are growing concerns regarding the reduced efficacy in some human-infective helminths. Understanding the mechanisms by which resistance evolves is the focus of increasing interest; robust genetic analysis of helminths is challenging, and although many candidate genes have been proposed, the genetic basis of resistance remains poorly resolved.

RESULTS

Here, we present a genome-wide analysis of two genetic crosses between ivermectin resistant and sensitive isolates of the parasitic nematode Haemonchus contortus, an economically important gastrointestinal parasite of small ruminants and a model for anthelmintic research. Whole genome sequencing of parental populations, and key stages throughout the crosses, identified extensive genomic diversity that differentiates populations, but after backcrossing and selection, a single genomic quantitative trait locus (QTL) localised on chromosome V was revealed to be associated with ivermectin resistance. This QTL was common between the two geographically and genetically divergent resistant populations and did not include any leading candidate genes, suggestive of a previously uncharacterised mechanism and/or driver of resistance. Despite limited resolution due to low recombination in this region, population genetic analyses and novel evolutionary models supported strong selection at this QTL, driven by at least partial dominance of the resistant allele, and that large resistance-associated haplotype blocks were enriched in response to selection.

CONCLUSIONS

We have described the genetic architecture and mode of ivermectin selection, revealing a major genomic locus associated with ivermectin resistance, the most conclusive evidence to date in any parasitic nematode. This study highlights a novel genome-wide approach to the analysis of a genetic cross in non-model organisms with extreme genetic diversity, and the importance of a high-quality reference genome in interpreting the signals of selection so identified.

Development of Onchocerca volvulus in humanized NSG mice and detection of parasite biomarkers in urine and serum

BACKGROUND

The study of Onchocerca volvulus has been limited by its host range, with only humans and non-human primates shown to be susceptible to the full life cycle infection. Small animal models that support the development of adult parasites have not been identified.

METHODOLOGY/PRINCIPAL FINDINGS

We hypothesized that highly immunodeficient NSG mice would support the survival and maturation of O. volvulus and alteration of the host microenvironment through the addition of various human cells and tissues would further enhance the level of parasite maturation. NSG mice were humanized with: (1) umbilical cord derived CD34+ stem cells, (2) fetal derived liver, thymus and CD34+ stem cells or (3) primary human skeletal muscle cells. NSG and humanized NSG mice were infected with 100 O. volvulus infective larvae (L3) for 4 to 12 weeks. When necropsies of infected animals were performed, it was observed that parasites survived and developed throughout the infection time course. In each of the different humanized mouse models, worms matured from L3 to advanced fourth stage larvae, with both male and female organ development. In addition, worms increased in length by up to 4-fold. Serum and urine, collected from humanized mice for identification of potential biomarkers of infection, allowed for the identification of 10 O. volvulus-derived proteins found specifically in either the urine or the serum of the humanized O. volvulus-infected NSG mice.

CONCLUSIONS/SIGNIFICANCE

The newly identified mouse models for onchocerciasis will enable the development of O. volvulus specific biomarkers, screening for new therapeutic approaches and potentially studying the human immune response to infection with O. volvulus.

Clinical validation of molecular markers of macrocyclic lactone resistance in Dirofilaria immitis

Prophylaxis with macrocyclic lactone (ML) endectocides is the primary strategy for heartworm control. Recent evidence has confirmed that ML-resistant Dirofilaria immitis isolates have evolved. Comparison of genomes of ML-resistant isolates show they are genetically distinct from wild-type populations. Previously, we identified single nucleotide polymorphisms (SNPs) that are correlated with phenotypic ML resistance. Since reliable in vitro assays are not available to detect ML resistance in L3 or microfilarial stages, the failure to reduce microfilaraemia in infected dogs treated with an ML has been proposed as a surrogate clinical assay for this purpose. The goal of our study was to validate the genotype-phenotype correlation between SNPs associated with ML resistance and failure to reduce microfilaraemia following ML treatment and to identify a minimal number of SNPs that could be used to confirm ML resistance. In this study, 29 participating veterinary clinics received a total of 148 kits containing supplies for blood collection, dosing and prepaid shipping. Patients recruited after a diagnosis of heartworm infection were treated with a single standard dose of Advantage Multi® and a blood sample taken pre- and approximately 2-4 weeks post-treatment. Each sample was processed by performing a modified Knott's Test followed by isolation of microfilariae, genomic DNA extraction and MiSeq sequencing of regions encompassing 10 SNP sites highly correlated with ML resistance. We observed significant correlation of SNP loci frequencies with the ML microfilaricidal response phenotype. Although all predictive SNP combination models performed well, a 2-SNP model was superior to other models tested. The predictive ability of these markers for ML-resistant heartworms should be further evaluated in clinical and epidemiological contexts.

Post-traumatic endophthalmitis prophylaxis with oral ciprofloxacin in comparison to intravenous cephazolin/gentamicin

BACKGROUND

Although posttraumatic endophthalmitis is an uncommon condition, it causes severe complications, so medical and pharmacological interventions for prevention of endophthalmitis after trauma are a major concern. The aim of this study was to evaluate the efficacy and clinical outcome of oral ciprofloxacin versus intravenous cefazolin/gentamicin for the prevention of endophthalmitis after penetrating ocular trauma.

MATERIALS AND METHODS

This was a retrospective, descriptive single-center study, including all cases of penetrating ocular trauma seen in the Feiz Hospital, a Tertiary Referral Eye Hospital in Isfahan, Iran, between 2011 and 2017. Data systemically recorded for each patient included clinical, ophthalmological, and demographic findings by a trained medical record abstractor or ophthalmologist reviewing patient records.

RESULTS

Six hundred and forty-five patients in cefazolin/gentamicin and 273 patients in oral ciprofloxacin groups were included in the study. Our study showed that the incidence of endophthalmitis was not significantly different between the two groups (P = 0.463). In patients with either sharp or blunt penetrating ocular trauma.

CONCLUSION

Oral ciprofloxacin as a prophylactic treatment could prevent posttraumatic endophthalmitis as effective as injectable cefazolin/gentamicin. Due to easier consumption of oral ciprofloxacin and lower systemic complications, in all patients with penetrating eye trauma, oral administration of ciprofloxacin is preferable to intravenous or intramuscular types of antibiotics to reduce the risk of posttraumatic endophthalmitis.

Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa

Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as Mycobacterium tuberculosis and parasites such as Plasmodium falciparum. This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients’ health records to give advice on treatment options as well as potential drug and vaccine interactions. However, despite accounting for the highest burden of infectious diseases, Africa has the lowest research output on infectious disease genomics. Here we review the contributions of genomics and bioinformatics to the management of infectious diseases of serious public health concern in Africa including tuberculosis (TB), dengue fever, malaria and filariasis. Furthermore, we discuss how genomics and bioinformatics can be applied to identify drug and vaccine targets. We conclude by identifying challenges to genomics research in Africa and highlighting how these can be overcome where possible.

Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles

Benzimidazoles (BZ) are essential components of the limited chemotherapeutic arsenal available to control the global burden of parasitic nematodes. The emerging threat of BZ resistance among multiple nematode species necessitates the development of novel strategies to identify genetic and molecular mechanisms underlying this resistance. All detection of parasitic helminth resistance to BZ is focused on the genotyping of three variant sites in the orthologs of the β-tubulin gene found to confer resistance in the free-living nematode Caenorhabditis elegans. Because of the limitations of laboratory and field experiments in parasitic nematodes, it is difficult to look beyond these three sites to identify additional mechanisms that might contribute to BZ resistance in the field. Here, we took an unbiased genome-wide mapping approach in the free-living nematode species C. elegans to identify the genetic underpinnings of natural resistance to the commonly used BZ, albendazole (ABZ). We found a wide range of natural variation in ABZ resistance in natural C. elegans populations. In agreement with known mechanisms of BZ resistance in parasites, we found that a majority of the variation in ABZ resistance among wild C. elegans strains is caused by variation in the β-tubulin gene ben-1. This result shows empirically that resistance to ABZ naturally exists and segregates within the C. elegans population, suggesting that selection in natural niches could enrich for resistant alleles. We identified 25 distinct ben-1 alleles that are segregating at low frequencies within the C. elegans population, including many novel molecular variants. Population genetic analyses indicate that ben-1 variation arose multiple times during the evolutionary history of C. elegans and provide evidence that these alleles likely occurred recently because of local selective pressures. Additionally, we find purifying selection at all five β-tubulin genes, despite predicted loss-of-function variants in ben-1, indicating that BZ resistance in natural niches is a stronger selective pressure than loss of one β-tubulin gene. Furthermore, we used genome-editing to show that the most common parasitic nematode β-tubulin allele that confers BZ resistance, F200Y, confers resistance in C. elegans. Importantly, we identified a novel genomic region that is correlated with ABZ resistance in the C. elegans population but independent of ben-1 and the other β-tubulin loci, suggesting that there are multiple mechanisms underlying BZ resistance. Taken together, our results establish a population-level resource of nematode natural diversity as an important model for the study of mechanisms that give rise to BZ resistance.

The effect of assortative mixing on stability of low helminth transmission levels and on the impact of mass drug administration: Model explorations for onchocerciasis

Background

Stable low pre-control prevalences of helminth infection are not uncommon in field settings, yet it is poorly understood how such low levels can be sustained, thereby challenging efforts to model them. Disentangling possible facilitating mechanisms is important, since these may differently affect intervention impact. Here we explore the role of assortative (i.e. non-homogenous) mixing and exposure heterogeneity in helminth transmission, using onchocerciasis as an example.

Methodology/Principal findings

We extended the established individual-based model ONCHOSIM to allow for assortative mixing, assuming that individuals who are relatively more exposed to fly bites are more connected to each other than other individuals in the population as a result of differential exposure to a sub-population of blackflies. We used the model to investigate how transmission stability, equilibrium microfilarial (mf) prevalence and intensity, and impact of mass drug administration depend on the assumed degree of assortative mixing and exposure heterogeneity, for a typical rural population of about 400 individuals. The model clearly demonstrated that with homogeneous mixing and moderate levels of exposure heterogeneity, onchocerciasis could not be sustained below 35% mf prevalence. In contrast, assortative mixing stabilised onchocerciasis prevalence at levels as low as 8% mf prevalence. Increasing levels of assortative mixing significantly reduced the probability of interrupting transmission, given the same duration and coverage of mass drug administration.

Conclusions/Significance

Assortative mixing patterns are an important factor to explain stable low prevalence situations and are highly relevant for prospects of elimination. Their effect on the pre-control distribution of mf intensities in human populations is only detectable in settings with mf prevalences <30%, where high skin mf density in mf-positive people may be an indication of assortative mixing. Local spatial variation in larval infection intensity in the blackfly intermediate host may also be an indicator of assortative mixing.

Most mathematical models for parasitic worm infections predict that at low prevalences transmission will fade out spontaneously because of the low mating probability of male and female worms. However, sustained low prevalence situations do exist in reality. Low prevalence areas have become of particular interest now that several worm infections are being targeted for elimination and the question arises whether transmission in such areas is driven locally and should be targeted with interventions. We hypothesise that an explanation for the existence of low prevalence areas is assortative mixing, which is the preferential mixing of high-risk groups among themselves and which has been shown to play an important role in transmission of other infectious diseases. For onchocerciasis, assortative mixing would mean that transmission is sustained by a sub-group of people and a connected sub-population of the blackfly intermediate host that mix preferentially with each other. Using a mathematical model, we study how assortative mixing allows for sustained low prevalences and show that it decreases the probability of interrupting transmission by means of mass drug administration. We further identify data sources that may be used to quantify the degree of assortative mixing in field settings.

From river blindness control to elimination: bridge over troubled water

BACKGROUND

An estimated 25 million people are currently infected with onchocerciasis (a parasitic infection caused by the filarial nematode Onchocerca volvulus and transmitted by Simulium vectors), and 99% of these are in sub-Saharan Africa. The African Programme for Onchocerciasis Control closed in December 2015 and the World Health Organization has established a new structure, the Expanded Special Project for the Elimination of Neglected Tropical Diseases for the coordination of technical support for activities focused on five neglected tropical diseases in Africa, including onchocerciasis elimination.

AIMS

In this paper we argue that despite the delineation of a reasonably well-defined elimination strategy, its implementation will present particular difficulties in practice. We aim to highlight these in an attempt to ensure that they are well understood and that effective plans can be laid to solve them by the countries concerned and their international partners.

CONCLUSIONS

A specific concern is the burden of disease caused by onchocerciasis-associated epilepsy in hyperendemic zones situated in countries experiencing difficulties in strengthening their onchocerciasis control programmes. These difficulties should be identified and programmes supported during the transition from morbidity control to interruption of transmission and elimination.

A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry

The parasitic nematode Haemonchus contortus is an economically and clinically important pathogen of small ruminants, and a model system for understanding the mechanisms and evolution of traits such as anthelmintic resistance. Anthelmintic resistance is widespread and is a major threat to the sustainability of livestock agriculture globally; however, little is known about the genome architecture and parameters such as recombination that will ultimately influence the rate at which resistance may evolve and spread. Here, we performed a genetic cross between two divergent strains of H. contortus, and subsequently used whole-genome resequencing of a female worm and her brood to identify the distribution of genome-wide variation that characterizes these strains. Using a novel bioinformatic approach to identify variants that segregate as expected in a pseudotestcross, we characterized linkage groups and estimated genetic distances between markers to generate a chromosome-scale F1 genetic map. We exploited this map to reveal the recombination landscape, the first for any helminth species, demonstrating extensive variation in recombination rate within and between chromosomes. Analyses of these data also revealed the extent of polyandry, whereby at least eight males were found to have contributed to the genetic variation of the progeny analyzed. Triploid offspring were also identified, which we hypothesize are the result of nondisjunction during female meiosis or polyspermy. These results expand our knowledge of the genetics of parasitic helminths and the unusual life-history of H. contortus, and enhance ongoing efforts to understand the genetic basis of resistance to the drugs used to control these worms and for related species that infect livestock and humans throughout the world. This study also demonstrates the feasibility of using whole-genome resequencing data to directly construct a genetic map in a single generation cross from a noninbred nonmodel organism with a complex lifecycle.

Patent landscape of neglected tropical diseases: an analysis of worldwide patent families

BACKGROUND

"Neglected Tropical Diseases" (NTDs) affect millions of people in Africa, Asia and South America. The two primary ways of strategic interventions are "preventive chemotherapy and transmission control" (PCT), and "innovative and intensified disease management" (IDM). In the last 5 years, phenomenal progress has been achieved. However, it is crucial to intensify research effort into NTDs, because of the emerging drug resistance. According to the World Health Organization (WHO), the term NTDs covers 17 diseases, namely buruli ulcer, Chagas disease, dengue, dracunculiasis, echinococcosis, trematodiasis, human African trypanosomiasis, leishmaniasis, leprosy, lymphatic filariasis, onchocerciasis, rabies, schistosomiasis, soil-transmitted helminthes, taeniasis, trachoma, and yaws. The aim of this study is to map out research and development (R&D) landscape through patent analysis of these identified NTDs. To achieve this, analysis and evaluation have been conducted on patenting trends, current legal status of patent families, priority countries by earliest priority years and their assignee types, technological fields of patent families over time, and original and current patent assignees.

MAIN BODY

Patent families were extracted from Patseer, an international database of patents from over 100 patent issuing authorities worldwide. Evaluation of the patents was carried out using the combination of different search terms related to each identified NTD. In this paper, a total number of 12,350 patent families were analyzed. The main countries with sources of inventions were identified to be the United States (US) and China. The main technological fields covered by NTDs patent landscape are pharmaceuticals, biotechnology, organic fine chemistry, analysis of biological materials, basic materials chemistry, and medical technology. Governmental institutions and universities are the primary original assignees. Among the NTDs, leishmaniasis, dengue, and rabies received the highest number of patent families, while human African trypanosomiasis (sleeping sickness), taeniasis, and dracunciliasis received the least. The overall trend of patent families shows an increase between 1985 and 2008, and followed by at least 6 years of stagnation.

CONCLUSION

The filing pattern of patent families analyzed undoubtedly reveals slow progress on research and development of NTDs. Involving new players, such as non-governmental organizations may help to mitigate and reduce the burden of NTDs.

Increased Expression of a MicroRNA Correlates with Anthelmintic Resistance in Parasitic Nematodes

Resistance to anthelmintic drugs is a major problem in the global fight against parasitic nematodes infecting humans and animals. While previous studies have identified mutations in drug target genes in resistant parasites, changes in the expression levels of both targets and transporters have also been reported. The mechanisms underlying these changes in gene expression are unresolved. Here, we take a novel approach to this problem by investigating the role of small regulatory RNAs in drug resistant strains of the important parasite Haemonchus contortus. microRNAs (miRNAs) are small (22 nt) non-coding RNAs that regulate gene expression by binding predominantly to the 3′ UTR of mRNAs. Changes in miRNA expression have been implicated in drug resistance in a variety of tumor cells. In this study, we focused on two geographically distinct ivermectin resistant strains of H. contortus and two lines generated by multiple rounds of backcrossing between susceptible and resistant parents, with ivermectin selection. All four resistant strains showed significantly increased expression of a single miRNA, hco-miR-9551, compared to the susceptible strain. This same miRNA is also upregulated in a multi-drug-resistant strain of the related nematode Teladorsagia circumcincta. hco-miR-9551 is enriched in female worms, is likely to be located on the X chromosome and is restricted to clade V parasitic nematodes. Genes containing predicted binding sites for hco-miR-9551 were identified computationally and refined based on differential expression in a transcriptomic dataset prepared from the same drug resistant and susceptible strains. This analysis identified three putative target mRNAs, one of which, a CHAC domain containing protein, is located in a region of the H. contortus genome introgressed from the resistant parent. hco-miR-9551 was shown to interact with the 3′ UTR of this gene by dual luciferase assay. This study is the first to suggest a role for miRNAs and the genes they regulate in drug resistant parasitic nematodes. miR-9551 also has potential as a biomarker of resistance in different nematode species.

Onchocerca volvulus: The Road from Basic Biology to a Vaccine

Human onchocerciasis - commonly known as river blindness - is one of the most devastating yet neglected tropical diseases, leaving many millions in sub-Saharan Africa blind and/or with chronic disabilities. Attempts to eliminate onchocerciasis, primarily through the mass drug administration of ivermectin, remains challenging and has been heightened by the recent news that drug-resistant parasites are developing in some populations after years of drug treatment. Needed, and needed now, in the fight to eliminate onchocerciasis are new tools, such as preventive and therapeutic vaccines. This review summarizes the progress made to advance the onchocerciasis vaccine from the research laboratory into the clinic.

Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta

Preventive chemotherapy has long been practiced against nematode parasites of livestock, leading to widespread drug resistance, and is increasingly being adopted for eradication of human parasitic nematodes even though it is similarly likely to lead to drug resistance. Given that the genetic architecture of resistance is poorly understood for any nematode, we have analyzed multidrug resistant Teladorsagia circumcincta, a major parasite of sheep, as a model for analysis of resistance selection. We introgressed a field-derived multiresistant genotype into a partially inbred susceptible genetic background (through repeated backcrossing and drug selection) and performed genome-wide scans in the backcross progeny and drug-selected F2 populations to identify the major genes responsible for the multidrug resistance. We identified variation linking candidate resistance genes to each drug class. Putative mechanisms included target site polymorphism, changes in likely regulatory regions and copy number variation in efflux transporters. This work elucidates the genetic architecture of multiple anthelmintic resistance in a parasitic nematode for the first time and establishes a framework for future studies of anthelmintic resistance in nematode parasites of humans.

Teladorsagia circumcincta is an economically significant nematode (roundworm) pathogen affecting sheep and goats in temperate regions of the world. The widespread use of prophylactic treatment has resulted in rapid selection for anthelmintic (anti-worm drug) resistance in this and other species of livestock parasites. The mechanism of resistance is not well understood because most studies have focused on the role of candidate genes using simplistic models of single gene selection, despite evidence that the evolution of resistance is more complex. Here, we report on a comprehensive whole-genome analysis that elucidated resistance-associated genes, which was facilitated by developing a pair of T. circumcincta strains sharing a largely common genetic background but differing markedly in their susceptibility to anthelmintic drugs. The results show that multiple genetic factors contribute to anthelmintic resistance in a variety of ways, including possible reduction/modulation in target site sensitivity, reduced target site expression, and increased drug efflux, to name a few. This suggests that drug resistance in these parasites is a multifactorial quantitative trait rather than a simple discrete Mendelian character. With this study, we established a genomics-based experimental paradigm for investigating anthelmintic resistance, at a time when its medical importance is rapidly increasing.