Detection of classic and cryptic Strongyloides genotypes by deep amplicon sequencing: A preliminary survey of dog and human specimens collected from remote Australian communities

Genomic analysis of Strongyloides stercoralis and Strongyloides fuelleborni in Bangladesh

BACKGROUND

About 600 million people are estimated to be infected with Strongyloides stercoralis, the species that causes most of the human strongyloidiasis cases. S. stercoralis can also infect non-human primates (NHPs), dogs and cats, rendering these animals putative sources for zoonotic human S. stercoralis infection. S. fuelleborni is normally found in old world NHPs but occasionally also infects humans, mainly in Africa. Dogs in southeast Asia carry at least two types of Strongyloides, only one of which appears to be shared with humans ("dog only" and "human and dog" types). For S. stercoralis with molecular taxonomic information, there is a strong sampling bias towards southeast and east Asia and Australia.

METHODOLOGY/PRINCIPLE FINDINGS

In order to extend the geographic range of sampling, we collected human and dog derived Strongyloides spp. and hookworms from two locations in Bangladesh and subjected them to molecular taxonomic and genomic analysis based on nuclear and mitochondrial sequences. All hookworms found were Necator americanus. Contrary to earlier studies in Asia, we noticed a rather high incidence of S. fuelleborni in humans. Also in this study, we found the two types of S. stercoralis and no indication for genetic isolation from the southeast Asian populations. However, we found one genomically "dog only" type S. stercoralis in a human sample and we found two worms in a dog sample that had a nuclear genome of the "dog only" but a mitochondrial genome of the "human and dog" type.

CONCLUSIONS/SIGNIFICANCE

S. fuelleborni may play a more prominent role as a human parasite in certain places in Asia than previously thought. The introgression of a mitochondria haplotype into the "dog only" population suggests that rare interbreeding between the two S. stercoralis types does occur and that exchange of genetic properties, for example a drug resistance, between the two types is conceivable.

A Pilot Study for the Characterization of Bacillus spp. and Analysis of Possible B. thuringiensis/Strongyloides stercoralis Correlation

Differentiating between Bacillus species is relevant in human medicine. Bacillus thuringiensis toxins might be effective against Strongyloides stercoralis, a nematode causing relevant human morbidity. Our first objective was to evaluate genomic and MALDI-TOF identification methods for B. thuringiensis. Our secondary objective was to evaluate a possible negative selection pressure of B. thuringiensis against S. stercoralis. PCR and Sanger were compared to MALDI-TOF on a collection of 44 B. cereus group strains. B. thuringiensis toxin genes were searched on 17 stool samples from S. stercoralis-infected and uninfected dogs. Metagenomic 16S rRNA was used for microbiome composition. The inter-rate agreement between PCR, Sanger, and MALDI-TOF was 0.631 k (p-value = 6.4 × 10-10). B. thuringiensis toxins were not found in dogs' stool. Bacteroidota and Bacillota were the major phyla in the dogs' microbiome (both represented >20% of the total bacterial community). Prevotella was underrepresented in all Strongyloides-positive dogs. However, the general composition of bacterial communities was not significantly linked with S. stercoralis infection. The genomic methods allowed accurate differentiation between B. thuringiensis and B. cereus. There was no association between B. thuringiensis and S. stercoralis infection, but further studies are needed to confirm this finding. We provide the first descriptive results about bacterial fecal composition in dogs with S. stercoralis infection.

Strongyloides stercoralis in two dogs from a household in temperate Australia

Strongyloides stercoralis is parasite affecting both humans and dogs and is most prevalent in tropical and subtropical areas of Australia. This case report describes two dogs from a household in Sydney, New South Wales, one with chronic gastrointestinal signs and the other who was asymptomatic who were subsequently diagnosed with S. stercoralis. Diagnosis can be challenging in humans and dogs due to intermittent shedding and low worm burdens and in this case the symptomatic dog had Strongyloides spp. rhabitiform larvae detected on a direct faecal smear and PCR, the asymptomatic dog on PCR only. Obtained sequences from the symptomatic dog confirmed the presence of the S. stercoralis clade affecting both dogs and humans. Infection does not respond to commonly used deworming drugs for dogs. Treatment in both cases was undertaken using off-label doses of ivermectin and follow-up PCR testing was negative. This case report should increase practitioner awareness of this parasite as present and transmissible in temperate areas of Australia.

High-throughput sequencing of Strongyloides stercoralis - a fatal disseminated infection in a dog

The rhabditid nematode Strongyloides stercoralis is known worldwide as the causative agent of strongyloidiasis in humans. In addition to public health concerns, S. stercoralis also infects dogs, which represent a possible reservoir for potentially zoonotic transmissions. We describe the first confirmed case of fatal disseminated infection in a dog in the Czech Republic. The microscopic and histological results were supported by a complex genotyping approach. Using high-throughput sequencing of the hypervariable region (HVR-IV) of 18S rDNA and Sanger sequencing of the partial cytochrome c oxidase subunit 1 gene (cox1), the potentially zoonotic haplotype/lineage A of S. stercoralis was confirmed, while the solely canine haplotype/lineage B was not found. The development of the disease is mainly associated with immunodeficiency, and in this case, it was triggered by inappropriate treatment, in particular the use of corticosteroids.

New insight into genetic diversity of zoonotic-potential Ancylostoma ceylanicum in stray cats living in Bangkok, Thailand, based on deep amplicon sequencing

AIMS

This study aimed to characterize feline hookworms from stray cats living in Bangkok.

METHODS AND RESULTS

A total of 56 hookworm-positive faecal samples were identified for hookworm species by using PCR targeting the ITS1, 5.8S, and ITS2 fragment and qPCR targeting ITS2. Of 56 samples, 96.4% (54/56) were identified as Ancylostoma ceylanicum and 1.8% (1/56) as Ancylostoma caninum. With qPCR, 89.3% (50/56) were identified as single A. ceylanicum infection and 5.4% (3/56) as coinfection of A. ceylanicum and A. caninum. For genetic characterization of A. ceylanicum, 10 samples were pooled, and the partial COI gene was amplified, followed by deep amplicon sequencing. Five pooled samples were analysed, and 99.73% were identified with A. ceylanicum sequences, which were allocated into 19 haplotypes (AC01-AC19). Genetic diversity findings for A. ceylanicum in Asia revealed that three of eight haplotypes considered of zoonotic significance occurred in humans, dogs, and cats, including haplotypes H01, H20, and H21. The predominant haplotype in this study, AC01, was clustered with H01-a zoonotic haplotype.

CONCLUSIONS

The diversity obtained by deep amplicon sequencing supported that the A. ceylanicum community had high genetic variation. Deep amplicon sequencing was a useful method to determine source, zoonotic potential, and host-parasite relationship.

Clinical insights to address canine strongyloidosis in daily practice

Canine strongyloidosis by Strongyloides stercoralis is a parasitic disease emerging in Europe, which represents both a veterinary clinical issue and a public health challenge because of the zoonotic potential. The disease, not yet frequent in Europe, could induce severe clinical signs in dogs; thus, an early diagnosis and appropriate treatment are desirable. The aim of the present work is to retrospectively investigate the clinical and paraclinical findings in sick dogs naturally infected by S. stercoralis, with particular attention to ultrasound (US) changes at the gastrointestinal level. Twelve dogs were included in the study. The diagnosis was made by means of larval morphological identification on faecal samples and PCR. Most dogs presented with gastrointestinal signs; diarrhea and weight loss were the most common presenting complaint. Only one dog showed respiratory signs, associated to a parasitic cutaneous nodule. Hypoproteinaemia, anaemia, leucocytosis and an increase in alpha2-globulin fraction at serum protein electrophoresis were common (>50%) but not constant findings. The most reported US picture was a fluid-filled, distended, atonic small intestine mostly associated with altered wall layering, while the wall thickness commonly associated with chronic enteritis was only rarely reported. These changes, associated with other clinical and paraclinical alterations, could increase the suspicion of canine strongyloidosis and may direct clinicians to include strongyloidosis in the differential diagnosis of dogs with diarrhea. The histological examination at the intestinal level, available in five dogs, revealed the presence of parasites from the full-thickness biopsy, but not from the endoscopic biopsy. The critical points of diagnosis in clinical practice are also discussed.

Strongyloides stercoralis genotyping in a human population in southwestern Iran

BACKGROUND

Strongyloidiasis is a neglected tropical disease (NTD) that is caused mainly by Strongyloides stercoralis, with an estimated 600 million people infected worldwide, and in fewer cases by Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. A number of studies have been conducted on the genetic diversity of S. stercoralis in East and Southeast Asia; however, there is very limited corresponding information from West Asian countries, including Iran.

METHODS

For Strongyloides worms collected from patients in southwestern Iran, the hypervariable regions I (HVR-I) and IV (HVR-IV) of the nuclear 18S ribosomal DNA (rDNA) locus (SSU) and a fragment of the subunit 1 mitochondrial cytochrome c oxidase gene (cox-1) were sequenced. For a subset of the worms, whole-genome sequencing data were generated.

RESULTS

The cox-1 sequences of 136 worms isolated from 23 patients indicated that all isolates were S. stercoralis. Among the cox-1 sequences, 33 polymorphic sites and 13 haplotypes were found. The phylogenetic analysis demonstrated that some sequences clustered fairly closely with sequences from humans and dogs from other parts of the world, while others formed a separate, Iran-specific group. Among 64 S. stercoralis analyzed, we found three of the previously described SSU HVR-I haplotypes, with haplotype II being the most frequent haplotype. In contrast to Southeast Asia, where S. stercoralis heterozygous for different haplotypes at the HVR-I locus are rare, we found 20 worms to be heterozygous for two different HVR-I haplotypes, 18 of which fell into the Iran-specific cox-1 cluster. SSU-heterozygous worms also showed elevated heterozygosity at the whole-genome level.

CONCLUSIONS

We conclude that the S. stercoralis population from the Khuzestan province shares much of the genetic diversity with the population in Southeast Asia, but there is an indication of additional genetic input. There appears to be some population structure with different subpopulations, which however do interbreed at least occasionally.

Strongyloides in non-human primates: significance for public health control

Primates are an important source of infectious disease in humans. Strongyloidiasis affects an estimated 600 million people worldwide, with a global distribution and hotspots of infection in tropical and subtropical regions. Recently added to the list of neglected tropical diseases, global attention has been demanded in the drive for its control. Through a literature review of Strongyloides in humans and non-human primates (NHP), we analysed the most common identification methods and gaps in knowledge about this nematode genus. The rise of molecular-based methods for Strongyloides detection is evident in both humans and NHP and provides an opportunity to analyse all data available from primates. Dogs were also included as an important host species of Strongyloides and a potential bridge host between humans and NHP. This review highlights the lack of molecular data across all hosts-humans, NHP and dogs-with the latter highly underrepresented in the database. Despite the cosmopolitan nature of Strongyloides, there are still large gaps in our knowledge for certain species when considering transmission and pathogenicity. We suggest that a unified approach to Strongyloides detection be taken, with an optimized, repeatable molecular-based method to improve our understanding of this parasitic infection. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.

Advancing Strongyloides omics data: bridging the gap with Caenorhabditis elegans

Among nematodes, the free-living model organism Caenorhabditis elegans boasts the most advanced portfolio of high-quality omics data. The resources available for parasitic nematodes, including Strongyloides spp., however, are lagging behind. While C. elegans remains the most tractable nematode and has significantly advanced our understanding of many facets of nematode biology, C. elegans is not suitable as a surrogate system for the study of parasitism and it is important that we improve the omics resources available for parasitic nematode species. Here, we review the omics data available for Strongyloides spp. and compare the available resources to those for C. elegans and other parasitic nematodes. The advancements in C. elegans omics offer a blueprint for improving omics-led research in Strongyloides. We suggest areas of priority for future research that will pave the way for expansions in omics resources and technologies. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.

Locally acquired strongyloidiasis in remote Australia: why are there still cases?

In Australia, strongyloidiasis primarily affects returned travellers, Vietnam veterans and refugees or asylum seekers, and First Nations people. Non-overseas acquired cases are seen almost exclusively in Australian First Nations remote communities. Australian First Nations communities have one of the highest rates of strongyloidiasis in the world. Our work has shown that strongyloidiasis is a disease of poverty. Acknowledging this is important-we need to shift the lens to socioeconomic factors, particularly environmental health hardware such as working toilets and sewerage systems, showers and laundries, and effective wastewater and rubbish removal. The rates of strongyloidiasis in First Nations communities is a result of decades of inadequate, poorly constructed and/or poorly maintained housing, and poor environmental health hardware (hereafter hardware). The solution lies in adequate funding, resulting in well designed and maintained housing and appropriate hardware. Governments need to allow First Nations communities themselves to take the lead role in funding allocation, and design, construction and maintenance of their housing and hardware. This will ensure housing and hardware fulfils cultural and physical needs and desires, and protects health. Improving housing and hardware will also improve other health outcomes. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.

A standard workflow for community-driven manual curation of Strongyloides genome annotations

Advances in the functional genomics and bioinformatics toolkits for Strongyloides species have positioned these species as genetically tractable model systems for gastrointestinal parasitic nematodes. As community interest in mechanistic studies of Strongyloides species continues to grow, publicly accessible reference genomes and associated genome annotations are critical resources for researchers. Genome annotations for multiple Strongyloides species are broadly available via the WormBase and WormBase ParaSite online repositories. However, a recent phylogenetic analysis of the receptor-type guanylate cyclase (rGC) gene family in two Strongyloides species highlights the potential for errors in a large percentage of current Strongyloides gene models. Here, we present three examples of gene annotation updates within the Strongyloides rGC gene family; each example illustrates a type of error that may occur frequently within the annotation data for Strongyloides genomes. We also extend our analysis to 405 previously curated Strongyloides genes to confirm that gene model errors are found at high rates across gene families. Finally, we introduce a standard manual curation workflow for assessing gene annotation quality and generating corrections, and we discuss how it may be used to facilitate community-driven curation of parasitic nematode biodata. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.

Is strongyloidiasis a zoonosis from dogs?

Strongyloides stercoralis infection remains a major veterinary and public health challenge globally. This chronic and potentially lifelong disease has fatal outcomes in immunosuppressed people and dogs. Currently, the role of dogs in the transmission cycle of human strongyloidiasis remains enigmatic. While zoonotic transmission to humans from companion animals has been proposed, this has not been confirmed. Modern molecular methods have allowed greater opportunity to explore the genotypes of S. stercoralis in dogs and humans. Work thus far has demonstrated that at least two distinct lineages exist, one apparently confined to canine hosts and one found in canine, feline, human and non-human primate hosts. Although genotyping of dog and human isolates from the same village has demonstrated identical genotypes in both species, coprophagia of human waste by dogs confounds interpretation. It remains unclear if dogs act as a zoonotic reservoir for human infection, or vice versa, or if this occurs only in some regions of the world and not in others. These questions must be answered before effective control strategies for strongyloidiasis can be instituted. This review explores the evidence for and against cross-species transmission of S. stercoralis between dogs and humans and summarizes future directions for research in this area. This article is part of the Theo Murphy meeting Issue 'Strongyloides: omics to worm-free populations'.

Human strongyloidiasis: complexities and pathways forward

Strongyloidiasis is a World Health Organization neglected tropical disease usually caused by Strongyloides stercoralis, a parasitic worm with a complex life cycle. Globally, 300-600 million people are infected through contact with fecally contaminated soil. An autoinfective component of the life cycle can lead to chronic infection that may be asymptomatic or cause long-term symptoms, including malnourishment in children. Low larval output can limit the sensitivity of detection in stool, with serology being effective but less sensitive in immunocompromise. Host immunosuppression can trigger catastrophic, fatal hyperinfection/dissemination, where large numbers of larvae pierce the bowel wall and disseminate throughout the organs. Stable disease is effectively treated by single-dose ivermectin, with disease in immunocompromised patients treated with multiple doses. Strategies for management include raising awareness, clarifying zoonotic potential, the development and use of effective diagnostic tests for epidemiological studies and individual diagnosis, and the implementation of treatment programs with research into therapeutic alternatives and medication safety.

Strongyloidiasis in humans and dogs in Southern Italy: an observational study

Strongyloidiasis is a clinical issue both in humans and in dogs. Moreover, there are concerns about its zoonotic potential. We aimed to explore Strongyloides stercoralis epidemiology in Southern Italy in humans and dogs sharing the same environment in three different settings: (1) kennels (group K); (2) livestock farms (group L) and (3) agricultural farms (group A). For humans, a commercial ELISA test was used for screening. RT-PCR on faecal samples was done for people testing positive or equivocal at serology. On dog's faecal samples, Baermann test and RT-PCR were performed. A total of 145 dogs and 139 persons were tested. Based on faecal tests in dogs and serology in humans, a S. stercoralis positivity of 4.1% and 6.5% was revealed, respectively. The sites where cases were found were different for animals and humans. In dogs the highest positivity was in group K (6.7% against 2% and 0% in L and A). Differently, in humans the proportion of positive results was similar between the groups (p = 0.883). Fifty percent (3/6) of positive dogs were healthy; the other dogs presented weight loss and/or diarrhoea. ELISA-positive persons (n=9) were all in health, but abdominal pain (37.5%), urticaria (22.2%) and asthma (22.2%) were reported, resolving after treatment with oral ivermectin 200 μg/kg. RT-PCR performed on 13 human faecal samples resulted negative. These findings suggest that strongyloidiasis is present in humans and dogs in Southern Italy, and screening in larger cohorts would be needed for more accurate estimates.

First identification of Strongyloides stercoralis infection in a pet dog in Argentina, using integrated diagnostic approaches

BACKGROUND

Strongyloides stercoralis is a soil-transmitted intestinal nematode with a complex life cycle that primarily affects humans, non-human primates, dogs, and occasionally cats. This study presents, to the best of our knowledge, the first case of S. stercoralis infection and its genotyping in a domestic dog from Argentina.

METHODS

The patient was a female wired-haired Teckel dog exhibiting recurrent coughing. Coproparasitological analysis using the Baermann technique revealed the presence of rhabditiform larvae morphologically compatible with S. stercoralis. To confirm this finding, molecular diagnosis (18S ribosomal RNA) and analysis of the cox1 gene were performed.

RESULTS

We identified a haplotype (HP20) that has previously only been related to S. stercoralis infection in dogs, but was found in the present study to be highly related to the haplotype (HP16) of a zoonotic variant and divergent from those previously described from human patients in Argentina. Furthermore, unlike in human cases following treatment with ivermectin, the dog was negative after moxidectin treatment according to polymerase chain reaction of the sampled faeces.

CONCLUSIONS

This case report shows the importance of further investigation into potential transmission events and prevalences of S. stercoralis in dogs and humans in South America. The results reported here should also encourage future work that examines different scenarios of infection with S. stercoralis in dogs and humans with the aim of integrating clinical management, diagnosis, treatment and follow-up strategies in the quest for new approaches for the treatment of this disease in animals and humans. The findings support the adoption of a One Health approach, which recognizes the interconnectedness between animal and human health, in addressing parasitic infections such as strongyloidiasis.

From past to present: opportunities and trends in the molecular detection and diagnosis of Strongyloides stercoralis

Strongyloides stercoralis is a soil-transmitted helminth that is mainly found in the tropical and subtropical regions and affects approximately 600 million people globally. The medical importance of strongyloidiasis lies in its capacity to remain asymptomatic and chronically unnoticed until the host is immunocompromised. Additionally, in severe strongyloidiasis, hyperinfection syndrome and larva dissemination to various organs can occur. Parasitological techniques such as Baermann-Moraes and agar plate culture to detect larvae in stool samples are the current gold standard. However, the sensitivity might be inadequate, especially with reduced worm burden. Complementing parasitological techniques, immunological techniques including immunoblot and immunosorbent assays are employed, with higher sensitivity. However, cross-reactivity to other parasites may occur, hampering the assay's specificity. Recently, advances in molecular techniques such as polymerase chain reaction and next-generation sequencing technology have provided the opportunity to detect parasite DNA in stool, blood, and environmental samples. Molecular techniques, known for their high sensitivity and specificity, have the potential to circumvent some of the challenges associated with chronicity and intermittent larval output for increased detection. Here, as S. stercoralis was recently included by the World Health Organization as another soil-transmitted helminth targeted for control from 2021 to 2030, we aimed to present a review of the current molecular techniques for detecting and diagnosing S. stercoralis in a bid to consolidate the molecular studies that have been performed. Upcoming molecular trends, especially next-generation sequencing technologies, are also discussed to increase the awareness of its potential for diagnosis and detection. Improved and novel detection methods can aid in making accurate and informed choices, especially in this era where infectious and non-infectious diseases are increasingly commonplace.

Genetic characterization of Strongyloides fuelleborni infecting free-roaming African vervets (Chlorocebus aethiops sabaeus) on the Caribbean island of St. Kitts

Human strongyloidiasis is an important neglected tropical disease primarily caused by the nematode Strongyloides stercoralis, and to a lesser extent Strongyloides fuelleborni which mainly infects non-human primates. Zoonotic sources of infection have important implications for control and prevention of morbidity and mortality caused by strongyloidiasis. Recent molecular evidence suggests that for S. fuelleborni, primate host specificity is variable among genotypes across the Old World, and consequently that these types likely vary in their capacity for human spillover infections. Populations of free-roaming vervet monkeys (Chlorocebus aethiops sabaeus), introduced to the Caribbean Island of Staint Kitts from Africa, live in close contact with humans, and concern has arisen regarding their potential to serve as reservoirs of zoonotic infections. In this study, we sought to determine the genotypes of S. fuelleborni infecting St. Kitts vervets to explore whether they are potential reservoirs for human-infecting S. fuelleborni types. Fecal specimens were collected from St. Kitts vervets and S. fuelleborni infections were confirmed microscopically and by PCR. Strongyloides fuelleborni genotypes were determined from positive fecal specimens using an Illumina amplicon sequencing-based genotyping approach targeting the mitochondrial cox1 locus and 18S rDNA hypervariable regions I and IV of Strongyloides species. Phylogenetic analysis of resultant genotypes supported that S. fuelleborni from St. Kitts vervets is of an exclusively African variety, falling within the same monophyletic group as an isolate which has been detected previously in a naturally infected human from Guinea-Bissau. This observation highlights that St. Kitts vervets may serve as potential reservoirs for zoonotic S. fuelleborni infection, which warrants further exploration.

Prevalence of Intestinal Parasites in Dog Faecal Samples from Public Environments in Qinghai Province, China

Dogs are popular companions in our daily lives for company, hunting, protection or shepherding, but they also serve as reservoirs for zoonotic parasites. We analysed faecal samples from urban and rural environments in Qinghai Province on the Qinghai-Tibet Plateau of China to determine the prevalence of intestinal parasites. A total of 682 faecal samples were collected from four urban and two rural environments from October 2019 to December 2020. The samples were analysed for common intestinal parasites using a species-specific PCR approach. The total number of samples with parasites was 40 (5.87%): 23 (3.37%) were positive for helminths, and 17 (2.49%) were positive for protozoa. The following parasites were identified, and their respective prevalence rates were calculated: Cryptosporidium canis (1.32%), Giardia duodenalis (1.17%, assemblages D (n = 6) and C (n = 2)), Taenia hydatigena (1.03%), Taenia multiceps (0.59%), Toxocara canis (0.59%), Echinococcus shiquicus (0.29%), Dipylidium caninum (0.29%), Taenia pisiformis (0.15%), Mesocestoides lineatus (0.15%), Trichuris vulpis (0.15%), and Ancylostoma spp. (0.15%). The overall prevalence was significantly higher in dog faecal samples from rural environments than in those from urban environments (16.19% vs. 3.99%). E. shiquicus, T. pisiformis, M. lineatus, T. vulpis, and Ancylostoma spp. were only found in dog faecal samples from rural environments. The results of the present study indicate that intestinal parasite-positive dogs are important sources of environmental contamination, suggesting a significant zoonotic infection risk in humans and other animals. This has implications for the ongoing control of intestinal parasite infections in dogs in Qinghai Province, China.

A systematic review and meta-analysis of human and zoonotic dog soil-transmitted helminth infections in Australian Indigenous communities

Soil-transmitted helminths (STH) infect 1.5 billion people and countless animals worldwide. In Australian Indigenous communities, STH infections have largely remained endemic despite control efforts, suggesting reservoirs of infection may exist. Dogs fulfil various important cultural, social and occupational roles in Australian Indigenous communities and are populous in these settings. Dogs may also harbour zoonotic STHs capable of producing morbidity and mortality in dogs and humans. This review provides an overview of human and zoonotic STH infections, identifies the Australian Indigenous locations affected and the parasite species and hosts involved. The meta-analysis provides estimates of individual study and pooled true prevalence of STH infections in Australian Indigenous communities and identifies knowledge gaps for further research on zoonotic or anthroponotic potential. A systematic literature search identified 45 eligible studies documenting the presence of Strongyloides stercoralis, Trichuris trichiura, Ancylostoma caninum, Ancylostoma duodenale, Ancylostoma ceylanicum, undifferentiated hookworm, and Ascaris lumbricoides. Of these studies, 26 were also eligible for inclusion in meta-analysis to establish true prevalence in the light of imperfect diagnostic test sensitivity and specificity by Rogan-Gladen and Bayesian methods. These studies revealed pooled true prevalence estimates of 18.9% (95% CI 15.8–22.1) for human and canine S. stercoralis infections and 77.3% (95% CI 63.7–91.0) for canine A. caninum infections indicating continued endemicity, but considerably more heterogenous pooled estimates for canine A. ceylanicum infections, and A. duodenale, undifferentiated hookworm and T. trichiura in humans. This review suggests that the prevalence of STHs in Australian Indigenous communities has likely been underestimated, principally based on imperfect diagnostic tests. Potential misclassification of hookworm species in humans and dogs due to outdated methodology, also obscures this picture. High-quality contemporary studies are required to establish current true prevalence of parasite species in all relevant hosts to guide future policy development and control decisions under a culturally sound One Health framework.

Soil-transmitted helminths include hookworms, threadworms, whipworms and roundworms. These worms may infect different hosts including humans and dogs, and some species are zoonotic, meaning that they are able to transmit between animals and humans. In many Australian Indigenous communities, people remain infected with these worms at high rates compared to other parts of the country despite various control strategies. Resource and health literacy inequalities are primary drivers for these differences. However, the potential for dogs to act as reservoirs for zoonotic worm infections in humans must also be considered. For this reason, it’s important to create a clear picture of the level of infection by location and host. Given that tests used to establish prevalence can produce false positive or negative results, we performed a meta-analysis allowing comparison of true prevalence estimates by location and host, regardless of the test used. This review suggests that threadworm and dog hookworm remain endemic in Australian Indigenous communities, though a gap exists to accurately inform the prevalence of the other worms. It also highlights the need for One Health strategies in research, policy and control where humans, all animal hosts and the environment are considered in a culturally relevant way.

The diagnosis of human and companion animal Strongyloides stercoralis infection: Challenges and solutions. A scoping review

Strongyloidiasis is the infection caused by soil-transmitted nematodes of Strongyloides species, infecting humans and some animals. Strongyloides stercoralis is the species with most clinical and epidemiological relevance in humans and dogs, due to its high prevalence and its capacity of inducing a life-threatening hyperinfection. Diagnosis of strongyloidiasis is challenging, due to the absence of a single reference standard test with high sensitivity and specificity, which also hampers the estimation of the accuracy of other diagnostic tests. In this chapter, we review the deployment and performance of the parasitological, immunological, molecular tests for the diagnosis of strongyloidiasis in humans and in dogs. Further, we comment the available evidence from genotyping studies that have addressed the zoonotic potential of S. stercoralis. Finally, we discuss the use of different diagnostic methods in relation to the purpose (i.e., screening, individual diagnosis, inclusion in a clinical trial) and the setting (endemic/non-endemic areas) and report the accuracy figures reported by systematic reviews on either parasitological, serological or molecular techniques published in literature.

Evaluation of various distance computation methods for construction of haplotype-based phylogenies from large MLST dataset

Multi-locus sequence typing (MLST) is widely used to investigate genetic relationships among eukaryotic taxa, including parasitic pathogens. MLST analysis workflows typically involve construction of alignment-based phylogenetic trees - i.e., where tree structures are computed from nucleotide differences observed in a multiple sequence alignment (MSA). Notably, alignment-based phylogenetic methods require that all isolates/taxa are represented by a single sequence. When multiple loci are sequenced these sequences may be concatenated to produce one tree that includes information from all loci. Alignment-based phylogenetic techniques are robust and widely used yet possess some shortcomings, including how heterozygous sites are handled, intolerance for missing data (i.e., partial genotypes), and differences in the way insertions-deletions (indels) are scored/treated during tree construction. In certain contexts, 'haplotype-based' methods may represent a viable alternative to alignment-based techniques, as they do not possess the aforementioned limitations. This is namely because haplotype-based methods assess genetic similarity based on numbers of shared (i.e., intersecting) haplotypes as opposed to similarities in nucleotide composition observed in an MSA. For haplotype-based comparisons, choosing an appropriate distance statistic is fundamental, and several statistics are available to choose from. However, a comprehensive assessment of various available statistics for their ability to produce a robust haplotype-based phylogenetic reconstruction has not yet been performed. We evaluated seven distance statistics by applying them to extant MLST datasets from the gastrointestinal parasite Cyclospora cayetanensis and two species of pathogenic nematode of the genus Strongyloides. We compare the genetic relationships identified using each statistic to epidemiologic, geographic, and host metadata. We show that Barratt's heuristic definition of genetic distance was the most robust among the statistics evaluated. Consequently, it is proposed that Barratt's heuristic represents a useful approach for use in the context of challenging MLST datasets possessing features (i.e., high heterozygosity, partial genotypes, and indel or repeat-based polymorphisms) that confound or preclude the use of alignment-based methods.

What lies behind the curtain: Cryptic diversity in helminth parasites of human and veterinary importance

Parasite cryptic species are morphologically indistinguishable but genetically distinct organisms, leading to taxa with unclear species boundaries. Speciation mechanisms such as cospeciation, host colonization, taxon pulse, and oscillation may lead to the emergence of cryptic species, influencing host-parasite interactions, parasite ecology, distribution, and biodiversity. The study of cryptic species diversity in helminth parasites of human and veterinary importance has gained relevance, since their distribution may affect clinical and epidemiological features such as pathogenicity, virulence, drug resistance and susceptibility, mortality, and morbidity, ultimately affecting patient management, course, and outcome of treatment. At the same time, the need for recognition of cryptic species diversity has implied a transition from morphological to molecular diagnostic methods, which are becoming more available and accessible in parasitology. Here, we discuss the general approaches for cryptic species delineation and summarize some examples found in nematodes, trematodes and cestodes of medical and veterinary importance, along with the clinical implications of their taxonomic status. Lastly, we highlight the need for the correct interpretation of molecular information, and the correct use of definitions when reporting or describing new cryptic species in parasitology, since molecular and morphological data should be integrated whenever possible.

Global prevalence of Strongyloides stercoralis in dogs: A systematic review and meta-analysis

Strongyloides stercoralis is an intestinal parasitic helminth that mainly affects humans and dogs throughout the world. Canine strongyloidosis is generally characterized by asymptomatic infection, with fatal disease in cases of immunodeficiency. This study was conducted in order to evaluate the global prevalence of S. stercoralis in dogs. Six electronic databases were searched for this purpose. The random effects model and 95% confidence intervals (CI) were applied to determine the overall and subgroup pooled prevalence. Heterogeneity was assessed by Cochran's Q test and I2 statistic. In total, 56 datasets from 50 studies from 1,202 peer-reviewed papers were included in the current meta-analysis. 20,627 dogs were assessed in 27 countries across six World Health Organization (WHO) regions. The global prevalence of S. stercoralis infection among dogs was 6% (95% CI 4–8%; 868/20,627). According to WHO regions, the estimated prevalence ranges 2% to 11% as follows: Western Pacific (11%, 0–31%); Africa (9%, 2–19%); America (6%, 3–11%); South-East Asia (5%, 1–13%)’ Europe (3%, 2–5%); and Eastern Mediterranean (2%, 0–6%). The pooled prevalence of S. stercoralis infection in dog owners was 7% (1–18%). The prevalence of S. stercoralis infection in studies based on serological assays was significantly higher than other techniques (29%, 20–39%). Younger female dogs, less than one year old, from rural areas had higher prevalence rates than their male counterparts, with no statistically significant differences. From this review, it is concluded that the low global prevalence of S. stercoralis in dogs may be strongly associated with low sensitivity diagnostic methods applied in most studies leading to the underestimation of infection rates. Therefore, the improvement of diagnostic techniques is recommended for precise evaluation of the disease.

Strongyloides genotyping: a review of methods and application in public health and population genetics

Strongyloidiasis represents a major medical and veterinary helminthic disease. Human infection is caused by Strongyloides stercoralis, Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi, with S.stercoralis accounting for the majority of cases. Strongyloides f. fuelleborni likely represents a zoonosis acquired from non-human primates (NHPs), while no animal reservoir for S. f. kellyi infection has been found. Whether S. stercoralis represents a zoonosis acquired from dogs and cats remains unanswered. Over the past two decades various tools have been applied to genotype Strongyloides spp. The most commonly sequenced markers have been the hyper-variable regions I and IV of the 18S rRNA gene and selected portions of the cytochrome c oxidase subunit I gene. These markers have been sequenced and compared in Strongyloides from multiple hosts and geographical regions. More recently, a machine learning algorithm multi-locus sequence typing approach has been applied using these markers, while others have applied whole genome sequencing. Genotyping of Strongyloides from dogs, cats, NHPs and humans has identified that S. stercoralis likely originated in dogs and adapted to human hosts. It has also been demonstrated that S. stercoralis is distinct from S. f. fuelleborni and S. f. kellyi. Two distinct genetic clades of S. stercoralis exist, one restricted to dogs and another infecting humans, NHPs, dogs and cats. Genotyping of S. f. fuelleborni has identified two separate clades, one associated with African isolates and another Indochinese peninsular clade. This review summarises the history and development of genotyping tools for Strongyloides spp. It describes the findings of major studies to date in the context of the epidemiology and evolutionary biology of these helminths, with a specific focus on human-infecting species.

Molecular detection of Strongyloides sp. in Australian Thoroughbred foals

Background

Strongyloides westeri is found in the small intestine of young horses, mainly in foals up to about 16 weeks of age. The main source of infection for foals is through transmammary transmission, and foals can develop acute diarrhoea, weakness, dermatitis and respiratory signs. The epidemiology of S. westeri in Australia is largely unknown. Further, molecular techniques have never been employed for detection of S. westeri in horses. This pilot study aimed to assess the utility of a molecular phylogenetic method for the detection of S. westeri in the faeces of foals.

Methods

Faecal samples were collected from a foal of less than 2 months of age, and eggs of Strongyloides sp. were detected using the modified McMaster technique. DNA was extracted from purified eggs, and a partial fragment of the small subunit of the nuclear ribosomal DNA (18S) was characterised using polymerase chain reaction, DNA sequencing and phylogenetic methods.

Results

Microscopic examination of faeces revealed small ellipsoidal eggs typical of Strongyloides sp. The 18S sequence generated by PCR in this study revealed 98.4% identity with that of a reference sequence of S. westeri available from GenBank. Phylogenetic analyses revealed a polyphyletic clustering of S. westeri sequences.

Conclusion

This is the first study reporting the detection of DNA of Strongyloides sp. in faeces of a foal using a molecular phylogenetic approach targeting the variable region of 18S rDNA. It is anticipated that this study will allow future molecular epidemiological studies on S. westeri in horses.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04966-1.

Examining the concept of One Health for indigenous communities: A systematic review

Purpose

This paper examines whether the usage of the concept of One Health in Canada-based research aligns with traditional Indigenous notions of health and wellness.

Methods

A comprehensive search of the literature was conducted using primary databases, including Scholars Portal, ProQuest Social Science, Sociological Abstracts (ProQuest), OVID Healthstar, Embase, Medline, Pubmed and Google Scholar. Papers discussing One Health and Indigenous Health were selected and analyzed through Nvivo12 to generate common themes across the studies.

Results

The analysis identified three major themes that focused on One Health as it relates to climate change, zoonosis, and social relationships between humans and animals. Climate change was seen to have affected the environmental health of Northern latitude areas where many Indigenous communities reside. Infectious diseases within Indigenous communities were a frequent topic of study and indicated that infections transmitted by dogs are likely to be addressed with One Health interventions. One Health interventions are likely to equally address the health of humans, animals, and the environment.

Conclusions

No significant connection between One Health and Indigenous knowledges was established in the analyzed articles. Articles discussed One Health as it pertains to epidemiological surveillance and research. The implications of utilizing One Health towards Indigenous Peoples and culture were not explicitly addressed.

Seropositivity and geographical distribution of Strongyloides stercoralis in Australia: A study of pathology laboratory data from 2012-2016

Background

There are no national prevalence studies of Strongyloides stercoralis infection in Australia, although it is known to be endemic in northern Australia and is reported in high risk groups such as immigrants and returned travellers. We aimed to determine the seropositivity (number positive per 100,000 of population and percent positive of those tested) and geographical distribution of S. stercoralis by using data from pathology laboratories.

Methodology

We contacted all seven Australian laboratories that undertake Strongyloides serological (ELISA antibody) testing to request de-identified data from 2012–2016 inclusive. Six responded. One provided positive data only. The number of people positive, number negative and number tested per 100,000 of population (Australian Bureau of Statistics data) were calculated including for each state/territory, each Australian Bureau of Statistics Statistical Area Level 3 (region), and each suburb/town/community/locality. The data was summarized and expressed as maps of Australia and Greater Capital Cities.

Principal findings

We obtained data for 81,777 people who underwent serological testing for Strongyloides infection, 631 of whom were from a laboratory that provided positive data only. Overall, 32 (95% CI: 31, 33) people per 100,000 of population were seropositive, ranging between 23/100,000 (95% CI: 19, 29) (Tasmania) and 489/100,000 population (95%CI: 462, 517) (Northern Territory). Positive cases were detected across all states and territories, with the highest (260-996/100,000 and 17–40% of those tested) in regions across northern Australia, north-east New South Wales and north-west South Australia. Some regions in Greater Capital Cities also had a high seropositivity (112-188/100,000 and 17–20% of those tested). Relatively more males than females tested positive. Relatively more adults than children tested positive. Children were under-represented in the data.

Conclusions/Significance

The study confirms that substantial numbers of S. stercoralis infections occur in Australia and provides data to inform public health planning.

Strongyloides stercoralis, a parasitic roundworm, is endemic in many countries world-wide. In Australia, groups at risk for strongyloidiasis include Aboriginal and/or Torres Strait Islander people, who acquired this parasite locally, and immigrants and returned travellers who acquired the infection outside Australia. We obtained deidentified results of ELISA IgG antibody tests for Strongyloides from diagnostic pathology laboratories during 2012 to 2016 and calculated the number of people who were positive at least once and the number who never had a positive result. We drew maps showing the number positive per 100,000 of population, the percent positive of those tested, and the number tested/100,000 for each region and the number positive in each suburb of residence according to the Australian Bureau of Statistics. The highest seropositivity (260-996/100,000 of population) was in Northern Australia, north-west South Australia and north-east New South Wales where many Aboriginal and Torres Strait Islander people live in remote communities. There were also some regions in Greater Capital Cities with a high number of people positive per 100,000 of population (112-188/100,000), likely reflecting higher populations of immigrants and returned travellers who were infected outside Australia.

HTLV-I and Strongyloides in Australia: The worm lurking beneath

Strongyloidiasis and HTLV-I (human T-lymphotropic virus-1) are important infections that are endemic in many countries around the world with an estimated 370 million infected with Strongyloides stercoralis alone, and 5-10 million with HTVL-I. Co-infections with these pathogens are associated with significant morbidity and can be fatal. HTLV-I infects T-cells thus causing dysregulation of the immune system which has been linked to dissemination and hyperinfection of S. stercoralis leading to bacterial sepsis which can result in death. Both of these pathogens are endemic in Australia primarily in remote communities in Queensland, the Northern Territory, and Western Australia. Other cases in Australia have occurred in immigrants and refugees, returned travellers, and Australian Defence Force personnel. HTLV-I infection is lifelong with no known cure. Strongyloidiasis is a long-term chronic disease that can remain latent for decades, as shown by infections diagnosed in prisoners of war from World War II and the Vietnam War testing positive decades after they returned from these conflicts. This review aims to shed light on concomitant infections of HTLV-I with S. stercoralis primarily in Australia but in the global context as well.

DISTRIBUTION OF STRONGYLOIDES STERCORALIS AMONG DOGS OF DIFFERENT HOUSING GROUPS IN KYIV AND KYIV REGION, CLINICAL MANIFESTATIONS AND DIAGNOSTIC METHODS

Strongyloidiasis in dogs, despite its uncertain zoonotic status, is potentially danger for dogs owners. It is considered that strongyloidiases characteristic for tropical and subtropical regions, but in recent years it is increasingly found in non-endemic countries. The aim. To determine the extent of the invasion, clinical signs and diagnostic methods of strongyloidiasis in dogs of different groups in Kyiv and Kyiv region. Materials and methods. A total of 364 dogs were studied (130 animals lived in shelters (Group 1) and 234 in homes (Group 2). Diagnosis of strongyloidiasis was performed by native smear and Baerman methods. Additionally, the sensitivity of the modified string test was tested. Samples of venous blood were taken from dogs with confirmed strongyloidiasis for haematological and biochemical analysis. Results. A study found that the extent of invasion (EI) in shelters and home dogs was 3.0±0.36 % (4/130; Group 1) and 2.5±0.25 % % (6/234; Group 2) respectively. It was found that three repetitions of the Baerman method test increased its efficiency to 90.5 %. The sensitivity of the modified string test was 100 %. Clinical manifestations included disorders of the respiratory (20 %: 2/10) and digestive systems (80 %: 8/10), weight loss (70 %: 7/10). Blood tests did not reveal changes specific to strongyloidiasis, eosinophilia was observed in only one dog in the acute stage of the disease. Conclusions. The results of our studies indicate the presence of strongyloidiasis in dogs in Kyiv and Kyiv region and probability of the spread of the pathogen in the environment. Symptoms in dogs with strongyloidiasis were nonspecific and cannot be used for diagnosis. A modified string test and Baerman method has demonstrated high efficacy and may be recommended to clarify the diagnosis of a chronic invasion.

Machine learning-based analyses support the existence of species complexes for Strongyloides fuelleborni and Strongyloides stercoralis

Human strongyloidiasis is a serious disease mostly attributable to Strongyloides stercoralis and to a lesser extent Strongyloides fuelleborni, a parasite mainly of non-human primates. The role of animals as reservoirs of human-infecting Strongyloides is ill-defined, and whether dogs are a source of human infection is debated. Published multi-locus sequence typing (MLST) studies attempt to elucidate relationships between Strongyloides genotypes, hosts, and distributions, but typically examine relatively few worms, making it difficult to identify population-level trends. Combining MLST data from multiple studies is often impractical because they examine different combinations of loci, eliminating phylogeny as a means of examining these data collectively unless hundreds of specimens are excluded. A recently-described machine learning approach that facilitates clustering of MLST data may offer a solution, even for datasets that include specimens sequenced at different combinations of loci. By clustering various MLST datasets as one using this procedure, we sought to uncover associations among genotype, geography, and hosts that remained elusive when examining datasets individually. Multiple datasets comprising hundreds of S. stercoralis and S. fuelleborni individuals were combined and clustered. Our results suggest that the commonly proposed 'two lineage' population structure of S. stercoralis (where lineage A infects humans and dogs, lineage B only dogs) is an over-simplification. Instead, S. stercoralis seemingly represents a species complex, including two distinct populations over-represented in dogs, and other populations vastly more common in humans. A distinction between African and Asian S. fuelleborni is also supported here, emphasizing the need for further resolving these taxonomic relationships through modern investigations.

Phylogenetic relationships of Strongyloides species in carnivore hosts

Strongyloides stercoralis is a parasitic nematode and a major pathogen responsible for human strongyloidiasis. The presence of this species in the dog population has led to an interest in studying the phylogenetic relationships among Strongyloides spp. in carnivore hosts. In the present study, Strongyloides spp. from various carnivore hosts (raccoon, Japanese badger, Siberian weasel, raccoon dog, masked palm civet, and domestic cat) were sought. Except for civets, Strongyloides spp. were identified in all host species. Based on 18S rDNA sequences, nine OTUs (operational taxonomy units) were identified. Molecular phylogenetic analyses using 18S28S rDNA and mitochondrial cox1 (cytochrome c oxidase subunit 1) sequences clustered them into two groups. The first group (named the stercoralis/procyonis group) was comprised of six OTUs and occurred in cats, raccoon dogs, raccoons (S. procyonis), Siberian weasels, and Japanese badgers and included S. stercoralis from humans and dogs. The second group (named the planiceps group) was made up of Strongyloides spp. from raccoon dogs (two OTUs) and one OTU from Siberian weasels. Subsequent analysis using almost the full-length nucleotide sequences of protein-coding genes in their mitochondrial genomes placed Strongyloides spp. of cats in a sister taxon position to S. stercoralis, whereas S. procyonis from raccoons was more distantly related to them. The presence of Strongyloides spp. from various carnivore hosts, which are close relatives of S. stercoralis, suggests this group of Strongyloides (the stercoralis/procyonis group) essentially evolved as parasites of carnivores, although more data on Strongyloides spp. from primate hosts are needed.

Opportunistic Mapping of Strongyloides stercoralis and Hookworm in Dogs in Remote Australian Communities

Both Strongyloides stercoralis and hookworms are common soil-transmitted helminths in remote Australian communities. In addition to infecting humans, S. stercoralis and some species of hookworms infect canids and therefore present both environmental and zoonotic sources of transmission to humans. Currently, there is limited information available on the prevalence of hookworms and S. stercoralis infections in dogs living in communities across the Northern Territory in Australia. In this study, 274 dog faecal samples and 11 faecal samples of unknown origin were collected from the environment and directly from animals across 27 remote communities in Northern and Central Australia. Samples were examined using real-time polymerase chain reaction (PCR) analysis for the presence of S. stercoralis and four hookworm species: Ancylostoma caninum, Ancylostoma ceylanicum, Ancylostoma braziliense and Uncinaria stenocephala. The prevalence of S. stercoralis in dogs was found to be 21.9% (60/274). A. caninum was the only hookworm detected in the dog samples, with a prevalence of 31.4% (86/274). This study provides an insight into the prevalence of S. stercoralis and hookworms in dogs and informs future intervention and prevention strategies aimed at controlling these parasites in both dogs and humans. A "One Health" approach is crucial for the prevention of these diseases in Australia.

Genomic studies on Strongyloides stercoralis in northern and western Thailand

Background

Strongyloidiasis is a soil borne helminthiasis, which in most cases is caused by Strongyloides stercoralis. Human infections with S. fuelleborni fuelleborni and S. fuelleborni kellyi also occur. Although up to 370 million people are currently estimated to be infected with S. stercoralis, this parasite is frequently overlooked. Strongyloides stercoralis is prevalent among humans in Thailand; however, S. fuelleborni fuelleborni has also been reported. Three recent genomic studies of individual S. stercoralis worms found genetically diverse populations of S. stercoralis, with comparably low heterozygosity in Cambodia and Myanmar, and less diverse populations with high heterozygosity in Japan and southern China that presumably reproduce asexually.

Methods

We isolated individual Strongyloides spp. from different localities in northern and western Thailand and determined their nuclear small ribosomal subunit rDNA (18S rDNA, SSU), in particular the hypervariable regions I and IV (HVR-I and HVR-IV), mitochondrial cytochrome c oxidase subunit 1 (cox1) and for a subset whole genome sequences. These sequences were then compared with each other and with published sequences from different geographical locations.

Results

All 237 worms isolated from 16 different human hosts were S. stercoralis, no S. fuelleborni was found. All worms had the common S. stercoralis SSU HVR IV haplotype A. Two different SSU HVR I haplotypes (I and II), both previously described in S. stercoralis, were found. No animal heterozygous for the two haplotypes was identified. Among the twelve cox1 haplotypes found, five had not been previously described. Based upon the mitochondrial cox1 and the nuclear whole genome sequences, S. stercoralis in Thailand was phylogenetically intermixed with the samples from other Southeast Asian countries and did not form its own branch. The genomic heterozygosity was even slightly lower than in the samples from the neighboring countries.

Conclusions

In our sample from humans, all Strongyloides spp. were S. stercoralis. The S. stercoralis from northern and western Thailand appear to be part of a diverse, intermixing continental Southeast Asian population. No obvious indication for genetic sub-structuring of S. stercoralis within Thailand or within the Southeast Asian peninsula was detected.

Dogs are reservoir hosts for possible transmission of human strongyloidiasis in Thailand: molecular identification and genetic diversity of causative parasite species

Human strongyloidiasis is a deleterious gastrointestinal disease mainly caused by Strongyloides stercoralis infection. We aimed to study the possible transmission of S. stercoralis between humans and pet animals. We isolated Strongyloides from humans and domestic dogs in the same rural community in north-east Thailand and compared the nucleotide sequences of derived worms using portions of the mitochondrial cytochrome c oxidase subunit 1 (cox1) and 18S ribosomal RNA (18S rRNA) genes. Twenty-eight sequences from the 18S rRNA gene were obtained from worms derived from humans (n = 23) and dogs (n = 5), and were identical with S. stercoralis sequences (from Thailand, Cambodia, Lao PDR and Myanmar) published in the GenBank database. The 28 cox1 sequences from humans and dogs showed high similarity to each other. The available published cox1 sequences (n = 150), in combination with our 28 sequences, represented 68 haplotypes distributed among four clusters. The 28 samples from the present study represented eight haplotypes including four new haplotypes. Dogs and humans shared the same haplotypes, suggesting the possibility of zoonotic transmission from pet dogs to humans. This is of concern since dogs and humans live in close association with each other.

From the feces to the genome: a guideline for the isolation and preservation of Strongyloides stercoralis in the field for genetic and genomic analysis of individual worms

Strongyloidiasis is a soil-borne helminthiasis, which, in spite of the up to 370 million people currently estimated to be infected with its causing agent, the nematode Strongyloides stercoralis, is frequently overlooked. Recent molecular taxonomic studies conducted in Southeast Asia and Australia, showed that dogs can carry the same genotypes of S. stercoralis that also infect humans, in addition to a presumably dog-specific Strongyloides species. This suggests a potential for zoonotic transmission of S. stercoralis from dogs to humans. Although natural S. stercoralis infections have not been reported in any host other than humans, non-human primates and dogs, other as yet unidentified animal reservoirs cannot be excluded. Molecular studies also showed that humans carry rather different genotypes of S. stercoralis. As a result, their taxonomic status and the question of whether they differ in their pathogenic potential remains open. It would therefore be very important to obtain molecular genetic/genomic information about S. stercoralis populations from around the world. One way of achieving this (with little additional sampling effort) would be that people encountering S. stercoralis in the process of their diagnostic work preserve some specimens for molecular analysis. Here we provide a guideline for the isolation, preservation, genotyping at the nuclear 18S rDNA and the mitochondrial cox1 loci, and for whole genome sequencing of single S. stercoralis worms. Since in many cases the full analysis is not possible or desired at the place and time where S. stercoralis are found, we emphasize when and how samples can be preserved, stored and shipped for later analysis. We hope this will benefit and encourage researchers conducting field studies or diagnostics to collect and preserve S. stercoralis for molecular genetic/genomic analyses and either analyze them themselves or make them available to others for further analysis.

A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing

Strongyloidiasis is a neglected tropical disease caused by the human infective nematodes Strongyloides stercoralis, Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. Previous large-scale studies exploring the genetic diversity of this important genus have focused on Southeast Asia, with a small number of isolates from the USA, Switzerland, Australia and several African countries having been genotyped. Consequently, little is known about the global distribution of geographic sub-variants of these nematodes and the genetic diversity that exists within the genus Strongyloides generally. We extracted DNA from human, dog and primate feces containing Strongyloides, collected from several countries representing all inhabited continents. Using a genotyping assay adapted for deep amplicon sequencing on the Illumina MiSeq platform, we sequenced the hyper-variable I and hyper-variable IV regions of the Strongyloides 18S rRNA gene and a fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene from these specimens. We report several novel findings including unique S. stercoralis and S. fuelleborni genotypes, and the first identifications of a previously unknown S. fuelleborni infecting humans within Australia. We expand on an existing Strongyloides genotyping scheme to accommodate S. fuelleborni and these novel genotypes. In doing so, we compare our data to all 18S and cox1 sequences of S. fuelleborni and S. stercoralis available in GenBank (to our knowledge), that overlap with the sequences generated using our approach. As this analysis represents more than 1,000 sequences collected from diverse hosts and locations, representing all inhabited continents, it allows a truly global understanding of the population genetic structure of the Strongyloides species infecting humans, non-human primates, and domestic dogs.

Strongyloidiasis is a neglected tropical disease caused by the human infective worms (nematodes) Strongyloides stercoralis, Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. Little is known about the genetic diversity of these nematodes and the possibility of geographically isolated genetic types is a particularly interesting research question, given the unique life cycle of these worms which includes both sexual and asexual stages. We extracted DNA from human, dog and primate feces containing Strongyloides, collected from several countries representing all inhabited continents. Using next-generation sequencing, we analyzed three Strongyloides DNA fragments from these specimens; two fragments of the 18S gene and one from the cytochrome c oxidase subunit 1 (cox1) gene. Using this approach, we discovered some unique S. stercoralis and S. fuelleborni genotypes, and identified a previously unknown S. fuelleborni infecting humans within Australia. We compared our data to all 18S and cox1 sequences of S. fuelleborni and S. stercoralis available in public databases and identified several patterns relating to the global distribution of certain genotypes. This knowledge could allow us to infer the origin of human Strongyloides infections in the future, and assess the role certain animals (non-human primates and dogs) might play in the transmission of Strongyloides to humans.