Multiplex PCR on single unembryonated Ascaris (roundworm) eggs

Development of allele-specific PCR methodology (AS-PCR) to screening A. lumbricoides and A. suum

Ascaris lumbricoides and Ascaris suum are described as helminths that infect humans and pigs, respectively. It is estimated that infection by A. lumbricoides affects about 447 million individuals living in tropical regions of developing countries. However, there is an increasing number of cases of human ascariasis in countries with no recent history of autochthonous infection by A. lumbricoides. In these places, pigs have been incriminated as the main source of human infection. Conventional parasitological diagnosis does not allow species-specific identification, and the real epidemiological scenario of human and swine ascariasis is still uncertain. Therefore, this work presents the application of a species-specific molecular diagnosis, based on the allele-specific PCR methodology (AS-PCR), using the Internal Transcript Space 1 (ITS-1) of the ribosomal DNA, as a target for differentiating between the two species, using DNA obtained from eggs. To validate the methodology, stool samples positive for Ascaris spp, were obtained from 68 humans from seven Brazilian states and from six pigs from the state of Minas Gerais. All samples obtained from humans were genotyped as A. lumbricoides and all samples obtained from swine were genotyped as A. suum. These results are in agreement with the literature, which demonstrates that in most endemic regions, transmission cycles are separate. Therefore, the execution of this work allowed the availability of a useful methodology for the differential diagnosis of the species, which may contribute to the characterization of the real epidemiological profile of human and swine ascariasis, and to the implementation of future control strategies.

Intestinal parasites of dogs (Canis lupus familiaris) in Svalbard (Norway): low prevalence and limited transmission with wildlife

Domesticated dogs (Canis lupus familiaris Linnaeus, 1758) are widely kept on all continents and could share parasites with free-living animals. To understand the transmission of intestinal parasites between dogs kept on the four dog stations and wildlife in Svalbard, 170 faecal samples from dogs and 203 faecal samples from wildlife, including Arctic fox (Vulpes lagopus (Linnaeus, 1758); n = 62), Svalbard reindeer (Rangifer tarandus platyrhynchus (Vrolik, 1829); n = 106), sibling vole (Microtus levis Miller, 1908; n = 63), Pink-footed Goose (Anser brachyrhynchus Baillon, 1834; n = 30), Little Auk (Alle alle (Linnaeus, 1758); n = 49), and Black-legged Kittiwake (Rissa tridactyla (Linnaeus, 1758); n = 18), were individually screened for the presence of intestinal parasites using microscopy and PCR and nucleotide sequencing methods. Additionally, the results of the study were compared with previous studies performed in the same area. The roundworm Toxascaris leonina (Linstow, 1902) was found microscopically and by PCR in a dog (n = 1). The specific DNA of three species of parasitic protists was detected in dogs from different yards. Phylogenetic analyses revealed the presence of Cryptosporidium canis Fayer, Trout, Xiao, Morgan, Lal and Dubey, 2001 (n = 1), Encephalitozoon cuniculi Levaditi, Nicolau and Schoen, 1923 genotype II (n = 4), and dog-specific Enterocytozoon bieneusi Desportes, Le Charpentier, Galian, Bernard, Cochand-Priollet, Lavergne, Ravisse and Modigliani, 1985 genotypes (n = 12). This study showed overall a low prevalence of intestinal parasites in dogs in Svalbard and possible but minimal transmission with wildlife.

Assessment of the exposure to Echinococcus multilocularis associated with carnivore faeces using real-time quantitative PCR and flotation technique assays

The eggs of Echinococcus multilocularis, the infectious stage, are spread into the environment through wild and domestic carnivore faeces. The spatial location of the faeces containing infective E. multilocularis eggs is a key parameter for studying areas of exposure and understanding the transmission processes to the intermediate hosts and humans. Echinococcus multilocularis faecal prevalence is often assessed by detecting E. multilocularis DNA, not necessarily eggs. This work aimed to determine the percentage of faeces containing E. multilocularis eggs in a rural town and its surroundings and whether this level of precision is relevant in assessing exposure to E. multilocularis. For this purpose, we developed a combined molecular and microscopic approach to investigate the E. multilocularis exposure of potential hosts in the environment from field-collected carnivore faeces. Carnivore defecation patterns were then spatialized to study the spatial distribution of E. multilocularis. Faeces were screened for E. multilocularis DNA using a specific real-time quantitative PCR (qPCR). Echinococcus multilocularis eggs were morphologically identified from E. multilocularis-specific qPCR-positive faeces after sucrose flotation and individually confirmed through specific PCR and sequencing. The spatial distribution of E. multilocularis was studied using Kulldorff statistics. Echinococcus multilocularis eggs were identified mostly in fox faeces positive for E. multilocularis DNA by qPCR (n = 27/70) and only from 1 of 15 copro-samples from dogs and 1 of 5 from cats. The faecal prevalence of E. multilocularis DNA and eggs was overdispersed, with the same geographical patterns. These data suggest that E. multilocularis DNA and/or egg detection in carnivore faeces, mainly that of foxes, is appropriate in ecological studies of E. multilocularis transmission.

Gastrointestinal parasites of arctic foxes (Vulpes lagopus) and sibling voles (Microtus levis) in Spitsbergen, Svalbard

The arctic fox (Vulpes lagopus), an apex predator with an omnipresent distribution in the Arctic, is a potential source of intestinal parasites that may endanger people and pet animals such as dogs, thus posing a health risk. Non-invasive methods, such as coprology, are often the only option when studying wildlife parasitic fauna. However, the detection and identification of parasites are significantly enhanced when used in combination with methods of molecular biology. Using both approaches, we identified unicellular and multicellular parasites in faeces of arctic foxes and carcasses of sibling voles (Microtus levis) in Svalbard, where molecular methods are used for the first time. Six new species were detected in the arctic fox in Svalbard, Eucoleus aerophilus, Uncinaria stenocephala, Toxocara canis, Trichuris vulpis, Eimeria spp., and Enterocytozoon bieneusi, the latter never found in the arctic fox species before. In addition, only one parasite was found in the sibling vole in Svalbard, the Cryptosporidium alticolis, which has never been detected in Svalbard before.

Molecular analysis of human- and pig-derived Ascaris in Honduras

Ascaris sp. is a soil-transmitted helminth (STH) significantly affecting the health of human and swine populations. Health inequities and poverty, with resulting deficiencies in water, sanitation and hygiene, are directly associated with Ascaris lumbricoides prevalence in humans. Resource constraints also lead to small-scale livestock production under unsanitary conditions. Free-ranging pigs, for instance, are exposed to a number of infectious agents, among which Ascaris suum is one of the most common. Under these conditions, close proximity between people and pigs can result in cross-contamination; that is, pigs harbouring human Ascaris and vice versa. Moreover, the potential interbreeding between these two Ascaris species has been demonstrated. The present study analysed Ascaris worms obtained from children and pigs in Honduras. Adult worms were collected from stool samples of children after pharmacological treatment, and from pigs’ intestines after slaughter for commercial purposes at a local abattoir. A nuclear ribosomal internal transcribed spacer (ITS) region was amplified by polymerase chain reaction (PCR) and digested with a restriction enzyme in order to separate putative human- and pig-derived Ascaris isolates. PCR products were also sequenced, and cladograms were constructed. All parasites isolated from children showed the typical human-derived genotype of Ascaris, whereas 91% of parasites from pigs showed the expected pig-derived genotype. Cross-infections between hosts were not demonstrated in this study. Nine per cent of pig-derived worms showed a restriction band pattern highly suggestive of a hybrid human–pig Ascaris genotype. These results contribute to the understanding of ascariasis epidemiology and its zoonotic potential in a highly endemic region.

Isothermal diagnostic assays for the detection of soil-transmitted helminths based on the SmartAmp2 method

Background

Diagnosis of soil-transmitted helminths (STHs) has traditionally relied on stool microscopy, which has a number of critical deficiencies. Molecular diagnostics are powerful tools to identify closely related species, but the requirement for costly equipment makes their implementation difficult in low-resource or field settings. Rapid, sensitive and cost-effective diagnostic tools are crucial for accurate estimation of STH infection intensity in MDA programmes in which the goal is to reduce morbidity following repeated rounds of chemotherapy.

Results

In this study, colourimetric isothermal assays were developed using SmartAmp2 primer sets and reagents in loop-mediated amplification (LAMP) assays. Species-specific primer sets, designed on a specific target sequence in the β-tubulin gene, were used to identify Necator americanus, Trichuris trichiura and Ascaris lumbricoides. After initial optimization on control plasmids and genomic DNA from adult worms, assays were evaluated on field samples. Assays showed high sensitivity and demonstrated high tolerance to inhibitors in spiked faecal samples. Rapid and sensitive colourimetric assays were successfully developed to identify the STHs in field samples using hydroxy napthol blue (HNB) dye.

Conclusions

Rapid and simple colourimetric diagnostic assays, using the SmartAmp2 method, were developed, with the potential to be applied in the field for detection of STH infections and the estimation of response to treatment. However, further validation on large numbers of field samples is needed.

Electronic supplementary material

The online version of this article (10.1186/s13071-017-2420-1) contains supplementary material, which is available to authorized users.

Human Ascariasis: Diagnostics Update

Soil-transmitted helminths (STHs) infect over one billion people worldwide. Ascariasis may mimic a number of conditions, and individual clinical diagnosis often requires a thorough work-up. Kato-Katz thick smears are the standard detection method for Ascaris and, despite low sensitivity, are often used for mapping and monitoring and evaluation of national control programmes. Although increased sampling (number of stools) and diagnostic (number of examinations per stool) efforts can improve sensitivity, Kato-Katz is less sensitive than other microscopy methods such as FLOTAC®. Antibody-based diagnostics may be a sensitive diagnostic tool; however, their usefulness is limited to assessing transmission in areas aiming for elimination. Molecular diagnostics are highly sensitive and specific, but high costs limit their use to individual diagnosis, drug - efficacy studies and identification of Ascaris suum. Increased investments in research on Ascaris and other STHs are urgently required for the development of diagnostic assays to support efforts to reduce human suffering caused by these infections.

Genetic blueprint of the zoonotic pathogen Toxocara canis

Toxocara canis is a zoonotic parasite of major socioeconomic importance worldwide. In humans, this nematode causes disease (toxocariasis) mainly in the under-privileged communities in developed and developing countries. Although relatively well studied from clinical and epidemiological perspectives, to date, there has been no global investigation of the molecular biology of this parasite. Here we use next-generation sequencing to produce a draft genome and transcriptome of T. canis to support future biological and biotechnological investigations. This genome is 317 Mb in size, has a repeat content of 13.5% and encodes at least 18,596 protein-coding genes. We study transcription in a larval, as well as adult female and male stages, characterize the parasite’s gene-silencing machinery, explore molecules involved in development or host–parasite interactions and predict intervention targets. The draft genome of T. canis should provide a useful resource for future molecular studies of this and other, related parasites.

Toxocara canis is a zoonotic parasite of major worldwide socioeconomic importance. Here, the authors sequence the genome and transcriptome of T. canis, and highlight potential mechanisms involved in development and host–parasite interactions that could support the pursuit of new drug interventions.

Genetic variations in the beta-tubulin gene and the internal transcribed spacer 2 region of Trichuris species from man and baboons

BACKGROUND

The whipworm Trichuris trichiura has been estimated to infect 604 - 795 million people worldwide. The current control strategy against trichuriasis using the benzimidazoles (BZs) albendazole (400 mg) or mebendazole (500 mg) as single-dose treatment is not satisfactory. The occurrence of single nucleotide polymorphisms (SNPs) in codons 167, 198 or 200 of the beta-tubulin gene has been reported to convey BZ-resistance in intestinal nematodes of veterinary importance. It was hypothesised that the low susceptibility of T. trichiura to BZ could be due to a natural occurrence of such SNPs. The aim of this study was to investigate whether these SNPs were present in the beta-tubulin gene of Trichuris spp. from humans and baboons. As a secondary objective, the degree of identity between T. trichiura from humans and Trichuris spp. from baboons was evaluated based on the beta-tubulin gene and the internal transcribed spacer 2 region (ITS2).

METHODS

Nucleotide sequences of the beta-tubulin gene were generated by PCR using degenerate primers, specific primers and DNA from worms and eggs of T. trichiura and worms of Trichuris spp. from baboons. The ITS2 region was amplified using adult Trichuris spp. from baboons. PCR products were sequenced and analysed. The beta-tubulin fragments were studied for SNPs in codons 167, 198 or 200 and the ITS2 amplicons were compared with GenBank records of T. trichiura.

RESULTS

No SNPs in codons 167, 198 or 200 were identified in any of the analysed Trichuris spp. from humans and baboons. Based on the ITS2 region, the similarity between Trichuris spp. from baboons and GenBank records of T. trichiura was found to be 98 - 99%.

CONCLUSIONS

Single nucleotide polymorphisms in codon 167, 198 and 200, known to confer BZ-resistance in other nematodes, were absent in the studied material. This study does not provide data that could explain previous reports of poor BZ treatment efficacy in terms of polymorphism in these codons of beta-tubulin. Based on a fragment of the beta-tubulin gene and the ITS2 region sequenced, it was found that T. trichiura from humans and Trichuris spp. isolated from baboons are closely related and may be the same species.

Phylogenetic analysis of Pomacea canaliculata isolates collected from rice fields in different origins of China by combined mitochondrial 12S and 16S genes

To study the genetic relationships of Pomacea canaliculata collected from rice fields in China, the mitochondrial (mt) 12S and 16S of 9 P. canaliculata isolates from 5 southern provinces in China were sequenced and analyzed. The intra-specific sequence variations of P. canaliculata were 0-1.1% for 12S and 0--0.6% for 16S, while the inter-specific variations among common Pomacea species in mt 12S and 16S were 3.0-11.7% and 2.3-10.1%, respectively. Phylogenetic analysis based on combined sequences of mt 12S and 16S revealed complex genetic structure of P. canaliculata in China. Two phylogenetic groups of P. canaliculata were indicated in China with one group sistered to P. canaliculata isolates from USA, and two groups were even found in the same province. The phylogenetic relationships of Pomacea spp. also could be effectively inferred by combined sequences of mt 12S and 16S. These findings provided basic information for further study of population genetics and diffusion pattern of P. canaliculata in China as well as in the world.

Clarifying Prehistoric Parasitism from a Complementary Morphological and Molecular Approach

This paper reports an approach to the identification of prehistoric parasitic infection, which integrates traditional morphological methods with molecular methods. The approach includes the strengths of each method while mitigating the limitations. Demonstrating the efficacy of this approach, we provide a case study from a 1,400 year old desiccated fecal sample from La Cueva de los Muertos Chiquitos, archaeological site, near Rio Zape, Durango, Mexico. Traditionally prepared microscope slides were processed via microscopy and tentative ascarids were identified. Information regarding the parasites' developmental stage was recorded. DNA was then extracted directly from the slide material. From this DNA extract, a small segment of the 18S ribosomal RNA gene variant that is specific to Ascaris, and its phylogenetically close relatives, was targeted for PCR amplification and sequencing. Phylogenetic analysis of the DNA sequence best matched a member of physalopterids, rather than ascarids, with a single exception of a match to Contracaecum spiculigerum. Subsequent extractions, amplifications and sequencing of the original rehydrated coprolite material confirmed these results. The C. spiculigerum sequence represented a phylogenetic anomaly and subsequent analysis determined the sequence was an error in the BLAST database, likely attributable to misidentification of juvenile specimens prior to sequencing and submission. Physaloptera are a difficult genus to identify morphologically and can carry major health burdens. They may be underreported in humans, in part, because of morphological similarities to the more common human parasites belonging to ascarids. We conclude that integrating traditional morphological methods with molecular methods can help resolve this issue, in both contemporary and prehistoric populations.

Real-time PCR detection for quantification of infection levels with Ostertagia ostertagi and Cooperia oncophora in cattle faeces

A quantitative real-time polymerase chain reaction (qPCR) based on hydrolysis (TaqMan) probes is described for robust and sensitive detection of the infection levels with eggs and third stage larvae (L3) of Cooperia oncophora and Ostertagia ostertagi isolated from cattle faeces. The current microscopic method for identification of strongyle nematodes in cattle faeces is labour-intensive where reliable species determination also requires trained expertise, which is increasingly lacking. The goal of this study was to develop a sustainable non-labour intensive diagnostic qPCR assay to detect and determine the levels of infection with the two most common gastro-intestinal nematodes (GIN) in cattle faeces targeting the second internal transcribed spacer of nuclear ribosomal DNA (ITS2) region (rDNA). According to our results, this procedure allows to reliably detect the relative proportions of eggs and L3 for each of the two species. This assay produced consistent results when mixtures with known numbers of L3 of both species were tested, although it was also demonstrated that the calculated copy numbers of ITS2 between single L3 sometimes varied very much. In addition, a positive correlation (r(2)=0.23) between the proportion of eggs and L3 in different paired samples collect in the field was observed for both species. Thus, for the first time a qPCR assay is reported, which can discriminate between the two most important cattle nematode parasites in temperate regions. This is of major importance to the livestock sector as it can be used with great precision to demonstrate strategic treatment efficacy that is important for the detection of anthelmintic resistance (AR).

Genetic variability of Baylisascaris schroederi from the Qinling subspecies of the giant panda in China revealed by sequences of three mitochondrial genes

The present study examined the variations in three mitochondrial (mt) DNA sequences, namely cytochrome b (cytb), cytochrome c oxidase subunit 3 (cox3) and NADH dehydrogenase subunit 5 (nad5), among Baylisascaris schroederi isolates from the Qinling subspecies of the giant panda in Shaanxi province, northwestern China. No differences in length were detected in the three mt fragments from different isolates. The intra-specific sequence variations within all B. schroederi samples were 0-2.6% for pcytb, 0-1.8% for pcox3 and 0-2.1% for pnad5, while the inter-specific sequence differences among members of the genus Baylisascaris were 8.2-15.2%, 6.2-15.9% and 8.4-16.0% for pcytb, pcox3, pnad5, respectively. A phylogenetic analysis of the combined sequences of pcytb, pcox3 and pnad 5 showed that all B. schroederi samples in the present study were located in two large clusters, with one cluster containing samples from giant pandas in Sichuan province. These findings provide basic information for further study of molecular epidemiology and control of B. schroederi infection in the Qinling subspecies of the giant panda and throughout China.

Genetic variation in mitochondrial DNA among Enterobius vermicularis in Denmark

Despite being the most prevalent nematode infections of man in Western Europe and North America, our knowledge of the genetic variability in Enterobius vermicularis is fragmented. We here report on a genetic study of pinworms in Denmark, performed using the cytochrome oxidase I (cox1) gene, with DNA extracted from individual eggs collected from clinical (human) samples. We collected cellophane-tape-test samples positive for pinworm eggs from 14 Departments of Clinical Microbiology in Denmark and surface-sterilized the eggs using a 1% hypochlorite solution before performing conventional PCR. Twenty-two haplotypes were identified from a total of 58 Danish patients. Cluster analysis showed that all Danish worms grouped together with human samples from Germany and Greece and with samples from Japanese chimpanzees designated as ‘type B’. Analysis of molecular variance showed no significant difference or trends in geographical distribution of the pinworms in Denmark, and several haplotypes were identical or closely related to samples collected in Germany, Greece and Japan. However, worms from the 4 countries were found to belong to different populations, with Fst values in the range of 0·16 to 0·47. This study shows pinworms in Denmark to be a homogenous population, when analysed using the cox1 mitochondrial gene.

Determination of Baylisascaris schroederi infection in wild giant pandas by an accurate and sensitive PCR/CE-SSCP method

It has been recognized that other than habitat loss, degradation and fragmentation, the infection of the roundworm Baylisascaris schroederi (B. schroederi) is one of the major causes of death in wild giant pandas. However, the prevalence and intensity of the parasite infection has been inconsistently reported through a method that uses sedimentation-floatation followed by a microscope examination. This method fails to accurately determine infection because there are many bamboo residues and/or few B. schroederi eggs in the examined fecal samples. In the present study, we adopted a method that uses PCR and capillary electrophoresis combined with a single-strand conformation polymorphism analysis (PCR/CE-SSCP) to detect B. schroederi infection in wild giant pandas at a nature reserve, and compared it to the traditional microscope approach. The PCR specifically amplified a single band of 279-bp from both fecal samples and positive controls, which was confirmed by sequence analysis to correspond to the mitochondrial COII gene of B. schroederi. Moreover, it was demonstrated that the amount of genomic DNA was linearly correlated with the peak area of the CE-SSCP analysis. Thus, our adopted method can reliably detect the infectious prevalence and intensity of B. schroederi in wild giant pandas. The prevalence of B. schroederi was found to be 54% in the 91 fecal samples examined, and 48% in the fecal samples of 31 identified individual giant pandas. Infectious intensities of the 91 fecal samples were detected to range from 2.8 to 959.2 units/gram, and from 4.8 to 959.2 units/gram in the fecal samples of the 31 identified giant pandas. For comparison, by using the traditional microscope method, the prevalence of B. schroederi was found to be only 33% in the 91 fecal samples, 32% in the fecal samples of the 31 identified giant pandas, and no reliable infectious intensity was observed.

Molecular detection of Capillaria aerophila, an agent of canine and feline pulmonary capillariosis

Capillaria aerophila, a trichuroid nematode causing pulmonary infections in wild and domestic carnivores, is occasionally and potentially poorly recognized in infections of humans due to clinicopathological mimicry and a lack of accurate, robust laboratory diagnostics. The present work evaluated the efficiency of a DNA-based assay amplifying a partial cytochrome c oxidase subunit 1 (cox1) gene of C. aerophila in the diagnosis of lung capillariosis. Fecal samples from 34 dogs and 10 cats positive at parasitological examination for C. aerophila and other endoparasites (i.e., other lungworms, whipworms, roundworms, hookworms, tapeworms, and/or coccidia) and from 44 animals negative for C. aerophila but positive for other endoparasites were molecularly examined. Of the 44 samples positive for C. aerophila at copromicroscopy, 43 scored positive (i.e., 33/34 dogs and 10/10 cats) in seminested PCR, resulting in a sensitivity of 97 to 100%. Samples that were copromicroscopy negative for C. aerophila although positive for other endoparasites never produced a PCR product or nonspecific amplicons. The specific PCR amplification of C. aerophila (i.e., specificity of 100%) was confirmed by a nucleotide sequence analysis of the cox1 amplicons. The potential implications of the molecular diagnosis of lung capillariosis are discussed.

Molecular evidence for sustained transmission of zoonotic Ascaris suum among zoo chimpanzees (Pan troglodytes)

Chimpanzees in the Copenhagen Zoo frequently excrete ascarid worms onto the cage floor in spite of a regular anthelmintic treatment program. Previously it had been shown that the source of the infections was of pig origin. However, it was unknown whether the recurrence of the infection was due to reintroduction of eggs from an external source or to a sustained transmission cycle within the zoo. We found that isolated eggs were able to embryonate to the infective J3 stage and PCR-RFLP analysis on the ITS region amplified from single embryonated eggs suggest these to be Ascaris suum. In addition, sequence analysis of the cox1 gene ('barcoding') on expelled worms followed by cluster analysis revealed that the chimpanzees are infected with pig A. suum which now, in spite of control efforts, has stabilized into a permanent transmission cycle in the zoo's chimpanzee troop.