PCR-based Species-Specific Amplification of ITS of Mecistocirrus digitatus and Its Application in Identification of GI Nematode Eggs in Bovine Faeces

Morphological and molecular identification of Cyclospora species in sheep and goat at Tamil Nadu, India

A total of 281 fresh fecal samples (65 sheeps and 216 goats) were examined for the presence of Cyclospora species in Tamil Nadu from October 2017 to April 2018. All the faecal samples were examined by direct smear method, saturated sucrose floatation technique and modified Ziehl-Neelsen staining method and it was confirmed-at genus level with PCR technique. Overall prevalence of Cyclospora infection in-small ruminant was 2.14%. The prevalence of Cyclospora species in sheep and goat was 3.08 and 1.85% respectively. Cyclospora oocyst was observed mostly during winter season (Dec-Feb) with 7.14% followed by summer (March and April) and Northeast mansoon (October and November) with 1.67 and 1.66% respectively. The oocyst detected from faecal sample through conventional faecal examination was confirmed by PCR.

Gross, histopathology and molecular diagnosis of oesophagostomosis in sheep

A total of 120 tissue samples (Rumen, reticulum, omasum, abomasum, small intestine and large intestine) were collected from slaughter houses in Chennai, Kanchipuram and Tiruvallur districts and five samples from necropsy room at Department of Veterinary Pathology, Madras Veterinary College, Chennai, Tamil Nadu. Overall prevalence of GI parasites was 52.00%. Among the positive samples, single infection was found to be more (53.84%) than themixed infection (46.15%). Out of which, oesophagostomosis was 17.00% and found as single infection. In oesophagostomosis, significant gross lesions observed in the small and large intestine were multiple small to large, round to irregular, hard, fibrotic, raised nodules. The wall of the large intestine was greatly thickened and oedematous and the nodules were seen projecting into the lumen and mucosal surface was intact. On histopathological examination, ileum of sheep showed parasitic nodules with central baso-eosinophilic necrotic area, larval stages in the necrotic area, surrounded by layers of inflammatory cells and finally encapsulated in a thick fibrous connective tissue capsule. Immunohistochemistry (IHC) with Vimentin showed intense cytoplasmic positive signals DAB Brown. PCR was carried out targeting ITS2 regions of the O. columbianum and O. venulosum. DNA isolated from both the faecal eggs and adult worms showed good amplification.

Genotyping of benzimidazole resistant and susceptible isolates of Haemonchus contortus from sheep by allele specific PCR

Extensive and indiscriminate use of the benzimidazole class of drugs has led to the onset of anthelmintic resistance. In tropical countries like India, Haemonchus contortus is the most pathogenic parasite infecting sheep and goats. The widespread presence of resistant helminths (especially H. contortus) threatens the livestock farming. The use of various drugs has led to single nucleotide polymorphism that causes specific amino acid substitutions in β-tubulin protein of H. contortus to confer resistance. This emphasizes the need for a survey on the present status of resistance in India. In this study, allele specific PCR was employed to screen the presence of a SNP, a thymine-to-adenine transversion which leads to substitution of amino acid in codon 200 of β-tubulin gene that is correlated specifically with BZ resistance. Third stage larvae (L3) from pooled faecal cultures of four organized sheep farms served as a source of genomic DNA for identification of H. contortus and further genotype analysis. A total of 1000 larvae was screened, out of which 673 larvae were identified as H. contortus. Among 673 H. contortus larvae, 539 larvae (80 %) were genotyped as homozygous resistant (rr) and remaining 134 (20 %) were heterozygous susceptible (Sr) by allele specific PCR. The concluded resistance status reasons out the failure of anthelmintic drug in treating ruminants. Immediate steps are needed to avoid further aggravation of the problem. Target selective treatment by reviewing the resistance status of individual drugs, appropriate use of anthelmintic drugs and other control strategies will provide a pragmatic option for delaying the further spread of anthelmintic resistance.

Exploring the Gastrointestinal "Nemabiome": Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities

Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. We describe the first application of deep amplicon sequencing to study parasitic nematode communities as well as introduce the concept of the gastro-intestinal “nemabiome”. The approach is analogous to 16S rDNA deep sequencing used to explore microbial communities, but utilizes the nematode ITS-2 rDNA locus instead. Gastro-intestinal parasites of cattle were used to develop the concept, as this host has many well-defined gastro-intestinal nematode species that commonly occur as complex co-infections. Further, the availability of pure mono-parasite populations from experimentally infected cattle allowed us to prepare mock parasite communities to determine, and correct for, species representation biases in the sequence data. We demonstrate that, once these biases have been corrected, accurate relative quantitation of gastro-intestinal parasitic nematode communities in cattle fecal samples can be achieved. We have validated the accuracy of the method applied to field-samples by comparing the results of detailed morphological examination of L3 larvae populations with those of the sequencing assay. The results illustrate the insights that can be gained into the species composition of parasite communities, using grazing cattle in the mid-west USA as an example. However, both the technical approach and the concept of the ‘nemabiome’ have a wide range of potential applications in human and veterinary medicine. These include investigations of host-parasite and parasite-parasite interactions during co-infection, parasite epidemiology, parasite ecology and the response of parasite populations to both drug treatments and control programs.

New multiplex PCR method for the simultaneous diagnosis of the three known species of equine tapeworm

Although several techniques exist for the detection of equine tapeworms in serum and feces, the differential diagnosis of tapeworm infection is usually based on postmortem findings and the morphological identification of eggs in feces. In this study, a multiplex polymerase chain reaction (PCR)-based method for the simultaneuos detection of Anoplocephala magna, Anoplocephala perfoliata and Anoplocephaloides mamillana has been developed and validated. The method simultaneously amplifies hypervariable SSUrRNA gene regions in the three tapeworm species in a single reaction using three pairs of primers, which exclusively amplify the internal transcribed spacer 2 (ITS-2) in each target gene. The method was tested on three types of sample: (a) 1/10, 1/100, 1/500, 1/1000, 1/2000 and 1/5000 dilutions of 70 ng of genomic DNA of the three tapeworm species, (b) DNA extracted from negative aliquots of sediments of negative control fecal samples spiked with 500, 200, 100, 50 and 10 eggs (only for A. magna and A. perfoliata; no A. mamillana eggs available) and (c) DNA extracted from 80, 50, 40, 30, 10 and 1 egg per 2 μl of PCR reaction mix (only for A. magna and A. perfoliata; no A. mamillana eggs available). No amplification was observed against the DNA of Gasterophilus intestinalis, Parascaris equorum and Strongylus vulgaris. The multiplex PCR method emerged as specific for the three tapeworms and was able to identify as few as 50 eggs per fecal sample and as little as 0.7 ng of control genomic DNA obtained from the three species. The method proposed is able to differentiate infections caused by the two most frequent species A. magna or A. perfoliata when the eggs are present in feces and is also able to detect mixed infections by the three cestode species.

Molecular and phylogenetic study on Toxocara vitulorum from cattle in the mid-Delta of Egypt

Toxocara vitulorum is an important intestinal nematode that commonly infects ruminants world-wide, notably in tropical and sub-tropical regions. In Egypt, T. vitulorum has a high prevalence rate in cattle and buffaloes calves. The current work aims to identify and verify T. vitulorum collected from cattle in El-Mahlla El-Kubra city in the mid-Delta of Egypt, using molecular and phylogenetic tools. The first internal transcribed spacer (ITS-1) and 18S genes of ribosomal DNA were amplified, sequenced, and compared with nucleotide sequences deposited in data bases, and also used to construct the phylogenetic trees. Our results confirm that T. vitulorum isolated from cattle in Egypt is genetically identical to those recorded in other countries. Moreover, the phylogenetic trees show a close relationship among different species of Toxocara, including the zoonotic species. Our results show that ITS genes can be targeted as genetic markers to diagnose and discriminate among different Toxocara spp. The data presented here may be helpful in the pursuit of further molecular and genetic studies of Toxocara species.

Development and validation of real-time PCR for rapid detection of Mecistocirrus digitatus

Hematophagous activity of Mecistocirrus digitatus, which causes substantial blood and weight loss in large ruminants, is an emerging challenge due to the economic loss it brings to the livestock industry. Infected animals are treated with anthelmintic drugs, based on the identification of helminth species and the severity of infection; however, traditional methods such as microscopic identification and the counting of eggs for diagnosis and determination of level of infection are laborious, cumbersome and unreliable. To facilitate the detection of this parasite, a SYBR green-based real-time PCR was standardized and validated for the detection of M. digitatus infection in cattle and buffaloes. Oligonucleotides were designed to amplify partial Internal Transcribed Spacer (ITS)-1 sequence of M. digitatus. The specificity of the primers was confirmed by non-amplification of DNA extracted from other commonly occurring gastrointestinal nematodes in ruminants. Plasmids were ligated with partial ITS-1 sequence of M. digitatus, serially diluted (hundred fold) and used as standards in the real-time PCR assay. The quantification cycle (Cq) values were plotted against the standard DNA concentration to produce a standard curve. The assay was sensitive enough to detect one plasmid containing the M. digitatus DNA. Clinical application of this assay was validated by testing the DNA extracted from the faeces of naturally infected cattle (n = 40) and buffaloes (n = 25). The results were compared with our standard curve to calculate the quantity of M. digitatus in each faecal sample. The Cq value of the assay depicted a strong linear relationship with faecal DNA content, with a regression coefficient of 0.984 and efficiency of 99%. This assay has noteworthy advantages over the conventional methods of diagnosis because it is more specific, sensitive and reliable.

Molecular basis for identification of species/isolates of gastrointestinal nematode parasites

Gastrointestinal (GI) parasitism is the most serious constraint throughout the world in small ruminants which causes significant production loss in animals. GI parasites are major contributor to reduce productivity in terms of meat, milk and wool in animals. Control of GI parasite is done primarily by anthelmintic treatment where choice and schedule of treatment is done after identification and quantitation of individual parasite. Identification of GI parasites is done through microscopic method by identifying specific morphological characteristics of egg and larva (L(3)). Since most of parasite eggs are having similar morphological characteristics, identification up to species level through microscopy is not possible in most of cases. To address this issue, molecular techniques are the viable alternative for identification of species as well as molecular level differences within a species (isolates) of parasites. Different DNA based molecular techniques viz. PCR, AFLP, RAPD, RFLP, PCR-SSCP, real time PCR, DNA microarray etc. have been used for identification and to assess the genetic diversity among parasite population. For identification of species, the characteristic sequence of genomic DNA of different species should differ to allow the delineation of species, but at the same time, no/minor variation within the species should exist. In contrast, for purpose of identifying population variants (strains/isolates), a considerable degree of variation in the sequence should exist within a species. Various target regions, including nuclear ribosomal DNA (rDNA), mitochondrial DNA (mtDNA) or repetitive DNA elements (microsatellite loci), which show considerable variation in the number of repeats within individuals have been employed to achieve the identification of parasites species or strain.

Multiplex PCR on single unembryonated Ascaris (roundworm) eggs

A sensitive and inexpensive method for DNA isolation and amplification by polymerase chain reaction (PCR) from single unembryonated Ascaris sp. eggs is described. The resistant shell of single eggs was crushed mechanically and PCR applied to the crude egg contents without any further purification steps. The ITS1 region of the rDNA and three regions of the mtDNA could be successfully amplified. Using two primer sets, it was possible to amplify the rDNA and mtDNA simultaneously in one single reaction. The ability to perform PCR on single unembryonated eggs may result in better and more precise species identification of eggs recovered from faecal material, environmental samples and possibly archaeological samples. In addition, single egg PCR makes it possible to perform population genetic studies without having to recover adult worms by deworming or autopsy.