IL-4 gene polymorphisms and their association with nematodes infection in Pakistani population

Background: Interleukin-4 (IL-4) plays a central role in the humoral immune defense against nematode parasite infections, inducing IgE switch and regulation of worm expulsion from the intestines. The present study aimed to investigate the polymorphisms in IL-4 gene and their association with socio-demographic and environmental factors among patients with gastrointestinal complaints. Method: The screened population comprised 305 patients aged 3-50 years from Rawalpindi and Jhelum districts of Pakistan. A well-prepared questionnaire was administered to collect data on socio-demographic and environmental factors. The data were analyzed by using multiple logistic regression models. Molecular analysis was done on 88 confirmed cases passing worms and eggs in stool by using PCR to amplify IL-4 gene. Results: The result showed higher GI nematodes prevalence in Rawalpindi 34.87% and Jhelum 23.1% among gastrointestinal patients. The multivariate logistic regression model showed significantly (p<0.05) increased risk of infection in participants who were residing in rural areas (OR=321.94; 22.5), having poor economic status (OR=0.34), consuming raw/unwashed vegetables (OR=1.73; 15.39) and did not practice handwashing (OR=2.77; OR=0.30). Sequence analysis showed three novel polymorphisms at SNP g.704_705 ins T, g.3763_3764 ins AC and g.3792 G >A in patients with acute severe infections. Two known polymorphisms SNPs g.8455A>G and g.8492C>A were found in the intron region. Conclusion: IL-4 gene polymorphisms showed disease susceptibility and consuming raw/unwashed vegetables, poor handwashing practices and poor economic status were the most associated factors with the disease. Keywords: Interleukin-4; SNPs; Nematodes; Risk Factors; Pakistan

Molecular confirmation of Dicrocoelium dendriticum in the Himalayan ranges of Pakistan

Lancet liver flukes of the genus Dicrocoelium (Trematoda: Digenea) are recognised parasites of domestic and wild herbivores. The aim of the present study was to confirm the species identity of Dicrocoeliid flukes collected from the Chitral valley in the Himalayan ranges of Pakistan. The morphology of 48 flukes belonging to eight host populations was examined; but overlapping traits prevented accurate species designation. Phylogenetic comparison of published D. dendriticum ribosomal cistron DNA, and cytochrome oxidase-1 (COX-1) mitochondrial DNA sequences with those from D. chinensis was performed to assess within and between species variation and re-affirm the use of species-specific single nucleotide polymorphism markers. PCR and sequencing of 34 corresponding fragments of ribosomal DNA and 14 corresponding fragments of mitochondrial DNA from the Chitral valley flukes, revealed 10 and 4 unique haplotypes, respectively. These confirmed for the first time the molecular species identity of Pakistani lancet liver flukes as D. dendriticum. This work provides a preliminary illustration of a phylogenetic approach that could be developed to study the ecology, biological diversity, and epidemiology of Dicrocoeliid lancet flukes when they are identified in new settings.•First molecular confirmation of Dicrocoelium dendriticum in Himalayan Pakistan.•Use of ribosomal and mitochondrial DNA phylogenetic markers.•Demonstration of the complementary value of morphological and molecular speciation methods for Dicrocoeliid flukes

Validation of deep amplicon sequencing of Dicrocoelium in small ruminants from Northern regions of Pakistan.

Dicrocoelium lancet flukes cause significant production loss in ruminant livestock. Although co-infection with multiple Dicrocoelium species within a host is common, techniques for studying the composition of these complex parasite communities are lacking. The pathogenicity, epidemiology, and therapeutic susceptibility of different helminth species vary, and little is known about the interactions that take place between co-infecting species and their hosts. Here, we describe the first applicationof metabarcoding deep amplicon sequencingmethod to studythe Dicrocoelium species in sheep and goats. First, rDNA ITS-2 sequences of four Dicrocoelium species (Dicrocoelium dendriticum, Dicrocoelium hospes, Dicrocoelium orientalis, and Dicrocoelium chinensis) were extracted from the NCBI public database. Phylogenetic analysis revealed separate clades of Dicrocoelium species; hence, molecular differentiation between each species is possible in co-infections. Second, 202 flukes belonging to seventeen host populations (morphologically verified as belonging to the Dicrocoelium genus) were evaluated to determine the deep amplicon sequencing read thresholdof an individual fluke for each of the four species. The accuracy of the method in proportional quantification of samples collected from single hosts was further assessed. Overall, 198 (98.01%) flukes were confirmed as D. dendriticum and 1.98% produced no reads. The comparison of genetic distances between rDNA ITS-2 revealed 86% to 98% identity between the Dicrocoelium species. Phylogenetic analysis demonstrated a distinct clustering of species, apart from D. orientalis and D. chinensis, which sit very close to each other in a singlelarge clade whereas D. hospes and D. dendriticum are separated into their own clade. In conclusion each sample was identified as D. dendriticum based on the proportion of MiSeq reads and validated the presence of this group of parasites in the Gilgit Baltistan and Khyber Pakhtunkhwa provinces of Pakistan. The metabarcoding deep amplicon sequencing technology and bioinformatics pathway have several potential applications, including speciesinteractions during co-infections, identifying the host and geographical distribution of Dicrocoelium in livestock, drug therapy response evaluation and understanding of the emergence and spread of drug resistance

Identification of genetic variants associated with a wide spectrum of phenotypes clinically diagnosed as Sanfilippo and Morquio syndromes using whole genome sequencing

Mucopolysaccharidoses (MPSs) are inherited lysosomal storage disorders (LSDs). MPSs are caused by excessive accumulation of mucopolysaccharides due to missing or deficiency of enzymes required for the degradation of specific macromolecules. MPS I-IV, MPS VI, MPS VII, and MPS IX are sub-types of mucopolysaccharidoses. Among these, MPS III (also known as Sanfilippo) and MPS IV (Morquio) syndromes are lethal and prevalent sub-types. This study aimed to identify causal genetic variants in cases of MPS III and MPS IV and characterize genotype-phenotype relations in Pakistan. We performed clinical, biochemical and genetic analysis using Whole Genome Sequencing (WGS) in 14 Pakistani families affected with MPS III or MPS IV. Patients were classified into MPS III by history of aggressive behaviors, dementia, clear cornea and into MPS IV by short trunk, short stature, reversed ratio of upper segment to lower segment with a short upper segment. Data analysis and variant selections were made based on segregation analysis, examination of known MPS III and MPS IV genes, gene function, gene expression, the pathogenicity of variants based on ACMG guidelines and in silico analysis. In total, 58 individuals from 14 families were included in the present study. Six families were clinically diagnosed with MPS III and eight families with MPS IV. WGS revealed variants in MPS-associated genes including NAGLU, SGSH, GALNS, GNPTG as well as the genes VWA3B, BTD, and GNPTG which have not previously associated with MPS. One family had causal variants in both GALNS and BTD. Accurate and early diagnosis of MPS in children represents a helpful step for designing therapeutic strategies to protect different organs from permanent damage. In addition, pre-natal screening and identification of genetic etiology will facilitate genetic counselling of the affected families. Identification of novel causal MPS genes might help identifying new targeted therapies to treat LSDs

Molecular identification of Paramphistomum epiclitum (Trematoda: Paramphistomidae) infecting buffaloes in an endemic area of Pakistan

This study determined the molecular characterization of Paramphistomum epiclitumusing the second internal transcribed spacer (ITS-2) grouping and secondary structure analysis from buffaloes in Khyber Pakhtunkhwa province, Pakistan. Paramphistomes were collected from the rumen of 25 infected buffaloes and their DNA was separated. DNAwas intensified, followed by sequencing. Phylogenetic examinations were carried out using the Maximum Composite Likelihood approach. The results revealed extensive intraspecific and interspecific varieties among different paramphistomid species. The sequences in the present study (GenBank accession number: MW481321 and MW481322)were compared to 46 reference sequences of Paramphistomum and other trematode data from GenBank. The results revealed the existence of two genotypes of P. epiclitumwith six intraspecific single nucleotide polymorphisms, most closely associated with Indian isolates with an evolutionary divergence in the range of 0.00-0.015. The phylogenetic tree analysis of Paramphistomumspp. with other representative isolates in different locations clearly showed the existence of two P. epiclitumgenotypes in Pakistan. The derived secondary structures for both genotypes presented structural similarities with the core four-helix domain structure. Likewise, the results showed the phylogenetic utility of the ITS-2 sequence -secondary structure information for inductions at higher ordered levels and the need for accurate species identification. The results of this study also have implications for the diagnosis and control of rumen flukes in the region

Serological diagnostic potential of the 38-72 kDa somatic antigen of Gastrothylax crumenifer in buffaloes using the Indirect Enzyme-Linked Immunosorbent Assay

Paramphistomosis, caused by digenetic trematodes of the superfamily Paramphistomoidea, causes heavy economic losses in terms of reduced fertility, milk, and meat production in the livestock industry. In the present study, somatic and excretory-secretory antigens isolated from 500 live Gastrothylax crumenifer were assessed for their diagnostic potential by using an antibody detection enzyme immunoassay. Before the enzyme immunoassay, the somatic and excretory/secretory (ES) antigens of G. crumenifer were subjected to SDS-PAGE and Western blot (WB) for the detection of immunogenic proteins. Indirect ELISA analysis was performed on sera from buffalos naturally infected with G. crumenifer, with control sera of buffalos infected with Gigantocotyle explanatum,Fasciola spp., Cot-ylophoron /Paramphistomum spp. The SDS-PAGE results of the somatic products of G. crumenifer identified proteins were between 10-123 kDa, showing a maximum abundance of 10, 15, 25-28, 36, 38-72, 95-123 kDa proteins. The most abundant proteins recorded in ES products were ≥95, 72, 55, and 40 kDa. The antigenic analysis of somatic proteins using WB revealed reactive polypeptides of a size between 55-70 kDa, while metabolic extracts did not show reactivity with naturally infected buffalo sera. The sensitivity and specificity of the ELISA test for 38-72 kDa somatic antigens were 85.71% and 89.74%, respectively. The cross-reactivity with other trematode sera was 16-20%. Antibodies were tested against the 38-72 kDa somatic antigens, and 19.69% (39/198) of buffalos were found positive, while 12.1% (24/198) presented infection in the faecal/postmortem examination. The study confirmed that ELISA established for the 38-72 kDa somatic antigens of G. crumenifer had diagnostic potential against paramphistome infections