Gene flow for Echinococcus granulosus metapopulations determined by mitochondrial sequences: A reliable approach for reflecting epidemiological drift of parasite among neighboring countries

Global distribution and definitive host range of Echinococcus species and genotypes: A systematic review

Echinococcus species (spp.) are regarded as neglected cestodes causing several potential zoonoses of global public health. This systematic review critically appraises the worldwide distribution of Echinococcus spp. and genotypes (Echinococcus spp.: recognized species in the genus; genotypes: variants identified within E. granulosus sensu lato.) in definitive hosts. We analyzed 82 studies from major databases, comprising 24 individual host species, including canids, felids, and a hyenid species. Canids, particularly dogs, were the most studied group among the host species, with E. granulosus sensu stricto (G1-G3) being the most frequently reported. E. granulosus s.s. was distributed across five major continents, while other Echinococcus spp. and genotypes exhibited an uneven continental distribution. The highest overlap of species existed among Asia, Europe, and Africa. Among the reported host species, 4.2 % were endangered (e.g. Lycaon pictus), 12.5 % species were vulnerable (e.g. Panthera leo, Panthera pardus, and Acinonyx jubatus), and 4.2 % were near threatened (e.g. Speothos venaticus). Overall, our review highlights the significance of canids, particularly dogs, as the core focus of scientific investigations, with E. granulosus s.s. being the most widely distributed species across five major continents, emphasizing the urgent need for continued research and public health efforts.

Genetic diversity and population genetics of Schistosoma haematobium isolated from children in Lusaka and Siavonga districts, Zambia

Urogenital schistosomiasis remains a pervasive health challenge in rural Zambian communities. This study explores the molecular epidemiology and genetic diversity of Schistosoma haematobium using mitochondrial genes (cox1 and nadh1). Urine samples from 421 children in Siavonga and Lusaka districts, Zambia, were collected between December 2020 and February 2022. Microscopy and DNA extraction facilitated the identification of S. haematobium, followed by amplification, sequencing, and phylogenetic analysis of cox1 and nadh1 genes. Phylogenetic analysis revealed clustering with samples from mainland African countries, emphasizing shared haplotypes. Both mitochondrial genes exhibited substantial diversity, with 5 haplotypes from 37 cox1 sequences and 12 haplotypes from 23 nadh1 sequences. High haplotype diversity (0.621-0.808) and low nucleotide diversity (0.00181-0.03288) were observed. Siavonga and Lusaka districts shared the majority of S. haematobium haplotypes. Molecular variance and genetic differentiation analysis indicated variations within populations rather than between populations (cox1: -0.025, nadh1: 0.01646). These findings suggest a limited differentiation between S. haematobium populations in Siavonga and Lusaka, potentially indicating gene flow. Tajima's test revealed negative values, indicating a departure from neutrality, introduction of rare alleles, and recent population expansion. This study contributes essential insights into S. haematobium population genetics, crucial for effective urogenital schistosomiasis control in Zambia.

In vitro and ex vivo protoscolicidal effects of hydroalcoholic extracts of Eucalyptus microtheca on protoscoleces of Echinococcus granulosus sensu stricto: A light and scanning electron microscopy (SEM) study

BACKGROUND

Cystic echinococcosis (CE) is one of the most widespread and important global helminth zoonoses. Treatment relies mainly on surgery and, or percutaneous interventions. However, spillage of live protoscoleces (PSCs) leading to recurrence is a problem during surgery. So, the application of protoscolicidal agents before surgery is required. This study aimed to investigate the activity and safety of hydroalcoholic extracts of E. microtheca against PSCs of Echinococcus granulosus sensu stricto (s.s.) both in vitro and also ex vivo, which is a simulation to Puncture, Aspiration, Injection, and Re-aspiration (PAIR) method.

METHODS

Considering the effects of heat on the protoscolicidal effecacy of Eucalyptus leaves, hydroalcoholic extraction was performed by both soxhlet extraction at 80 °C and percolation at room temperature. The protoscolicidal action of hydroalcoholic extracts was assessed by in vitro and ex vivo assessments. Infected sheep livers were collected from the slaughterhouse. Then, the genotype of hydatid cysts (HCs) was confirmed by sequencing and, isolates were limited to E. granulosus s.s. In the next step, ultrastructural changes of Eucalyptus-exposed PSCs were studied by scanning electron microscopy (SEM). Finally, a cytotoxicity test was conducted by (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay to evaluate the safety of E. microtheca.

RESULTS

The prepared extracts by soxhlet extraction and percolation were, successfully exerted strong protoscolicidal effects in both in vitro and ex vivo tests. The results of in vitro assessment indicated that hydroalcoholic extract of E. microtheca prepared by percolation at room temperature (EMP) and hydroalcoholic extract of E. microtheca prepared by soxhlet extraction at 80 °C (EMS) killed all PSCs (100%) at concentrations of 10 and 12.5 mg/mL, respectively. Also, EMP showed 99% protoscolicidal action after 20 min in an ex vivo setting compared to EMS. SEM micrographs confirmed potent protoscolicidal and destructive effects of E. microtheca against PSCs. The cytotoxicity of EMP was tested on the Hela cell line using MTT assay. The value of 50% cytotoxic concentration (CC50) was calculated at 46.5 μg/mL after 24h.

CONCLUSION

Both hydroalcoholic extracts showed potent protoscolicidal activity and, especially EMP produced remarkable protoscolicidal effects compared to the control group.

Update on the genetic diversity and population structure of Echinococcus granulosus in Gansu Province, Tibet Autonomous Region, and Xinjiang Uygur Autonomous Region, Western China, inferred from mitochondrial cox1, nad1, and nad5 sequences

The identification of additional Echinococcus granulosus sensu lato (s.l.) complex species/genotypes in recent years raises the possibility that there might be more variation among this species in China than is currently understood. The aim of this study was to explore intra- and inter-species variation and population structure of Echinococcus species isolated from sheep in three areas of Western China. Of the isolates, 317, 322, and 326 were successfully amplified and sequenced for cox1, nad1, and nad5 genes, respectively. BLAST analysis revealed that the majority of the isolates were E. granulosus s.s., and using the cox1, nad1, and nad5 genes, respectively, 17, 14, and 11 isolates corresponded to Elodea canadensis (genotype G6/G7). In the three study areas, G1 genotypes were the most prevalent. There were 233 mutation sites along with 129 parsimony informative sites. A transition/transversion ratio of 7.5, 8, and 3.25, respectively, for cox1, nad1, and nad5 genes was obtained. Every mitochondrial gene had intraspecific variations, which were represented in a star-like network with a major haplotype with observable mutations from other distant and minor haplotypes. The Tajima's D value was significantly negative in all populations, indicating a substantial divergence from neutrality and supporting the demographic expansion of E. granulosus s.s. in the study areas. The phylogeny inferred by the maximum likelihood (ML) method using nucleotide sequences of cox1-nad1-nad5 further confirmed their identity. The nodes assigned to the G1, G3, and G6 clades as well as the reference sequences utilized had maximal posterior probability values (1.00). In conclusion, our study confirms the existence of a significant major haplotype of E. granulosus s.s. where G1 is the predominant genotype causing of CE in both livestock and humans in China.

Prevalence of Cystic Echinococcosis Genotypes in Iranian Animals: A Systematic Review and Meta-Analysis

Background

Cystic echinococcosis is considered a public health problem that if left untreated can have dangerous consequences for the person. The disease is caused by Echinococcus granulosus sensu lato larvae. The main risk factors for this parasitic infection are habitat, direct contact with dogs, use of raw vegetables, and use of unwashed vegetables. The most important factors affecting the prevalence of HCD are economic, occupational, agricultural, educational, and factors related to public health and cultural habits of the general public in that geographical area.

Objectives

The purpose of this study was to investigate the prevalence of the types of cystic echinococcosis genotypes (E. granulosus sensu stricto (G₁-G₃) and E. Canadensis (G₆ and G₇)) in livestock in Iran.

Method

This systematic review was conducted, using Medline/PubMed, Scopus, Web of Sciences, and Google Scholar databases, to identify studies of cystic echinococcosis in animals published from 2010 to April 14, 2021. Finally, 28 studies were selected for meta-analysis, which was analyzed using Stata software version 14. The cystic echinococcosis prevalence with 95% confidence intervals of animals was synthesized using the random effect model. Heterogeneity was evaluated and in cases where the I² index was higher than 75%, subgroup analysis was performed according to the types of animals.

Result

The highest prevalence of cystic echinococcosis infection was related to G₁ genotype (P = 0.91 (95% CI = 0.84, 0.97)) and the prevalence was related to G₂ genotype (P = 0.07(95% CI = 0.00, 0.18)). The results of the subgroup analysis showed that in the G₁ genotype the highest prevalence was observed in Goats and Buffaloes with P = 1 (95% CI = 0.96, 1) and P = 1 (95% CI = 0.97, 1), in the G₃ and G₆ genotypes the highest prevalence was observed in camels with P = 0.50 (95% CI = 0.31, 0.69), and P = 0.45 (95% CI = 0.22, 0.69), respectively.

Conclusion

The cystic echinococcosis genotypes vary from region to region or from country to country and also from host to host, and according to the results, it should always be stopped in areas where the prevalence of such genomes suitable for livestock as well as human food sources to prevent infection of livestock and thus human exposure to cystic echinococcosis.

Gene migration of giardiasis in Iran; a microevolutionary scale for reflecting transmission patterns of Giardia lamblia assemblages in symptomatic patients

In the microevolutionary scale of Giardia lamblia, the gene migration indicates how G. lamblia assemblages have transmitted between adjacent counties. 33 positive fecal samples were taken from patients suffering gastrointestinal disorders (nausea, bloating, burping constipation and fatty diarrhea) at Tabriz and Ardabil cities, where located in the cold regions of northwest Iran. Following parasitological examinations, DNA samples were extracted, amplified and digested by single-step PCR-RFLP assay, targeting the glutamate dehydrogenase (gdh) locus to distinguish within and between assemblages A and B. PCR products were directly sequenced to reconfirm their heterogeneity traits and phylogenetic analysis. Of the 33 isolates, 81.9% (n: 27), 9% (n: 3) and 9% (n: 3) were successfully identified as assemblages A (genotype AII), B (genotype BIII) and the mixed of genotypes AII and B, respectively. Despite the presence of heterogeneous clinical backgrounds, a low genetic diversity of sub-assemblage AII was identified among symptomatic cases. A low value of pairwise fixation index showed that G. lamblia sub-assemblage AII is not genetically differentiated among northwest regions of Iran. The occurrence of haplotypes TAB-1/ARD-1 between two regional populations indicates that there is a dawn of G. lamblia gene flow due to transfer of alleles through host mobility and/or ecological alterations. To assess the hypothetical evolutionary scenario, further studies are essential for multilocus genotyping of G. lamblia in tropical regions of Iran and neighboring countries.

Phylogeography and Genetic Diversity of Human Hydatidosis in Bordering the Caspian Sea, Northern Iran by Focusing on Echinococcus granulosus Sensu Stricto Complex

Background:

Human Echinococcosisis a cyclo-zoonotic infection caused by tapeworms of the Echinococcus granulosus sensu stricto complex. The detection of mitochondrial genome data of genus Echinococcus can reflect the taxonomic status, genetic diversity, and population structure genetics.

Methods:

Totally, 52 formalin-fixed paraffin-embedded (FFPE) tissue samples from patients with histologically confirmed CE were collected from Mazandaran province, Iran in the period of Mar 1995 to May 2018. All extracted DNAs from (FFPE) tissue samples were subjected to amplify by polymerase chain reactions method targeting cytochrome c oxidase subunit 1 (cox1) gene. All PCR amplicons were sequenced to phylogenetic analysis and genetic diversity.

Results:

Molecular analysis showed that 50(96.1%) and 2 (3.84%) isolates were identified as G1 andG3 E. granulosus genotypes, respectively. DNA sequence analyses indicated a high gene diversity for G1 (Haplotype diversity: 0.830) and G3 genotypes (Hd: 1.00). Based on multiple sequence alignment analyses, 7 (13.46%; G1 genotype) and 2 (3.84%; G3 genotype) new haplotypes were unequivocally identified.

Conclusion:

G3 genotype (Buffalo strain) was identified from two human hydatidosis isolates in the region. Present study strengthens our knowledge about taxonomic status, transmission patterns of Echinococcus parasite to human and heterogeneity aspects of this parasite in clinical CE isolates of Northern Iran.

Assessment of the global paradigms of genetic variability in Strongyloides stercoralis infrapopulations determined by mitochondrial DNA sequences

Microevolutionary data of Strongyloides stercoralis infrapopulations are regarded as a requirement for determining the global genetic structure and transmission paradigms of this neglected tropical nematode among the neighboring countries of the world. English databases were searched from 2010 to 2019, analyzing a total of 10 publications. The cytochrome c oxidase subunit 1 sequences of S. stercoralis isolated from Asian and African continents were subjected to calculate the diversity indices and genetic differentiation. A parsimonious haplotype network indicated a star-like trait a total of 106 (Homo sapiens) and 48 haplotypes (Canid) being grouped into four distinct geographical haplogroups. A significant genetic diversity was identified in human-derived S. stercoralis (Haplotype diversity: 0.78) and those with dog (Hd: 0.86) origins. Cladistic phylogenetic tree indicated the Japanese, Thailandish, and Myanmarese clades have a sister relationship with the Laotian clade. The statistically significant Fst values indicated that human S. stercoralis populations of Japanese-Thailandish, Japanese-Myanmarese, and Japanese-Laotian origins were genetically differentiated (Fst: 0.48430 to 0.54903). We conclude that a high gene migration of human strongyloidiasis is being unequivocally shared between the Laotion-Myanmarese and Laotion-Thailandish population pairs. The current findings enhance our knowledge to assess the transmission dynamics and the evolutionary patterns of S. stercoralis in various geographical regions of the globe; also it will serve as a basis for public health policy to control human strongyloidiasis particularly in immunocompromised individuals. Besides, the infected canids and other environmental reservoirs for zoonotic transmission of S. stercoralis to humans should be de-wormed along with their owners.

Assessment of the global pattern of genetic diversity in Echinococcus multilocularis inferred by mitochondrial DNA sequences

The aim of this review was to assess our current knowledge on phylogeography and global genetic structure of Echinococcus multilocularis populations originating from rodents, wild canid hosts, and human. Six bibliographic databases were searched from 1990 to 2017, identifying a total of 110 publications. The cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) sequences of E. multilocularis from Asia, Europe, and North Americas were analyzed to estimate the diversity and neutrality indices, and genetic differentiation. A total of 69 (cox1, 36.7%) and 16 haplotypes (cytb, 19.2%) were grouped into various geographical clades. A parsimonious haplotype network demonstrated a star-like feature with haplo-groups Em2 (Asia: 36%), Em105 (Eastern Tibetan plateau: 4.8%), Em46 (Europe: 9.1%), Em73, (Europe: 2.7%) and Em92 (North Americas: 4.3%) as the most common haplotypes. A relatively high level of genetic diversity was detected in rodent-derived E. multilocularis isolates (Haplotype diversity: 0.944), wild canids (Hd: 0.912), and human origin (Hd: 0.704). The highest number of haplotypes (n = 59) and the highest haplotype diversity (0.969) were identified in the Asian and European populations, respectively. Cladistic phylogenetic tree indicated the European clade has a sister relationship with the Asian clade. However, some North American haplotypes were assigned to the European clade together with haplotypes from Poland. The statistically significant Fst values indicated that E. multilocularis populations of Asian-European, Asian-North American, and European-North American origins were genetically differentiated (Fst: 0.22624 to 0.43059). An occurrence of distinct parasite populations suggests that E. multilocularis derived from glacial refugia have been plausibly sustained by indigenous hosts during the Pleistocene Epoch.

Molecular evaluation of pvdhfr and pvmdr-1 mutants in Plasmodium vivax isolates after treatment with sulfadoxine/pyrimethamine and chloroquine in Iran during 2001-2016

The rising use of sulfadoxine/pyrimethamine (SP) in the treatment of chloroquine (CQ)-resistant Plasmodium falciparum has resulted in increased exposure to P. vivax isolates in Iran, where both species are being circulated. In this investigation, the frequency of pvdhfr and pvmdr-1 mutants was assessed in P. vivax strains during 2001-2016 after the introduction of SP/CQ in malarious areas of Iran. The P. vivax isolates (n, 52) were obtained from autochthonous samples in Southeast Iran during 2015-2016. The genomic DNA was extracted and examined using nested polymerase chain reaction-(PCR) and sequencing. Mutations were detected in pvdhfr codons P33L (21.2%), T61 M (25%), S93H (3.9%), and S117 T (1.9%) and 5 isolates showed double mutations (33 L/61 M, 7.7%; 33 L/117 T, 1.9%). No mutation was identified in pvdhfr codons F57 and S58. The pvmdr-1 1076 L mutation was detected in 93.3% of P. vivax isolates. The findings indicated that the frequency of three codons of pvdhfr F57/S58/S117 has decreased from 2001 (1.05%/7.0%/16.9%) to 2016 (0%/0%/1.9%). Genomic analysis of pvmdr-1 showed that the frequency of 1076 L has gradually increased from 2013 (93%) to 2016 (93.3%) (P > .05). The results demonstrated that P. vivax isolates are probably being exited under SP pressure, which reflects the appropriate level of training for field microscopists, as established by Iranian policymakers. Emergent pvdhfr codons 33L, 61M, and 93H should be noticed in plausible drug tolerance and treatment plans. The high prevalence of pvmdr-1 1076L mutation shows that efficacy of CQ combination with primaquine may be in danger of being compromised, however further investigations are needed to evaluate the clinical importance of CQ-resistant P. vivax isolates.

The potential role of toll-like receptor 4 Asp299Gly polymorphism and its association with recurrent cystic echinococcosis in postoperative patients

The study of pathogenesis mechanisms of larval stages in the Taeniidae has recently focused on host genetic factors, particularly toll-like receptor (TLR) variations. However, the potential role of TLR4 polymorphism in hydatidosis has not yet been sufficiently elucidated in postoperative patients. In this case-control investigation, 80 patients from Iran, including 40 with acute hydatidosis (AH) and 40 with recurrent hydatidosis (RH), and 80 ethnically matched controls were evaluated from February 2015 to February 2017. Hydatidosis patients were confirmed using radiological, immunological, and histopathological examinations. Genotyping of Asp299Gly and Thr399Ile of TLR4 single-nucleotide polymorphisms was determined by restriction fragment length polymorphism, sequencing, and phylogenetic strategies. The heterozygous mutant-type TLR4 Asp299Gly genotype indicated a tendency to be associated with the occurrence of RH (P = 0.060) and conferred a 3-fold risk for susceptibility. There was no difference in genotype frequency of Asp299Gly between patients with AH and healthy controls (P = 0.42; OR, 1.82; 95% CI, 0.11-30.1%). Interestingly, a frequency of the G allele (12%: Gly) was observed to be a risk factor for susceptibility to RH patients (P = 0.050; OR, 7.08; 95% CI, 0.97-51.5%). A relative genetic variability of TLR4 Asp299Gly was found in RH patients (haplotype diversity: 0.700) compared to AH patients and healthy controls (Hd: 0.000). The Asp299Gly genotype was dominantly identified in patients with hepatic hydatid cysts. The TLR4 Thr399Ile codon was not detected except in a patient with a pulmonary hydatid cyst. The current findings enhance our knowledge regarding the TLR4 Asp299Gly polymorphism potentially leading to the development of RH, by skewing the immune system towards a Th2 response. Identification of the Asp299Gly codon may be a diagnostic hallmark in RH patients who have undergone unsuccessful postoperative intervention. However, further studies with a higher case number are needed on ethnic population from various geographic regions, in order to confirm this hypothesis.

Genetic variability and transcontinental sharing of Giardia duodenalis infrapopulations determined by glutamate dehydrogenase gene

Microevolutionary data of Giardia duodenalis sub-assemblages is a prerequisite for determining the invasion zoonotic patterns of the parasite. To infer transmission patterns that could not be differentiated by the phenotypic features, a population genetic investigation is crucial for the elucidation of the genetic structure of G. duodenalis among the continents. Forty G. duodenalis positive fecal samples were collected from different foci of Northwest Iran. The specimens were subjected to Trichrome staining and sucrose gradient flotation. DNA samples were extracted, amplified, and sequenced by targeting glutamate dehydrogenase (gdh) gene. The global gdh sequences of sub-assemblages AII and BIV retrieved from NCBI GenBank were analyzed to estimate diversity indices, neutrality indices, and gene migration tests. Sequencing analyses indicated various levels of genetic variability of sub-assemblages AII and BIV among the five continents. Sub-assemblage BIV had greater genetic variability (haplotype diversity: 0.975; nucleotide diversity: 0.04246) than sub-assemblage AII. The statistical Fst value demonstrated that the genetic structure of sub-assemblages AII and BIV are moderately differentiated between European-American populations (Fst: 0.05352-0.15182), whereas a significant differentiation was not seen among other geographical population pairs. We conclude that a high gene flow of G. duodenalis sub-assemblages AII and BIV is unequivocally sharing among the continents. The current findings strengthen our knowledge to assess the evolutionary patterns of G. duodenalis in endemic foci of the world and it will become the basis of public health policy to control human giardiasis.

New insights into mitogenomic phylogeny and copy number in eight indigenous sheep populations based on the ATP synthase and cytochrome c oxidase genes

The origins and phylogeny of different sheep breeds has been widely studied using polymorphisms within the mitochondrial hypervariable region. However, little is known about the mitochondrial DNA (mtDNA) content and phylogeny based on mtDNA protein-coding genes. In this study, we assessed the phylogeny and copy number of the mtDNA in eight indigenous (population size, n=184) and three introduced (n=66) sheep breeds in China based on five mitochondrial coding genes (COX1, COX2, ATP8, ATP6 and COX3). The mean haplotype and nucleotide diversities were 0.944 and 0.00322, respectively. We identified a correlation between the lineages distribution and the genetic distance, whereby Valley-type Tibetan sheep had a closer genetic relationship with introduced breeds (Dorper, Poll Dorset and Suffolk) than with other indigenous breeds. Similarly, the Median-joining profile of haplotypes revealed the distribution of clusters according to genetic differences. Moreover, copy number analysis based on the five mitochondrial coding genes was affected by the genetic distance combining with genetic phylogeny; we also identified obvious non-synonymous mutations in ATP6 between the different levels of copy number expressions. These results imply that differences in mitogenomic compositions resulting from geographical separation lead to differences in mitochondrial function.

Phylogeography, genetic variability and structure of Acanthamoeba metapopulations in Iran inferred by 18S ribosomal RNA sequences: A systematic review and meta-analysis

OBJECTIVE

To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country.

METHODS

We searched electronic databases including Medline, PubMed, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran.

RESULTS

T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5 (Acanthamoeba lenticulata), T6, T9, T11, T13 and T15 (Acanthamoeba jacobsi). A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6 (34.1%) and IR7 (31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity (0.612-0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index (F_ST) was from low to high values (0.02433-0.41892). The statistically F_ST points out that T4 is genetically differentiated between north-west, north-south and central-south metapopulations, but not differentiated between west-central, west-south, central-south, and north-central isolates.

CONCLUSIONS

An occurrence of IR6 and IR7 displays that possibly a gene flow of Acanthamoeba T4 occurred after the founder effect or bottleneck experience through ecological changes or host mobility. This is the first systematic review and meta-analysis providing new approaches into gene migration and transmission patterns of Acanthamoeba sp, and targeting at the high-risk individuals/sources among the various regions of Iran.