Genetic diversity and distribution of Fasciola hepatica haplotypes in Iran: Molecular and phylogenetic studies

Assessment of genetic markers for multilocus sequence typing (MLST) of Fasciola isolates from Iran

BACKGROUND

Several markers have been described to characterise the population structure and genetic diversity of Fasciola species (Fasciola hepatica (F. hepatica) and Fasciola gigantica (F. gigantica). However, sequence analysis of a single genomic locus cannot provide sufficient resolution for the genetic diversity of the Fasciola parasite whose genomes are ∼1.3 GB in size.

OBJECTIVES

To gain a better understanding of the gene diversity of Fasciola isolates from western Iran and to identify the most informative markers as candidates for epidemiological studies, five housekeeping genes were evaluated using a multilocus sequence typing (MLST) approach.

METHODS

MLST analysis was developed based on five genes (ND1, Pepck, Pold, Cyt b and HSP70) after genomic DNA extraction, amplification and sequencing. Nucleotide diversity and phylogeny analysis were conducted on both concatenated MLST loci and each individual locus. A median joining haplotype network was created to examine the haplotypes relationship among Fasciola isolates.

RESULTS

Thirty-three Fasciola isolates (19 F. hepatica and 14 F. gigantica) were included in the study. A total of 2971 bp was analysed for each isolate and 31 sequence types (STs) were identified among the 33 isolates (19 for F. hepatica and 14 for F. gigantica isolates). The STs produced 44 and 42 polymorphic sites and 17 and 14 haplotypes for F. hepatica and F. gigantica, respectively. Haplotype diversity was 0.982 ± 0.026 and 1.000 ± 0.027 and nucleotide diversity was 0.00200 and 0.00353 ± 0.00088 for F. hepatica and F. gigantica, respectively. There was a high degree of genetic diversity with a Simpson's index of diversity of 0.98 and 1 for F. hepatica and F. gigantica, respectively. While HSP70 and Pold haplotypes from Fasciola species were separated by one to three mutational steps, the haplotype networks of ND1 and Cyt b were more complex and numerous mutational steps were found, likely due to recombination.

CONCLUSIONS

Although HSP70 and Pold genes from F. gigantica were invariant over the entire region of sequence coverage, MLST was useful for investigating the phylogenetic relationship of Fasciola species. The present study also provided insight into markers more suitable for phylogenetic studies and the genetic structure of Fasciola parasites.

Multiplex PCR and Sequence Analysis to Investigate Genetic Diversity of Fasciola Isolates from Cattle and Sheep in Turkey

Fasciolosis is a highly prevalent helminthic infection caused by Fasciola hepatica and F. gigantica. With the aim of identifying hybrid Fasciola flukes, multiplex PCR was performed to amplify the pepck gene. Furthermore, to determine Fasciola haplotypes, mitochondrial nad1 gene was amplified and sequenced, and phylogenetic analyses were performed. Adult Fasciola isolates were collected from 51 cattle and 51 sheep, genomic DNA was isolated, and one-step multiplex PCR was subsequently performed to amplify pepck. Isolates that generated a 510 bp band were identified as F. gigantica, those that generated a 241 bp band were identified as F. hepatica, and those that generated both bands were identified as hybrid (aspermic) flukes. Multiplex PCR data identified four isolates as F. gigantica and 84 as F. hepatica. Fourteen hybrid isolates (five cattle and nine sheep) were identified. On unidirectional DNA sequence analysis of nad1 PCR products, three sequences were identified as F. gigantica and 99 as F. hepatica. In addition, only 4 of 87 haplotypes detected for F. hepatica nad1 sequences were found to be previously reported, while the remaining 83 are unique to this study. To summarize, this study is the first to report the existence of hybrid Fasciola flukes and 83 unique haplotypes of F. hepatica in Turkey.

New Insights Into the Genetic Variability of Fasciola Hepatica (Trematoda) in Algeria and Relationships with Other Geographic Regions Revealed By Mitochondrial DNA

This study aims to investigate the level of genetic variability of Fasciola hepatica flukes isolated from cattle in Algeria and to determine the phylogenetic and phylogeographic relationships with sequences isolated worldwide. Mitochondrial (Cytochrome c Oxidase subunit I gene - COI) and nuclear markers (Internal Transcribed Spacers of nuclear ribosomal DNA - ITS) for 24 F. hepatica flukes isolated from 12 cattle in North Algeria were characterised. Only two haplotypes were obtained for the COI gene, resulting in a low level of genetic variation. The analysis of variation among the COI sequences isolated from around the world did not show high levels of genetic divergence, and the phylogenetic analysis revealed a genetic similarity among F. hepatica isolates from different areas of the world. The analysis of the ITS region showed a low level of variability, which prevented obtaining informative phylogenetic and phylogeographic results. The present study also revealed that specimens of F. hepatica are genetically similar in different hosts, indicating that the genetic structure among populations of this parasite is not influenced by the host species. The low levels of genetic variation for COI and ITS regions among fluke isolates from all continents are consistent with a common origin for the flukes’ worldwide distribution.

Molecular characteristics and genetic diversity of Fasciola hepatica from sheep in Xinjiang, China

Introduction

Fasciola hepatica is a trematode infecting ruminants worldwide and occasionally affecting other animal species, including humans. It causes significant economic losses. Geographic distribution and patterns of infection must be considered before control and management measures are developed for this parasite. DNA molecular markers are useful for the identification of flukes and elucidation of their genetic evolution. Therefore, the population structure of F. hepatica was studied using this method in sheep in Xinjiang, China.

Material and Methods

The molecular characteristics, genetic relationships within the population and dispersal patterns of F. hepatica isolates were analysed based on the cox1 and nad1 genes. The population structure of F. hepatica from three regions of Xinjiang was explored and a neutrality test was conducted.

Results

The cox1 and nad1 genes have 21 and 42 variable sites, respectively, which can be classified into 34 and 33 haplotypes. Median-joining network and phylogenetic tree analyses showed that there was no significant variation in F. hepatica isolates between the three geographical regions. Analysis of variance revealed that the genetic variation of F. hepatica was mainly present within the populations. The neutrality test indicated that the populations were relatively stable but the Hami population may have undergone short-term expansion.

Conclusion

This study revealed for the first time the molecular characteristics, genetic diversity and dispersal patterns of F. hepatica isolates from sheep in Xinjiang, thus providing new insights into the genetic variation and haplotype diversity of F. hepatica from indigenous sheep.

Bionomics and phylo-molecular analysis of Leishmania species isolated from human lesions using ITS1 genes in north-east of Iran

Leishmaniasis is a zoonotic infectious disease caused by Leishmania species. The identification of parasite species and the type of disease is beneficial for treatment and preventive modalities. Leishmania tropica and L. major have been reported as the main etiological agents of cutaneous leishmaniasis (CL) in Iran. The incidence of zoonotic CL has increased and different in distinct loci of Iran. Hence, we perused the Leishmania species and its genetic traits in the North East of Iran. The investigation was conducted on 200 positive smears prepared from patients' lesions suffering from CL referred to the health care centers of northeastern provinces in Iran from 2013 to 2019. The obtained positive microscopy samples were divided to score the ranges from + 1 to + 6, of them 40 smears exhibited low-parasitemia. Leishmania species analyzed using PCR-RFLP, genetic diversity indices evaluation, phylogenetic analysis, and sequencing comparison with other species in the GeneBank based on ITS1 gene. The isolated L. major strains were similar to other Iranian isolates in this region. Pairwise fixation index (F_ST) index was statistically significant in different L. major populations and showed the genetic differences in pairwise population of different geographical locations of Iran. The current study confirmed an old pattern endemicity of zoonotic CL in North-east of Iran. Therefore, in order to assess the hybrid formation, more epidemiological, ecological, and gene polymorphism studies are needed to understand the pathogenic role of Leishmania species in Iran.

Molecular Characterization of Fasciola spp. from a Donkey (Equus asinus) Using Partial Sequencing of cox1 and nad1

Background

Fasciola hepatica as an important parasite affects health of humans and animals in some tropical and subtropical areas of the world, including Iran. Little is known about the molecular diversity of Fasciola in Equidae. Therefore, this study aimed to characterize the genetic polymorphisms among parasites.

Methods

Eight adult Fasciola spp. isolates were collected from a working donkey after necropsy in Shiraz, southwestern Iran, in 2018. Primarily, various parameters were measured morphologically. Subsequently, DNA was extracted from each fluke and molecular markers of cytochrome C oxidase (cox1) and NADH dehydrogenase 1(nad1) from individual Fasciola isolates were amplified using PCR assay and sequence data were employed for molecular and phylogenetic analysis. Genetic diversity between isolates was evaluated by comparing the sequences of these two mitochondrial regions.

Results

Based on the morphological and analyzed mitochondrial sequences, all of eight donkey isolates (100%) were identified as F. hepatica. Moreover, nine and five nucleotide polymorphisms were identified in the cox1and nad1 region sequences, respectively.

Conclusion

Accordingly, phylogenetic data revealed five and four haplotypes among donkey isolates based on the cox1and nad1 markers. Similarly, some of these haplotypes have been previously reported from different host species in Iran as well as all around the world.

Molecular phylogenetic and genetic variability of Fasciola gigantica in Kermanshah province, western Iran with an overview to understand haplotypes distribution in Asia and Africa

Over the last decade, diagnostic tools to detect and differentiate Fasciola species have improved, but our understanding of the distribution of haplotypes and population structure of this parasite is less clear. This study was designed to survey this gap in the F. gigantica epidemiology in Kermanshah province, western Iran from 2015 to 2017. Sixty-eight Fasciola isolates were collected from slaughterhouses from this province. We evaluated the PCR-RFLP assay of the ITS1 genes for the identification of Fasciola species using the RsaI enzyme. After Fasciola species identification, the partial sequence of mitochondrial NADH dehydrogenase subunit 1 (ND1) gene of F. gigantica was used for subsequent construction of the phylogenetic tree and network analysis. Based on the PCR-PRFLP profile, one (6.25%) of sheep isolates and 19 (39.60%) of cattle isolates were detected as F. gigantica, whereas 93.75% of sheep isolates, 60.40% of cattle isolates and all of the goat isolates were F. hepatica. In the 20 analyzed flukes, five ND1 haplotypes were detected. Statistically significant genetic differentiation was demonstrated between the Iran population and all the other populations. Evidence is presented for the existence of two well-separated populations: African and West Asian gigantica flukes and East Asian gigantica flukes. Genetic relationships among haplotypes were associated with geographical divisions. Also, our results have heightened our knowledge about the genetic diversity of F. gigantic, providing the first evidence for the existence of two well-separated populations of this parasite.

Genetic diversity and relationships of the liver fluke Fasciola hepatica (Trematoda) with native and introduced definitive and intermediate hosts

Fasciolosis is a worldwide spread parasitosis mainly caused by the trematode Fasciola hepatica. This disease is particularly important for public health in tropical regions, but it can also affect the economies of many developed countries due to large infections in domestic animals. Although several studies have tried to understand the transmission by studying the prevalence of different host species, only a few have used population genetic approaches to understand the links between domestic and wildlife infections. Here, we present the results of such genetic approach combined with classical parasitological data (prevalence and intensity) by studying domestic and wild definitive hosts from Camargue (southern France) where fasciolosis is considered as a problem. We found 60% of domestic hosts (cattle) infected with F. hepatica but lower values in wild hosts (nutria, 19%; wild boars, 4.5%). We explored nine variable microsatellite loci for 1,148 adult flukes recovered from four different populations (non-treated cattle, treated cattle, nutria and wild boars). Populations from the four groups differed, though we found a number of migrants particularly non-treated cattle and nutria. Overall, we detected 729 different multilocus genotypes (from 783 completely genotyped individuals) and only 46 genotypes repeated across samples. Finally, we experimentally infected native and introduced intermediate snail hosts to explore their compatibility with F. hepatica and assess the risks of fasciolosis expansion in the region. The introduced species Galba truncatula and Pseudosuccinea columella attained the higher values of overall compatibility in relation to the European species. However, concerning the origin, sympatric combinations of G. truncatula were more compatible (higher prevalence, intensity and survival) than the allopatric tested. According to our results, we should note that the assessment of epidemiological risks cannot be limited to a single host-parasite system, but should focus on understanding the diversity of hosts in the heterogeneous environment through space and time.

Occurrence, Morphometric, and Molecular Investigation of Cattle and Buffalo Liver Adult Fluke in Peninsular Malaysia Main Abattoirs

Fascioliasis is a parasitic disease of human and animal caused by Fasciola gigantica (F. gigantica) and Fasciola hepatica (F. hepatica). More than 700 million of grazing animals and over 180 million human population are at the risk of fascioliasis. This study was conducted in Banting, Ipoh, Shah Alam, and Taiping abattoirs within Peninsular Malaysia to determine the occurrence and identify the species of liver flukes, causing liver condemnation in cattle and buffaloes. Within a study period from January to December 2018, a total of 25 condemned bovine livers were collected from Banting, Ipoh, Shah Alam, and Taiping abattoirs and analyzed. Taiping abattoir had the highest occurrence of fascioliasis [14/1014 (1.38%)], and Shah Alam abattoir had the least occurrence [1/3377 (0.03%)]. From all the sampled livers, the average number of adult flukes recorded ranged from 1 to 83. A total of 440 adult flukes were studied morphometrically, using parameters such as body length (BL), body width (BW), cone length (CL), cone width (CL), body area (BA), body perimeter (BP), the distance between the ventral sucker and posterior end of body (VS-P), BL/BW ratio, BL/V-SP, and body roundness (BR). Furthermore, molecular analysis was conducted using PCR-RFLP methods to distinguish between F. gigantica and F. hepatica involving ITS1 primer and RsaI restriction enzyme. RFLP pattern with RsaI produced a consistent pattern of 360,100 and 60 bp fragments in F. hepatica, whereas F. gigantica worms had a profile of 360,170, and 60 bp in size. The morphometric and molecular analysis results indicated that cattle and buffaloes slaughtered at Banting, Shah Alam, Taiping, and Ipoh abattoirs were infected with F. gigantica.