New insight into genetic variation and haplotype diversity of Fasciola hepatica from Algeria

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 sequencing method 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 threshold of 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 single large 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 species interactions 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.

Genetic variation and population structure of Fasciola hepatica: an in silico analysis

Fasciola hepatica is a trematode leading to heavy economic setbacks to the livestock sector globally. The population's genetic information and intimate kinship level are frequently assessed using analysis of mitochondrial DNA. In this analysis, we retrieved cox1 (n = 247) and nad1 (n = 357) sequences of F. hepatica from the NCBI GenBank database and aligned the sequences with the respective reference sequences using MEGA software. The median joining network was drawn using PopArt software while neutrality and diversity indices were estimated with the help of DnaSp software. Neighbor-joining phylogenetic tree was constructed using the MEGA software package. A total of 46 and 98 distinctive haplotypes were observed for cox1 and nad1 genes, respectively. Diversity indices indicated high haplotype and nucleotide diversities in both genes. Positive Tajima's D and Fu's Fs values were found for the entire population of both the genes under study. The cox1 and nad1 gene segments in this study showed high Tajima's D values, suggesting a low likelihood of future population growth. The Tajima's D value of the nad1 gene sequence is lower (2.14910) than that of the cox1 gene sequence (3.40314), which suggests that the former is growing at a slower rate. However, the region-wise analysis revealed that both the cox1 and nad1 genes showed deviation from neutrality suggesting a recent population expansion as a result of an excess of low-frequency polymorphism. Furthermore, the overall host-wise analysis showed positive and significant Tajima's D values for the cox1 and nad1 gene sequences. To the best of our knowledge, this is the first attempt to provide insights into genetic variations and population structure of F. hepatica at a global scale using cox1 and nad1 genes. Our findings suggest the existence of specific variants of F. hepatica in different parts of the world and provide information on the molecular ecology of F. hepatica. The results of this study also mark a critical development in upcoming epidemiological investigations on F. hepatica and will also contribute to understanding the global molecular epidemiology and population structure of F. hepatica.

New perspectives for fascioliasis in Upper Egypt's new endemic region: Sociodemographic characteristics and phylogenetic analysis of Fasciola in humans, animals, and lymnaeid vectors

BACKGROUND

Fascioliasis is a significant vector-borne disease that has emerged in numerous tropical and subtropical countries causing severe health problems. Egypt is one of the fascioliasis endemic regions; however, the current situation in Upper Egypt is understudied, with only sporadic human cases or outbreaks. This study aims to highlight the sociodemographic characteristics of human fascioliasis in a newly emerged endemic area in Upper Egypt, along with risk factors analysis and the molecular characteristics of the fasciolid population in humans, animals, and lymnaeid snails.

METHODOLOGY/PRINCIPAL FINDINGS

The study reported Fasciola infection in patients and their close relatives by analyzing the risk of human infection. Morphological and molecular characterization was performed on lymnaeid snails. Multigene sequencing was also used to characterize fasciolids from human cases, cattle, and pooled snail samples. The study identified asymptomatic Fasciola infection among family members and identified the presence of peridomestic animals as a significant risk factor for infection. This is the first genetic evidence that Radix auricularia exists as the snail intermediate host in Egypt.

CONCLUSIONS/SIGNIFICANCE

This study revealed that Assiut Governorate in Upper Egypt is a high-risk area for human fascioliasis that requires additional control measures. Fasciola hepatica was the main causative agent infecting humans and snail vectors in this newly emerged endemic area. In addition, this is the first report of R. auricularia as the snail intermediate host transmitting fascioliasis in Upper Egypt. Further research is required to clarify the widespread distribution of Fasciola in Egypt's various animal hosts. This provides insight into the mode of transmission, epidemiological criteria, and genetic diversity of fasciolid populations in Upper Egypt.\.

Human and Animal Fascioliasis: Origins and Worldwide Evolving Scenario

Fascioliasis is a plant- and waterborne zoonotic parasitic disease caused by two trematode species: (i) Fasciola hepatica in Europe, Asia, Africa, the Americas, and Oceania and (ii) F. gigantica, which is restricted to Africa and Asia. Fasciolid liver flukes infect mainly herbivores as ruminants, equids, and camelids but also omnivore mammals as humans and swine and are transmitted by freshwater Lymnaeidae snail vectors. Two phases may be distinguished in fasciolid evolution. The long predomestication period includes the F. gigantica origin in east-southern Africa around the mid-Miocene, the F. hepatica origin in the Near-Middle East of Asia around the latest Miocene to Early Pliocene, and their subsequent local spread. The short postdomestication period includes the worldwide spread by human-guided movements of animals in the last 12,000 years and the more recent transoceanic anthropogenic introductions of F. hepatica into the Americas and Oceania and of F. gigantica into several large islands of the Pacific with ships transporting livestock in the last 500 years. The routes and chronology of the spreading waves followed by both fasciolids into the five continents are redefined on the basis of recently generated knowledge of human-guided movements of domesticated hosts. No local, zonal, or regional situation showing disagreement with historical records was found, although in a few world zones the available knowledge is still insufficient. The anthropogenically accelerated evolution of fasciolids allows us to call them "peridomestic endoparasites." The multidisciplinary implications for crucial aspects of the disease should therefore lead the present baseline update to be taken into account in future research studies.

Potential Hybridization of Fasciola hepatica and F. gigantica in Africa-A Scoping Review

The occurrence of Fasciola gigantica and F. hepatica in Africa is well documented; however, unlike in Asia, there is a paucity of information on the existence of hybrids or parthenogenetic species on the continent. Nonetheless, these hybrid species may have beneficial characteristics, such as increased host range and pathogenicity. This study provides evidence of the potential existence of Fasciola hybrids in Africa. A literature search of articles published between 1980 and 2022 was conducted in PubMed, Google Scholar, and Science Direct using a combination of search terms and Boolean operators. Fasciola species were documented in 26 African countries with F. hepatica being restricted to 12 countries, whilst F. gigantica occurred in 24 countries, identified based on morphological features of adult Fasciola specimens or eggs and molecular techniques. The co-occurrence of both species was reported in 11 countries. However, the occurrence of potential Fasciola hybrids was only confirmed in Egypt and Chad but is suspected in South Africa and Zimbabwe. These were identified based on liver fluke morphometrics, assessment of the sperms in the seminal vesicle, and molecular techniques. The occurrence of intermediate host snails Galba truncatula and Radix natalensis was reported in Ethiopia, Egypt, South Africa, Tanzania, and Uganda, where F. hepatica and F. gigantica co-occurrences were reported. The invasive Pseudosuccinea columella snails naturally infected with F. gigantica were documented in South Africa and Egypt. In Zimbabwe, P. columella was infected with a presumed parthenogenetic Fasciola. This suggests that the invasive species might also be contributing to the overlapping distributions of the two Fasciola species since it can transmit both species. Notwithstanding the limited studies in Africa, the potential existence of Fasciola hybrids in Africa is real and might mimic scenarios in Asia, where parthenogenetic Fasciola exist in most Asian countries. In South Africa, aspermic F. hepatica and Fasciola sp. have been reported already, and Fasciola hybrids have been reported? in Chad and Egypt. Thus, the authors recommend future surveys using molecular markers recommended to identify Fasciola spp. and their snail intermediate hosts to demarcate areas of overlapping distribution where Fasciola hybrids and/or parthenogenetic Fasciola may occur. Further studies should also be conducted to determine the presence and role of P. columella in the transmission of Fasciola spp. in these geographical overlaps to help prevent parasite spillbacks.

Identification and Genetic Characterization of Fasciola hepatica Isolated from Cattle in Jeddah, Saudi Arabia Based on Sequence Analysis of Mitochondrial (COI) Gene

Background

In Saudi Arabia, more than US$ 0.2 million annual losses are caused by liver condemnations due to fascioliasis. Data obtained from the genetic characterization of Fasciola population sheds light on parasite transmission which could eventually help in development of effective parasite control measures. So, the aim of this study was to investigate the genetic diversity of Fasciola spp. isolated from cattle in Saudi Arabia by sequence analyses of COI gene.

Materials and Methods

A total of 325 cows slaughtered at the central municipal abattoir in Jeddah city, Jeddah Province, Saudi Arabia were examined for fascioliasis in the period from 1^st of June to 1^st of July 2020. DNA was extracted from adult Fasciola worms and used for PCR and DNA sequence using a primer pair targeting COI gene. Analysis of the obtained sequences was done using BLAST search and phylogenetic analysis.

Results

Bovine fascioliasis was diagnosed in 18 out of 325 cattle (5.5%). Forty-eight flukes were extracted from infected animals and DNA was successfully amplified from all flukes. Overall 12 different DNA sequences were obtained. BLAST search showed that all obtained sequences were F. hepatica and had >97% similarity with F. hepatica isolates from Tanzania, Europe and Iran. Phylogenetic analysis of the obtained sequences showed that Fasciola isolates from the current study were clustered in one subclade closely related to isolates from North and South Africa and Italy.

Conclusion

Reports on the molecular characterization of Fasciola spp. in Saudi Arabia are limited. In the current study, our findings showed that F. hepatica was the only Fasciola species parasitizing cattle in Jeddah city, Saudi Arabia. Further studies using a large number of samples from different localities in Saudi Arabia are needed to provide data that will help the development of control measures against fascioliasis.

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.

The causative agents of fascioliasis in animals and humans: Parthenogenetic Fasciola in Asia and other regions

Parthenogenetic Fasciola is the causative agent of fascioliasis in animals and humans and is widely distributed in Asian countries, such as Japan, South Korea, China, Vietnam, Thailand, the Philippines, Myanmar, Bangladesh, Nepal, and India. Parthenogenetic Fasciola geographically originated from central and eastern China, where it exists between the habitats of Fasciola hepatica and Fasciola gigantica; it likely appeared thousands of years ago following hybridization between F. hepatica and F. gigantica. Parthenogenetic Fasciola consists of diploids and triploids that possess nuclear genome of both F. hepatica and F. gigantica and mitochondrial genome of either F. hepatica or F. gigantica. Maternal parents of parthenogenetic Fasciola are either F. hepatica having Fh-C4 haplotype or F. gigantica having Fg-C2 haplotype in mitochondrial NADH dehydrogenase subunit 1 (ND1) nucleotide sequences. Parthenogenetic Fasciola flukes with the Fh-C4 haplotype have spread from China to South Korea and Japan, whereas the flukes with the Fg-C2 haplotype have not only spread to Korea and Japan but also southward to Vietnam, Thailand, the Philippines, Myanmar, Bangladesh, Nepal, and India. Parthenogenetic Fasciola can be distinguished from F. hepatica and F. gigantica using combinational DNA sequence analysis of nuclear phosphoenolpyruvate carboxykinase (pepck) and DNA polymerase delta (pold) along with mitochondrial ND1 markers. The establishment of parthenogenetic Fasciola is expected as follows: parthenogenetic diploids with the Fh-C4 and Fg-C2 haplotypes first appeared based on single or multiple interspecific hybridization events; subsequently, parthenogenetic triploids emerged via backcross events between the maternal parthenogenetic diploid and either paternal bisexual F. hepatica or F. gigantica. Parthenogenetic Fasciola diploids and triploids then survived for thousands of years by clonal parthenogenetic reproduction, and generated descendants with ND1 haplotypes, which were derived from the Fh-C4 and Fg-C2 due to nucleotide substitution. Thus, the emergence of parthenogenetic Fasciola may be due to extremely uncommon and accidental events. Parthenogenetic Fasciola should be treated as a new asexual hybrid species.

Whole Genome Sequence Analysis of Mycobacterium bovis Cattle Isolates, Algeria

Mycobacterium bovis (M. bovis), a Mycobacterium tuberculosis complex species responsible for tuberculosis in cattle and zoonotic tuberculosis in humans, is present in Algeria. In Algeria however, the M. bovis population structure is unknown, limiting understanding of the sources and transmission of bovine tuberculosis. In this study, we identified the whole genome sequence (WGS) of 13 M. bovis strains isolated from animals exhibiting lesions compatible with tuberculosis, which were slaughtered and inspected in five slaughterhouses in Algeria. We found that six isolates were grouped together with reference clinical strains of M. bovis genotype-Unknown2. One isolate was related to M. bovis genotype-Unknown7, one isolate was related to M. bovis genotype-Unknown4, three isolates belonged to M. bovis genotype-Europe 2 and there was one new clone for two M. bovis isolates. Two isolates from Blida exhibited no pairwise differences in single nucleotide polymorphisms. None of these 13 isolates were closely related to four zoonotic M. bovis isolates previously characterized in Algeria. In Algeria, the epidemiology of bovine tuberculosis in cattle is partly driven by cross border movements of animals and animal products.

Molecular characterization and phylogenetic analysis of Fasciola hepatica from high- plateau and steppe areas in Algeria

A previous study based on mitochondrial DNA markers reported the presence of Fasciola hepatica in Algeria. However, a precise species identification is still required. In this report, a total of 68 Fasciola isolates, collected from high-plateau (Bordj-Bou-Arreridj) and steppe (Djelfa) areas of Algeria, were identified at the species level by multiplex PCR and PCR-restriction fragment length polymorphism (RFLP) for nuclear phosphoenolpyruvate carboxykinase (pepck) and DNA polymerase delta (pold), respectively. The result of the multiplex PCR conflicted with that of the PCR-RFLP; however, subsequent nucleotide sequencing of pepck clearly showed that all isolates should be classified as F. hepatica. The two mitochondrial markers, NADH dehydrogenase subunit I (nad1) and cytochrome c oxidase subunit 1 (cox1), revealed a close relationship between the parasite populations from the plateau and those from the steppe. A dispersal direction from the high plateau to the steppe was indicated because the former population was more diversified than the latter. Moreover, these populations were more closely related to populations from Spain than those from Egypt or Afghanistan. Given the population characteristic of F. hepatica in Spain and the history of cattle trade, it seems likely that the parasite was introduced to Algeria from Europe through a route across the Mediterranean Sea.

Genetically 'pure' Fasciola gigantica discovered in Algeria: DNA multimarker characterization, trans-Saharan introduction from a Sahel origin and spreading risk into north-western Maghreb countries

Fascioliasis is a freshwater snail-borne zoonotic helminth disease caused by two species of trematodes: Fasciola hepatica of almost worldwide distribution and the more pathogenic F. gigantica restricted to parts of Asia and most of Africa. Of high pathological impact in ruminants, it underlies large livestock husbandry losses. Fascioliasis is moreover of high public health importance and accordingly included within the main neglected tropical diseases by WHO. Additionally, this is an emerging disease due to influences of climate and global changes. In Africa, F. gigantica is distributed throughout almost the whole continent except in the north-western Maghreb countries of Morocco, Algeria and Tunisia where only F. hepatica is present. The present study concerns the DNA multimarker characterization of the first finding of F. gigantica in sheep in Algeria by the complete sequences of rDNA ITS-1 and ITS-2 and mtDNA cox1 and nad1 genes. Sequence comparisons and network analyses show sequence identities and similarities suggesting a south-north trans-Saharan geographical origin, with introduction from Ghana, through the Sahel countries of Burkina Faso and Mali into Algeria. This way perfectly fits with nomadic pastoralism according to interconnecting intranational and transborder herd transhumance routes traditionally followed in this western part of Africa from very long ago. The risk for further spread throughout the three north-western Maghreb countries is multidisciplinarily analysed, mainly considering the present extensive motorization of the intranational transhumance system in Algeria, the lymnaeid snail vector species present throughout the north-western Maghreb, the increasing demand for animal products in the growing cities of northern Algeria and the continued human infection reports. Control measures should assure making anti-fasciolid drugs available and affordable for herders from the beginning and along their transhumant routes and include diffusion and rules within the regional regulatory framework about the need for herd treatments.

Multilocus approach reveals discordant molecular markers and corridors for gene flow between North African populations of Fasciola hepatica

Fasciolosis is a foodborne trematodosis characterised by a worldwide distribution. Various approaches have been developed for the study of the causative agents of this parasitic infection: Fasciola hepatica, Fasciola gigantica and the aspermic intermediated forms (hybrid and introgressed). In the present study, novel and common molecular markers (pepck and pold, ITS, CO1, ND1 and CO1-trnT-rrnL) were used to characterise Fasciola flukes from the Tunisian-Algerian border, to estimate the gene flow between these populations and to evaluate the reliability of different molecular markers. All nuclear and mitochondrial markers, apart from pepck, supported the monophyly of the studied flukes identified as F. hepatica. Multiplex PCR for pepck revealed three different genotypes corresponding to F. hepatica (pepck-Fh), F. gigantica (pepck-Fg) and the aspermic Fasciola flukes (pepck-Fh/Fg). Sequence analysis of pepck revealed high polymorphism, length variation, within this intronic marker. The observed inconsistencies were due to the position of the forward primer within the intronic region. Pepck sequences showed different level of heterozygosity and homozygosity with length polymorphisms in the introns. Pepck multiplex PCR patterns could not differentiate between Fasciola species. All studies based on only pepck multiplex PCR with mitochondrial markers should be revised. Nuclear and mitochondrial markers revealed an important gene flow between Tunisian and Algerian populations of F. hepatica. The combination of nuclear and mitochondrial sequence analysis is still the best method to distinguish these taxa. Effective measures are needed in order to better control cross-country illegal trade of vector.