A molecular phylogeographic study based on DNA sequences from individual metacercariae of Paragonimus mexicanus from Guatemala and Ecuador

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General overview of the current status of human foodborne trematodiasis

Foodborne trematodes (FBT) of public health significance include liver flukes (Clonorchis sinensis, Opisthorchis viverrini, O. felineus, Fasciola hepatica and F. gigantica), lung flukes (Paragonimus westermani and several other Paragonimus spp.) and intestinal flukes, which include heterophyids (Metagonimus yokogawai, Heterophyes nocens and Haplorchis taichui), echinostomes (Echinostoma revolutum, Isthmiophora hortensis, Echinochasmus japonicus and Artyfechinostomum malayanum) and miscellaneous species, including Fasciolopsis buski and Gymnophalloides seoi. These trematode infections are distributed worldwide but occur most commonly in Asia. The global burden of FBT diseases has been estimated at about 80 million, however, this seems to be a considerable underestimate. Their life cycle involves a molluscan first intermediate host, and a second intermediate host, including freshwater fish, crustaceans, aquatic vegetables and freshwater or brackish water gastropods and bivalves. The mode of human infection is the consumption of the second intermediate host under raw or improperly cooked conditions. The major pathogenesis of C. sinensis and Opisthorchis spp. infection includes inflammation of the bile duct which leads to cholangitis and cholecystitis, and in a substantial number of patients, serious complications, such as liver cirrhosis and cholangiocarcinoma, may develop. In lung fluke infections, cough, bloody sputum and bronchiectasis are the most common clinical manifestations. However, lung flukes often migrate to extrapulmonary sites, including the brain, spinal cord, skin, subcutaneous tissues and abdominal organs. Intestinal flukes can induce inflammation in the intestinal mucosa, and they may at times undergo extraintestinal migration, in particular, in immunocompromised patients. In order to control FBT infections, eating foods after proper cooking is strongly recommended.

Lung flukes of the genus Paragonimus: ancient and re-emerging pathogens

The title of this article refers to Table 1 in Zhou (2022, Infectious diseases of poverty: progress achieved during the decade gone and perspectives for the future. Infectious Diseases of Poverty 11, 1), in which it is indicated that Paragonimus species, like many other foodborne trematodes, are ancient pathogens that are also re-emerging to cause disease in modern times. This article provides a general overview of Paragonimus species and the disease they cause. This is followed by comments on several specific topics of current interest: taxonomy and distribution of members of the genus; details of the life cycle; global and regional prevalence of paragonimiasis; genomics of lung flukes and possible effects of global environmental change. Unresolved questions relating to these topics are discussed and gaps in knowledge identified.

The effect of landscape and human settlement on the genetic differentiation and presence of Paragonimus species in Mesoamerica

Foodborne diseases are a neglected research area, and despite the existence of many tools for diagnosis and genetic studies, very little is known about the effect of the landscape on the genetic diversity and presence of parasites. One of these foodborne disease is paragonimiasis, caused by trematodes of the genus Paragonimus, which is responsible for a high number of infections in humans and wild animals. The main Paragonimus sp reported in Mesoamerica is Paragonimus mexicanus, yet there are doubts about its correct identification as a unique species throughout the region. This, together with a lack of detailed knowledge about their ecology, evolution and differentiation, may complicate the implementation of control strategies across the Mesoamerican region. We had the goal of delimiting the species of P. mexicanus found throughout Mesoamerica and determining the effect of landscape and geology on the diversity and presence of the parasite. We found support for the delimitation of five genetic groups. The genetic differentiation among these groups was positively affected by elevation and the isolation of river basins, while the parasite's presence was affected negatively only by the presence of human settlements. These results suggest that areas with lower elevation, connected rivers basins, and an absence of human settlements have low genetic differentiation and high P. mexicanus presence, which may increase the risk of Paragonimus infection. These demonstrate the importance of accurate species delimitation and consideration of the effect of landscape on Paragonimus in the proposal of adequate control strategies. However, other landscape variables cannot be discarded, including temperature, rainfall regime, and spatial scale (local, landscape and regional). These additional variables were not explored here, and should be considered in future studies.

Morphological and molecular characterization of Paragonimus caliensis Little, 1968 (Trematoda: Paragonimidae) from Medellin and Pichinde, Colombia

Paragonimiasis is a subacute to chronic inflammatory granulomatous lung disease caused by the genus Paragonimus. In Latin America Paragonimus mexicanus Miyazaki & Ishii, 1968 is the only confirmed species to cause human infections. Paragonimus caliensis Little, 1968 is an uncommon species often regarded as a synonym of P. mexicanus. Recently, the study of two types of Paragonimus metacercariae from Costa Rica has provided new molecular and morphological evidence that P. caliensis is a separate species from P. mexicanus. In the present study, molecular, morphological and phylogenetic tools have been used to characterize two populations of Paragonimus located at west of Medellin, Antioquia and at Pichinde, Valle del Cauca (type locality of P. caliensis), Colombia. Adults and metacercariae obtained from Medellin, and metacercariae from Pichinde were analyzed. For morphological observations we used light microscopy and scanning electron microscopy (SEM). Morphology of metacercariae and adults matched with the holotype of P. caliensis. The number and arrangement of sensory papillae in the acetabulum region differs from the morphotypes reported for P. caliensis in Costa Rica. Two morphotypes in branching patterns of ovary and two morphotypes in branching patterns of testes were identified. The main morphological differences between P. caliensis and P. mexicanus corresponded to the size of gonads and their relative positions in the body, and the occasional presence of a cyst wall in P. caliensis metacercariae. The molecular and phylogenetic analyses (using nuclear ribosomal ITS2 and partial cytochrome c oxidase subunit 1 CO1 sequences) confirmed that P. caliensis from the type locality is the same species from Medellin and Costa Rica. Furthermore, these analyses also suggest genetic as well as geographical separation of P. caliensis populations between Colombia and Costa Rica. Currently, P. mexicanus and P. caliensis are sympatric in the Colombian Pacific bioregion, and specific diagnosis based on their egg size is not possible. Therefore, it is necessary to determine the biogeographic distribution ranges of both species and to implement molecular techniques to establish the role of P. caliensis in human paragonimiasis in Colombia.

Hypolobocera guayaquilensis (Decapoda: Pseudothelphusidae): A New Crab Intermediate Host of Paragonimus mexicanus in Manabí Province, Ecuador

To determine that Paragonimus sp. is actively transmitted in a tropical area of the Pacific region of Ecuador where human cases of pulmonary paragonimiasis have recently been documented, a total of 75 freshwater crabs were collected from 2 different streams in the Pedernales area of Manabí Province, Ecuador. All collected crabs were identified as Hypolobocera guayaquilensis based on morphological characteristics of the male gonopods. The hepatopancreas of each crab was examined by compressing it between 2 glass plates followed by observation under a stereomicroscope. Excysted Paragonimus metacercariae were detected in 39 (52.0%) crabs and their densities varied from 1 to 32 per infected crab. There was a positive relationship between crab size and metacercarial density. Sequences of the second internal transcribed spacer region of the ribosomal RNA gene of the Paragonimus metacercariae obtained in this study were identical to those of Paragonimus mexicanus deposited in the DDBJ/EMBL/GenBank database. Thus, the present study is the first to confirm that the crab species H. guayaquilensis is the second intermediate host of P. mexicanus in Manabí Province, Ecuador. Because this crab might be the possible source of human infections in this area, residents should pay attention to improper crab-eating habits related with a neglected parasitic disease, i.e., paragonimiasis.

Diversity of helminth parasites in aquatic invertebrate hosts in Latin America: how much do we know?

Helminths in aquatic invertebrate hosts have been overlooked in comparison with vertebrate hosts. Therefore, the known diversity, ecology and distribution of these host-parasite systems are very limited in terms of their taxonomic diversity, habitat and geographic regions. In this study we examined the published literature on helminth parasites of aquatic invertebrates from Latin America and the Caribbean (LAC) to identify the state of the knowledge in the region and to identify patterns of helminth diversity. Results showed that 67% of the literature is from Argentina, Mexico and Brazil. We found records for 772 host-parasite associations. Most records relate to medically or economically important hosts. Molluscs were the most studied host group with 377 helminth records (80% trematodes). The lymnaeids and planorbids were the most studied molluscs across LAC. Arthropods were the second most studied host group with 78 helminth records (trematodes 38%, cestodes 24% and nematodes 20%), with shrimps and crabs being the most studied hosts. Host species with the largest number of helminth taxa were those with a larger sampling effort through time, usually in a small country region. No large geographical-scale studies were identified. In general, the knowledge is still too scarce to allow any zoogeographical or helminth diversity generalization, as most hosts have been studied locally and the studies on invertebrate hosts in LAC are substantially uneven among countries.

Current status of Paragonimus and paragonimiasis in Ecuador

A review of national and international publications on paragonimiasis in Ecuador, epidemiological records from the Ministry of Public Health and unpublished research data was conducted to summarise the current status of the parasite/disease. The purpose of the review is to educate physicians, policy-makers and health providers on the status of the disease and to stimulate scientific investigators to conduct further research. Paragonimiasis was first diagnosed in Ecuador 94 years ago and it is endemic to both tropical and subtropical regions in 19 of 24 provinces in the Pacific Coast and Amazon regions. Paragonimus mexicanus is the only known species in the country, with the mollusc Aroapyrgus colombiensis and the crabs Moreirocarcinus emarginatus, Hypolobocera chilensis and Hypolobocera aequatorialis being the primary and secondary intermediate hosts, respectively. Recent studies found P. mexicanus metacercariae in Trichodactylus faxoni crabs of the northern Amazon. Chronic pulmonary paragonimiasis is commonly misdiagnosed and treated as tuberculosis and although studies have demonstrated the efficacy of praziquantel and triclabendazole for the treatment of human infections, neither drug is available in Ecuador. Official data recorded from 1978-2007 indicate an annual incidence of 85.5 cases throughout the 19 provinces, with an estimated 17.2% of the population at risk of infection. There are no current data on the incidence/prevalence of infection, nor is there a national control programme.

Detection of multiple species of human Paragonimus from Mexico using morphological data and molecular barcodes

Paragonimus mexicanus is the causal agent of human paragonimiasis in several countries of the Americas. It is considered to be the only species of the genus present in Mexico, where it is responsible for human infection. Through the investigation of P. mexicanus specimens from several places throughout Mexico, we provide morphological, molecular and geographical evidence that strongly suggests the presence of at least three species from this genus in Mexico. These results raise questions regarding the diagnosis, treatment, prophylaxis and control of human paragonimiasis in Mexico. We also provide a brief discussion regarding biodiversity inventories and the convenience of providing molecular and morphological information in biodiversity studies.

Evidence of new species of Haematoloechus (Platyhelminthes: Digenea) using partial cox1 sequences

BACKGROUND AND AIMS

Haematoloechus, digeneans parasites of amphibians, is a species-rich genus with more than 50 species around the globe. Establishing an accurate taxonomy for this group has been difficult due to high intraspecific variability. Nuclear DNA sequences have given independent information about species validity and phylogeny of the group.

MATERIALS AND METHODS

In this paper, I test the performance of partial sequences of the mitochondrial cytochrome c oxidase subunit I (cox1) gene in the differentiation of recognized species of the genus and in the detection of potential new taxa. Samples from 13 nominal species were sequenced, plus four samples that could not be assigned to any described species based on morphology.

RESULTS

Parsimony analysis of the amplified 360 bp fragment resulted in six most parsimonious trees showing the same grouping of samples, differing in the samples' arrangement within those groups. All 13 species were recovered on the trees, and five potential new species are shown.

CONCLUSION

Additional sampling and sequencing is necessary to support this hypothesis, but with this preliminary information the search for diagnostic characters that allow the description of the new taxa is less difficult.

Phylogenetic analysis of nuclear and mitochondrial DNA reveals a complex of cryptic species in Crassicutis cichlasomae (Digenea: Apocreadiidae), a parasite of Middle-American cichlids

We obtained nuclear ITS-1 and mitochondrial cox1 sequences from 225 Crassicutis cichlasomae adults collected in 12 species of cichlids from 32 localities to prospect for the presence of cryptic species. This trematode is commonly found in species of cichlids over a wide geographic range in Middle-America. Population-level phylogenetic analyses of ITS-1 and cox1, assessments of genetic and haplotype diversity, and morphological observations revealed that C. cichlasomae represents a complex of seven cryptic species for which no morphological diagnostic characters have been discovered thus far. Bayesian and Maximum Likelihood analyses of concatenated datasets (906 bp) recovered eight lineages of C. cichlasomae, all with high posterior probabilities and bootstrap branch support. Values of genetic divergence between clades ranged from 1.0% to 5.2% for ITS-1, and from 7.2% to 30.0% for cox1. Morphological study of more than 300 individuals did not reveal structural diagnostic traits for the species defined using molecular evidence. These observations indicate that some traditional morphological characters (e.g., testes position) have substantial intra-specific variation, and should be used with caution when classifying C. cichlasomae and their sister taxa. Additionally, phylogenetic analyses did not reveal a strict correlation between these cryptic species and their host species or geographic distribution, however it appears that genetic distinctiveness of these cryptic species was influenced by the diversification and biogeographical history of Middle-American cichlids.

North American paragonimiasis (Caused by Paragonimus kellicotti) in the context of global paragonimiasis

Paragonimus species are highly evolved parasites with a complex life cycle that involves at least three different hosts, i.e., snails, crustaceans, and mammals. The adult forms of Paragonimus species reside and mate in the lungs of a variety of permissive mammalian hosts, including humans. Although human paragonimiasis is uncommonly encountered in North America, both autochthonous and imported disease may be encountered. Paragonimus kellicotti, the species endemic to North America, is a well-known pathogen in wild and domestic animals. Five patients with North American paragonimiasis have been reported in the recent medical literature. The biologic, clinical, radiologic, and laboratory features of paragonimiasis are reviewed, with emphasis on North American paragonimiasis whenever possible.

Making the most of mitochondrial genomes--markers for phylogeny, molecular ecology and barcodes in Schistosoma (Platyhelminthes: Digenea)

An increasing number of complete sequences of mitochondrial (mt) genomes provides the opportunity to optimise the choice of molecular markers for phylogenetic and ecological studies. This is particularly the case where mt genomes from closely related taxa have been sequenced; e.g., within Schistosoma. These blood flukes include species that are the causative agents of schistosomiasis, where there has been a need to optimise markers for species and strain recognition. For many phylogenetic and population genetic studies, the choice of nucleotide sequences depends primarily on suitable PCR primers. Complete mt genomes allow individual gene or other mt markers to be assessed relative to one another for potential information content, prior to broad-scale sampling. We assess the phylogenetic utility of individual genes and identify regions that contain the greatest interspecific variation for molecular ecological and diagnostic markers. We show that variable characters are not randomly distributed along the genome and there is a positive correlation between polymorphism and divergence. The mt genomes of African and Asian schistosomes were compared with the available intraspecific dataset of Schistosoma mansoni through sliding window analyses, in order to assess whether the observed polymorphism was at a level predicted from interspecific comparisons. We found a positive correlation except for the two genes (cox1 and nad1) adjoining the putative control region in S. mansoni. The genes nad1, nad4, nad5, cox1 and cox3 resolved phylogenies that were consistent with a benchmark phylogeny and in general, longer genes performed better in phylogenetic reconstruction. Considering the information content of entire mt genome sequences, partial cox1 would not be the ideal marker for either species identification (barcoding) or population studies with Schistosoma species. Instead, we suggest the use of cox3 and nad5 for both phylogenetic and population studies. Five primer pairs designed against Schistosoma mekongi and Schistosoma malayensis were tested successfully against Schistosoma japonicum. In combination, these fragments encompass 20-27% of the variation amongst the genomes (average total length approximately 14,000bp), thus providing an efficient means of encapsulating the greatest amount of variation within the shortest sequence. Comparative mitogenomics provides the basis of a rational approach to molecular marker selection and optimisation.

Morphological and molecular identification of two Paragonimus spp., of which metacercariae concurrently found in a land crab, Potamiscus tannanti, collected in Yenbai Province, Vietnam

Paragonimosis is an important food-borne zoonosis especially in Asian countries. Among Paragonimus species, Paragonimus westermani followed by P. skrjabini complex are the major pathogens for human paragonimosis in Asia. In addition, P. heterotremus is an important pathogen in southern China and the Indochina Peninsula and is the only proven species to cause human paragonimosis in Vietnam. During a recent survey in Yenbai Province in northern Vietnam, we found small and large types of Paragonimus metacercariae often concurrently in mountainous crabs, Potamiscus tannanti. Adult worms from those small and large metacercariae were obtained separately by experimental infection in dogs and cats. Morphological and molecular phylogenetic study based on sequences of ITS2 and a part of CO1 genes were performed for the identification of small and large metacercariae and their adults. The results showed that small metacercariae and their adults are completely identical with P. heterotremus in morphology and molecular genetic profiles. In contrast, large metacercariae and their adults have some morphological similarities with P. skrjabini and P. harinasutai, but are unidentifiable from each other by morphology alone. Molecular phylogenetic tree analyses on ITS2 and CO1 genes revealed that large metacercariae and their adults were grouped in the same clade and different from any known Paragonimus species. Although they share the same ancestor with P. skrjabini complex, their genetic distance was considerably different from two other known subspecies, P. skrjabini skrjabini and P. skrjabini miyazakii. Our results provide a new insight on the phylogeny of the genus Paragonimus.

Advances and Trends in the Molecular Systematics of the Parasitic Platyhelminthes

The application of molecular systematics to the parasitic Platyhelminthes (Cestoda, Digenea and Monogenea) over the last decade has advanced our understanding of their interrelationships and evolution substantially. Here we review the current state of play and the early works that led to the molecular-based hypotheses that now predominate in the field; advances in their systematics, taxonomy, classification and phylogeny, as well as trends in species circumscription, molecular targets and analytical methods are discussed for each of the three major parasitic groups. A by-product of this effort has been an ever increasing number of parasitic flatworms characterized genetically, and the useful application of these data to the diagnosis of animal and human pathogens, and to the elucidation of life histories are presented. The final section considers future directions in the field, including taxon sampling, molecular targets of choice, and the current and future utility of mitochondrial and nuclear genomics in systematic study.

The Use and Implications of Ribosomal DNA Sequencing for the Discrimination of Digenean Species

In just over a decade, the use of molecular approaches for the recognition of parasites has become commonplace. For trematodes, the internal transcribed spacer region of ribosomal DNA (ITS rDNA) has become the default region of choice. Here, we review the findings of 63 studies that report ITS rDNA sequence data for about 155 digenean species from 19 families, and then review the levels of variation that have been reported and how the variation has been interpreted. Overall, complete ITS sequences (or ITS1 or ITS2 regions alone) usually distinguish trematode species clearly, including combinations for which morphology gives ambiguous results. Closely related species may have few base differences and in at least one convincing case the ITS2 sequences of two "good" species are identical. In some cases, the ITS1 region gives greater resolution than the ITS2 because of the presence of variable repeat units that are generally lacking in the ITS2. Intraspecific variation is usually low and frequently apparently absent. Information on geographical variation of digeneans is limited but at least some of the reported variation probably reflects the presence of multiple species. Despite the accepted dogma that concerted evolution makes the individual representative of the entire species, a significant number of studies have reported at least some intraspecific variation. The significance of such variation is difficult to assess a posteriori, but it seems likely that identification and sequencing errors account for some of it and failure to recognise separate species may also be significant. Some reported variation clearly requires further analysis. The use of a "yardstick" to determine when separate species should be recognised is flawed. Instead, we argue that consistent genetic differences that are associated with consistent morphological or biological traits should be considered the marker for separate species. We propose a generalised approach to the use of rDNA to distinguish trematode species.

Genomic characterization of lung flukes, Paragonimus heterotremus, P. siamensis, P. harinasutai, P. westermani and P. bangkokensis by RAPD markers

Random amplified polymorphic DNA (RAPD) markers were assayed in an attempt to discriminate among five species of Paragonimus. Genomic DNAs of two strains of Paragonimus heterotremus from two provinces in Thailand, Saraburi and Phitsanulok, as well as of P. siamensis, P. harinasutai, P. westermani and P. bangkokensis were extracted and amplified by an arbitrary primer, namely P2 (5-GTTTCGCTCC-3). RAPD patterns showed that those five species were genetically distinct, although they shared genomic DNA to some extent. This primer could also distinguish between two strains of P. heterotremus. The polymorphism observed allowed to construct a relationship dendrogram. The phylogenetic dendrogram showed that the P. heterotremus strains were closest to P. harinasutai, followed by P. siamensis, P. bangkokensis and P. westermani.