Molecular characterization and phylogenetic analysis of ascarid nematodes from twenty-one species of captive wild mammals based on mitochondrial and nuclear sequences

Helminths of the rock lizards Darevskia dahli and D. armeniaca in their invaded range in Ukraine

This study investigated the helminths of the mixed invasive population of Darevskia armeniaca and D. dahli, collected during two field trips in Denyshy, Zhytomyr region, Ukraine, in 2023. In total, 67 adult lizards (35 D. armeniaca and 32 D. dahli) were examined. Molecular and morphological approaches were used to identify the parasites. The analyses revealed six helminth species, including four nematodes (Toxocara cati, Strongyloides darevskyi, Oswaldocruzia sp., and Spirurida gen. sp.), one trematode (Pleurogenes claviger), and one cestode (Mesocestoides litteratus). Toxocara cati had the highest prevalence, found in cysts located primarily on the liver and in the body cavity of the hosts. The qualitative and quantitative comparative assessment of the helminth community suggests that, due to the introduction of these lizards, most helminth species from their native range have been lost. Additionally, most local helminth species have not yet adapted to parasitising these lizards as normal hosts of their life cycle.

First report of Hexametra angusticaecoides Chabaud & Brygoo, 1960 (Nematoda: Ascarididae) in a population of captive central bearded dragons, Pogona vitticeps Ahl (Squamata: Agamidae)

Between 2022 and 2023 ascaridoid nematodes of the genus Hexametra were recovered from two captive central bearded dragons (Pogona vitticeps Ahl) in the Extremadura region of Spain. These nematodes were identified by an integrative approach combining morpho-anatomical and molecular data. We used two rRNA regions (D2-D3 expansion segments of the 28S, and ITS fragments), and the partial region of the cytochrome oxidase I gene (COI mtDNA) sequences. Hexametra angusticaecoides Chabaud & Brygoo, 1960 (Ascarididae) was morphologically characterized and illustrated using light and scanning electron microscopy. Bayesian inference (BI) and Maximum Likelihood (ML) phylogenetic trees for these genetic markers established relationships that highlight the importance of using molecular and phylogenetic data for accurate species identification within the genus Hexametra. Phylogenetic trees indicated that the Spanish isolates of H. angusticaecoides were clustered in a well-supported clade together with other isolates from Central Europe of the same species. Molecular phylogenetic findings also reflect that there was a higher intraspecific variation for ITS genetic markers at the intraspecific level. Phylogenetic results based on 28S rRNA suggest that Ascarididea was divided into three monophyletic major clades. To our knowledge, this is the first report of this species parasitizing bearded dragons, extending the host range of this species. These findings represent the first formal record of H. angusticaecoides in Spain.

Prevalence of Gastrointestinal Parasites in Zoo Animals and Phylogenetic Characterization of Toxascaris leonina (Linstow, 1902) and Baylisascaris transfuga (Rudolphi, 1819) in Jiangsu Province, Eastern China

The burden of gastrointestinal parasites in zoo animals has serious implications for their welfare and the health of veterinarians and visitors. Zhuyuwan Zoo is located in the eastern suburb of Yangzhou city in eastern China, in which over 40 species of zoo animals are kept. In order to understand the infection status of GI parasites in Zhuyuwan Zoo, a total of 104 fresh fecal samples collected randomly from birds (n = 19), primates (n = 19), and non-primate mammals (n = 66) were analyzed using the saturated saline flotation technique and nylon sifter elutriation and sieving method for eggs/oocysts, respectively. Two Ascaris species were molecularly characterized. The results showed that the overall prevalence of parasitic infection was 42.3% (44/104). The parasitic infection rate in birds, primates, and non-primate mammals were 26.3% (5/19), 31.6% (6/19), and 50.0% (33/66), respectively. A total of 11 species of parasites were identified, namely, Trichostrongylidae, Capillaria sp., Trichuris spp., Strongyloides spp., Amidostomum sp., Toxascaris leonina, Baylisascaris transfuga, Parascaris equorum, Paramphistomum spp., Fasciola spp., and Eimeria spp. Paramphistomum spp. eggs were first detected from the captive Père David's deer, and Fasciola spp. eggs were first reported from sika deer in zoo in China. A sequence analysis of ITS-2 and cox1 showed that the eggs isolated from the African lion (Panthera leo Linnaeus, 1758) were T. leonina, and the eggs from the brown bear (Ursus arctos Linnaeus, 1758) were B. transfuga. The public health threat posed by these potential zoonotic parasitic agents requires attention. These results lay a theoretical foundation for prevention and control of wild animal parasitic diseases at zoos in China.

Mitogenomic phylogenies suggest the resurrection of the subfamily Porrocaecinae and provide insights into the systematics of the superfamily Ascaridoidea (Nematoda: Ascaridomorpha), with the description of a new species of Porrocaecum

BACKGROUND

The family Toxocaridae is a group of zooparasitic nematodes of veterinary, medical and economic significance. However, the evolutionary relationship of Porrocaecum and Toxocara, both genera currently classified in Toxocaridae, and the monophyly of the Toxocaridae remain under debate. Moreover, the validity of the subgenus Laymanicaecum in the genus Porrocaecum is open to question. Due to the scarcity of an available genetic database, molecular identification of Porrocaecum nematodes is still in its infancy.

METHODS

A number of Porrocaecum nematodes collected from the Eurasian marsh harrier Circus aeruginosus (Linnaeus) (Falconiformes: Accipitridae) in the Czech Republic were identified using integrated morphological methods (light and scanning electron microscopy) and molecular techniques (sequencing and analyzing the nuclear 18S, 28S and ITS regions). The complete mitochondrial genomes of the collected nematode specimens and of Porrocaecum (Laymanicaecum) reticulatum (Linstow, 1899) were sequenced and annotated for the first time. Phylogenetic analyses of ascaridoid nematodes based on the amino acid sequences of 12 protein-coding genes of mitochondrial genomes were performed using maximum likelihood and Bayesian inference.

RESULTS

A new species of Porrocaecum, named P. moraveci n. sp., is described based on the morphological and genetic evidence. The mitogenomes of P. moraveci n. sp. and P. reticulatum both contain 36 genes and are 14,517 and 14,210 bp in length, respectively. Comparative mitogenomics revealed that P. moraveci n. sp. represents the first known species with three non-coding regions and that P. reticulatum has the lowest overall A + T content in the mitogenomes of ascaridoid nematodes tested to date. Phylogenetic analyses showed the representatives of Toxocara clustered together with species of the family Ascarididae rather than with Porrocaecum and that P. moraveci n. sp. is a sister to P. reticulatum.

CONCLUSIONS

The characterization of the complete mitochondrial genomes of P. moraveci n. sp. and P. reticulatum is reported for the first time. Mitogenomic phylogeny analyses indicated that the family Toxocaridae is non-monophyletic and that the genera Porrocaecum and Toxocara do not have an affinity. The validity of the subgenus Laymanicaecum in Porrocaecum was also rejected. Our results suggest that: (i) Toxocaridae should be degraded to a subfamily of the Ascarididae that includes only the genus Toxocara; and (ii) the subfamily Porrocaecinae should be resurrected to include only the genus Porrocaecum. The present study enriches the database of ascaridoid mitogenomes and provides a new insight into the systematics of the superfamily Ascaridoidea.

Morphology and genetic characterization of Physaloptera sibirica Petrow & Gorbunov, 1931 (Spirurida: Physalopteridae), from the hog-badger Arctonyx collaris Cuvier (Carnivora: Mustelidae), with molecular phylogeny of Physalopteridae

BACKGROUND

Nematodes of the family Physalopteridae (Spirurida: Physalopteroidea) commonly parasitize the alimentary canal of all major vertebrate groups. However, many physalopterid species are not adequately described, especially regarding the detailed morphology of the cephalic end. The current genetic database for Physaloptera species is still very limited, which seriously hampers molecular-based species identification. Additionally, the systematic status of some genera and the evolutionary relationships of the subfamilies in the Physalopteridae remain under debate.

METHODS

New morphological data for Physaloptera sibirica was gathered using light and scanning electron microscopy based on newly collected specimens from the hog badger Arctonyx collaris Cuvier (Carnivora: Mustelidae) in China. Six different genetic markers, including nuclear small ribosomal DNA (18S), large ribosomal DNA (28S) and internal transcribed spacer (ITS), mitochondrial cytochrome c oxidase subunit 1 (cox1) and subunit 2 (cox2), and the 12S small subunit ribosomal RNA gene of P. sibirica were sequenced and analyzed for the first time to our knowledge. Additionally, to construct a basic molecular phylogenetic framework for the Physalopteridae, phylogenetic analyses were performed based on the cox1 and 18S + cox1 genes using maximum likelihood (ML) and Bayesian inference (BI) methods.

RESULTS

Scanning electron microscopy (SEM) observation displayed the details of the cephalic structures, deirids, excretory pore, caudal papillae, vulva, phasmids and egg of P. sibirica for the first time to our knowledge. Pairwise comparison of the sequences obtained for P. sibirica did not reveal intraspecific divergence regarding the 18S, 28S, cox1 and 12S genetic markers and a low level of divergence in the ITS (0.16%) and cox2 (2.39%) regions. Maximum likelihood and Bayesian inference analyses showed that the representatives of Physalopteridae formed two major clades (species of Physalopterinae + Thubunaeinae parasitic in terrestrial vertebrates and Proleptinae only occurring in marine or freshwater fishes). Turgida turgida was found nested among representatives of Physaloptera. Physaloptera sibirica clustered together with P. rara. Physalopteroides sp. (Thubunaeinae) formed a sister relationship to the physalopterine Abbreviata caucasica.

CONCLUSIONS

Physaloptera sibirica was redescribed, which is the fourth nematode parasite reported from the hog badger A. collaris, and A. collaris represents a new host for P. sibirica. The phylogenetic results challenged the validity of the subfamily Thubunaeinae and of the genus Turgida and supported dividing the family Physalopteridae into two subfamilies, Physalopterinae and Proleptinae. However, we do not make any immediate systematic changes in the Physalopteridae, because a more rigorous study with broader representation of the Physalopteridae is required. These present findings contribute to morphologically identifying P. sibirica more accurately and provide new insights into the systematics of the Physalopteridae.

First Study of Ascaris lumbricoides from the Semiwild Population of the Sumatran Orangutan Pongo abelii in the Context of Morphological Description and Molecular Phylogeny

There is little evidence that the already described and accepted taxa of ascarids (Ascaris lumbricoides, A. suum, and A. ovis) infecting individuals of taxonomically distant groups (hominids, pigs, sheep, goats, and dogs) can be genetically or morphologically distinguished. However, despite described morphological differences, e.g., due to intraspecific variation, these are insufficient for species determination and may indicate differences amongst ascarids because of cross infections, hybrid production, and specific adaptations to hosts. Herein, the results of a molecular and morphological analysis of ascarids parasitising Sumatran orangutans (Pongo abelii Lesson, 1827) in native populations are presented. The research took place in the Bukit Lawang area, Indonesia, in 2009. Throughout the year, fresh faecal samples were collected regularly from 24 orangutans, and all were examined for the presence of nematode adults. Only five adult worms from two orangutan females were found during regular collection. Using the integrative taxonomic approach, the nematodes found were identified as A. lumbricoides. The significance of the find and its rarity is documented by the fact that this is the first confirmed finding of adult ascarids from an original orangutan site (not from a zoo) in more than 130 years (including the long-term study spanning the last 20 years focusing on orangutan parasites and natural antiparasitic drugs). More accurate morphometric parameters and genetic differences for the identification of ascarids were established. These parameters will be helpful for other findings in great apes and will also be suitable for further and precise determination of this parasite. The details distinguishing between male and female specimens are also stated and well defined. A comprehensive evaluation of the situation of Ascaris species parasitising orangutans, including a comparison with previously described orangutan parasite (i.e., A. satyri-species inquirenda), is discussed.

Molecular data reveal a new species of Seuratascaris Sprent, 1985 (Nematoda: Ascaridoidea) from Quasipaa exilispinosa (Liu & Hu) (Amphibia: Anura)

The genus Seuratascaris Sprent, 1985 is a group of obligate nematode parasites of amphibians. In the present study, a new species of Seuratascaris, S. physalis sp. n. was described using light and scanning electron microscopy based on specimens collected from Quasipaa exilispinosa (Liu & Hu) (Amphibia: Anura) in China. The new species differs from S. numidica (Seurat, 1917) by the cuticle of the cervical region distinctly inflated to form a cephalic vesicle-like structure and the absence of single medio-ventral precloacal papilla. The molecular characterization of the nuclear large ribosomal DNA (28S) and internal transcribed spacer (ITS) and the mitochondrial cytochrome c oxidase subunit 1 (cox1), cytochrome c oxidase subunit 2 (cox2) and 12S small subunit ribosomal RNA gene of S. physalis sp. n., together with the 28S, cox2 and 12S of S. numidica are provided for the first time. Molecular analysis revealed the presence of high level of interspecific genetic variation between the two species in the ITS (5.50%), cox1 (13.3%), cox2 (10.6%) and 12S regions (10.5%), which strongly supported that S. physalis sp. n. represented a different species from S. numidica. Angusticaecum ranae Wang, Zhao & Chen, 1978 reported from the frog Quasipaa spinosa (David) (Anura: Dicroglossidae) in China was transferred into the genus Seuratascaris as S. ranae (Wang, Zhao & Chen, 1978) comb. n. based on the morphology of lips and the presence of very short and robust spicules without alae and small numbers of precloacal papillae. The present study provided useful genetic data for molecular identification of species of Seuratascaris and provides the foundation for being able to determine if S. numidica represents a species complex of some sibling species or a single species.

Genetic and population diversity of Toxocara cati (Schrank, 1788) Brumpt, 1927, on the basis of the internal transcribed spacer (ITS) region

The present investigation was aimed to study the sequence, phylogenetic and haplotype analyses of Toxocara cati based on the ITS region, along with the genetic diversity, demographic history and population-genetic structure. The maximum likelihood tree based on Kimura 2-parameter model was constructed using the complete ITS region of all the nucleotide sequences (n = 57) of Toxocara spp. and other related ascarid worms available in the GenBank™. It placed all the sequences of T. cati into four major clades designated as T. cati genotypes 1-4 (TcG1-G4). A total of 66 signature nucleotides were identified in the ITS region between genotypes. The median-joining haplotype network displayed a total of 24 haplotypes, with China exhibiting the highest number of haplotypes (h = 20) followed by India (h = 4), and Japan and Russia (h = 1). It indicated a clear distinction between all the four genotypes. The pairwise F_ST values between all the genotypes indicated huge genetic differentiation (> 0.25) between different T. cati genotypes. Moreover, the gene flow (Nm) between T. cati genotypes was very low. Results of AMOVA revealed higher genetic variation between genotypes (92.82%) as compared to the variation within genotypes (7.18%). The neutrality indices and mismatch distributions for the G1-G4 genotypes, Indian isolates and the overall dataset of T. cati indicated either a constant population size or a slight population increase. The geographical distribution of all the genotypes of T. cati is also reported. This is the first report of genotyping of T. cati on the basis of the ITS region.

Gene rearrangements in the mitochondrial genome of ten ascaris species and phylogenetic implications for Ascaridoidea and Heterakoidea families

The Ascaridoidea family and Heterakoidea family are the most common and typical representative of large parasites. Although our understanding of these parasites' diversity has expanded by analyses of some mitochondrial genes, there is limited information on these species' evolutionary rates. Here we determined ten complete mitogenome sequences of five subfamilies of Ascaridoidea and one subfamily of Heterakoidea. The phylogenetic tree divided the Ascaridoidea into six monophyletic major clades, and the divergence time of Heterakoidea family and Ascaridoidea family can be placed during the early Carboniferous Period (300-360 Mya). The reconstruction of the ancestral state showed that the gene orders of all species in Ascaridoidea were conserved, and the Heterakoidea had obvious genome rearrangement. The conserved blocks between them were divided into five and the main types are tandem-duplication/random loss (TDRL). These results will help to better understand the gene rearrangements and evolutionary position of ascaris species.

Morphology, genetic characterization and molecular phylogeny of the poorly known nematode parasite Cissophyllus leytensis Tubangui & Villaamil, 1933 (Nematoda: Ascaridida) from the Philippine sailfin lizard Hydrosaurus pustulatus (Eschscholtz, 1829) (Reptilia: Squamata)

Background

The genus Cissophyllus (Cosmocercoidea: Kathlaniidae) is a rare group of nematodes parasitic in turtles and lizards. To date, only four species have been reported in Asia and North America. However, most of them are inadequately described. The species Cissophyllus leytensis has never been reported since it was originally described by Tubangui and Villaamil in 1933 from the Philippine sailfin lizard Hydrosaurus pustulatus (Eschscholtz, 1829) (Reptilia: Squamata). Furthermore, the systematic status of Cissophyllus/Cissophyllinae in the family Kathlaniidae of the superfamily Cosmocercoidea remains under debate.

Methods

The detailed morphology of C. leytensis was studied using light microscopy (LM) and, for the first time, scanning electron microscopy (SEM), based on newly collected specimens from the type host H. pustulatus. Six different genetic markers, including nuclear sequences [small ribosomal subunit (18S), internal transcribed spacer (ITS) and large ribosomal subunit (28S)], plus mitochondrial genes [cytochrome c oxidase subunit 1 (cox1), cytochrome c oxidase subunit 2 (cox2) and 12S small subunit ribosomal RNA gene] of C. leytensis were sequenced. Additionally, in order to test the validity of the subfamily Cissophyllinae and clarify the phylogenetic relationships of Cissophyllus and the other genera in the family Kathlaniidae, phylogenetic analyses based on 18S + 28S and ITS sequence data were performed using maximum likelihood (ML) and Bayesian inference (BI) analyses, respectively.

Results

Our observations using LM and SEM revealed some previously unreported morphological features, necessitating the redescription of this poorly known species. The presence of remarkable morphological variation in the isthmus and the position of excretory pore among different individuals was found. Molecular analysis showed no intraspecific nucleotide divergence detected in the 18S, ITS, 28S, cox2 and 12S regions among different individuals of C. leytensis, but a low level of intraspecific genetic variation was found in the cox1 (0.52%). Our phylogenetic results showed the representatives of the Cosmocercoidea divided into four large clades (Cosmocerca + Aplectana + Cosmocercoides representing the family Cosmocercidae, Cruzia representing the subfamily Cruzinae of Kathlaniidae, Falcaustra + Cissophyllus + Megalobatrachonema representing the subfamily Kathlaniinae of Kathlaniidae, and Orientatractis + Rondonia representing the family Atractidae). The genus Cissophyllus clustered together with the genus Megalobatrachonema in both the ML and BI trees using ITS sequence data, but displayed a sister relationship to the genus Falcaustra in the ML tree and to the genera Falcaustra + Megalobatrachonema in the BI tree using 18S + 28S sequence data.

Conclusions

Molecular phylogenetic results further confirmed that the family Kathlaniidae is not a monophyletic group. The subfamily Cruziinae should be moved from the hitherto-defined family Kathlaniidae and elevated as a separate family Cruziidae. The present phylogenetic results also negated the validity of the subfamily Cissophyllinae and supported the genus Cissophyllus assigned in the subfamily Kathlaniinae. Molecular analysis indicated that the morphological variation in the isthmus and position of excretory pore among different individuals should be considered as intraspecific variation. Moreover, some characters important for the specific diagnosis of C. leytensis are reported for the first time: the number of acuminate denticles (lamellae) on each lip, the chitinized pharynx with three flabellate pharyngeal plates, the presence of single medioventral precloacal papilla and the detailed morphology of caudal papillae. The present study is only the second record of C. leytensis.

Graphical Abstract

PHYLOGEOGRAPHY OF BAYLISASCARIS PROCYONIS (RACCOON ROUNDWORM) IN NORTH AMERICA

Sequences of the mitochondrial cytochrome c oxidase 1 (COI) gene of 115 Baylisascaris procyonis individuals from 13 U.S. states and 1 Canadian province were obtained from 44 raccoon hosts to assess genetic variation and geographic structure. The maximum genetic distance between individuals was low (1.6%), consistent with a single species. Moderate COI haplotype (h = 0.60) and nucleotide (π = 0.0053) diversity were found overall. Low haplotype diversity was found among samples east of the Mississippi River (h = 0.036), suggesting that historical growth and expansion of raccoon populations in this region could be responsible for high parasite gene flow or a selective sweep of B. procyonis mtDNA. There was low genetic structure (average Φst = 0.07) for samples east of the continental divide, but samples from Colorado showed higher diversity and differentiation from midwestern and eastern samples. There was marked genetic structure between samples from east and west of the continental divide, with no haplotypes shared between these regions. There was no significant isolation by distance among any of these geographic samples. The phylogeographic patterns for B. procyonis are similar to genetic results reported for their raccoon definitive hosts. The phylogeographic divergence of B. procyonis from east and west of the continental divide may involve vicariance resulting from Pleistocene glaciation and associated climate variation.

The morphological and molecular characterization of Baylisascaris devosi Sprent, 1952 (Ascaridoidea, Nematoda), collected from Pine marten (Martes martes) in Iran

Background

Baylisascaris devosi is an intestinal nematode found in several carnivores including fisher, wolverine, Beech marten, American marten and sable in different parts of the world, but this nematode has not been reported from Pine marten. Therefore, this study aimed to identify Baylisascaris isolated from a Pine marten in Iran using morphological and molecular approaches.

Methods

Specimens of B. devosi were collected from one road-killed Pine marten in northern Iran. Morphological features were evaluated using scanning electron microscopy, energy dispersive x-ray analysis and ion sectioning. The molecular characterization was carried out using partial Cox1, LSU rDNA and ITS-rDNA genes.

Results

The nematodes isolated from the Pine marten were confirmed to be B. devosi based on the morphological features and the sequence of ribosomal and mitochondrial loci. X-ray scans (EDAX) were completed on gallium cut structures (papillae, eggs, male spike and mouth denticles) of B. devosi using a dual-beam scanning electron microscope. The male spike and mouth denticles had a high level of hardening elements (Ca, P, S), helping to explain the chemical nature and morphology of the worm. Based on these genetic marker analyses, our sequence had the greatest similarity with Russian B. devosi isolated from sable.

Conclusions

In this study, to our knowledge, the occurrence of B. devosi infection in Pine marten is reported for the first time. Molecular analysis showed that these three genes are suitable molecular markers for identification and inferring phylogenetic relationships of Baylisascaris species. Furthermore, the high divergence of Cox1 between Baylisascaris species indicates that Cox1 could be used for their phylogenetic and taxonomic studies.

Molecular characterization of ascaridoid parasites from captive wild carnivores in China using ribosomal and mitochondrial sequences

BACKGROUND

Despite the public health importance of toxocariasis/toxascariasis, only a few species of these ascaridoid parasites from wild canine and feline carnivores have been studied at the molecular level so far. Poor understanding of diversity, host distribution and the potential (zoonotic) transmission of the ascaridoid species among wild animals negatively affects their surveillance and control in natural settings. In this study, we updated previous knowledge by profiling the genetic diversity and phylogenetic relationships of ascaridoid species among eleven wild canine and feline animals on the basis of a combined analysis of the ribosomal internal transcribed spacer region (ITS) gene and the partial mitochondrial cytochrome c oxidase subunit 2 (cox2) and NADH dehydrogenase subunit 1 (nad1) genes.

RESULTS

In total, three genetically distinct ascaridoid lineages were determined to be present among these wild carnivores sampled, including Toxocara canis in Alopex lagopus and Vulpes vulpes, Toxocara cati in Felis chaus, Prionailurus bengalensis and Catopuma temmincki and Toxascaris leonina in Canis lupus, Panthera tigris altaica, Panthera tigris amoyensis, Panthera tigris tigris, Panthera leo and Lynx lynx. Furthermore, it was evident that T. leonina lineage split into three well-supported subclades depending on their host species, i.e. wild felids, dogs and wolves and foxes, based on integrated genetic and phylogenetic evidence, supporting that a complex of T. leonina other than one species infecting these hosts.

CONCLUSIONS

These results provide new molecular insights into classification, phylogenetic relationships and epidemiological importance of ascaridoids from wild canids and felids and also highlight the complex of the taxonomy and genetics of Toxascaris in their wild and domestic carnivorous hosts.

Molecular phylogenetics and species-level systematics of Baylisascaris

Nucleotide sequences representing nine genes and five presumptive genetic loci were used to infer phylogenetic relationships among seven Baylisascaris species, including one species with no previously available molecular data. These genes were used to test the species status of B. procyonis and B. columnaris using a coalescent approach. Phylogenetic analysis based on combined analysis of sequence data strongly supported monophyly of the genus and separated the species into two main clades. Clade 1 included B. procyonis, B. columnaris, and B. devosi, species hosted by musteloid carnivores. Clade 2 included B. transfuga and B. schroederi from ursids, B. ailuri, a species from the red panda (a musteloid), and B. tasmaniensis from a marsupial. Within clade 2, geographic isolates of B. transfuga, B. schroederi (from giant panda), and B. ailuri formed a strongly supported clade. In certain analyses (e.g., some single genes), B. tasmaniensis was sister to all other Baylisascaris species rather than sister to the species from ursids and red panda. Using one combination of priors corresponding to moderate population size and shallow genetic divergence, the multispecies coalescent analysis of B. procyonis and B. columnaris yielded moderate support (posterior probability 0.91) for these taxa as separate species. However, other prior combinations yielded weak or no support for delimiting these taxa as separate species. Similarly, tree topologies constrained to represent reciprocal monophyly of B. columnaris and B. procyonis individuals (topologies consistent with separate species) were significantly worse in some cases, but not others, depending on the dataset analyzed. An expanded analysis of SNPs and other genetic markers that were previously suggested to distinguish between individuals of B. procyonis and B. columnaris was made by characterization of additional individual nematodes. The results suggest that many of these SNPs do not represent fixed differences between nematodes derived from raccoon and skunk hosts.

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A phylogenetic hypothesis for Baylisascaris species was produced using nine genes.

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Genetic data was generated for two new species- B. devosi and B. tasmaniensis.

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Baylisascaris devosi and B. tasmaniensis were part of a monophyletic Baylisascaris.

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B. procyonis (raccoon) and B. columnaris (skunk) could not be reliably distinguished.

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Established SNPs may not be diagnostic for Baylisascaris from raccoons and skunks.

A frequent roundworm Baylisascaris transfuga in overpopulated brown bears (Ursus arctos) in Slovakia: a problem worthy of attention

The genus Baylisascaris (order Ascaridida) includes numerous relatively host-specific nematodes, which are common in intestines of wild mammals. Some of them may have impact on veterinary and public health, as their larvae have the potential to cause visceral, ocular, and/or neural larva migrans in a wide range of mammals, birds, and humans. Baylisascaris transfuga is a parasite occurring in a range of bear species throughout the world. We present the current data on B. transfuga occurrence in brown bears from a relatively restricted territory of the Poľana Protected Landscape Area in Central Slovakia, obtained by traditional methods (faecal examination, morphology). Species affiliation was confirmed by employing molecular markers generating nuclear 28S and mitochondrial cox1 sequences in adult worms. Based on 17 examined samples (15 excrements and two intestines of young bear females), the occurrence of B. transfuga in the surveyed area was assessed as 52.9%. Both bear females were infected with adult and juvenile worms. Due to the high density of bears in the locality, the high infection rate with ascarids, and the huge number of eggs produced by the parasites, it is apparent that the respective environment, including the inhabited areas, might be markedly contaminated by Baylisascaris eggs. The ability of B. transfuga to serve as a zoonotic agent has not been unambiguously proved; however, this attribute should be considered and subjected to further research.

Parasites of the Giant Panda: A Risk Factor in the Conservation of a Species

The giant panda, with an estimated population size of 2239 in the world (in 2015), is a global symbol of wildlife conservation that is threatened by habitat loss, poor reproduction and limited resistance to some infectious diseases. Of these factors, some diseases caused by parasites are considered as the foremost threat to its conservation. However, there is surprisingly little published information on the parasites of the giant panda, most of which has been disseminated in the Chinese literature. Herein, we review all peer-reviewed publications (in English or Chinese language) and governmental documents for information on parasites of the giant pandas, with an emphasis on the intestinal nematode Baylisascaris schroederi (McIntosh, 1939) as it dominates published literature. The purpose of this chapter is to: (i) review the parasites recorded in the giant panda and describe what is known about their biology; (ii) discuss key aspects of the pathogenesis, diagnosis, treatment and control of key parasites that are reported to cause clinical problems and (iii) conclude by making some suggestions for future research. This chapter shows that we are only just 'scratching the surface' when it comes to parasites and parasitological research of the giant panda. Clearly, there needs to be a concerted research effort to support the conservation of this iconic species.

Beyond the raccoon roundworm: The natural history of non-raccoon Baylisascaris species in the New World

A total of 10 species of Baylisascaris, a genus of ascaridoid nematodes, occur worldwide and 6 of them occur in the New World. Most of the Baylisascaris species have a similar life cycle with carnivorous mammals or marsupials serving as definitive hosts and a smaller prey host serving as paratenic (or intermediate) hosts. However, one species in rodents is unique in that it only has one host. Considerable research has been conducted on B. procyonis, the raccoon roundworm, as it is a well-known cause of severe to fatal neurologic disease in humans and many wildlife species. However, other Baylisascaris species could cause larva migrans but research on them is limited in comparison. In addition to concerns related to the potential impacts of larva migrans on potential paratenic hosts, there are many questions about the geographic ranges, definitive and paratenic host diversity, and general ecology of these non-raccoon Baylisascaris species. Here, we provide a comprehensive review of the current knowledge of New World Baylisascaris species, including B. columnaris of skunks, B. transfuga and B. venezuelensis of bears, B. laevis of sciurids, B. devosi of gulonids, B. melis of badgers, and B. potosis of kinkajou. Discussed are what is known regarding the morphology, host range, geographic distribution, ecoepidemiology, infection dynamics in definitive and paratenic hosts, treatment, and control of these under-studied species. Also, we discuss the currently used molecular tools used to investigate this group of parasites. Because of morphologic similarities among larval stages of sympatric Baylisascaris species, these molecular tools should provide critical insight into these poorly-understood areas, especially paratenic and definitive host diversity and the possible risk these parasites pose to the health to the former group. This, paired with traditional experimental infections, morphological analysis, and field surveys will lead to a greater understanding of this interesting and important nematode genus.

Baylisascaris potosis n. sp., a new ascarid nematode isolated from captive kinkajou, Potos flavus, from the Cooperative Republic of Guyana

We describe a new nematode species, Baylisascaris potosis n. sp., isolated from captive kinkajou, Potos flavus, from the Cooperative Republic of Guyana. The nematode was found in fecal specimens, identified morphologically, and confirmed genetically. The new species is similar to Baylisascaris procyonis, Baylisascaris columnaris, and other Baylisascaris species, but is distinguished by the position of the male phasmidial pole. Nuclear and mitochondrial DNA sequence analyses confirmed that the new species is phylogenetically distinct from all the members of the genus Baylisascaris, and groups with B. procyonis and B. columnaris. This nematode is the 10th species assigned to the genus Baylisascaris.

Complete mitochondrial genomes of chimpanzee- and gibbon-derived Ascaris isolated from a zoological garden in southwest China

Roundworms (Ascaridida: Nematoda), one of the most common soil-transmitted helminths (STHs), can cause ascariasis in various hosts worldwide, ranging from wild to domestic animals and humans. Despite the veterinary and health importance of the Ascaridida species, little or no attention has been paid to roundworms infecting wild animals including non-human primates due to the current taxon sampling and survey bias in this order. Importantly, there has been considerable controversy over the years as to whether Ascaris species infecting non-human primates are the same as or distinct from Ascaris lumbricoides infecting humans. Herein, we first characterized the complete mitochondrial genomes of two representative Ascaris isolates derived from two non-human primates, namely, chimpanzees (Pan troglodytes) and gibbons (Hylobates hoolock), in a zoological garden of southwest China and compared them with those of A. lumbricoides and the congeneric Ascaris suum as well as other related species in the same order, and then used comparative mitogenomics, genome-wide nucleotide sequence identity analysis, and phylogeny to determine whether the parasites from chimpanzees and gibbons represent a single species and share genetic similarity with A. lumbricoides. Taken together, our results yielded strong statistical support for the hypothesis that the chimpanzee- and gibbon-derived Ascaris represent a single species that is genetically similar to A. lumbricoides, consistent with the results of previous morphological and molecular studies. Our finding should enhance public alertness to roundworms originating from chimpanzees and gibbons and the mtDNA data presented here also serves to enrich the resource of markers that can be used in molecular diagnostic, systematic, population genetic, and evolutionary biological studies of parasitic nematodes from either wild or domestic hosts.

Molecular analysis of Baylisascaris columnaris revealed mitochondrial and nuclear polymorphisms

Background

Baylisascaris species are intestinal nematodes of skunks, raccoons, badgers, and bears belonging to the genus Ascarididae. Oral uptake of embryonated Baylisascaris sp. eggs by a wide variety of mammals and birds can lead to visceral, ocular and neurological larva migrans. B. procyonis, the raccoon roundworm, is known to cause severe illness in intermediate hosts and in humans, whereas the skunk roundworm B. columnaris is probably less pathogenic. Skunks and raccoons are kept as pets in Europe, sometimes together with cats and dogs, living in close contact with humans. B. procyonis and B. columnaris are difficult to differentiate based on morphological criteria and molecular and phylogenetic information concerning B. columnaris is missing. This is the first study on the genetic characterisation of B. columnaris, based on mitochondrial and nuclear molecular markers.

Methods

B. columnaris worms were isolated from pet skunks, and used for molecular analysis. PCR primers targeted at mitochondrial cytochrome c oxidase 1 and 2 (CO1 and CO2), ribosomal ITS1-5.8S-ITS2 and ribosomal 28S genes were used. DNA sequences from B. columnaris, B. procyonis and B. transfuga from bears were analysed by cluster analysis.

Results

Four different multi-locus genotypes were found in B. columnaris, based on 14 single nucleotide polymorphisms (SNPs) and two insertions / deletions in CO1, CO2, ITS1-5.8S-ITS2 and 28S.

Conclusions

The genetic characteristics of B. columnaris show close resemblance to those of B. procyonis, but in contrast to B. procyonis, show several polymorphisms in both mitochondrial and nuclear markers. These polymorphisms could be used as a tool to differentiate B. columnaris from B. procyonis in molecular diagnostic assays, and to identify B. columnaris by PCR, in addition to or replacing morphometric analysis. This might lead to more insight into the zoonotic relevance of B. columnaris in humans.

Conveniently pre-tagged and pre-packaged: extended molecular identification and metagenomics using complete metazoan mitochondrial genomes

BACKGROUND

Researchers sorely need markers and approaches for biodiversity exploration (both specimen linked and metagenomics) using the full potential of next generation sequencing technologies (NGST). Currently, most studies rely on expensive multiple tagging, PCR primer universality and/or the use of few markers, sometimes with insufficient variability.

METHODOLOGY/PRINCIPAL FINDINGS

We propose a novel approach for the isolation and sequencing of a universal, useful and popular marker across distant, non-model metazoans: the complete mitochondrial genome. It relies on the properties of metazoan mitogenomes for enrichment, on careful choice of the organisms to multiplex, as well as on the wide collection of accumulated mitochondrial reference datasets for post-sequencing sorting and identification instead of individual tagging. Multiple divergent organisms can be sequenced simultaneously, and their complete mitogenome obtained at a very low cost. We provide in silico testing of dataset assembly for a selected set of example datasets.

CONCLUSIONS/SIGNIFICANCE

This approach generates large mitogenome datasets. These sequences are useful for phylogenetics, molecular identification and molecular ecology studies, and are compatible with all existing projects or available datasets based on mitochondrial sequences, such as the Barcode of Life project. Our method can yield sequences both from identified samples and metagenomic samples. The use of the same datasets for both kinds of studies makes for a powerful approach, especially since the datasets have a high variability even at species level, and would be a useful complement to the less variable 18S rDNA currently prevailing in metagenomic studies.