Whole genome amplification and exome sequencing of archived schistosome miracidia

Adult schistosomes live in the blood vessels and cannot easily be sampled from humans, so archived miracidia larvae hatched from eggs expelled in feces or urine are commonly used for population genetic studies. Large collections of archived miracidia on FTA cards are now available through the Schistosomiasis Collection at the Natural History Museum (SCAN). Here we describe protocols for whole genome amplification of Schistosoma mansoni and Schistosome haematobium miracidia from these cards, as well as real time PCR quantification of amplified schistosome DNA. We used microgram quantities of DNA obtained for exome capture and sequencing of single miracidia, generating dense polymorphism data across the exome. These methods will facilitate the transition from population genetics, using limited numbers of markers to population genomics using genome-wide marker information, maximising the value of collections such as SCAN.

Molecular Characterization and Identification of Stubby Root Nematode Species From Multiple States in the United States

Stubby root nematodes (SRN) are important plant parasites infecting many crops and widely distributed in many regions of the United States. SRN transmit Tobacco rattle virus, which causes potato corky ringspot disease, thereby having a significant economic impact on the potato industry. In 2015 to 2017, 184 soil samples and 16 nematode suspensions from North Dakota, Minnesota, Idaho, Oregon, Washington, South Carolina, North Carolina, and Florida were assayed for the presence of SRN. SRN were found in 106 soil samples with population densities of 10 to 320 SRN per 200 g of soil and in eight of the nematode suspensions. Sequencing of ribosomal DNA (rDNA) or species-specific polymerase chain reaction assays revealed the presence of four SRN species, including Paratrichodorus allius, P. minor, P. porosus, and Trichodorus obtusus. Accordingly, their rDNA sequences were characterized by analyzing D2-D3 of 28S rDNA, 18S rDNA, and internal transcribed spacer (ITS) rDNA obtained in this study and retrieved from GenBank. Both intra- and interspecies variations were higher in ITS rDNA than 18S rDNA and D2-D3 of 28S rDNA. Based on phylogenetic analysis, the four SRN species formed a monophyletic group, with P. allius more closely related to P. porosus than P. minor and T. obtusus. Indel variation of ITS2 rDNA was present in P. allius populations from the same geographic regions. This study documented the occurrence of SRN species across multiple states. The intra- and interspecies genetic diversity of rDNA in this study will provide more information for understanding the evolutionary relationships of SRN and will be valuable for future studies of SRN species identification and management.

Gene expression studies using a miniaturized thermal cycler system on board the International Space Station

The distance and duration of human spaceflight missions is set to markedly increase over the coming decade as we prepare to send astronauts to Mars. However, the health impact of long-term exposure to cosmic radiation and microgravity is not fully understood. In order to identify the molecular mechanisms underpinning the effects of space travel on human health, we must develop the capacity to monitor changes in gene expression and DNA integrity in space. Here, we report successful implementation of three molecular biology procedures on board the International Space Station (ISS) using a miniaturized thermal cycler system and C. elegans as a model organism: first, DNA extraction–the initial step for any type of DNA analysis; second, reverse transcription of RNA to generate complementary DNA (cDNA); and third, the subsequent semi-quantitative PCR amplification of cDNA to analyze gene expression changes in space. These molecular procedures represent a significant expansion of the budding molecular biology capabilities of the ISS and will permit more complex analyses of space-induced genetic changes during spaceflight missions aboard the ISS and beyond.

Quantitative Polymerase Chain Reaction for Diagnosis of Soil-Transmitted Helminth Infections: A Comparison with a Flotation-Based Technique and an Investigation of Variability in DNA Detection

Appropriate diagnostic techniques are crucial to global soil-transmitted helminth (STH) control efforts. The recommended Kato-Katz method has low sensitivity in low-transmission settings. Quantitative polymerase chain reaction (qPCR) is a highly sensitive alternative diagnostic option. However, little is known about the variability in qPCR results, and there are few published comparisons between qPCR and other microscopy-based techniques such as sodium nitrate flotation (SNF). Using 865 stool samples collected from 571 individuals, we compared SNF and qPCR in terms of diagnostic sensitivity and infection intensity measurements. In addition, we conducted repeated examinations on a single Necator americanus-positive stool sample over a 6-month period. Results showed good diagnostic agreement between SNF and qPCR for Ascaris spp. (κ = 0.69, P < 0.001), and moderate agreement for hookworm (κ = 0.55, P < 0.001) and Trichuris spp. (κ = 0.50, P < 0.001). Quantitative polymerase chain reaction demonstrated higher sensitivity than SNF for Ascaris spp. (94.1% versus 68.1%) and hookworm (75.7% versus 66.9%) but not for Trichuris spp. (53.1% versus 81.3%), which had very low prevalence. Sodium nitrate flotation and qPCR infection intensity measurements were strongly correlated for Ascaris spp. (ρ = 0.82, P < 0.001) and moderately correlated for hookworm (ρ = 0.58, P < 0.001). Repeated examinations using qPCR showed that N. americanus cycle threshold values decreased significantly at 1 month and remained stable thereafter. Results confirm the high diagnostic sensitivity of qPCR for Ascaris spp. and hookworm, particularly for light-intensity infections, which is ideal for settings approaching transmission elimination. Results support the potential for qPCR to be used as a quantitative assay for STH. Further research is needed in settings where Trichuris trichiura is endemic.

Epidemiological and genetic characterization of larval stages of Fasciola gigantica in snail intermediate hosts in Karnataka State, India

Fasciolosis in ruminants in India is caused by the liver fluke Fasciola gigantica. Radix (Lymnaea) spp. are known to carry the infective stages of this parasite. Understanding the seasonal prevalence of F. gigantica infection in the intermediate host is of extreme importance in order to elucidate the transmission dynamics of the parasite. So the present study was designed to determine the bioclimatic distribution of larval stages of F. gigantica in Radix spp. snails as well as to explore the genetic diversity of F. gigantica in three geographical regions (Deccan plateau, Western Ghats and coastal region) of Karnataka. The lymnaeid snails were sampled (n = 2077) for a period of one year (June 2015 to May 2016) at 24 sites. The snails were morphologically identified and the infection status was established through cercarial shedding and nested polymerase chain reaction (PCR) based technique targeting second internal transcribed spacers (ITS-2) of nuclear ribosomal DNA. The sensitivity of PCR (8.2%) for detection of F. gigantica infection within snail is significantly higher than cercarial shedding (4.3%) with an overall prevalence of 5.1%. The prevalence of infection was higher in winter than in the rainy and summer seasons (6.2% instead of 4.6% and 4.3% respectively). Deccan plateau (5.8%) showed a higher prevalence of infection compared to Western Ghats (5.2%) and Coastal region (3.6%). The sequencing ITS-2 region permitted the identification of the parasite as F. gigantica which is having high implication in studying the population genetic structure of the parasite in the country. In conclusion, overall results indicated that Radix spp. snails harboured F. gigantica developmental stages throughout the year and nested PCR was found to be sensitive and specific for detection of F. gigantica infection in snails compared to routine parasitological techniques.

Morphological and molecular study of Neorhadinorhynchus nudus (Harada, 1938) (Acanthocephala: Cavisomidae) from Auxis thazard Lacepede (Perciformes: Scombridae) in the South China Sea

In the present study, Neorhadinorhynchus nudus (Harada, 1938) is reported from the frigate tuna Auxis thazard (Lacepéde) (Perciformes: Scombridae), in the South China Sea for the first time. The detailed morphology of N. nudus was studied using light and scanning electron microscopy based on the newly collected material. The results showed some morphometric variability between our specimens and previous studies, including the number of hooks per longitudinal row and the size of copulatory bursa and eggs. Our SEM observations also revealed all proboscis hooks emerged from elevated round rims on proboscis surface. In addition, N. nudus was firstly characterised using molecular methods by sequencing and analysing the ribosomal ITS and mitochondrial cox1 regions. There is no nucleotide divergence found in the ITS sequences, but a low level of nucleotide variability detected in the cox1 regions (the level of intraspecific nucleotide variability being 0.75% to 2.54%). The DNA sequence data obtained herein will indeed be a useful reference for rapid and accurate species identification of Neorhadinorhynchus.

Ascaridia galli isolates with ITS1-5.8rRNA-ITS2 fragment homologous to Ascaridia columbae

Ascaridia (A.) galli is one of the most commonly occurring nematodes in poultry worldwide, often in hens and broiler chickens. The infection with Ascaridia galli in free-range chickens was even 70%. There is not much information about A. galli genetic features. The present study was conducted to assess the genetic diversity of A. galli isolated from hens in Poland by analyzing the nucleotide sequence of the region ITS1-5.8rRNA-ITS2 and to define its homology within the family Ascaridiidae. Adult A. galli were collected from the intestines of naturally infected hens from two flocks of free-run laying hens from the Wielkopolska region in Poland. From all parasites an identical ITS1-5.8rRNA-ITS2 sequence was obtained, which was homologous in 99% with A. columbae (JQ995321.1) sequence. The high homology sequences of A. galli (KX683286) from Poland and A. columbae (JQ995321.1) isolate from the USA, support the observations of other authors suggesting that A. galli and A. columbae might be closely related. It is the first whole ITS1-5.8rRNA-ITS2 of A. galli in the GenBank database, so there is not enough data for detailed phylogenetic analysis of A. galli. Detailed genetic analysis is necessary to get better insight into the birds' Ascaridia species.

Molecular phylogenetic position of Haplometroides intercaecalis (Digenea, Plagiorchiidae)

Three valid species of Haplometroides Odhner, 1910 parasitise snakes and amphisbaenians from South America. This study provides additional data on morphometric and molecular phylogenetic position inferred from the nuclear ribosomal gene 28S (partial). DNA sequences were isolated from Haplometroides intercaecalis Silva, Ferreira and Strüssmann, 2007 found in one specimen of Phalotris matogrossensis Lema, D'Agostini and Cappellari, 2005. Five digenean specimens were recovered from the esophagus of this snake, and four specimens were used for morphometrical studies and one specimen for molecular analysis. Phylogenetic analysis using maximum likelihood and Bayesian methods was conducted with sequences available for the order Plagiorchiida and its phylogenetic position places H. intercaecalis among the brachycoeliids Brachycoelium (Dujardin, 1845) Stiles and Hassall, 1898 and Parabrachycoelium Pérez-Ponce de León, Mendoza-Garfias, Razo-Mendivil and Parra-Olea, 2011, and the mesocoeliid Mesocoelium Odhner, 1910, not closely related to plagiorchids as expected. Due to morphological differences among these families, it may be necessary to create a new family to accommodate Haplometroides spp. However, more genera/taxa as well as other molecular markers should be added in future studies to confirm our results and resolve this matter. This is the first phylogenetic positioning of digeneans of the genus Haplometroides, contributing to the systematic analysis of the helminthological biodiversity of Neotropical snakes.

First molecular identification of an agent of diplostomiasis, Diplostomum pseudospathaceum (Niewiadomska 1984) in the United Kingdom and its genetic relationship with populations in Europe

Trematode genus Diplostomum comprises of parasitic species which cause diplostomiasis, the 'white eye' disease in fish and heavy infection can result in mortality. The increasing availability of DNA sequences of accurately identified Diplostomum species on public data base presently enables the rapid identification of species from novel sequences. We report the first molecular evidence of the occurrence of D. pseudospathaceum in the United Kingdom. Two gene regions, nuclear internal transcribed spacer cluster (ITS1-5.8S-ITS2) and mitochondrial cytochrome c oxidase subunit 1 (cox1) of cercariae from infected aquatic snails, Lymnaea stagnalis collected in several locations in Southern England were sequenced. Phylogenetic analysis based on both sequenced genes revealed that the novel sequences were D. pseudospathaceum. Molecular diversity analysis of published D. pseudospathaceum cox1 sequences from seven countries in Europe and the novel sequences from the present study revealed high diversity, but low nucleotide divergence and a lack of gene differentiation between the populations. Haplotype network analysis depicted a star-like pattern and revealed a lack of geographic structure in the population. Fixation indices confirmed gene flow between populations and we suspect high levels of dispersal facilitated by highly mobile second intermediate (fish) and definitive (piscivorous birds) host may be driving gene flow between populations. Neutrality tests and mismatch distribution indicated recent population growth/expansion for D. pseudospathaceum in Europe.

Reverse taxonomy applied to the Brachionus calyciflorus cryptic species complex: Morphometric analysis confirms species delimitations revealed by molecular phylogenetic analysis and allows the (re)description of four species

The discovery and exploration of cryptic species have been profoundly expedited thanks to developments in molecular biology and phylogenetics. In this study, we apply a reverse taxonomy approach to the Brachionus calyciflorus species complex, a commonly studied freshwater monogonont rotifer. By combining phylogenetic, morphometric and morphological analyses, we confirm the existence of four cryptic species that have been recently suggested by a molecular study. Based on these results and according to an exhaustive review of the taxonomic literature, we name each of these four species and provide their taxonomic description alongside a diagnostic key.

Angiostrongylus cantonensis DNA in Cerebrospinal Fluid of Persons with Eosinophilic Meningitis, Laos

Definitive identification of Angiostrongylus cantonensis parasites from clinical specimens is difficult. As a result, regional epidemiology and burden are poorly characterized. To ascertain presence of this parasite in patients in Laos with eosinophilic meningitis, we performed quantitative PCRs on 36 cerebrospinal fluid samples; 4 positive samples confirmed the parasite’s presence.

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity

Although animals are among the best studied organisms, we still lack a full description of their diversity, especially for microscopic taxa. This is partly due to the time-consuming and costly nature of surveying animal diversity through morphological and molecular studies of individual taxa. A powerful alternative is the use of high-throughput environmental sequencing, providing molecular data from all organisms sampled. We here address the unknown diversity of animal phyla in marine environments using an extensive dataset designed to assess eukaryotic ribosomal diversity among European coastal locations. A multi-phylum assessment of marine animal diversity that includes water column and sediments, oxic and anoxic environments, and both DNA and RNA templates, revealed a high percentage of novel 18S rRNA sequences in most phyla, suggesting that marine environments have not yet been fully sampled at a molecular level. This novelty is especially high among Platyhelminthes, Acoelomorpha, and Nematoda, which are well studied from a morphological perspective and abundant in benthic environments. We also identified, based on molecular data, a potentially novel group of widespread tunicates. Moreover, we recovered a high number of reads for Ctenophora and Cnidaria in the smaller fractions suggesting their gametes might play a greater ecological role than previously suspected.

Transrenal DNA-based diagnosis of Strongyloides stercoralis (Grassi, 1879) infection: Bayesian latent class modeling of test accuracy

For epidemiological work with soil transmitted helminths the recommended diagnostic approaches are to examine fecal samples for microscopic evidence of the parasite. In addition to several logistical and processing issues, traditional diagnostic approaches have been shown to lack the sensitivity required to reliably identify patients harboring low-level infections such as those associated with effective mass drug intervention programs. In this context, there is a need to rethink the approaches used for helminth diagnostics. Serological methods are now in use, however these tests are indirect and depend on individual immune responses, exposure patterns and the nature of the antigen. However, it has been demonstrated that cell-free DNA from pathogens and cancers can be readily detected in patient’s urine which can be collected in the field, filtered in situ and processed later for analysis. In the work presented here, we employ three diagnostic procedures—stool examination, serology (NIE-ELISA) and PCR-based amplification of parasite transrenal DNA from urine–to determine their relative utility in the diagnosis of S. stercoralis infections from 359 field samples from an endemic area of Argentina. Bayesian Latent Class analysis was used to assess the relative performance of the three diagnostic procedures. The results underscore the low sensitivity of stool examination and support the idea that the use of serology combined with parasite transrenal DNA detection may be a useful strategy for sensitive and specific detection of low-level strongyloidiasis.

As international bodies focus efforts on control of the world’s neglected tropical diseases, the critical importance of accurate and sensitive diagnosis becomes a key factor. The problem arises when the infection load in a community is reduced to a level where the standard diagnostic methodologies are insufficiently sensitive to detect the residual infection in the community. There is a need to develop improved diagnostic strategies for many parasitic diseases. One of the more difficult to diagnose helminth parasites is the nematode Strongyloides stercoralis. We have introduced a new approach that detects parasite-specific cell free DNA in urine as a sensitive measure of parasite presence. In the work presented here, we compare the performance of parasitological, serological and urine/DNA-based diagnosis of S. stercoralis infection. Using a Bayesian Latent Class Analysis approach, we provide evidence for the enhanced utility of using both urine and blood for the diagnosis of this parasite.

First ocular report of Gurltia paralysans (Wolffhügel, 1933) in cat

A two-year-old cat from Tenerife, Canary Islands (Spain), presented with two months history of uveitis in the left eye. It had been treated for two months but still showed an active uveitis. After new treatment, eye examination showed a mobile worm in the anterior chamber. Following surgical removal, the worm was obtained. Morphological study revealed that it was a male metastrongyloid nematode (Nematoda: Metastrongyloidea) with caudal bursa and two similar spicules. Molecular tools based on the 18Sr RNA gene sequence identified the parasite as Gurltia paralysans, which is a neurotropic nematode previously found in South America. Therefore, this article describes the first report of ophthalmic case of parasitism by G. paralysans, and cites for first time this species out of South America.

Morphological and molecular characterization of Seuratascaris numidica (Seurat, 1917) (Ascaridida: Ascarididae)

Seuratascaris numidica (Seurat, 1917) is a specialized nematode species parasitizing amphibians only. In the present study, the detailed morphology of this poorly known species was studied using light and scanning electron microscopy based on the newly material collected from Hoplobatrachus chinensis (Osbeck) (Amphibia: Anura) in China. We found that the relative length of intestinal caecum in our male specimens (representing 68.4-71.1% of oesophageal length) is slighter longer than the previously reported data (not over 60.0% of oesophageal length). Our SEM observations also revealed the presence of ca. 64-76 small conical denticles on each lip. In addition, Angusticaecum wuyiensis Wang, 1981, collected from Rana schmackeri Boettger (Amphibia: Anura) from Wuyi Mountain in Fujian Province, China was considered as a new synonym of S. numidica. The ITS and cox1 sequences of S. numidica were also sequenced for the first time and there is no nucleotide variability detected in both regions. The present supplementary morphological and molecular data (especially the ITS and cox1 sequences) obtained herein is extremely important and useful to determine the morphological variability, population genetics and phylogenetic position of S. numidica in the future.

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.

Metazoan parasite fauna of migrating common garfish, Belone belone (L.), in the Baltic Sea

A total of 35 common garfish, Belone belone (Linnaeus, 1761), were studied for metazoan parasites on their spawning grounds in the western Baltic Sea. Nine parasite species were found, and six new locality records could be established for German coastal waters (Axine belones, Monogenea; Proteocephalus sp., Cestoda; Anisakis simplex (s.s.), Contracaecum rudolphii A and Hysterothylacium aduncum, Nematoda; Echinorhynchus gadi, Acanthocephala). For the first time, the marine ectoparasite A. belones was recorded from the gills of garfish inside the Baltic Sea, indicating its ability to survive the spawning migration as well as the brackish water conditions at its reproduction grounds. This is alike the endohelminth A. simplex (s.s.), that was identified by molecular analyses of the internal transcribed spacer (ITS-1, 5.8S, ITS-2) region. Almost all isolated metazoans were parasites commonly recorded from the northeast Atlantic Ocean and the North Sea. The lower number of typical generalist Baltic Sea parasites indicates the rapid migration of common garfish onto the spawning grounds, reducing the access and uptake of these species.

A Rapid Diagnostic for Detection of Aphelenchoides besseyi and A. fujianensis Based on Real-Time PCR

Aphelenchoides besseyi and A. fujianensis have been frequently found in mixed populations associated with forage grass seed in Brazil. The morphological similarity between both species has previously led A. fujianensis to be erroneously identified as A. besseyi. A. besseyi is a quarantine pest in many countries that import Brazilian forage seed; however, there is no current evidence suggesting that A. fujianensis is a plant-parasitic species. Two real-time polymerase chain reaction (qPCR) diagnostics were developed to detect each species and an operational envelope was established. A set of primers and hydrolysis probes for each species was designed targeting the large subunit (LSU) region. To assess their specificity, primers and probes sets were tested with samples of nontarget Aphelenchoides and Paraphelenchus sp. also frequently associated with forage seed. Experiments using dilutions of purified plasmid standards underpinned the sensitivity of the qPCR assays, which detected as few as 10 copies of target nematode ribosomal DNA. Thus, the developed diagnostics were sufficiently sensitive to detect DNA extracted from a fragment of a single target nematode. There was a positive correlation between copy number of the target species and nematode abundance, suggesting the potential of this method for quantification. Evidence of intra-individual variability among cloned sequences of the LSU region in a single A. besseyi population is also reported.

Development of a lateral flow recombinase polymerase assay for the diagnosis of Schistosoma mansoni infections

Infection with Schistosoma mansoni causes intestinal schistosomiasis, a major health problem across Africa. The accurate diagnosis of intestinal schistosomiasis is vital to inform surveillance/control programs. Diagnosis mainly relies on microscopic detection of eggs in faecal samples but many factors affect sensitivity. Molecular diagnostics are sensitive and specific but application is limited as necessary infrastructure, financial resources and skilled personnel are often lacking in endemic settings. Recombinase Polymerase Amplification (RPA) is an isothermal DNA amplification/detection technology that is practical in nearly any setting. Here we developed a RPA lateral flow (LF) assay targeting the 28S rDNA region of S. mansoni. The 28S LF-RPA assay's lower limit of detection was 10pg DNA with the lower test parameters permitting sufficient amplification being 6 min and 25°C. Optimal assay parameters were 40-45°C and 10 min with an analytical sensitivity of 10² copies of DNA. Additionally the PCRD3 lateral flow detection cassettes proved more robust and sensitive compared to the Milenia HybriDetect strips. This 28S LF-RPA assay produces quick reproducible results that are easy to interpret, require little infrastructure and is a promising PON test for the field molecular diagnosis of intestinal schistosomiasis.

Molecular xenomonitoring for post-validation surveillance of lymphatic filariasis in Togo: no evidence for active transmission

BACKGROUND

Lymphatic filariasis (LF) is a mosquito-borne filarial disease targeted for elimination by the year 2020. The Republic of Togo undertook mass treatment of entire endemic communities from 2000 to 2009 to eliminate the transmission of the disease and is currently the first sub-Saharan African country to be validated by WHO for the elimination of LF as a public health problem. However, post-validation surveillance activities are required to ensure the gains achieved are sustained. This survey assessed the mosquito vectors of the disease and determined the presence of infection in these vectors, testing the hypothesis that transmission has already been interrupted in Togo.

METHOD

Mosquitoes were collected from 37 villages located in three districts in one of four evaluation units in the country. In each district, 30 villages were selected based on probability proportionate to size; eight villages (including one of the 30 villages already selected) where microfilaremia-positive cases had been identified during post-treatment surveillance activities were intentionally sampled. Mosquitoes were collected using pyrethrum spray collections (PSC) in households randomly selected in all villages for five months. In the purposefully selected communities, mosquitoes were also collected using human landing collections (HLC) and exit traps (ET). Collected mosquitoes were identified morphologically, and the identification of Wuchereria bancrofti DNA in the mosquitoes was based on the pool screening method, using the LAMP assay.

RESULTS

A total of 15,539 mosquitoes were collected during the study. Anopheles gambiae (72.6%) was the predominant LF vector collected using PSC. Pool screen analysis of 9191 An. gambiae in 629 pools revealed no mosquitoes infected with W. bancrofti (0%; CI: 0-0.021).

CONCLUSIONS

These results confirm the findings of epidemiological transmission assessment surveys conducted in 2012 and 2015, which demonstrated the absence of LF transmission in Togo. The challenges of implementing molecular xenomonitoring are further discussed.

Population structure analysis of the neglected parasite Thelazia callipaeda revealed high genetic diversity in Eastern Asia isolates

Background

Thelazia callipaeda is the causative agent of thelaziasis in canids, felids and humans. However, the population genetic structure regarding this parasite remains unclear.

Methodology/principal findings

In this study, we first explored the genetic variation of 32 T. callipaeda clinical isolates using the following multi-molecular markers: cox1, cytb, 12S rDNA, ITS1 and 18S rDNA. The isolates were collected from 13 patients from 11 geographical locations in China. Next, the population structure of T. callipaeda from Europe and other Asian countries was analyzed using the cox1 sequences collected during this study and from the GenBank database. In general, the Chinese clinical isolates of T. callipaeda expressed high genetic diversity. Based on the cox1 gene, a total of 21 haplotypes were identified. One only circulated in European countries (Hap1), while the other 20 haplotypes were dispersed in Korea, Japan and China. There were five nucleotide positions in the cox1 sequences that were confirmed as invariable among individuals from Europe and Asia, but the sequences were distinct between these two regions. Population differences between Europe and Asian countries were greater than those among China, Korea and Japan. The T. callipaeda populations from Europe and Asia should be divided into two separate sub-populations. These two groups started to diverge during the middle Pleistocene. Neutrality tests, mismatch distribution and Bayesian skyline plot (BSP) analysis all rejected possible population expansion of T. callipaeda.

Conclusions

The Asian population of T. callipaeda has a high level of genetic diversity, but further studies should be performed to explore the biology, ecology and epidemiology of T. callipaeda.

Thelazia callipaeda is the causative agent of thelaziasis canids, felids and humans. Despite the existing threat of thelaziosis in China, the genetic diversity of T. callipaeda has not been investigated across its wide geographical distribution in China, yet such information may provide insight into the disease epidemiology and the development of specific control measures. In this study, the genetic variation of 32 T. callipaeda clinical isolates collected from 13 patients from 11 geographical locations in China were explored using the following multi-molecular markers: cox1, cytb, 12S rDNA, ITS1 and 18S rDNA. In addition, the population structure of T. callipaeda from Europe and other Asian countries was analyzed using the cox1 sequences collected during this study and from the GenBank database. In general, the Chinese clinical isolates of T. callipaeda demonstrated high genetic diversity. Based on the cox1 gene, a total of 21 haplotypes were identified, one circulated in European countries (Hap1), while the other 20 haplotypes were dispersed in Korea, Japan and China. There were five nucleotide positions in the cox1 that were confirmed as invariable among individuals from Europe and Asia, but the sequences were distinct between these two regions. Population differences between Europe and Asian countries were greater than those among China, Korea and Japan, such that the T. callipaeda population from Europe and Asia should be divided into two separate sub-populations. These two groups started to diverge during the middle Pleistocene.

Molecular identification of Trichinella species by multiplex PCR: new insight for Trichinella murrelli

In order to identify Trichinella at the species level, the commonly used test is a multiplex PCR, allowing the discrimination of nine out of the twelve taxa described so far. This test is based on five primer pairs amplifying fragments of the large subunit rDNA. Each taxon produces one or two bands of different sizes, resulting in a specific band pattern. By multiplex PCR, Trichinella murrelli shows two bands of 127 bp and 316 bp. However, a third band of 256 bp can occur. This band can lead to misidentification, since it is similar to the 253 bp band displayed by Trichinella britovi. BLAST analysis confirmed that the 256 bp band is from T. murrelli. The aim of this short note is to inform analysts that T. murrelli larvae may display either two- or three-band patterns.

Updated molecular phylogenetic data for Opisthorchis spp. (Trematoda: Opisthorchioidea) from ducks in Vietnam

BACKGROUND

An opisthorchiid liver fluke was recently reported from ducks (Anas platyrhynchos) in Binh Dinh Province of Central Vietnam, and referred to as "Opisthorchis viverrini-like". This species uses common cyprinoid fishes as second intermediate hosts as does Opisthorchis viverrini, with which it is sympatric in this province. In this study, we refer to the liver fluke from ducks as "Opisthorchis sp. BD2013", and provide new sequence data from the mitochondrial (mt) genome and the nuclear ribosomal transcription unit. A phylogenetic analysis was conducted to clarify the basal taxonomic position of this species from ducks within the genus Opisthorchis (Digenea: Opisthorchiidae).

METHODS

Adults and eggs of liver flukes were collected from ducks, metacercariae from fishes (Puntius brevis, Rasbora aurotaenia, Esomus metallicus) and cercariae from snails (Bithynia funiculata) in different localities in Binh Dinh Province. From four developmental life stage samples (adults, eggs, metacercariae and cercariae), the complete cytochrome b (cob), nicotinamide dehydrogenase subunit 1 (nad1) and cytochrome c oxidase subunit 1 (cox1) genes, and near-complete 18S and partial 28S ribosomal DNA (rDNA) sequences were obtained by PCR-coupled sequencing. The alignments of nucleotide sequences of concatenated cob + nad1 + cox1, and of concatenated 18S + 28S were separately subjected to phylogenetic analyses. Homologous sequences from other trematode species were included in each alignment.

RESULTS

Phylogenetic trees were inferred from concatenated (cob + nad1 + cox1) nucleotide sequences and combined 18S + 28S nucleotide sequences of five Opisthorchis sp. BD2013 samples and additional reference taxa. Both trees demonstrated the anticipated clustering of taxa within the superfamily Opisthorchioidea, the paraphyly of the genus Opisthorchis and the sister-species relationship of Opisthorchis sp. BD2013 with O. viverrini.

CONCLUSIONS

While it is likely that Opisthorchis sp. BD2013 is distinct from O. viverrini, it is clearly a sister taxon of O. viverrini within the limited number of Opisthorchis species for which appropriate sequence data are available. The new sequences provided here will assist the diagnosis and the taxonomic clarification of the opisthorchiid species.

[Genetic variation of Thelazia callipaeda among isolates collected from patients in Zunyi City, Guizhou Province]

OBJECTIVE

To identify the genetic variation and possible sources of Thelazia callipaeda isolates collected from patients in Zunyi City, Guizhou Province.

METHODS

Seven cases of T. callipaeda infection in Zunyi City, 2016 were verified, and DNA (s) were extracted from the T. callipaeda's body collected from the thelaziasis patients. A mitochondrial COX1 fragment was amplified and sequenced. The sequence alignment and phylogenetical analysis were performed to compare the genetic variation of the gene sequence with the homologous sequences downloaded from Genebank.

RESULTS

COX1 genes of T. callipaeda were differed among the samples from the seven cases, which had low variation.

CONCLUSIONS

Zunyi City is a new area with endemic of thelaziasis. The isolates from Zunyi City include either Asian origin or European origin of T. callipaeda. Moreover, at least four haplotypes are identified among the seven isolates.