Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation

Maintaining genome integrity is particularly important in germ cells to ensure faithful transmission of genetic information across generations. Here we systematically describe germ cell mutagenesis in wild-type and 61 DNA repair mutants cultivated over multiple generations. ~44% of the DNA repair mutants analysed showed a >2-fold increased mutagenesis with a broad spectrum of mutational outcomes. Nucleotide excision repair deficiency led to higher base substitution rates, whereas polh-1(Polη) and rev-3(Polζ) translesion synthesis polymerase mutants resulted in 50-400 bp deletions. Signatures associated with defective homologous recombination fall into two classes: 1) brc-1/BRCA1 and rad-51/RAD51 paralog mutants showed increased mutations across all mutation classes, 2) mus-81/MUS81 and slx-1/SLX1 nuclease, and him-6/BLM, helq-1/HELQ or rtel-1/RTEL1 helicase mutants primarily accumulated structural variants. Repetitive and G-quadruplex sequence-containing loci were more frequently mutated in specific DNA repair backgrounds. Tandem duplications embedded in inverted repeats were observed in helq-1 helicase mutants, and a unique pattern of 'translocations' involving homeologous sequences occurred in rip-1 recombination mutants. atm-1/ATM checkpoint mutants harboured structural variants specifically enriched in subtelomeric regions. Interestingly, locally clustered mutagenesis was only observed for combined brc-1 and cep-1/p53 deficiency. Our study provides a global view of how different DNA repair pathways contribute to prevent germ cell mutagenesis.

Recruitment of MRE-11 to complex DNA damage is modulated by meiosis-specific chromosome organization

DNA double-strand breaks (DSBs) are one of the most dangerous assaults on the genome, and yet their natural and programmed production are inherent to life. When DSBs arise close together they are particularly deleterious, and their repair may require an altered form of the DNA damage response. Our understanding of how clustered DSBs are repaired in the germline is unknown. Using laser microirradiation, we examine early events in the repair of clustered DSBs in germ cells within Caenorhabditis elegans. We use precise temporal resolution to show how the recruitment of MRE-11 to complex damage is regulated, and that clustered DNA damage can recruit proteins from various repair pathways. Abrogation of non-homologous end joining or COM-1 attenuates the recruitment of MRE-11 through distinct mechanisms. The synaptonemal complex plays both positive and negative regulatory roles in these mutant contexts. These findings indicate that MRE-11 is regulated by modifying its accessibility to chromosomes.

Genetic variability, cryptic species and phylogenetic relationship of six cyathostomin species based on mitochondrial and nuclear sequences

Cyathostomins are important intestinal nematode parasites of equines and include 50 accepted species. Their taxonomy has been frequently revised and the presence of cryptic species suggested. Furthermore, usually molecular- and morphology-based phylogenetic analyses give divergent results. In this study, the nucleotide sequences of the nuclear second internal transcribed spacer (ITS-2) and the mitochondrial partial cytochrome c oxidase subunit I (COI) were determined for adults of six cyathostomin species (Coronocyclus coronatus, Coronocyclus labiatus, Cylicocyclus nassatus, Cylicostephanus calicatus, Cylicostephanus longibursatus, Cylicostephanus minutus) collected from different equine species within two geographic regions. Maximum likelihood trees were calculated for ITS-2, COI, and concatenated data. No obvious differentiation was observed between geographic regions or equine host species. As previously reported, Coronocyclus coronatus and Cylicostephanus calicatus revealed a close relationship. Cryptic species were detected in Cylicostephanus minutus and Cylicostephanus calicatus. Cylicocyclus nassatus and Coronocyclus labiatus showed diverse mitochondrial and nuclear haplotypes occurring in different combinations, while Cylicostephanus longibursatus was comparatively homogenous. In conclusion, a combined analysis of nuclear and mitochondrial haplotypes improved resolution of the phylogeny and should be applied to the remaining cyathostomin species and across additional equine host species and geographic regions.

Genetic characterization of nodular worm infections in Asian Apes

Parasitic nematodes of Oesophagostomum spp., commonly known, as 'nodular worms' are emerging as the most widely distributed and prevalent zoonotic nematodes. Oesophagostomum infections are well documented in African non-human primates; however, the taxonomy, distribution and transmission of Oesophagostomum in Asian non-human primates are not adequately studied. To better understand which Oesophagostomum species infect Asian non-human primates and determine their phylogeny we analysed 55 faecal samples from 50 orangutan and 5 gibbon individuals from Borneo and Sumatra. Both microscopy and molecular results revealed that semi-wild animals had higher Oesophagostomum infection prevalence than free ranging animals. Based on sequence genotyping analysis targeting the Internal transcribed spacer 2 of rDNA, we report for the first time the presence of O. aculeatum in Sumatran apes. Population genetic analysis shows that there is significant genetic differentiation between Bornean and Sumatran O. aculeatum populations. Our results clearly reveal that O. aculeatum in free-ranging animals have a higher genetic variation than those in semi-wild animals, demonstrating that O. aculeatum is circulating naturally in wildlife and zoonotic transmission is possible. Further studies should be conducted to better understand the epidemiology and dynamics of Oesophagostomum transmission between humans, non-human primates and other wild species and livestock in Southeast Asia.

Genetic identification of Anisakis spp. (Nematoda: Anisakidae) from cetaceans of the Southwestern Atlantic Ocean: ecological and zoogeographical implications

Adult Anisakis Dujardin, 1845 were found in two specimens of killer whale Orcinus orca and one specimen of franciscana Pontoporia blainvillei stranded from off the coast of Buenos Aires Province, Argentina. Genetic identification of the nematodes (N = 144) was performed by sequence analysis of the mitochondrial (mtDNA cox2) and the nuclear (nas 10 nDNA) gene loci. Anisakis pegreffii and Anisakis berlandi were detected in the two individuals of O. orca, while Anisakis typica and A. pegreffii were identified in P. blainvillei. Morphological and morphometric analysis also carried out on adult specimens of A. pegreffii and A. berlandi has allowed to underlining the usefulness of genetic/molecular markers in their recognition. This represents the first record of A. pegreffii in O. orca and P. blainvillei and of A. berlandi in O. orca. This is also the first sympatric and syntopic occurrence, as adults, of A. pegreffii and A. berlandi from the Austral Region of the Atlantic Ocean waters. These results provide insights into the knowledge of the host ranges and geographical distribution of these parasites in the basin waters of the region. Pontoporia blainvillei showed low abundance values of infection with Anisakis spp., which is the general pattern for coastal dolphins in the area, whereas O. orca harboured higher abundance of Anisakis spp. than those previously recorded among cetacean species in the Argentine Sea. Differences in the Anisakis spp. distribution and their parasitic loads, observed among the three host specimens, are discussed in relation to the oceanographic parameters, as well as to the host ecology. The usefulness of genetic/molecular markers in the recognition of adults of the sibling species A. pegreffii and A. berlandi with considerable overlapping in morphometric and morphological characters was underlined. The distribution of Anisakis species from Southwestern Atlantic waters is discussed in relation to their value as indicators for studies on the zoogeography of their hosts at a regional-scale level.

A new molecular nomenclature for Taenia hydatigena: mitochondrial DNA sequences reveal sufficient diversity suggesting the assignment of major haplotype divisions

Cysticercosis caused by the metacestode larval stage of Taenia hydatigena formerly referred to as Cysticercus tenuicollis is a disease of veterinary importance that constitutes a significant threat to livestock production worldwide, especially in endemic regions due to condemnation of visceral organs and mortality rate of infected young animals. While the genetic diversity among parasites is found to be potentially useful in many areas of research including molecular diagnostics, epidemiology and control, that of T. hydatigena across the globe remains poorly understood. In this study, analysis of the mitochondrial DNA (mtDNA) of adult worms and larval stages of T. hydatigena isolated from dogs, sheep and a wild boar in China showed that the population structure consists of two major haplogroups with very high nucleotide substitutions involving synonymous and non-synonymous changes. Compared with other cestodes such as Echinococcus spp., the genetic variation observed between the haplogroups is sufficient for the assignment of major haplotype or genotype division as both groups showed a total of 166 point-mutation differences between the 12 mitochondrial protein-coding gene sequences. Preliminary analysis of a nuclear protein-coding gene (pepck) did not reveal any peculiar changes between both groups which suggests that these variants may only differ in their mitochondrial makeup.

Molecular phylogenetic identification and morphological characteristics of Raillietina echinobothrida (Cestoda: Cyclophyllidea: Davaineidae) in commercial chickens in North China

Raillietina echinobothrida (R. echinobothrida) is one of the most pathogenic and prevalent tapeworms threat to the commercial chickens in China. However, there is a lack of research on their molecular identification and morphological characteristics. This study explored the molecular identification markers for R. echinobothrida in North China based on 18s ribosomal RNA (18s rRNA) gene and the ribosomal DNA second internal transcribed spacer (ITS-2) gene. The BLAST results of 18s rRNA (1643 bp) and ITS-2 (564 bp) gene sequences showed that the isolated intestinal tapeworms were R. echinobothrida. Phylogenetic trees obtained by maximum likelihood (ML) or neighbor-joining (NJ) method revealed that the R. echinobothrida in North China had the closest evolutionary relationship with the species found on the Qinghai-Tibet plateau, China. Morphological observations by hematoxylin staining and scanning electron microscope showed four round suckers and a retractable rostellum on the spherical scolex of R. echinobothrida. Two rows of alternately arranged hooks distributed around the rostellum. There were 30-40 testes in each mature segment. A well-developed cirrus pouch lied outside the excretory duct of mature segment. The gravid segment contained 200-400 eggs and there was a well-developed oncosphere in each egg. In addition, abundant ultrastructural features in mature proglottid of R. echinobothrida in North China were identified by transmission electron microscopy. In conclusion, the present study established ways of molecular phylogenetic identification for R. echinobothrida based on 18s rRNA and ITS-2 gene, and identified the morphological and ultrastructural characteristics of R. echinobothrida in North China.

Usual or unusual presentations of Dirofilaria repens in two sibling dogs: a case report

This study describes two different manifestations of Dirofilaria repens infection in sibling dogs with microfilaremia. Dog 1, asymptomatic, harbored a gravid female of D. repens on the parietal layer of tunica vaginalis of one testicle and showed a marked circulating eosinophilia (3.3·103/μL). Both testicles were normal in shape and size without any gross lesions. Dog 2 had a pyotraumatic dermatitis. The cases were confirmed by PCR and sequencing. The sequences obtained showed 100% identity with those of D. repens isolated from human scrotum in Croatia. The treatment with moxidectin 2.5% and imidacloprid 10%/kg was effective in eliminating microfilariae after just one application, as demonstrated by negative modified Knott's tests and PCR analyses of blood samples. This status was maintained during the post-treatment observation period. The classical localization of D. repens in dogs is in subcutaneous tissues, within nodules or free; however, it can also occur with some frequency in testicles, as described in humans. The infection can be associated with circulating eosinophilia or pyotraumatic dermatitis, as reported in this study. Thus, in endemic areas, it is advisable to carefully inspect the removed testicles at neutering since parasite localization can take place without any macroscopic changes. Moreover, in the case of circulating eosinophilia or pyotraumatic dermatitis, investigations should include modified Knott's test and PCR to ensure that D. repens is not the cause of these alterations. Rapid and sensitive tests for the early detection of infected animals would help to prevent or limit the spread of this zoonosis.

Experimental evidence for the lack of sensitivity of in vivo faecal egg count reduction testing for the detection of early development of benzimidazole resistance

The objective of this study was to compare the results of an in vitro egg hatch test (EHT), micro-agar larval development test (MALDT) and in vivo faecal egg count reduction test (FECRT) between worm strains obtained from goats and sheep identically infected with the gastrointestinal parasitic nematode Haemonchus contortus. Results from the in vivo and in vitro tests were compared with benzimidazole (BZ)-resistance-associated β-tubulin allele frequencies determined using Pyrosequencing™. BZ resistance was not detected by the in vivo FECRT, where reductions of > 99% for both the resistant and the susceptible H. contortus strains were detected in both species. Discriminating doses in EHT and MALDT for the resistant strain indicated a low level (approx. 25%) of resistant individuals. Genotyping indicated that the susceptible strain had 10% BZ-resistant β-tubulin codon 200 alleles and the resistant strain had 26% respective resistant alleles. The in vitro tests and allele-frequency distribution suggested low levels of resistance in both strains; however, the FECRT did not support the evidence of resistant individuals of either strain in either species, suggesting a potential underestimation of low-level resistance in sheep and goats when employing this test.

Comprehensive Chromosome End Remodeling during Programmed DNA Elimination

Germline and somatic genomes are in general the same in a multicellular organism. However, programmed DNA elimination leads to a reduced somatic genome compared to germline cells. Previous work on the parasitic nematode Ascaris demonstrated that programmed DNA elimination encompasses high-fidelity chromosomal breaks and loss of specific genome sequences including a major tandem repeat of 120 bp and ~1,000 germline-expressed genes. However, the precise chromosomal locations of these repeats, breaks regions, and eliminated genes remained unknown. We used PacBio long-read sequencing and chromosome conformation capture (Hi-C) to obtain fully assembled chromosomes of Ascaris germline and somatic genomes, enabling a complete chromosomal view of DNA elimination. We found that all 24 germline chromosomes undergo comprehensive chromosome end remodeling with DNA breaks in their subtelomeric regions and loss of distal sequences including the telomeres at both chromosome ends. All new Ascaris somatic chromosome ends are recapped by de novo telomere healing. We provide an ultrastructural analysis of Ascaris DNA elimination and show that eliminated DNA is incorporated into double membrane-bound structures, similar to micronuclei, during telophase of a DNA elimination mitosis. These micronuclei undergo dynamic changes including loss of active histone marks and localize to the cytoplasm following daughter nuclei formation and cytokinesis where they form autophagosomes. Comparative analysis of nematode chromosomes suggests that chromosome fusions occurred, forming Ascaris sex chromosomes that become independent chromosomes following DNA elimination breaks in somatic cells. These studies provide the first chromosomal view and define novel features and functions of metazoan programmed DNA elimination.

Possible transmission of Strongyloides fuelleborni between working Southern pig-tailed macaques (Macaca nemestrina) and their owners in Southern Thailand: Molecular identification and diversity

Human strongyloidiasis is caused by Strongyloides stercoralis, S. fuelleborni fuelleborni and Strongyloides f. kellyi. Strongyloides fuelleborni is a soil-transmitted nematode parasite typically infecting non-human primates. The southern pig-tailed macaque (Macaca nemestrina) is distributed throughout the southern part of Thailand and could be a source of zoonotic transmission of this nematode. Here, we extracted DNA from Strongyloides speciescultured from the feces of southern pig-tailed macaques and their owners. Using PCR and sequencing of the extracted DNA, we compared the nucleotide sequences of these worms using portions of the 18S rDNA hypervariable region IV (HVR-IV) and the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. Sequences from the 18S rRNA gene were obtained from worms from 23 southern pig-tailed macaques and from one owner. These sequences were identical with each other and with all East and Southeast Asian S. fuelleborni sequences (from Japan, Thailand, and Lao PDR) in the GenBank database. A median-joining network of published cox1 sequences (n = 123), in combination with the present 24 new sequences, represented 107 haplotypes distributed among six clusters, which corresponded to geographical localities but did not relate to host species. The S. fuelleborni cox1 sequences from some southern pig-tailed macaques and the one infected owner shared the same cox1 haplotype. This is the first evidence of likely zoonotic transmission of S. fuelleborni from a reservoir host, M. nemestrina.

Current Knowledge of Small Flukes (Digenea: Heterophyidae) from South America

Fish-borne heterophyid trematodes are known to have a zoonotic potential, since at least 30 species are able to infect humans worldwide, with a global infection of around 7 million people. In this paper, a ‘state-of-the-art’ review of the South American heterophyid species is provided, including classical and molecular taxonomy, parasite ecology, host-parasite interaction studies and a list of species and their hosts. There is still a lack of information on human infections in South America with undetected or unreported infections probably due to the information shortage and little attention by physicians to these small intestinal flukes. Molecular tools for specific diagnoses of South American heterophyid species are still to be defined. Additional new sequences of Pygidiopsis macrostomum, Ascocotyle pindoramensis and Ascocotyle longa from Brazil are also provided.

Phylogeny and systematics of the Proterodiplostomidae Dubois, 1936 (Digenea: Diplostomoidea) reflect the complex evolutionary history of the ancient digenean group

The Proterodiplostomidae Dubois, 1936 is a relatively small family of diplostomoidean digeneans parasitising the intestines of reptilian hosts associated with freshwater environments in tropical and subtropical regions. The greatest diversity of proterodiplostomids is found in crocodilians, although some parasitise snakes and turtles. According to the most recent revision, the Proterodiplostomidae included 17 genera within 5 subfamilies. Despite the complex taxonomic structure of the family, availability of testable morphology-based phylogenetic hypotheses and ancient hosts, molecular phylogenetic analyses of the group were practically lacking. Herein, we use novel DNA sequence data of the nuclear lsrRNA gene and mitochondrial cox1 gene from a broad range of proterodiplostomid taxa obtained from crocodilian, fish, and snake hosts on four continents to test the monophyly of the family and evaluate the present morphology-based classification system of the Proterodiplostomidae in comparison with the molecular phylogeny. This first detailed phylogeny for the Proterodiplostomidae challenges the current systematic framework. Combination of molecular phylogenetic data with examination of freshly collected quality specimens and re-evaluation of morphological criteria resulted in a number of systematic and nomenclatural changes along with a new phylogeny-based classification of the Proterodiplostomidae. As the result of our molecular and morphological analyses: (i) the current subfamily structure of the Proterodiplostomidae is abolished; (ii) three new genera, Paraproterodiplostomum n. g., Neocrocodilicola n. g. and Proteroduboisia n. g., are described and Pseudoneodiplostomoides Yamaguti, 1954 is restored and elevated from subgenus to genus level; (iii) two new species, Paraproterodiplostomum currani n. g., n. sp. and Archaeodiplostomum overstreeti n. sp., are described from the American alligator in Mississippi, USA. Comparison of the structure of terminal ducts of the reproductive system in all proterodiplostomid genera did not support the use of these structures for differentiation among subfamilies (or major clades) within the family, although they proved to be useful for distinguishing among genera and species. Our study includes the first report of proterodiplostomids from Australia and the first evidence of a snake acting as a paratenic host for a proterodiplostomid. A key to proterodiplostomid genera is provided. Questions of proterodiplostomid-host associations parasitic in crocodilians are discussed in connection with their historical biogeography. Our molecular phylogeny of the Proterodiplostomidae closely matches the current molecular phylogeny of crocodilians. Directions for future studies of the Proterodiplostomidae are outlined.

Morphological and genetic characterisation of Centrorhynchus clitorideus (Meyer, 1931) (Acanthocephala: Centrorhynchidae) from the little owl Athene noctua (Scopoli) (Strigiformes: Strigidae) in Pakistan

Centrorhynchus Lühe, 1911 is a large genus of acanthocephalans mainly parasitic in various strigiform and falconiform birds. Some species of Centrorhynchus have not been adequately described. Here, the detailed morphology of C. clitorideus (Meyer, 1931) was studied using light and, for the first time, scanning electron microscopy, based on newly collected specimens from the little owl Athene noctua (Scopoli) (Strigiformes: Strigidae) in Pakistan. Partial sequences of the 18S and 28S nuclear ribosomal RNA genes and the mitochondrial cytochrome c oxidase subunit 1 (cox1) of C. clitorideus were generated for the first time. No nucleotide variation was detected for the partial 18S and 28S regions, but 3.30% of intraspecific nucleotide divergence was found for the cox1 gene. Phylogenetic analyses based on 28S and 18S sequence data showed that C. clitorideus formed a sister relationship with Centrorhynchus sp. MGV-2005 or Centrorhynchus sp. MGV-2005 + C. microcephalus (Bravo-Hollis, 1947), respectively.

The complete mitochondrial genome of the Columbia lance nematode, Hoplolaimus columbus, a major agricultural pathogen in North America

BACKGROUND

The plant-parasitic nematode Hoplolaimus columbus is a pathogen that uses a wide range of hosts and causes substantial yield loss in agricultural fields in North America. This study describes, for the first time, the complete mitochondrial genome of H. columbus from South Carolina, USA.

METHODS

The mitogenome of H. columbus was assembled from Illumina 300 bp pair-end reads. It was annotated and compared to other published mitogenomes of plant-parasitic nematodes in the superfamily Tylenchoidea. The phylogenetic relationships between H. columbus and other 6 genera of plant-parasitic nematodes were examined using protein-coding genes (PCGs).

RESULTS

The mitogenome of H. columbus is a circular AT-rich DNA molecule 25,228 bp in length. The annotation result comprises 12 PCGs, 2 ribosomal RNA genes, and 19 transfer RNA genes. No atp8 gene was found in the mitogenome of H. columbus but long non-coding regions were observed in agreement to that reported for other plant-parasitic nematodes. The mitogenomic phylogeny of plant-parasitic nematodes in the superfamily Tylenchoidea agreed with previous molecular phylogenies. Mitochondrial gene synteny in H. columbus was unique but similar to that reported for other closely related species.

CONCLUSIONS

The mitogenome of H. columbus is unique within the superfamily Tylenchoidea but exhibits similarities in both gene content and synteny to other closely related nematodes. Among others, this new resource will facilitate population genomic studies in lance nematodes from North America and beyond.

Morphological and molecular data show no evidence of the proposed replacement of endemic Pomphorhynchus tereticollis by invasive P. laevis in salmonids in southern Germany

Changes in parasite communities might result in new host-parasite dynamics and may threaten local fish populations. This phenomenon has been suggested for acanthocephalan parasites in the river Rhine and Danube where the species Pomphorhynchus tereticollis is becoming replaced by the Ponto-Caspian P. laevis. Developing knowledge on morphologic, genetic and behavioural differences between such species is important to follow such changes. However, disagreements on the current phylogeny of these two acanthocephalan species are producing conflicts that is affecting their correct identification. This study is offering a clearer morphological and genetic distinction between these two species. As P. tereticollis is found in rhithral tributaries of the Rhine, it was questioned whether the local salmonid populations were hosts for this species and whether P. laevis was expanding into the Rhine watershed as well. In order to test for this, brown trout, Salmo trutta, and grayling, Thymallus thymallus from South-Western Germany watersheds have been samples and screened for the occurrence of acanthocephalan parasites. For the first time, both species were confirmed to be hosts for P. tereticollis in continental Europe. P. tereticollis was found to be common, whereas P. leavis was found only at a single location in the Danube. This pattern suggest either that the expansion of P. laevis through salmonid hosts into rhithral rivers has not yet occurred, or that not yet ascertained biotic or abiotic features of rhithral rivers hinder P. laevis to spread into these areas.

High-throughput multiplex qPCRs for the surveillance of zoonotic species of canine hookworms

The canine hookworms Ancylostoma braziliense, Ancylostoma ceylanicum, Ancylostoma caninum and Uncinaria stenocephala are not only capable of producing morbidity and mortality in dogs but are also neglected tropical zoonoses. Each hookworm species differs considerably in its geographical distribution, life cycle, biology, pathogenic impacts on both canine and human hosts, zoonotic potential, and response to treatment with anthelminthics. Here we describe the development and validation of two Taq-Man based multiplex PCR assays capable of detecting and differentiating all four canine hookworm species in faeces of naturally infected dogs. The analytical sensitivity of both assays was assessed using 10-fold serial dilutions of synthetic gene block fragments containing individual sequence targets of each hookworm species. The sensitivity of the assays and ability to detect mixed species infections were compared to a conventional PCR-Restriction Fragment Length Polymorphism based-approach when applied to laboratory and field samples from endemic areas. The qPCRs detected at least one species of hookworms in 82.4% of PCR-RFLP-negative but microscopy-positive samples. The qPCRs detected an additional 68% mixed infections with different species of canine hookworms, and additional single species infection with A. caninum (47%), U. stenocephala (33%) and A. ceylanicum (0.02%) that were missed by PCR-RFLP. These multiplex qPCR assays will assist field based epidemiological surveillance studies towards an accurate and sensitive monitoring of canine hookworm infections in dogs, to inform their species-specific zoonotic risks to populations living in endemic areas, globally.

Comparison of multi-parallel qPCR and double-slide Kato-Katz for detection of soil-transmitted helminth infection among children in rural Bangladesh

There is growing interest in local elimination of soil-transmitted helminth (STH) infection in endemic settings. In such settings, highly sensitive diagnostics are needed to detect STH infection. We compared double-slide Kato-Katz, the most commonly used copromicroscopic detection method, to multi-parallel quantitative polymerase chain reaction (qPCR) in 2,799 stool samples from children aged 2–12 years in a setting in rural Bangladesh with predominantly low STH infection intensity. We estimated the sensitivity and specificity of each diagnostic using Bayesian latent class analysis. Compared to double-slide Kato-Katz, STH prevalence using qPCR was almost 3-fold higher for hookworm species and nearly 2-fold higher for Trichuris trichiura. Ascaris lumbricoides prevalence was lower using qPCR, and 26% of samples classified as A. lumbricoides positive by Kato-Katz were negative by qPCR. Amplicon sequencing of the 18S rDNA from 10 samples confirmed that A. lumbricoides was absent in samples classified as positive by Kato-Katz and negative by qPCR. The sensitivity of Kato-Katz was 49% for A. lumbricoides, 32% for hookworm, and 52% for T. trichiura; the sensitivity of qPCR was 79% for A. lumbricoides, 93% for hookworm, and 90% for T. trichiura. Specificity was ≥ 97% for both tests for all STH except for Kato-Katz for A. lumbricoides (specificity = 68%). There were moderate negative, monotonic correlations between qPCR cycle quantification values and eggs per gram quantified by Kato-Katz. While it is widely assumed that double-slide Kato-Katz has few false positives, our results indicate otherwise and highlight inherent limitations of the Kato-Katz technique. qPCR had higher sensitivity than Kato-Katz in this low intensity infection setting.

Soil-transmitted helminth infections (STH) (e.g., Ascaris, hookworm, Trichuris) contribute to a large burden of disease among children in low- and middle-income countries. There is increasing interest in implementing large-scale deworming programs to eliminate STH in certain settings. Efforts to monitor whether local elimination has occurred require sensitive diagnostic tests that will not miss positive cases. Kato-Katz, a microscopy-based diagnostic test, has commonly been used to identify STH eggs in stool, but in settings where infection intensity is low, this method frequently misses positive samples because it requires visual identification of small numbers of eggs, and hookworm eggs may degrade prior to visualization. Quantitative polymerase chain reaction (qPCR) is a molecular diagnostic method for detecting STH. It may detect more low intensity infections than Kato-Katz because it identifies STH DNA in stool; DNA can be detected in very small quantities and is less likely to degrade than STH ova. Thus, qPCR is likely to be more accurate than Kato-Katz. This study compared the performance of double-slide Kato-Katz and qPCR using 2,799 stool samples from children aged 2–12 years in a setting in rural Bangladesh with predominantly low STH infection intensity. qPCR was more sensitive than Kato-Katz for hookworm and Trichuris infections. 26% of samples were classified as Ascaris positive by Kato-Katz and negative by qPCR. DNA sequencing of 10 samples confirmed that Ascaris was absent in samples classified as positive by Kato-Katz and negative by qPCR. We conclude that Kato-Katz likely produced false positive results for Ascaris and that qPCR had a higher sensitivity than double-slide Kato-Katz in this low infection intensity setting.

Morphological and molecular characterization of Maritrema kostadinovae n. sp. (Digenea: Microphallidae) from the yellow-crowned night heron Nyctanassa violacea (Aves: Ardeidae) in Mexico

A new species of microphallid trematode was collected from the intestine of the yellow-crowned night heron Nyctanassa violacea (L.) (Pelecaniformes: Ardeidae) from Veracruz, Mexico. Maritrema kostadinovae n. sp. differs distinctly from other members of Maritrema Nicoll, 1907 from the Americas by its smaller body size (262-435 × 242-363 μm), the extension of caeca (reaching to anterior level of ventral sucker), the size and shape of the cirrus (short, tubular and unarmed) and metraterm (simple and thin-walled), the position of the genital pore (sinistrolateral to ventral sucker) and the arrangement of the vitellaria (horseshoe-shaped with posteriorly directed opening). Maximum likelihood and Bayesian inference analyses, based on partial 28S rDNA sequences, depicted M. kostadinovae n. sp. within the genus Maritrema with strong support. The new species is in a sister position to other available members of Maritrema, except for M. subdolum Jägerskiöld, 1909 that branches as the early divergent species in the Maritrema clade. The new species is the third species of Maritrema described from birds in Mexico. Comparative morphometric data for Maritrema taxa from birds and mammals from the Americas is provided.

Field evaluation of DNA detection of human filarial and malaria parasites using mosquito excreta/feces

We recently developed a superhydrophobic cone-based method for the collection of mosquito excreta/feces (E/F) for the molecular xenomonitoring of vector-borne parasites showing higher throughput compared to the traditional approach. To test its field applicability, we used this platform to detect the presence of filarial and malaria parasites in two villages of Ghana and compared results to those for detection in mosquito carcasses and human blood. We compared the molecular detection of three parasites (Wuchereria bancrofti, Plasmodium falciparum and Mansonella perstans) in mosquito E/F, mosquito carcasses and human blood collected from the same households in two villages in the Savannah Region of the country. We successfully detected the parasite DNA in mosquito E/F from indoor resting mosquitoes, including W. bancrofti which had a very low community prevalence (2.5-3.8%). Detection in the E/F samples was concordant with detection in insect whole carcasses and human blood, and a parasite not vectored by mosquitoes was detected as well.Our approach to collect and test mosquito E/F successfully detected a variety of parasites at varying prevalence in the human population under field conditions, including a pathogen (M. perstans) which is not transmitted by mosquitoes. The method shows promise for further development and applicability for the early detection and surveillance of a variety of pathogens carried in human blood.

A Whole Genome Re-Sequencing Based GWA Analysis Reveals Candidate Genes Associated with Ivermectin Resistance in Haemonchus contortus

The most important and broad-spectrum drug used to control the parasitic worms to date is ivermectin (IVM). Resistance against IVM has emerged in parasites, and preserving its efficacy is now becoming a serious issue. The parasitic nematode Haemonchus contortus (Rudolphi, 1803) is economically an important parasite of small ruminants across the globe, which has a successful track record in IVM resistance. There are growing evidences regarding the multigenic nature of IVM resistance, and although some genes have been proposed as candidates of IVM resistance using lower magnification of genome, the genetic basis of IVM resistance still remains poorly resolved. Using the full magnification of genome, we herein applied a population genomics approach to characterize genome-wide signatures of selection among pooled worms from two susceptible and six ivermectin-resistant isolates of H. contortus, and revealed candidate genes under selection in relation to IVM resistance. These candidates also included a previously known IVM-resistance-associated candidate gene HCON_00148840, glc-3. Finally, an RNA-interference-based functional validation assay revealed the HCON_00143950 as IVM-tolerance-associated gene in H. contortus. The possible role of this gene in IVM resistance could be detoxification of xenobiotic in phase I of xenobiotic metabolism. The results of this study further enhance our understanding on the IVM resistance and continue to provide further evidence in favor of multigenic nature of IVM resistance.

Targeted Sequencing of Genomic Repeat Regions Detects Circulating Cell-free Echinococcus DNA

Background

Echinococcosis is a chronic zoonosis caused by tapeworms of the genus Echinococcus. Treatment of the disease is often expensive and complicated, sometimes requiring extensive surgery. Ultrasonographic imaging is currently the main technique for diagnosis, while immunological analysis provides additional information. Confirmation still needs pathological analysis. However, these diagnostic techniques generally detect infection in late stages of the disease. An accurate, early and non-invasive molecular diagnostic method is still unavailable.

Methodology/Principal findings

We sequenced the cell-free DNA (cfDNA) from plasma of echinococcosis patients and confirmed the presence of Echinococcus DNA. To improve detection sensitivity, we developed a method based on targeted next-generation sequencing of repeat regions. Simulation experiments demonstrate that the targeted sequencing is sensitive enough to detect as little as 0.1% of an Echinococcus genome in 1 mL of plasma. Results obtained using patient plasma shows that the Area Under the Curve (AUC) of the method is 0.862, with a detection sensitivity of 62.50% and specificity of 100%, corresponding to a Youden-index of 0.625.

Conclusions/Significance

This study provides evidence that hydatid cysts release cfDNA fragments into patient plasma. Using the repeat region targeted sequencing method, highly specific detection of Echinococcus infection was achieved. This study paves a new avenue for potential non-invasive screening and diagnosis of echinococcosis.

Echinococcosis is a severe chronic parasitic disease caused by tapeworms of the genus Echinococcus. According to the World Health Organization, there are more than 1 million people living with echinococcosis worldwide. For decades, little progress has been made to develop a molecular diagnosis and specific treatment for the disease. Although imaging and immunological detection are used for diagnosis, these technologies are either only effective for late stages of the disease or hardly conclusive. The detection of cell-free DNA has been a powerful tool for precise diagnosis. In this study, we showed the presence of Echinococcus-derived cell-free DNA in plasma of echinococcosis patients. We further established an assay to detect parasite DNA in blood samples based on amplification of Echinococcus specific repeat regions followed by targeted next-generation sequencing. This technique provides a new method for potential extensive screening and precision diagnosis of echinococcosis with high specificity.

Global genetic diversity of Spirometra tapeworms

Spirometra larvae are etiological agents of human sparganosis. However, the systematics of spirometrid cestodes has long been controversial. In order to determine the current knowledge on the evolution and genetic structure of Spirometra, an exhaustive population diversity analysis of spirometrid cestodes using the mitochondrial gene: cytochrome c oxidase subunit 1 (cox1) was performed. All publicly available cox1 sequences available in the GenBank and 127 new sequencing genes from China were used as the dataset. The haplotype identify, network, genetic differentiation and phylogenetic analysis were conducted successively. A total of 488 sequences from 20 host species, representing four spirometrid tapeworms (S. decipiens, S. ranarum, S. erinaceieuropaei and Sparganum proliferum) and several unclassified American and African isolates from 113 geographical locations in 17 countries, identified 45 haplotypes. The genetic analysis revealed that there are four clades of spirometrid cestodes: Clade 1 (Brazil + USA) and Clade 2 (Argentina + Venezuela) included isolates from America, Clade 3 contained African isolates and one Korean sample, and the remainders from Asia and Australia belonged to Clade 4; unclassified Spirometra from America and Africa should be considered the separate species within the genus; and the taxonomy of two Korea isolates (S. erinaceieuropaei KJ599680 and S. decipiens KJ599679) was still ambiguous and needs to be further identified. In addition, the demographical analyses supported population expansion for the total spirometrid population. In summary, four lineages were found in the spirometrid tapeworm, and further investigation with deeper sampling is needed to elucidate the population structure.

Molecular detection of Trichostrongylus species through PCR followed by high resolution melt analysis of ITS-2 rDNA sequences

Polymerase chain reaction followed by high resolution melting (PCR-HRM) analysis is a simple, rapid and accurate method for molecular detection of various nematode species. The objective of the present study was, for the first time, to develop a PCR-HRM assay for the detection of various animal Trichostrongylus spp. A pair of primers targeting the ITS-2 rDNA region of the Trichostrongylus spp. was designed for the development of the HRM assay. DNA samples were extracted from 30 adult worms of Trichostrongylus spp., the ITS-2-rDNA region was amplified using PCR, and the resultant products were sequenced and characterized. Afterwards, the PCR-HRM analysis was conducted to detect and discriminate Trichostrongylus spp. Molecular sequence analysis revealed that 24, 4, and 1 of the samples were T. colubriformis, T. vitrinus and T. capricola, respectively. Results from PCR-HRM indicated that complete agreement was relatively found between speciation by HRM analysis and DNA sequencing for the detection of Trichostrongylus species. The PCR-HRM analysis method developed in the present study is fast and low-cost; the method can be comparable with other molecular detection techniques, representing a reliable tool for the identification of various species within the Trichostrongylus genus.

[Complete mitochondrial genomes of Paragonimus westermani in China and phylogenetic analysis of various geographical isolates]

OBJECTIVE

To compare the complete mitochondrial genome sequences of two phenotypes of Paragonimus westermani isolated from Fujian Province with different sizes of metacercariae, and perform a phylogenetic analysis of various geographical isolates of P. westermani from Asia, so as to identify the possible genetic characteristics associated with the P. westermani phenotypes.

METHODS

P. westermani metacercariae with different sizes (large metacercariae, 380-420 μm in diameter; small metacercariae, 320-340 μm) isolated from freshwater crabs were used to infect dogs, and the eggs and adult worms of P. westermani were collected from the dog stool samples and lung tissues. Then, the egg size and morphology were compared. In addition, genomic DNA was extracted from the adult worms of the two phenotypes of P. westermani and used for the PCR amplification to yield the complete mitochondrial genome sequence. Sequence structure and phylogenetic analyses were performed based on the complete mitochondrial genome of P. westermani.

RESULTS

Following infection with large and small P. westermani metacercariae, the adult worms recovered from the dog lung had a thick body, and had oral and ventral suckers. The ventral sucker was located slightly in front of the midline of the body, and testes, ovary and vitelline gland were seen in the adult worms. Following fixation, the adults appeared oval, with an approximately 1.7∶1 of the length-width ratio. The length and width of the eggs isolated from the fecal samples of dogs infected with large and small P. westermani metacercariae varied significantly, and the large metacercariae produced bigger eggs than the smaller metacercariae. Based on the morphological features of adults and eggs and the ITS2 sequences, both phenotypes were identified as P. westermani. The complete mitochondrial genome sequence analysis of adults showed almost consistent sequences in the protein-coding region of the mitochondrial genome of adult worms derived from large and small metacercariae, with a major variation seen in the former non-coding region. Sliding window analysis revealed the most polymorphic region within the ND4 gene across the mitochondrial genome from various geographical isolates of P. westermani, and phylogenetic analysis showed that both phenotypes were clustered into the Chinese branch of P. westermani, which was close to the Japanese branch and distinct from the South/Southeast Asian branch.

CONCLUSIONS

The genetic distance between the phenotypes of P. westermani isolated from Fujian Province is near at a mitochondrial genome level, with no remarkable genetic differentiation seen; however, the mutation and structural changes in the non-coding region may result in the phenotypic variations. In addition, there is a distinct variation of the evolutionary rate in the mitochondrial coding genes, suggesting the selection of appropriate molecular markers during the phylogenic researches.