Mitochondrial Genome Sequence of Echinostoma revolutum from Red-Crowned Crane (Grus japonensis)

Development and utilization of a visual loop-mediated isothermal amplification coupled with a lateral flow dipstick (LAMP-LFD) assay for rapid detection of Echinostomatidae metacercaria in edible snail samples

Trematodes belonging to the family Echinostomatidae are food-borne parasites which cause echinostomiasis in animals and humans. This is a global public health issue, particularly in East and Southeast Asia. A method to detect the infective stage of Echinostomatidae species is required to prevent transmission to humans. In this study, a loop-mediated isothermal amplification coupled with a lateral flow dipstick (LAMP-LFD) assay was developed for visual detection of the metacercarial stage in edible snails of the genus Filopaludina from local markets in Thailand. The LAMP-LFD method can be performed within 70 min at a consistent temperature of 66 °C, and the results can be interpreted with the naked eye. The detection limits of the assay using Echinostoma mekongi, E. macrorchis, E. miyagawai and Hypoderaeum conoideum genomic DNA were equal between the four species at 50 pg/μL. A specificity evaluation demonstrated that the LAMP-LFD assay had no cross-reaction with another parasite (Thapariella species) or with the snail host species (Filopaludina martensi martensi, F. sumatrensis speciosa, and F. s. polygramma). Clinical test assessments were compared to microscopic examination in 110 edible snail samples. The clinical sensitivity and specificity of the tests were 84.62 % and 100 %, respectively, with a strong level of agreement based on the kappa statistic and the results of both methods were not significantly different (p > 0.05) per McNemar's test. The test successfully developed in this study may be useful for the detection of the metacercarial stage in edible snails for epidemiological investigations, control, surveillance, and to prevent future echinostomiasis health issues.

First molecular insights into gastrointestinal helminths of domestic birds in the Caspian Sea Littoral of Iran with an emphasis on the One Health concern

The current investigation was carried out during the period from July 2022 to March 2023, aiming to investigate the prevalence of gastrointestinal helminths in domestic birds collected from traditional markets in Guilan province. One hundred forty-eight domestic birds, including chickens (Gallus gallus domesticus), domestic ducks (Anas platyrhynchos domesticus), greylag geese (Anser anser), and domestic turkeys (Meleagris gallopavo domesticus) were examined. Totally, 42.56% of the investigated birds were positive for helminthic parasites. Morphological analysis revealed varying infection rates among birds: Echinostoma revolutum (5.40%), Hypoderaeum conoideum (2.02%), Cloacotaenia megalops (0.67%), Hymenolepididae family (4.05%), Ascaridia galli (16.89%), and Heterakis gallinarum (4.72%). The investigation involved molecular analysis of the 18S and ITS1 + 5.8S + ITS2 rRNA gene regions. The findings indicated that the 18S region of nematode isolates exhibited a similarity of 92 to 100% with sequences in the GenBank, whereas trematode and cestode isolates showed a gene similarity ranging from 88 to 99%. The ITS regions of nematode, trematode, and cestode isolates exhibited genetic similarities ranging from 87 to 100%, 73-99%, and 75-99%, respectively. Furthermore, phylogenetic analysis confirmed the categorization of the identified species within the Ascaridiidae, Heterakidae, Hymenolepididae, and Echinostomatidae families, indicating their close affinity with previously documented species. Implementing precise control measures such as consistent monitoring, adequate sanitation protocols, and administering anthelmintic treatments is crucial for effectively managing parasitic infections in free-range and backyard poultry farms. Additionally, conducting further surveys is advisable to assess the impact of these parasites on the health and productivity of poultry in the investigated area.

A report on the complete mitochondrial genome of the trematode Azygia robusta Odhner, 1911, its new definitive host from the Russian Far East, and unexpected phylogeny of Azygiidae within Digenea, as inferred from mitogenome sequences

New data on the complete mitochondrial genome of Azygia robusta (Azygiidae) were obtained by the next-generation sequencing (NGS) approach. The mitochondrial DNA (mtDNA) of A. robusta had a length of 13 857 bp and included 12 protein-coding genes, two ribosomal genes, 22 transfer RNA genes, and two non-coding regions. The nucleotide sequences of the complete mitochondrial genomes of two A. robusta specimens differed from each other by 0.12 ± 0.03%. Six of 12 protein-coding genes demonstrated intraspecific variation. The difference between the nucleotide sequences of the complete mitochondrial genomes of A. robusta and Azygia hwangtsiyui was 26.95 ± 0.35%; the interspecific variation of protein-coding genes between A. robusta and A. hwangtsiyui ranged from 20.5 ± 0.9% (cox1) to 30.7 ± 1.2% (nad5). The observed gene arrangement in the mtDNA sequence of A. robusta was identical to that of A. hwangtsiyui. Codon usage and amino acid frequencies were highly similar between A. robusta and A. hwangtsiyui. The results of phylogenetic analyses based on mtDNA protein-coding regions showed that A. robusta is closely related to A. hwangtsiyui (belonging to the same suborder, Azygiida) that formed a distinct early-diverging branch relative to all other Digenea. A preliminary morphological analysis of paratypes of the two azygiid specimens studied showed visible morphological differences between them. The specimen extracted from Sakhalin taimen (Parahucho perryi) was most similar to A. robusta. Thus, we here provide the first record of a new definitive host, P. perryi, for A. robusta and also molecular characteristics of the trematode specimens.

Characterization of complete mitochondrial genome and ribosomal operon for Carassotrema koreanum Park, 1938 (Digenea: Haploporidae) by means of next-generation sequencing data

We obtained new data on the complete mitochondrial DNA (mtDNA) and the ribosomal operon of the trematode Carassotrema koreanum (Digenea: Haploporata: Haploporidae), an intestinal parasite of Carassius auratus, using next-generation sequencing. The mtDNA of C. koreanum contained 13,965 bp, including 12 protein-coding genes, two ribosomal genes, 22 transport RNA (tRNA) genes and a non-coding region. The ribosomal operon of C. koreanum was 10,644 bp in length, including ETS1 (1449 bp), 18S ribosomal RNA (rRNA) gene (1988 bp), ITS1 ribosomal DNA (rDNA) (558 bp), 5.8S rRNA gene (157 bp), ITS2 rDNA (274 bp), 28S rRNA gene (4152 bp) and ETS2 (2066 bp). Phylogenetic analysis based on mtDNA protein-coding regions showed that C. koreanum was closely related to Parasaccocoelium mugili, a species from the same suborder Haploporata. Bayesian phylogenetic tree topology was the most reliable and confirmed the validity of the Haploporata. The results of sequence cluster analysis based on codon usage bias demonstrated some agreement with the results of the phylogenetic analysis. In particular, Schistosoma spp. were differentiated from the other members of Digenea and the members of Pronocephalata were localized within the same cluster. Carassotrema koreanum and P. mugili fell within different clusters. The grouping of C. koreanum and P. mugili within the same cluster was obtained on the basis of frequencies of 13 specified codons, of which three codon pairs were degenerate. A similarity was found between two haploporid species and two Dicrocoelium spp. in the presence of TTG start codon of the mitochondrial nad5 gene. Our results confirmed the taxonomical status of the Haploporata identified in the previous studies and revealed some characteristic features of the codon usage in its representatives.

Mitophylogenomics of the zoonotic fluke Echinostoma malayanum confirms it as a member of the genus Artyfechinostomum Lane, 1915 and illustrates the complexity of Echinostomatidae systematics

The complete mitochondrial genome (mitogenome or mtDNA) of the trematode Echinostoma malayanum Leiper, 1911 was fully determined and annotated. The circular mtDNA molecule comprised 12 protein-coding genes (PCGs) (cox1 - 3, cob, nad1 - 6, nad4L, atp6), two mitoribosomal RNAs (MRGs) (16S or rrnL and 12S or rrnS), and 22 transfer RNAs (tRNAs or trn), and a non-coding region (NCR) rich in long and short tandem repeats (5.5 LRUs/336 bp/each and 7.5 SRUs/207 bp/each). The atp8 gene is absent and the 3' end of nad4L overlaps the 5' end of nad4 by 40 bp. Special DHU-arm missing tRNAs for Serine were found for both tRNA^Ser1(AGN) and tRNA^Ser2(UCN). Codons of TTT (for phenylalanine), TTG (for leucine), and GTT (for valine) were the most, and CGC (for Arginine) was the least frequently used. A similar usage pattern was seen in base composition, AT and GC skewness for PCGs, MRGs, and mtDNA* (coding cox3 to nad5) in E. malayanum and Echinostomatidae. The nucleotide use is characterized by (T > G > A > C) for PCGs/mtDNA*, and by (T > G ≈ A > C) for MRGs. E. malayanum exhibited the lowest genetic distance (0.53%) to Artyfechinostomum sufrartyfex, relatively high to the Echinostoma congeners (13.20-13.99%), higher to Hypoderaeum conoideum (16.18%), and the highest to interfamilial Echinochasmidae (26.62%); Cyclocoelidae (30.24%); and Himasthlidae (25.36%). Topology indicated the monophyletic position between E. malayanum/A. sufrartyfex and the group of Echinostoma caproni, Echinostoma paraensei, Echinostoma miyagawai, and Echinostoma revolutum, rendering Hypoderaeum conoideum and unidentified Echinostoma species paraphyletic. The strictly closed genomic/taxonomic/phylogenetic features (including base composition, skewness, codon usage/bias, genetic distance, and topo-position) reinforced Echinostoma malayanum to retake its generic validity within the Artyfechinostomum genus.

The mitochondrial genome sequence analysis of Ophidascaris baylisi from the Burmese python (Python molurus bivittatus)

Ophidascaris species are parasitic roundworms that inhabit the python gut, resulting in severe granulomatous lesions or even death. However, the classification and nomenclature of these roundworms are still controversial. Our study aims to identify a snake roundworm from the Burmese python (Python molurus bivittatus) and analyze the mitochondrial genome. We identified this roundworm as Ophidascaris baylisi based on the morphology and cytochrome c oxidase subunit I (cox1) sequence. Ophidascaris baylisi complete mitochondrial genome was 14,784 bp in length, consisting of two non-coding regions and 36 mitochondrial genes (12 protein-coding genes, 22 tRNA genes, and two rRNA genes). The protein-coding genes used TTG, ATG, ATT, or TTA as start codons and TAG, TAA, or T as stop codons. All tRNA genes showed a TV-loop structure, except trnS1^AGN and trnS2^UCN revealed a D-loop structure. The mitochondrial large ribosomal subunit 16S (rrnL) and small ribosomal subunit 12S (rrnS) were 956 bp and 700 bp long, respectively. Phylogenetic analysis based on O. baylisi mitochondrial protein-coding genes demonstrated that O. baylisi clustered with the family Ascarididae members and was most closely related to Ophidascaris wangi. These results may enhance the nematode mitochondrial genome database and provide valuable molecular markers for further research on the taxonomy, phylogeny, and genetic relationships of Ophidascaris nematodes.