Cystic echinococcosis in wild boars (Sus scrofa) from southern Italy: Epidemiological survey and molecular characterization.

Cystic Echinococcosis (CE) caused by Echinococcus granulosus sensu lato (s.l.) is one of the most important parasitic zoonotic diseases in the world and it represents an important public health and socio-economic concern. In the Mediterranean basin, CE is widespread and it is endemic in Italy, with major prevalence in southern areas. Several studies have investigated CE in domestic pigs, however, such data in wild boars are scant. In the last decades the wild boar population in Italy has increased and this ungulate could play an important role in the spreading ofCEinthewild.Here wereporton theprevalenceandfertility rateofhydatid cystsinwildboarsthat were shot during two hunting seasons (2016–2017) in the Campania region of southern Italy. For each animal, a detailed inspection of the carcass and organs (lungs, liver and spleen) was performed and when cysts were found, their number, morphology and fertility were determined by visual and microscopic examination. Cysts were classified morphologically as fertile, sterile, caseous and calcified. Protoscoleces and germinal layers were collected from individual cysts and DNA was extracted to identify different strains/genotypes of E. granulosus s.l. Outofatotalof2108wildboars93(4.4%)werefoundpositiveforCE.Infectedanimalswere45malesand48 females, aged between 1 and 8 years. The average number of cysts per wild boar was 1.3 (min 1 - max 13). The total number of cysts collected was 123, of which 118 (95.9%) in the liver, 4 (3.3%) in the lungs and 1 (0.8%) in the spleen. Of all analyzed cysts, 70 (56.9%) were fertile and 53 (43.1%) sterile/acephalous. The presence of fertile cysts in 19.4% of CE-positive animals is noteworthy. Overall, molecular diagnosis showed 19 wild boars infected with the pig strain (G7)

Concatenated protein gene sequences of 183 Clonorchis sinensis specimens

This data set contains aligned concatenated protein gene sequences of 183 Clonorchis sinensis (phylum Platyhelminthes; class Trematoda; family Opisthorchiidae) specimens. The alignment includes polymorphic positions represented by IUPAC ambiguity characters; this polymorphism likely represents heteroplasmy as a result of multiple, distinct mitochondrial genomes being present within an individual worm. Sequence names correspond to specimen nos

Concatenated protein gene sequences of 183 Clonorchis sinensis specimens

This data set contains aligned concatenated protein gene sequences of 183 Clonorchis sinensis (phylum Platyhelminthes; class Trematoda; family Opisthorchiidae) specimens. The alignment includes polymorphic positions represented by IUPAC ambiguity characters; this polymorphism likely represents heteroplasmy as a result of multiple, distinct mitochondrial genomes being present within an individual worm. Sequence names correspond to specimen nos

Concatenated protein gene sequences of 183 Clonorchis sinensis specimens

This data set contains aligned concatenated protein gene sequences of 183 Clonorchis sinensis (phylum Platyhelminthes; class Trematoda; family Opisthorchiidae) specimens. The alignment includes polymorphic positions represented by IUPAC ambiguity characters; this polymorphism likely represents heteroplasmy as a result of multiple, distinct mitochondrial genomes being present within an individual worm. Sequence names correspond to specimen nos

Alignment of 303 Echinococcus granulosus sensu stricto mtDNA sequences

Fasta file with 303 aligned E. granulosus s. s. mtDNA sequences. The alignment contains gaps: the strings of NNN-s represent gaps of estimated length based on the reference sequence (AB786664 in GenBank)

Concatenated protein gene sequences of 183 Clonorchis sinensis specimens

This data set contains aligned concatenated protein gene sequences of 183 Clonorchis sinensis (phylum Platyhelminthes; class Trematoda; family Opisthorchiidae) specimens. The alignment includes polymorphic positions represented by IUPAC ambiguity characters; this polymorphism likely represents heteroplasmy as a result of multiple, distinct mitochondrial genomes being present within an individual worm. Sequence names correspond to specimen nos

First record of a tandem-repeat region within the mitochondrial genome ofClonorchis sinensisusing a long-read sequencing approach

BACKGROUND: Mitochondrial genomes provide useful genetic markers for systematic and population genetic studies of parasitic helminths. Although many such genome sequences have been published and deposited in public databases, there is evidence that some of them are incomplete relating to an inability of conventional techniques to reliably sequence non-coding (repetitive) regions. In the present study, we characterise the complete mitochondrial genome-including the long, non-coding region-of the carcinogenic Chinese liver fluke, Clonorchis sinensis, using long-read sequencing. METHODS: The mitochondrial genome was sequenced from total high molecular-weight genomic DNA isolated from a pool of 100 adult worms of C. sinensis using the MinION sequencing platform (Oxford Nanopore Technologies), and assembled and annotated using an informatic approach. RESULTS: From > 93,500 long-reads, we assembled a 18,304 bp-mitochondrial genome for C. sinensis. Within this genome we identified a novel non-coding region of 4,549 bp containing six tandem-repetitive units of 719-809 bp each. Given that genomic DNA from pooled worms was used for sequencing, some variability in length/sequence in this tandem-repetitive region was detectable, reflecting population variation. CONCLUSIONS: For C. sinensis, we report the complete mitochondrial genome, which includes a long (> 4.5 kb) tandem-repetitive region. The discovery of this non-coding region using a nanopore-sequencing/informatic approach now paves the way to investigating the nature and extent of length/sequence variation in this region within and among individual worms, both within and among C. sinensis populations, and to exploring whether this region has a functional role in the regulation of replication and transcription, akin to the mitochondrial control region in mammals. Although applied to C. sinensis, the technological approach established here should be broadly applicable to characterise complex tandem-repetitive or homo-polymeric regions in the mitochondrial genomes of a wide range of taxa

Alignment of 170 Echinococcus granulosus sensu stricto G1 near-complete mtDNA sequences

Fasta file with aligned near-complete E. granulosus s. s. G1 mtDNA sequences. The alignment contains 170 haplotypes, which comprises 211 genotype G1 samples sequenced (for additional data on the haplotypes see Table S3). The alignment contains gaps: the strings of NNN-s represent gaps of estimated length based on a reference sequence (AB786664 in GenBank)