Simone M. Cacciò
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View article: Host range expansion of asexual parasite can be explained by loss of adaptions in Muller’s Ratchet
Host range expansion of asexual parasite can be explained by loss of adaptions in Muller’s Ratchet Open
Sexual recombination is a hallmark of eukaryotic evolution. Without recombination, asexual eukaryotes should succumb to deleterious mutations and more rapidly evolving pathogens. Giardia duodenalis, a parasitic protist, sits within one of …
View article: Parapipe: a pipeline for parasite next-generation sequencing data analysis applied to Cryptosporidium
Parapipe: a pipeline for parasite next-generation sequencing data analysis applied to Cryptosporidium Open
Graphical abstract An outline of Parapipe's workflow, illustrating its five core modules: quality control, variant calling, polyclonality detection, clustering, and report generation.
View article: Molecular Epidemiology of Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi in Guizhou Angus Calves: Dominance of Angus Cattle-Adapted Genotypes and Zoonotic Potential of E. bieneusi
Molecular Epidemiology of Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi in Guizhou Angus Calves: Dominance of Angus Cattle-Adapted Genotypes and Zoonotic Potential of E. bieneusi Open
Limited molecular data exist on zoonotic parasites Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi in Angus calves from Guizhou, China. This study constitutes the first molecular epidemiological survey of these pathog…
View article: Parapipe: A Pipeline for Parasite Next-Generation Sequencing Data Analysis Applied to Cryptosporidium
Parapipe: A Pipeline for Parasite Next-Generation Sequencing Data Analysis Applied to Cryptosporidium Open
Cryptosporidium, a protozoan parasite of significant public health concern, is responsible for severe diarrheal disease, particularly in immunocompromised individuals and young children in resource-limited settings. Analysis of whole genom…
View article: Detection of parasites in food and water matrices by shotgun metagenomics: A narrative review
Detection of parasites in food and water matrices by shotgun metagenomics: A narrative review Open
View article: Parapipe: A Pipeline for Parasite Next-Generation Sequencing Data Analysis Applied to Cryptosporidium
Parapipe: A Pipeline for Parasite Next-Generation Sequencing Data Analysis Applied to Cryptosporidium Open
2. Abstract Cryptosporidium, a protozoan parasite of significant public health concern, is responsible for severe diarrheal disease, particularly in immunocompromised individuals and young children in resource-limited settings. Analysis of…
View article: Parapipe: a Pipeline for Handling Parasite NGS Datasets and its Application to Cryptosporidium
Parapipe: a Pipeline for Handling Parasite NGS Datasets and its Application to Cryptosporidium Open
0.0 Abstract Cryptosporidium , a protozoan parasite of significant public health concern, is responsible for severe diarrheal diseases, particularly in immunocompromised individuals and young children in resource-limited settings. Analysis…
View article: Design, development, and testing of a new multi-locus sequence typing scheme for the zoonotic pathogen Cryptosporidium parvum
Design, development, and testing of a new multi-locus sequence typing scheme for the zoonotic pathogen Cryptosporidium parvum Open
The zoonotic parasite Cryptosporidium parvum is an important global cause of diarrheal disease in humans and young ruminants. Molecular typing is essential to track transmission routes and identify clusters of cases. Here, we develo…
View article: Host range expansion of asexual parasite can be explained by loss of adaptions in Muller’s Ratchet
Host range expansion of asexual parasite can be explained by loss of adaptions in Muller’s Ratchet Open
Sexual recombination is a hallmark of eukaryotic evolution. Without recombination, asexual eukaryotes should succumb to deleterious mutations and more rapidly evolving pathogens. Giardia duodenalis, a parasitic protist, sits within one of …
View article: Comprehensive analysis of flavohemoprotein copy number variation in Giardia intestinalis: exploring links to metronidazole resistance
Comprehensive analysis of flavohemoprotein copy number variation in Giardia intestinalis: exploring links to metronidazole resistance Open
Background Giardiasis, caused by the protozoan parasite Giardia intestinalis , often presents a treatment challenge, particularly in terms of resistance to metronidazole. Despite extensive research, markers for metronidazole resistance hav…
View article: Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries
Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries Open
View article: Comparative genomics of <i>Cryptosporidium parvum</i> reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
Comparative genomics of <i>Cryptosporidium parvum</i> reveals the emergence of an outbreak-associated population in Europe and its spread to the United States Open
The zoonotic parasite Cryptosporidium parvum is a global cause of gastrointestinal disease in humans and ruminants. Sequence analysis of the highly polymorphic gp60 gene enabled the classification of C. parvum isolates into multiple groups…
View article: Novel strategy to quantify the viability of oocysts of Cryptosporidium parvum and C. hominis, a risk factor of the waterborne protozoan pathogens of public health concern
Novel strategy to quantify the viability of oocysts of Cryptosporidium parvum and C. hominis, a risk factor of the waterborne protozoan pathogens of public health concern Open
While waters might be contaminated by oocysts from >40 Cryptosporidium species, only viable oocysts of C. parvum and C. hominis truly pose the main health risk to the immunocompetent population. Oocyst viability is also an important but of…
View article: Mitochondrial genetic diversity and phylogenetic relationships of Echinococcus multilocularis in Europe
Mitochondrial genetic diversity and phylogenetic relationships of Echinococcus multilocularis in Europe Open
The cestode Echinococcus multilocularis is the causative agent of alveolar echinococcosis, a fatal zoonotic parasitic disease of the northern hemisphere. Red foxes are the main reservoir hosts and, likely, the main drivers of the geographi…
View article: Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method
Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method Open
Purpose A new high-resolution next-generation sequencing (NGS)-based method was established to type closely related European type II Toxoplasma gondii strains. Methods T. gondii field isolates were collected from different parts of Europe …
View article: Highly contiguous genomes of Giardia duodenalis isolates
Highly contiguous genomes of Giardia duodenalis isolates Open
High-quality genome data sets for Giardia duodenalis are scarce. Here, we generated highly contiguous genomes by a hybrid PacBio/Illumina sequencing approach of four assemblage A (one AI from a cat, and three AII from humans) and five asse…
View article: Highly contiguous genomes of Giardia duodenalis isolates
Highly contiguous genomes of Giardia duodenalis isolates Open
High-quality genome data sets for Giardia duodenalis are scarce. Here, we generated highly contiguous genomes by a hybrid PacBio/Illumina sequencing approach of four assemblage A (one AI from a cat, and three AII from humans) and five asse…
View article: Comparative genomics reveals the emergence of an outbreak-associated<i>Cryptosporidium parvum</i>population in Europe and its spread to the USA
Comparative genomics reveals the emergence of an outbreak-associated<i>Cryptosporidium parvum</i>population in Europe and its spread to the USA Open
The zoonotic parasite Cryptosporidium parvum is a global cause of gastrointestinal disease in humans and ruminants. Sequence analysis of the highly polymorphic gp60 gene enabled the classification of C. parvum isolates into multiple groups…
View article: European Union Reference Laboratories support the National food, feed and veterinary Reference Laboratories with rolling out whole genome sequencing in Europe
European Union Reference Laboratories support the National food, feed and veterinary Reference Laboratories with rolling out whole genome sequencing in Europe Open
The Inter European Union Reference Laboratories (EURLs) Working Group on Next Generation Sequencing (NGS) involves eight EURLs for microbiological food and feed hazards and has been working since 2017 to promote the adoption of NGS by the …
View article: Highly contiguous genomes of human clinical isolates of Giardia duodenalis reveal assemblage- and sub-assemblage-specific presence–absence variation in protein-coding genes
Highly contiguous genomes of human clinical isolates of Giardia duodenalis reveal assemblage- and sub-assemblage-specific presence–absence variation in protein-coding genes Open
Giardia duodenalis (syn. G. intestinalis, G. lamblia ) is a widespread gastrointestinal protozoan parasite with debated taxonomic status. Currently, eight distinct genetic sub-groups, termed assemblages A–H, are defined based on a few gene…
View article: Extensive testing of a multi-locus sequence typing scheme for Giardia duodenalis assemblage A confirms its good discriminatory power
Extensive testing of a multi-locus sequence typing scheme for Giardia duodenalis assemblage A confirms its good discriminatory power Open
Background The flagellated parasite Giardia duodenalis is a major and global cause of diarrhoeal disease. Eight genetically very distinct groups, known as assemblages A to H, have been recognized in the G. duodenalis species complex, two o…
View article: Deliverable D-JRP-TOXOSOURCES-WP5.3 Report on the inter-laboratory comparison and the pilot studies of WP5
Deliverable D-JRP-TOXOSOURCES-WP5.3 Report on the inter-laboratory comparison and the pilot studies of WP5 Open
Deliverable D-JRP-TOXOSOURCES-WP5.3 Report on the inter-laboratory comparison and the pilot studies of WP5
View article: D-JRP19-WP1.2: Report of the Y4 meeting of the PARADISE project
D-JRP19-WP1.2: Report of the Y4 meeting of the PARADISE project Open
This is the report of the Y4 annual meeting of the “OHEJP Project: PARADISE, which was held virtually on October 26 via the Teams platform. This report is a deliverable of the project.
View article: D-JRP19-WP1.3: Report of the Y5 Final meeting of the OHEJP PARADISE project
D-JRP19-WP1.3: Report of the Y5 Final meeting of the OHEJP PARADISE project Open
This is the report of the Y5 Final meeting of the OHEJP project: PARADISE, which was hold in Uppsala (Sweden) on June 22-23, 2022. This report is a deliverable of the project.
View article: D-JRP-PARADISE-WP3-3
D-JRP-PARADISE-WP3-3 Open
This is a report of the OHEJP project: PARADISE, concenring the development of Standard Operating Procedures (SOPs) for the C. parvum and G. duodenalis Multi Locus Typing Schemes (MLST)
View article: D-JRP-PARADISE-WP3.2: Report on the identification of markers for multi-locus sequence typing of Cryptosporidium parvum and Giardia duodenalis
D-JRP-PARADISE-WP3.2: Report on the identification of markers for multi-locus sequence typing of Cryptosporidium parvum and Giardia duodenalis Open
This is a report of the OHEJP project: PARADISE, which details the procedures undertaken for in silico detection of variable regions suitable for subsequent selection of markers for C. parvum and G. duodenalis.
View article: VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses
VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses Open
Large-scale comparative genomics- and population genetic studies generate enormous amounts of polymorphism data in the form of DNA variants. Ultimately, the goal of many of these studies is to associate genetic variants to phenotypes or fi…
View article: An outbreak of cryptosporidiosis associated with drinking water in north-eastern Italy, August 2019: microbiological and environmental investigations
An outbreak of cryptosporidiosis associated with drinking water in north-eastern Italy, August 2019: microbiological and environmental investigations Open
Cryptosporidium is a leading global cause of waterborne disease, with many reported outbreaks related to main water supplies. In August 2019, an outbreak of cryptosporidiosis involving 80 cases occurred among 114 vacationers in a small mun…
View article: Clustering of Cryptosporidium species infections among sheep and cattle but not children in remote highland communities of Madagascar
Clustering of Cryptosporidium species infections among sheep and cattle but not children in remote highland communities of Madagascar Open
View article: Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen <i>Cryptosporidium parvum</i>
Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen <i>Cryptosporidium parvum</i> Open
Cryptosporidium parvum is a globally distributed zoonotic pathogen and a major cause of diarrhoeal disease in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur be…