Adria Matoute’s research while affiliated with Pasteur Institute of Lille and other places

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Publications (3)


Fatal case of imported visceral leishmaniasis in a dog caused by Leishmania infantum in French Guiana
  • Article

August 2024

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26 Reads

Veterinary Parasitology Regional Studies and Reports

Mona Saout

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Théo Pinheiro

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Virginie da Costa

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[...]

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Geographical origin distribution of the individuals analysed.
Apicomplexa relative frequency in wildlife samples. For each sample, the relative frequency of reads assigned to Apicomplexa for Illumina and Nanopore matched samples at level 6 (i.e., up to genus) is reported. G0***L1 indicates the host ID, the first four elements indicate its code, followed by the letter representing the organ studied (P: lung; L or LD: tongue; CR: heart; R: spleen), and then the number representing the organ number.
Nanopore and Illumina relative frequency at level 6. For each sample, the relative frequency of genera identified using Nanopore and Illumina platforms was reported, and those showing a marked difference between the two platforms were labelled with the genus name. Dots are coloured according to sample.
Distribution of host species studied.
Demultiplexed sequence counts summary.

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Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana
  • Article
  • Full-text available

April 2024

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45 Reads

French Guiana, located in the Guiana Shield, is a natural reservoir for many zoonotic pathogens that are of considerable medical or veterinary importance. Until now, there has been limited data available on the description of parasites circulating in this area, especially on protozoan belonging to the phylum Apicomplexa; conversely, the neighbouring countries describe a high parasitic prevalence in animals and humans. Epidemiological surveillance is necessary, as new potentially virulent strains may emerge from these forest ecosystems, such as Amazonian toxoplasmosis. However, there is no standard tool for detecting protozoa in wildlife. In this study, we developed Meat-Borne-Parasite, a high-throughput meta-barcoding workflow for detecting Apicomplexa based on the Oxford Nanopore Technologies sequencing platform using the 18S gene of 14 Apicomplexa positive samples collected in French Guiana. Sequencing reads were then analysed with MetONTIIME pipeline. Thanks to a scoring rule, we were able to classify 10 samples out of 14 as Apicomplexa positive and reveal the presence of co-carriages. The same samples were also sequenced with the Illumina platform for validation purposes. For samples identified as Apicomplexa positive by both platforms, a strong positive correlation at up to the genus level was reported. Overall, the presented workflow represents a reliable method for Apicomplexa detection, which may pave the way for more comprehensive biomonitoring of zoonotic pathogens.

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Distribution of animal species studied.
Demultiplexed sequences counts summary.
Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Workflow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana

February 2024

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41 Reads

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3 Citations

French Guiana, located in the Guiana Shield, is a natural reservoir for many zoonotic pathogens that are of considerable medical or veterinary importance. Until now, there are few data available on the description of parasites circulating in this area, especially on protozoan belonging to the phy-lum Apicomplexa; conversely, the neighbouring countries describe a high parasitic prevalence in animals and humans. Epidemiological surveillance is necessary, as new potentially virulent strains may emerge from these forest ecosystems, such as Amazonian toxoplasmosis. However, there is no standard tool for detecting protozoa in wildlife. In this study, we developed Meat-Borne-Parasite, a high-throughput meta-barcoding workflow for detecting Apicomplexa based on Oxford Nanopore Technologies sequencing platform using the 18S gene of fourteen Apicomplexa-positive samples collected in French Guiana. Sequencing reads were then analysed with MetONTIIME pipeline. Thanks to a scoring rule, we were able to classify as Apicom-plexa-positive 10 samples out of 14 and reveal the presence of co-carriages. The same samples were also sequenced with Illumina platform, for validation purposes. On samples identified as Apicomplexa-positive by both platforms, a strong positive correlation at up to genus level was reported. Overall, the presented workflow represents a reliable method for Apicomplexa detec-tion, which may pave the way for more comprehensive biomonitoring of zoonotic pathogens.

Citations (1)


... Downstream analysis was performed utilizing the MetONTIIME pipeline [25] developed for long-read analysis in the QIIME 2 [4] environment with the Docker (version 4.27.1) [27] container interface. ...

Reference:

Microbial composition on microplastics mediated by stream impairment
Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Workflow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana