{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T02:14:15Z","timestamp":1790820855419,"version":"4.1.0"},"reference-count":47,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2024,4,24]],"date-time":"2024-04-24T00:00:00Z","timestamp":1713916800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European funding (ERDF\/FEDER)","award":["GY0012553"],"award-info":[{"award-number":["GY0012553"]}]},{"name":"European funding (ERDF\/FEDER)","award":["CEBA: ANR-10-LABEX-25-01"],"award-info":[{"award-number":["CEBA: ANR-10-LABEX-25-01"]}]},{"name":"Investissement d\u2019Avenir grants of the the Agence Nationale de la Recherche","award":["GY0012553"],"award-info":[{"award-number":["GY0012553"]}]},{"name":"Investissement d\u2019Avenir grants of the the Agence Nationale de la Recherche","award":["CEBA: ANR-10-LABEX-25-01"],"award-info":[{"award-number":["CEBA: ANR-10-LABEX-25-01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["CIMB"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/cimb46050237","type":"journal-article","created":{"date-parts":[[2024,4,24]],"date-time":"2024-04-24T03:56:31Z","timestamp":1713930991000},"page":"3810-3821","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana"],"prefix":"10.3390","volume":"46","author":[{"given":"Adria","family":"Matoute","sequence":"first","affiliation":[{"name":"Tropical Biome and Immunopathophysiology (TBIP), Universit\u00e9 de Guyane, 97300 Cayenne, France"},{"name":"U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Universit\u00e9 Lille, 59000 Lille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1192-0684","authenticated-orcid":false,"given":"Simone","family":"Maestri","sequence":"additional","affiliation":[{"name":"Tropical Biome and Immunopathophysiology (TBIP), Universit\u00e9 de Guyane, 97300 Cayenne, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mona","family":"Saout","sequence":"additional","affiliation":[{"name":"Tropical Biome and Immunopathophysiology (TBIP), Universit\u00e9 de Guyane, 97300 Cayenne, France"},{"name":"U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Universit\u00e9 Lille, 59000 Lille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laure","family":"Laghoe","sequence":"additional","affiliation":[{"name":"Tropical Biome and Immunopathophysiology (TBIP), Universit\u00e9 de Guyane, 97300 Cayenne, France"},{"name":"U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Universit\u00e9 Lille, 59000 Lille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"St\u00e9phane","family":"Simon","sequence":"additional","affiliation":[{"name":"Tropical Biome and Immunopathophysiology (TBIP), Universit\u00e9 de Guyane, 97300 Cayenne, France"},{"name":"U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Universit\u00e9 Lille, 59000 Lille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H\u00e9l\u00e8ne","family":"Blanquart","sequence":"additional","affiliation":[{"name":"GenoScreen, 5900 Lille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9960-0561","authenticated-orcid":false,"given":"Miguel Angel","family":"Hernandez Martinez","sequence":"additional","affiliation":[{"name":"Laboratoire Associ\u00e9 du CNR Leishmaniose, Laboratoire Hospitalo-Universitaire de Parasitologie et Mycologie, Centre Hospitalier Andr\u00e9e Rosemon, 97300 Cayenne, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3414-0821","authenticated-orcid":false,"given":"Magalie","family":"Pierre Demar","sequence":"additional","affiliation":[{"name":"Tropical Biome and Immunopathophysiology (TBIP), Universit\u00e9 de Guyane, 97300 Cayenne, France"},{"name":"U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Universit\u00e9 Lille, 59000 Lille, France"},{"name":"Laboratoire Associ\u00e9 du CNR Leishmaniose, Laboratoire Hospitalo-Universitaire de Parasitologie et Mycologie, Centre Hospitalier Andr\u00e9e Rosemon, 97300 Cayenne, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,4,24]]},"reference":[{"key":"ref_1","first-page":"102","article-title":"Three cases of human Sarcocystis infection with a review of human muscular sarcocystosis in Malaysia","volume":"44","author":"Pathmanathan","year":"1992","journal-title":"Trop. 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