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Matoute A, Maestri S, Saout M, Laghoe L, Simon S, Blanquart H, Hernandez Martinez MA, Pierre Demar M. Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana. Curr Issues Mol Biol 2024; 46:3810-3821. [PMID: 38785505 PMCID: PMC11119736 DOI: 10.3390/cimb46050237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/06/2024] [Accepted: 04/03/2024] [Indexed: 05/25/2024] Open
Abstract
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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Affiliation(s)
- Adria Matoute
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
- U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Université Lille, 59000 Lille, France
| | - Simone Maestri
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
| | - Mona Saout
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
- U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Université Lille, 59000 Lille, France
| | - Laure Laghoe
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
- U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Université Lille, 59000 Lille, France
| | - Stéphane Simon
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
- U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Université Lille, 59000 Lille, France
| | | | - Miguel Angel Hernandez Martinez
- Laboratoire Associé du CNR Leishmaniose, Laboratoire Hospitalo-Universitaire de Parasitologie et Mycologie, Centre Hospitalier Andrée Rosemon, 97300 Cayenne, France;
| | - Magalie Pierre Demar
- Tropical Biome and Immunopathophysiology (TBIP), Université de Guyane, 97300 Cayenne, France; (A.M.); (S.M.); (M.S.); (L.L.); (S.S.)
- U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, CHU Lille, INSERM, CNRS, Université Lille, 59000 Lille, France
- Laboratoire Associé du CNR Leishmaniose, Laboratoire Hospitalo-Universitaire de Parasitologie et Mycologie, Centre Hospitalier Andrée Rosemon, 97300 Cayenne, France;
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Sundararaman B, Shapiro K, Packham A, Camp LE, Meyer RS, Shapiro B, Green RE. Whole genome enrichment approach for genomic surveillance of Toxoplasma gondii. Food Microbiol 2024; 118:104403. [PMID: 38049278 DOI: 10.1016/j.fm.2023.104403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/26/2023] [Accepted: 10/15/2023] [Indexed: 12/06/2023]
Abstract
Pathogenic bacteria, viruses, fungi, and protozoa can cause food and waterborne diseases. Surveillance methods must therefore screen for these pathogens at various stages of water distribution and of food from production to consumption. Detection using nucleic acid amplification methods offer rapid identification, but such methods have limited utility for characterizing populations, variant types or virulence traits of pathogens. Whole genome sequencing (WGS) can be used to determine this information. However, pathogens must be isolated and cultured to yield sufficient DNA for WGS, which is laborious or not feasible for certain stages of parasites like oocysts of Toxoplasma gondii. We previously developed the Circular Nucleic acid Enrichment Reagent (CNER) method to make whole genome enrichment (WGE) baits for difficult-to-grow bacterial pathogens. WGE using CNERs facilitates direct sequencing of pathogens from samples without the need to isolate and grow them. Here, we made WGE-CNERs for T. gondii to demonstrate the use of the CNER method to make baits to enrich the large genomes of water and foodborne protozoan pathogens. By sequencing, we detected as few as 50 parasites spiked in an oyster hemolymph matrix. We discuss the use of WGE-CNERs for genomic surveillance of food and waterborne pathogens.
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Affiliation(s)
| | - Karen Shapiro
- One Health Institute, UC Davis, USA; Department of Pathology, Microbiology, and Immunology, UC Davis, USA.
| | | | - Lauren E Camp
- Department of Pathology, Microbiology, and Immunology, UC Davis, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, UC Santa Cruz, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, UC Santa Cruz, USA; Howard Hughes Medical Institute, UC Santa Cruz, USA
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