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Mise à jour le 13 décembre 2022 à 08:17 am

Épidémiologie moléculaire d’Histoplasma capsulatum sur le plateau des Guyanes et en Amérique du Sud

Madame Tani LY, présentera ses travaux en vue de l’obtention du Doctorat


Sujet : Épidémiologie moléculaire d’Histoplasma capsulatum sur le plateau des Guyanes et en Amérique du Sud
Directeurs de thèse :  Monsieur Mathieu NACHER, PU-PH, Directeur CIC INSERM 1424 au CH de Cayenne et à l’Université de Guyane.

Spécialité : Physiologie et biologie des organismes des populations

Date : mercredi 15 septembre 2021 à 10h00, Université de Guyane Département de Formation et de Recherche Santé en salle P2

Résumé

Introduction : Histoplasmosis is the most common opportunistic infection and the leading cause of death in people living with HIV, particularly in South America. Historically, Histoplasma capsulatum was classified into 3 varieties : capsulatum, duboisii and farciminosum. Then, the species was subdivided into 8 clades, 2 of which were specific to Latin America : LAm A and LAm B. Recently, other studies show that Latin America hosts at least 7 new clades, 5 of which circulate in Brazil. However, no isolates came from French Guiana, which is also part of the Amazon known to be a unique diversity hotspot.

The primary objective of this thesis was therefore to update and improve our phylogenetic knowledge of the Histoplasma capsulatum species by including isolates from the three Guianas in our analysis using the most recent technologies and methods.

The secondary objective is to determine the prevalence of histoplasmosis in wildlife in French Guyana.

Material and methods : Cultures from the routine diagnosis of histoplasmosis at the Cayenne Hospital and those from collaborations were selected and subcultured on solid medium. Each culture was used as a template for DNA extraction. A PCR check was performed to verify the identity of the species for each isolate included in the study. Kasuga’s method was initiated by PCR amplifying portions of the arf, H-anti, ole, and tub genes for each isolate. The resulting PCR products were sequenced and then whole genome sequencing was performed on the Hiseq and NextSeq platforms. The gene and genome sequences were used for phylogenetic analysis using Maximum Likelihood and then for population study using Neighbor-joining, Principal Component Analysis, FastStructure and Admixture plots. To study the prevalence of histoplasmosis in wildlife, biological samples were collected from several local species and DNA was extracted. Then DNA was extracted from them. The prevalence of histoplasmosis was assessed by real-time PCR targeting the ITS gene.

Results : 85 whole genomes are newly sequenced, 37 of which come from French Guiana. The phylogenetic analysis identified 4 different putative phylogenetic species of Histoplasma capsulatum present in French Guiana, 3 of which were written for the first time : Amazon I, II and III. They form 7 groups by genetic similarity with pre-existing clades. The current genetic diversity of the genus Histoplasma is the result of the evolution of at least 6 ancestral populations.

The prevalence study was conducted on 97 species of Amazonian mammals from French Guiana collected along the coastline : 49 armadillos, 12 cabiais and packs, 4 porcupines and tamanduas, 2 hinds, sloth mustangs, pakiras and Dasypus kappleri armadillos, and 1 agouti, baboon, jaguarondi, kinkajou, macaque, margay, mirmidon, saimiri, tapir and tayra. The biological samples were : heart (94.8%), brain, lungs, liver, spleen, kidneys and blood. The prevalence was more important in the ground sniffers – pack, armadillo and cabiai -, and on the lung, liver and spleen samples. The prevalence rate of histoplasmosis in the wildlife of French Guiana was estimated to be up to 56%.

In conclusion, these studies have allowed us to improve the resolution of the Histoplasma capsulatum phylogenetic tree by identifying 3 new clades in addition to the 7 already existing in Latin America. This supports the idea that Latin America has the greatest diversity of histoplasmas. On the other hand, these studies have identified for the first time the prevalence of histoplasmosis in wildlife with a higher prevalence in soil sniffers. This corroborates the relationship between infectivity and frequency of contact or degree of exposure.

Abstract

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École doctorale

M. Bertrand DE TOFFOL
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Mme Rachelle HO-COUI-YOUN
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