Evaluation of Next-Generation Sequencing Applied to and Epidemiological Study.

Fiche publication

Date publication

août 2022

Journal

Pathogens (Basel, Switzerland)

Auteurs

Membres identifiés du Cancéropôle Est :
Mr DUFFOURD Yannis

Tous les auteurs :
Bailly E, Valot S, Vincent A, Duffourd Y, Grangier N, Chevarin M, Costa D, Razakandrainibe R, Favennec L, Basmaciyan L, Dalle F

Lien Pubmed

https://www.ncbi.nlm.nih.gov/pubmed/36015058

Résumé

. Nowadays, most of the and epidemiological studies are based on gp60 gene subtyping using the Sanger sequencing (SgS) method. Unfortunately, SgS presents the limitation of being unable to detect mixed infections. Next-Generation Sequencing (NGS) seems to be an interesting solution to overcome SgS limits. Thus, the aim of our study was to (i) evaluate the reliability of NGS as a molecular typing tool for cryptosporidiosis, (ii) investigate the genetic diversity of the parasite and the frequency of mixed infections, (iii) assess NGS usefulness in sp. outbreak investigations, and (iv) assess an interpretation threshold of sequencing data. . 108 DNA extracts from positive samples were sequenced by NGS. Among them, two samples were used to validate the reliability of the subtyping obtained by NGS and its capacity to detect DNA mixtures. In parallel, 106 samples from French outbreaks were used to expose NGS to epidemic samples. . NGS proved suitable for sp. subtyping at the gp60 gene locus, bringing more genetic information compared to SgS, especially by working on many samples simultaneously and detecting more diversity. . This study confirms the usefulness of NGS applied to and epidemiological studies, especially aimed at detecting minority variants.