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Poster

A web tool for analysis the genotyping of mycobacterium avium subsp. paratuberculosis strains and other mac members

Abstract : Background: Genotyping applied to strains of Mycobacterium avium subsp. paratuberculosis (MAP) becomes an indispensable tool for epidemiological surveillance of this significant veterinary pathogen. For MAP, multilocus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRUs) and other variable number variable-number tandem repeats (VNTRs) was established using 8 markers. Within the past 5 years this standard, portable, reproducible and discriminatory typing method has been frequently use alone or in combinations with other molecular method. As such, a number of genotypes (termed INVM) of strains of diverse origins have been identified in our laboratory. However, no web tools are available for knowing the already existing INMV profiles and storing newly defined genotypes. Objective: To develop a web application called “Mac INMV database”. This freely accessible service allows users to compare the genotyping data of their strains analysed by MLVA with those of existing reference strains. Results: a freely accessible database was created with genotyping data of strains of MAP and of other M. avium complex (MAC) members. This database gathers all INMV profiles obtained in the laboratory and those published in the literature. The database information include incrementing species and subspecies status, INMV profiles with corresponding alleles/repeat numbers at each locus, and combined numerical genotypes. The user can consult and query all the existing INMV profiles in order to see if profiles identified in his lab already exist. If profiles are not known, the user can request new attribution numbers online. All information can be exported under EXCEL or PDF format. An extensive documentation regarding the genotyping method, protocols, primer sequences, marker information, is available to the users.
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Poster
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https://hal.inrae.fr/hal-02743915
Déposant : Migration Prodinra <>
Soumis le : mercredi 3 juin 2020 - 06:44:25
Dernière modification le : mardi 29 septembre 2020 - 17:02:02

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  • HAL Id : hal-02743915, version 1
  • PRODINRA : 276492

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Thierry Cochard, Maxime Branger, Virginie Thibault, Philip Supply, Franck Biet. A web tool for analysis the genotyping of mycobacterium avium subsp. paratuberculosis strains and other mac members. 12. International Colloquium on Paratuberculosis, Jun 2014, Parme, Italy. 234 p., 2014. ⟨hal-02743915⟩

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