MAC-INMV-plus : a web application dedicated to genotyping of Mycobacterium avium subsp. paratuberculosis strains and other MAC members

Background: Genotyping applied to strains of Mycobacterium avium subsp. paratuberculosis (MAP) has become an indispensable tool for epidemiological surveillance of this significant veterinary pathogen. For MAP, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRUs) and other variable-number tandem repeats (VNTRs) was established using 8 markers. Within the past years this standard, portable, reproducible and discriminatory typing method has been frequently applied alone or in combinations with short-sequence-repeat (SSR) sequencing. As such, a number of genotypes of strains of diverse origins have been identified in laboratories worldwide. With the large diffusion of these genotyping methods standardization between laboratories and knowledge of existing INMV profiles and archiving of newly defined genotypes need to be managed. Objective: To develop a web application called “Mac INMV plus database” including MLVA and SSR. This freely accessible service allows users to compare VNTR and SSR subtype data of their strains analyzed by MLVA and with those of existing reference strains.Results: A freely accessibledatabase was created with genotyping data of strains of MAP and of other M. avium complex (MAC) members. This database gathers all profiles obtained in the laboratory and those published in the literature. The database information include incrementing species and subspecies status, INMV and SSR profiles with corresponding alleles/repeat numbers at each locus, and combined numerical genotypes. The user can consult and query all the existing profiles in order to see if profiles identified in their 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, and associated isolate specific metadata is available to the users