MAC-INMV-SSR: a web application dedicated to genotyping members of Mycobacterium avium complex (MAC) including Mycobacterium avium subsp. paratuberculosis strains

Infect Genet Evol. 2020 Jan:77:104075. doi: 10.1016/j.meegid.2019.104075. Epub 2019 Oct 18.

Abstract

Genotyping of Mycobacterium avium subsp. paratuberculosis (Map) is an indispensable tool for 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 variable-number tandem repeats (VNTRs) was established using 8 markers. In the recent past this standard, portable, reproducible and discriminatory typing method has been frequently applied alone or in combinations with multi-locus short-sequence-repeat (MLSSR) sequencing. With the widespread use of these genotyping methods, standardization between laboratories needs to be managed, and knowledge of existing profiles and newly defined genotypes should be indexed and shared. To meet this need, a web application called "MAC-INMV-SSR database" was developed. This freely accessible service allows users to compare MLVA and MLSSR subtype data of their strains with those of existing reference strains analyzed with the same genotyping methods.

Keywords: Database; Genotyping; MAC complex; MLSSR; MLVA; Mycobacterium avium subsp. paratuberculosis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Genetic Markers
  • Genotyping Techniques / methods
  • Genotyping Techniques / standards*
  • Internet
  • Microsatellite Repeats
  • Minisatellite Repeats
  • Multilocus Sequence Typing / methods
  • Multilocus Sequence Typing / standards
  • Mycobacterium avium Complex / classification*
  • Mycobacterium avium Complex / genetics
  • Mycobacterium avium subsp. paratuberculosis / classification
  • Mycobacterium avium subsp. paratuberculosis / genetics
  • Software

Substances

  • Genetic Markers