Genotyping of Mycobacterium Avium Complex Organisms Using Multispacer Sequence Typing

Microbiology. 2010 Mar;156(Pt 3):687-94. doi: 10.1099/mic.0.033522-0. Epub 2009 Nov 19.

Abstract

Mycobacterium avium complex (MAC) currently comprises eight species of environmental and animal-associated, slowly-growing mycobacteria: Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium chimaera, Mycobacterium colombiense, Mycobacterium arosiense , Mycobacterium bouchedurhonense, Mycobacterium marseillense and Mycobacterium timonense. In humans, MAC organisms are responsible for opportunistic infections whose unique epidemiology remains poorly understood, in part due to the lack of a genotyping method applicable to all eight MAC species. In this study we developed multispacer sequence typing (MST), a sequencing-based method, for the genotyping of MAC organisms. An alignment of the genome sequence of M. avium subsp. hominissuis strain 104 and M. avium subsp. paratuberculosis strain K-10 revealed 621 intergenic spacers <1000 bp. From these, 16 spacers were selected that ranged from 300 to 800 bp and contained a number of variable bases, <50 within each of the 16 spacers. Four spacers were successfully PCR-amplified and sequenced in 11 reference strains. Combining the sequence of these four spacers in 106 MAC organisms, including 83 M. avium, 11 M. intracellulare , six M. chimaera, two M. colombiense and one each of M. arosiense, M. bouchedurhonense, M. marseillense and M. timonense, yielded a total of 45 spacer types, with an index of discrimination of 0.94. Each spacer type was specific for a species and certain spacer types were specific for subspecies of M. avium. MST is a new method for genotyping of organisms belonging to any one of the eight MAC species tested in this study.

MeSH terms

  • Bacterial Typing Techniques / methods*
  • DNA Primers
  • DNA, Bacterial / genetics
  • DNA, Ribosomal Spacer / genetics
  • Genotype
  • Molecular Sequence Data
  • Mycobacterium avium Complex / classification*
  • Mycobacterium avium Complex / genetics
  • Phylogeny
  • Polymerase Chain Reaction
  • Polymorphism, Restriction Fragment Length
  • Sequence Analysis, DNA

Substances

  • DNA Primers
  • DNA, Bacterial
  • DNA, Ribosomal Spacer

Associated data

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