Mycobacterium avium in the postgenomic era

Abstract

The past several years have witnessed an upsurge of genomic data pertaining to the Mycobacterium avium complex (MAC). Despite clear advances, problems with the detection of MAC persist, spanning the tests that can be used, samples required for their validation, and the use of appropriate nomenclature. Additionally, the amount of genomic variability documented to date greatly outstrips the functional understanding of epidemiologically different subsets of the organism. In this review, we discuss how postgenomic insights into the MAC have helped to clarify the relationships between MAC organisms, highlighting the distinction between environmental and pathogenic subsets of M. avium. We discuss the availability of various genetic targets for accurate classification of organisms and how these results provide a framework for future studies of MAC variability. The results of postgenomic M. avium study provide optimism that a functional understanding of these organisms will soon emerge, with genomically defined subsets that are epidemiologically distinct and possess different survival mechanisms for their various niches. Although the status quo has largely been to study different M. avium subsets in isolation, it is expected that attention to the similarities and differences between M. avium organisms will provide greater insight into their fundamental differences, including their propensity to cause disease.

FIG. 1.

hsp65 gene phylogeny based on nucleotide differences (277), superimposed with genetic variation based on LSPs (239). IS901⁺ strains cluster in one lineage, and all lack LSP^A17. IS900⁺ strains cluster in a lineage identified by codes 5 and 6, and all lack LSP^A8. M. intracellulare serves as the outgroup for the M. avium subspecies. M. avium subsp. silvaticum presents with an identical genetic profile to that of code 4. Bar, 5 nucleotides.