Molecular epidemiology of nontuberculous mycobacteria.

The emergence of nontuberculous mycobacteria (NTM) as important environmental pathogens has stimulated the search for molecular markers to identify NTM sources, determine virulence mechanisms and describe their population structure. The availability of genome sequence data for a number of NTM isolates has permitted a more definitive approach to classification of these organisms based on sequence analysis of polymorphic targets, such as 16S rRNA, hsp65 and the internal transcribed spacer. An alternative approach, based on assessment of conserved inserted and deleted elements, also permits robust branding of clinical and laboratory isolates. Complementary to 'top-down' approaches that classify organisms at the species, subspecies and strain level, 'bottom-up' methods to determine the genetic similarity of pairs or groups of isolates have also been developed and used. Analysis of large restriction fragments by pulsed-field gel electrophoresis, restriction fragment length polymorphisms of insertion sequences, repetitive genetic elements, arbitrary primed PCR fragments and multilocus sequencing have largely supplanted phenotypic methods for strain comparison, such as serotyping, biotyping and multilocus enzyme electrophoresis. Together, these two sets of tools can provide an enhanced portrait of the NTM and be useful in epidemiologic investigations of the geographic and ecologic provenance of NTM infections. With further study, it is anticipated that the application of these genetic tools to well-defined collections of organisms will not only lead to an improved understanding of the source of NTM infection, but also help identify clinically relevant bacterial subtypes and eventually uncover genetic markers of bacterial virulence.