10.2217/FMB.09.75 © 2009 Future Medicine ISSN 1746-0913 Future Microbiol. (2009) 4(8), 1009–1020 part of Future Microbiology 1009 Review Nontuberculous mycobacteria The term nontuberculous mycobacteria (NTM) refers to a diverse collection of opportunistic mycobacteria that differ in habitat, growth requirements and metabolic capabilities [1] . Some also infect and cause disease in mam- mals (including humans), birds and fish [2] . Classically, this group has been defined by exclusion; indeed, in this review we will use NTM to refer to members of the genus that are not obligate host-associated pathogens, such as Mycobacterium tuberculosis and Mycobacterium leprae. The NTM have previously been called atypical mycobacteria but this moniker is inap- propriate on a number of grounds. Statistically, host-associated pathogens are atypical among the genus, forming a small minority of recognized species. In addition, the observation that patho- genic members of the genus evolve through a process that includes genomic deletions (termed reductive genomics) may also be atypical [3] . As such, we will use the term NTM to refer to a mix of two conceptual sets of organisms: environ- mental bacteria that are normal inhabitants of soils, natural waters and drinking-water distribu- tion systems; and host-associated pathogens that may occasionally cause spill-over infections in humans, such as the poultry, animal and human pathogen Mycobacterium avium subsp. avium and the agent of Johne’s disease, Mycobacterium avium subsp. paratuberculosis [4] . The environmental NTM are normal inhabit- ants of soils, natural waters, and potable water from drinking-water distribution systems [1] and household plumbing [5] . As these NTM are oligotrophic, they grow in these ecosystems [6] . Because of the high cell-surface hydrophobicity of NTM [7] , numbers are high on particulates, surfaces of pipes (biofilms) and at air–water inter- faces (surface slimes) [8,9] . As a consequence of their ubiquitous distribution, humans and other mammals are commonly surrounded by such NTM. Recent evidence has shown that NTM isolates from approximately 50% of households of NTM patients belong to the same species and share the same DNA fingerprint as the patient isolate [Falkinham JO III, Unpublished Data] . The host-associated pathogenic NTM are prob- ably encountered less frequently and/or in fewer numbers than the environmental NTM; despite this, pathogenic NTM represent a disproportion- ate subject of concern, because of their proven Molecular epidemiology of nontuberculous mycobacteria Marcel A Behr † & Joseph O Falkinham III † Author for correspondence: Division of Infectious Diseases & Medical Microbiology, McGill University, A5.156, Montreal General Hospital, 1650 Cedar Avenue, Montreal H3G 1A4, Canada n Tel.: +1 514 934 1934 ext. 42815 n Fax: +1 514 934 8423 n marcel.behr@mcgill.ca 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. Keywords molecular epidemiology n mycobacteria n typing For reprint orders, please contact: reprints@futuremedicine.com