## 1 Introduction: Mycobacteria and the Host  
The _Mycobacterium_ genus includes a high diversity of species, with differential phenotypic and genotypic traits, as well as epidemiological relevance, including several important human and animal pathogens [1]. _Mycobacterium_ species can be included in three groups: (1) mycobacteria that cause tuberculosis (TB), (2) mycobacteria that cause leprosy, and (3) the non-tuberculous mycobacteria (NTM), a wider diverse group of species also referred in the literature as atypical or environmental mycobacteria [2]. Moreover, a differentiation according to host-pathogen relationships can be drawn, with pathogens capable to survive and replicate in the environment (free-living or facultative pathogens),while others cannot replicate outside the host (obligate or strict pathogens) [3]. _M. tuberculosis_ and _M. leprae_ are strict pathogens that together account for hundreds of thousands of new TB and leprae cases, respectively, and to a striking number of human deaths every year. Research interest is mainly focused on these two members, as well as on the animal-adapted TB ecotype, _M. bovis_, however, the number of reports of human and non-human infections caused by environmental or nosocomial NTM increased in the last decade, possibly resulting from global changes that impacted infection dynamics, better diagnostics, and/or increased awareness. The steady rise of the incidence of NTM infection has consolidated the attentiveness of academic and clinical communities, easing the identification of new cases and accelerating research in NTM-related topics [2]. NTM are opportunistic pathogens (i.e., microorganisms that can become pathogenic upon a perturbation of their host, such as a prior disease, co-infection, immunodeficiency, or aging) that can be found in natural and anthropogenic-related environments. The numbers of described NTM species have been increasing, posing challenges to their correct identification based on conventional methods that explore phenotypic traits and also the molecular approaches [4]. A wide variety of new methodologies have become available for the detection, identification, and differentiation of NTM species. These topics are reviewed further ahead. The recognition of NTM as opportunistic pathogens began in the 1950's with a number of patients suffering from underlying pulmonary disease being reported in the literature [5] Chronologically, three distinct phases could be drawn: in the pre-HIV era, the majority of patients with NTM pulmonary infection were men, whose risk factors included lung damage from other conditions (e.g., emphysema, cystic fibrosis, TB), smoking and occupational dust exposure [6], or World War II veterans with smoking and alcohol abuse habits; in a second stage, the infections became associated with patients with concomitant human immunodeficiency virus infection and loss of T-cells. Afterwards, reports describe taller, slender, and elderly women (and some men) as being more affected [7]. However, these bacteria only attracted more attention from the medical community when disseminated _Mycobacterium avium_ complex (MAC) was recognized as one of the major opportunistic bacterial infections affecting acquired-immunodeficient syndrome (AIDS) patients [7]. After this acknowledgment, pulmonary infection in immunocompetent patients by NTM also became a concern, namely in developed countries, wherein trends for NTM infection have increased as pulmonary TB decreases [7]. Nowadays, the number of infection cases due to NTM almost outweighs those of TB in developed countries where NTM infection has been growing due to population aging, immunodeficiency, comorbidity with chronic diseases, and immunosuppressive therapy [8]. Contrary to TB, reporting of NTM infection is not mandatory, narrowing the epidemiological understanding of disease burden, especially in developing countries, where the prevalence of pulmonary TB infection is still high and NTM infection is poorly documented.