The genus Mycobacteria comprises over 190 different species with a division of classification of species into either typical or atypical mycobacteria or tuberculous and non-tuberculous mycobacteria. Typical mycobacteria describes the Mycobacterium tuberculosis complex which is a well-known cause of human infection. The atypicals include many other well-known species such as Mycobacterium leprae, Mycobacterium ulcerans and the rapidly growing mycobacteria such as the Mycobacterium abscessus complex, Mycobacterium chelonae, and the Mycobacterium fortuitum complex to name a few. Mycobacterial infections in humans is not restricted to a specific body part with the possibility of infection sites endless. Many of the atypical species are naturally present within the environment.
Identification of a specific isolate can be challenging due to the extensive number of different species, as is the determination of clinical significance of species that are predominantly environmental. Rapid accurate diagnosis from human samples is necessary to determine clinical relevance, with culture from primary material remaining as the gold standard. Isolate identification still involves the use of a combination of traditional methods based on cultivation on specialist media, with consideration of morphological characteristics such as growth rates, preferred growth temperature, pigmentation together with smear morphology, through to ICT assays and genomic sequencing. Molecular diagnosis from primary samples remains limited for many species with continued reliance on isolation. The slow growing nature of many mycobacteria leads to protracted results. A rise in the incidence of clinically relevant atypical mycobacterial infections may cause an advancement of technology in this area.
With such a diverse number of species, a breakdown of identification methods that are currently available to determine species identification will be discussed with some tips and traps for scientists new to mycobacteriology.