Standard operating procedure for optimal identification of mycobacteria using 16S rRNA gene sequences

Genetic sequencing is increasingly used for the identification of bacteria and for many of them, including mycobacteria, the analysis of the 16S rRNA gene represents the gold standard. Sequencing technology has greatly improved in recent years and now allows one to obtain good quality electropherograms also in non specialized settings. The interpretation of the electropherograms still lacks however precise rules and the achievement of an incorrect identification from an excellent sequence is very frequent, in particular for organism like mycobacteria which are very closely related to each other at the genetic level. Without claiming to be authoritative or comprehensive, this note aims to provide a few simple directions suitable to steer the choice of the best possible identification.