NGS-based approach for diagnostically unidentified Mycobacterium saskatchewanense, a rare non-tuberculous mycobacterium

Introduction: The implementation of advanced technologies and algorithms for diagnosis and genome analysis has made a fundamental contribution to pathogens’ identification and investigation. Methods: The study of non-tuberculous mycobacteria (NTM) benefited from a next-generation sequencing (NGS) approach, making it possible to describe sequences of rare pathogens. This study identified 20 diagnostically unknown isolates as Mycobacterium saskatchewanense ST 691, an environmental NTM. The isolates were sequenced on two different platforms to compare their throughput and to investigate shared and unique single nucleotide polymorphism (SNP) counts, phylogeny based on concatenated 16S, hsp65, and rpoB genes, and core-genome multilocus sequence typing (MLST), in order to broaden the current knowledge of Mycobacterium saskatchewanense. Results: Principal component analysis on the three genes combined with the mutations’ annotation suggests that rpoB may serve as a suitable marker to distinguish M. saskatchewanense from other NTM. Discussion: Our results show that frontier studies performed using NGS can help in overcoming the limits of traditional diagnostic assays and deepen the knowledge on rare and uncommon NTM that are raising clinical concern.