Table 1.

Synopsis of the reference-free sorting and assembly outcomes of consensus sequences for the three Mycobacterium spp. target genes (hsp65, rpoB, 16S rRNA) included in the culture-independent next-generation sequencing approach.

	hsp65	rpoB	16S rRNA
Mycobacterium tuberculosis complex (MTBC)	49	54	52
Non-tuberculous mycobacteria (NTM)	3	0	2
MTBC + NTM	4	1	0
Total	56	55a	54b

The mycobacterial DNA detection and composition of the mycobacteriome varied depending on the three independent targets. Notably, the shorter target PCR (hsp65) demonstrated the ability to identify the highest proportion of mycobacteria, with amplification and Mycobacterium spp. sequences detected in 93.3% of the samples tested (56/60). The rpoB PCR displayed the highest sensitivity for MTBC detection, identifying MTBC in 91.7% of all samples included (55/60).

^aOne sample could not be amplified using the rpoB target.

^bFor two samples (NB18154 and KS19028), the 16S rRNA consensus sequences were classified as organisms not belonging to the Mycobacterium genus. Further analysis using NCBI Basic Local Alignment Search Tool (BLAST) identified the presence of Niallia sp. in NB18154 and Streptomyces sp. in KS19028.