Genomic_Diversity_MTBC

Whole Genome Sequencing (WGS) of diagnostic samples from patients with tuberculosis still represents a challenge due to the complexity and heterogeneity of this type of samples (high contamination level and low amount of Mycobacterium tuberculosis complex (MTBC) DNA). As of today, clinical samples are cultured in solid/liquid media for diagnosis and research purposes to amplify the amount of MTBC at expense of the delay in the obtention of results, due to the slow growth rate of M. tuberculosis. In addition, it is not clear if the overall population diversity of diagnostic samples is represented in culture. Different research groups tried to sequence directly from clinical samples, focusing mainly in drug-resistance prediction and lineage identification for a rapid and complete diagnosis. However, the sequencing depth/coverage they obtained was not enough to perform comparative genomics. Thus, there is still no evidence if the diversity of sequences from culture is comparable from that coming from clinical samples. In addition, this problem is likely inherited by the lack of standardised pipelines and control of false genetic variation for culture-free WGS data analysis. The main aims of this study are: i) to recover the genome of MTBC from leftovers of diagnostic samples from two different (high and upper-moderate burden-TB) settings, Mozambique and Georgia; ii) to design a specific pipeline for diagnostic samples analysis; and (iii) to compare the genetic variability between sputum-culture paired samples.