Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis

Mariner-Llicer, C.; Goig, G. A.; Torres-Puente, M.; Vashakidze, S.; Villamayor, L.; Saavedra-Cervera, B.; Mambuque, E.; Khurtsilava, I.; Avaliani, Z.; Rosenthal, A.; Gabrielian, A.; Shurgaia, M.; Shubladze, N.; Garcia-Basteiro, A. L.; Lopez, M.; Comas, I.

doi:10.1101/2024.01.30.577772

bioRxiv · 10.1101/2024.01.30.577772

Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis

Mariner-Llicer, C.·Goig, G. A.·Torres-Puente, M.·Vashakidze, S.·Villamayor, L.·Saavedra-Cervera, B.·Mambuque, E.·Khurtsilava, I.·Avaliani, Z.·Rosenthal, A.·Gabrielian, A.·Shurgaia, M.·Shubladze, N.·Garcia-Basteiro, A. L.·Lopez, M.·Comas, I.

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Abstract

Culturing Mycobacterium tuberculosis (MTB) from tuberculosis cases is the basis for many research and clinical applications. Paradoxically, it is assumed to impose a diversity bottleneck, which, if true, would entail unexplored consequences. The alternative, culture-free sequencing from diagnostic samples, is a promising but challenging approach both to obtain and analyse the MTB genome from the complex sample. This study obtains high-quality genomes of sputum-culture pairs from two different settings after developing a workflow for sequencing from sputum and a tailored bioinformatics pipeline. Our approach reveals that 88% of variants called in culture-free sequencing analysis are false positives due to supplementary alignments, mostly in enriched-sputa samples. Overall, contrary to the bottleneck dogma, we identify a 97% variant agreement within sputum-culture pairs, with a high correlation also in the variants frequency (0.98). Our findings extrapolate to all publicly available data, thus demonstrating that in most cases culture accurately mirrors clinical samples.

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Mariner-Llicer, C., Goig, G. A., Torres-Puente, M., Vashakidze, S., Villamayor, L., Saavedra-Cervera, B., Mambuque, E., Khurtsilava, I., Avaliani, Z., Rosenthal, A., Gabrielian, A., Shurgaia, M., Shubladze, N., Garcia-Basteiro, A. L., Lopez, M., Comas, I.. 2024-01-31. Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis. https://doi.org/10.1101/2024.01.30.577772

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