Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis across different settings
Culturing and genomic sequencing of Mycobacterium tuberculosis (MTB) from tuberculosis (TB) cases is the basis for many research and clinical applications. The alternative, culture-free sequencing from diagnostic samples, is promising but poses challenges to obtain and analyse the MTB genome. Paradoxically, culture is assumed to impose a diversity bottleneck, which, if true, would entail unexplored consequences. To unravel this paradox we generate high-quality genomes of sputum-culture pairs from two different settings after developing a workflow for sequencing from sputum and a tailored bioinformatics analysis. Careful downstream comparisons reveal sources of sputum-culture incongruences due to false positive/negative variation associated with factors like low input MTB DNA or variable genomic depths. After accounting for these factors, 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). The combined analysis from five different settings and more than 100 available samples shows that our results can be extrapolated to different TB epidemic scenarios, demonstrating that for the cases tested culture accurately mirrors clinical samples.
Authors
- Belén Saavedra (ORCID: https://orcid.org/0000-0002-4057-0214)
- Manuela Torres‐Puente (ORCID: https://orcid.org/0000-0002-8352-180X)
- Zaza Avaliani (ORCID: https://orcid.org/0000-0002-8790-3282)
- Mariana G. López (ORCID: https://orcid.org/0000-0002-2216-9232)
- Sergo A. Vashakidze (ORCID: https://orcid.org/0000-0001-5907-4870)
- Edson Mambuque (ORCID: https://orcid.org/0000-0002-9106-1444)
- Alex Rosenthal (ORCID: https://orcid.org/0000-0003-4190-9045)
- Natalia Shubladze (ORCID: https://orcid.org/0000-0003-0580-9629)
- Carla Mariner-Llicer (ORCID: https://orcid.org/0000-0002-8230-5785)
- Iza Khurtsilava
- Luis M. Villamayor
- Marika Shurgaia
- Alberto L. García‐Basteiro (ORCID: https://orcid.org/0000-0002-2038-5505)
- Galo Adrián Goig (ORCID: https://orcid.org/0000-0002-4136-6610)
- Iñaki Comas (ORCID: https://orcid.org/0000-0001-5504-9408)
- Andrei Gabrielian (ORCID: https://orcid.org/0000-0002-8392-924X)
Institutions
- Swiss Tropical and Public Health Institute (CH)
- University of Basel (CH)
- Wellcome Sanger Institute (GB)
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (ES)
- Centro de Investigación Biomédica en Red (ES)
- Manhiça Health Research Centre (MZ)
- National Center for Tuberculosis and Lung Disease (GE)
- University of Georgia (GE)
- National Institute of Allergy and Infectious Diseases (US)
- Barcelona Institute for Global Health (ES)
- Instituto de Biomedicina de Valencia (ES)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (ES)
- Universitat de Barcelona (ES)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-09-05
- DOI
- https://doi.org/10.1038/s41467-024-51266-0
- Citations
- 16
- Primary Topic
- Mycobacterium research and diagnosis
- Type
- article
- Field-Weighted Citation Impact
- 6.19
Funders
- Horizon 2020 Framework Programme