Sequencing Pathogens Directly from Sputum: Promise, Progress, and Challenges | GenomeWeb
October 06, 2016
Sponsored by
Agilent Technologies

Sequencing Pathogens Directly from Sputum: Promise, Progress, and Challenges


Co-director of the Division of Infection and Immunity at University College London; Clinical Lead for Virology,
Great Ormond Street Hospital for Children

This webinar discussed recent advances toward sequencing pathogens directly from sputum via novel enrichment methods.

Antimicrobial resistance in pathogens such as Mycobacterium tuberculosis has risen over the last decade, driving interest in methods to more rapidly and accurately detect resistance. Whole-genome sequencing of M. tuberculosis samples would allow simultaneous identification of all known resistance mutations as well as markers for monitoring transmission, but this process currently takes weeks because it requires prior bacterial enrichment by culturing.

During the webinar, Judith Breuer of University College London discussed an effort to enable rapid whole-genome sequencing of hard-to-culture pathogens directly from sputum using a new enrichment technology. The UCL team compared direct WGS of M. tuberculosis for determining resistance with standard phenotypic culture methods well as rapid molecular tests and the recently developed mycobacterial growth indicator tube (MGIT) enriched sequencing method.

Data from the study shows that, using enriched methods, the time to drug resistance profile is between 24 and 96 hours depending on the extent of sequencing and the method used. The results also indicate that direct sequencing is both sensitive and specific for M. tuberculosis first- and second-line drug resistance and that whole-genome sequencing provides sufficient genetic data to identify transmission clusters. Furthermore, direct sequencing from sputum provides more information on population diversity than sequencing of MGIT enriched cultures.

For Research Use Only. Not for use in diagnostic procedures. 

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