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Sequencing Quickly Identifies Resistant TB

Whole-genome sequencing offers a means of rapid characterization of multidrug-resistant tuberculosis to guide clinical decision-making, according to authors of a case report.

Investigators obtained DNA from a sputum sample that became culture-positive after 3 days in a mycobacterial growth indicator tube. Whole genome sequencing identified two distantly related Beijing strains of Mycobacterium tuberculosis.

Standard genotyping did not identify mixed infection on three additional samples from the same patient.

"These findings have important implications for distinguishing relapse from reinfection and for identifying secondary cases of infection," Sharon J. Peacock, PhD, of the University of Cambridge in England, and co-authors stated in correspondence to the New England Journal of Medicine.

Researchers analyzed genes with known resistance to 39 different antibiotics. Results from a reference laboratory showed phenotypic resistance to nine drugs. Susceptibility was demonstrated for amikacin, capreomycin, clofazimine, and linezolid, findings consistent with genotyping, the authors said.

Genomic sequencing also revealed mutations consistent with resistance to several agents not tested by the reference laboratory: amithiozone, gatifloxacin, levofloxacin, rifapentine, and rifabutin.

Susceptibility to para-aminosalicylic acid was indicated, consistent with the majority strain. However, the minority strain harbored a mutation involved in the activation of the drug, with unknown consequences.

"This retrospective study revealed the potential of rapid whole-genome sequencing to reduce the time taken to diagnose [multidrug resistant] tuberculosis from weeks to days, depending on the time to culture positivity and the turnaround time for sequencing and analysis," the authors concluded. "In well-resourced countries, rapid whole-genome sequencing may replace current methods of identifying and typing M. tuberculosis complex, since it offers the ultimate molecular resolution for outbreak investigations."

Whole-genome sequencing cannot replace phenotypic susceptibility for all antibiotics, they added, but can be used for rapid identification of resistance when mutations associated with resistance are detected.


Peacock S "Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis" N Engl J Med 2013; DOI: 10.1056/NEJMc1215305.

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