What is it about?
The traditional method for testing for TB (tuberculosis) is expensive and slow (could be 2 months). Most of that time is spent growing the bacteria that gives the disease. In our paper, we show that you can get the DNA of the bacteria directly from a patient's sputum, and then decode the DNA, check if it is TB and spot drug resistance, all within 48 hours. The key step is getting the DNA, and our method for this is cheap, and doesn't require a special lab. We also show the DNA analysis can be done on a handheld "USB-stick" DNA sequencing machine, opening up the possibility of doing this in the field.
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Why is it important?
There were over 10 million cases of TB in 2015 - it kills more than any other single infectious organism. New strains of the bug are spreading which cannot be killed by standard drugs ("drug resistance"). There's a huge need to be able to cheaply and rapidly test for TB and spot drug resistance, in a way that could be done across the world, not just in well-equipped labs.
Perspectives
This is a proof of concept paper, but the implications are significant. There is a tremendous desire across the world to apply molecular testing to TB, to access more patients, and to better manage the growth of drug resistance. Whole genome sequencing has the benefit of allowing sharing of bacterial DNA information, to allow global surveillance of spread of strains and resistance. By showing this can be done with both mature (Illumina) and new, portable (Nanopore) technology, we make a big step towards removing technical barriers for this. Considerable technical work still needs to be done, to improve the handling of contamination (from other bugs living in patients mouths/airways), stabilising the new nanopore tech, etc. Beyond that, there are always the bigger challenges of how to integrate into public health. However it is worth noting that Public Health England announced this year (2017) that they now sequence all TB cases by default (in addition to the traditional pipeline). It's hard to predict how this will all fall out, but there is a real chance this could significantly change TB management across the world.
Zamin Iqbal
University of Oxford
Read the Original
This page is a summary of: Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples, Journal of Clinical Microbiology, March 2017, ASM Journals,
DOI: 10.1128/jcm.02483-16.
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