DNA analysis of bacteria taken from sick patients has been shown to be 96% accurate for the diagnosis of tuberculosis (TB) and related diseases, and 99% accurate for predicting resistance to the most common antibiotics used for TB treatment, when compared to existing laboratory tests.

Tuberculosis is more common in the UK than most people realise. On top of that, there are many related organisms in the same family, (known as non-tuberculous mycobacteria) which also cause disease, but which require different drugs to treat them. These related organisms are increasingly being found in sick patients and therefore being able to differentiate between them is becoming more and more important.
Whole Genome Sequencing (WGS) is a relatively new technology which attempts to produce a map of the entire genetic code that makes up an organism. Comparing the DNA code sequence generated from an (initially unknown) organism found in a particular patient to a library of known ‘reference’ sequences, we can identify the exact species based purely on its DNA code. Similarly, we can predict whether the organism is likely to be resistant to certain drugs by looking at specific sections of its genetic code that have previously been shown to be associated with resistance.

Researchers here at MMM and Public Health England tested the new DNA-based technology for a year at the National Mycobacterial Reference Service in Birmingham, (which serves dozens of NHS hospitals across the Midlands and North of England) in order to see how WGS fared compared to existing laboratory methods in a real-life, large-scale environment. We found that although there is still some more work to be done to increase the proportion of samples that yield enough DNA for analysis, when WGS predictions were made, they were very accurate.

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The original paper can be found at:  http://jcm.asm.org/content/56/2/e01480-17.full

Author: T. Phuong Quan, Statistician and First Author

This work was supported by the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), the NIHR Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Oxford University, in partnership with Public Health England (PHE) and by the Department of Health and the Wellcome Trust, through the Health Innovation Challenge (HIC) Fund.