Advanced Test Detects Drug Resistant TB

The Translational Genomics Research Institute (TGen), an affiliate of City of Hope, and Advanced Biological Laboratories (ABL) have recently announced plans to roll out an advanced test for tuberculosis (TB), DeepChek®-TB.

Caused by the bacteria Mycobacterium tuberculosis, TB is one of the top 10 causes of death worldwide, accounting for 1.6 million deaths in 2017, 95% of which were in developing countries. Anti-TB drugs are available, but their success relies on the accurate and timely detection of the disease and strict adherence to the drug schedule. Inappropriate use of anti-TB drugs is contributing to the development of drug resistance strains, a problem which needs to be addressed if the Sustainable Development Goal to end the TB epidemic by 2030 is to be achieved. Tools that enable faster and more accurate detection of drug resistance will be pivotal in ensuring patients are treated with the right drugs at the right time.

To learn more about the development of the DeepChek®-TB test and how it works to detect  resistance to TB drugs, we spoke to Dr. David Engelthaler, Associate Professor and Co-Director, Pathogen and Microbiome Division, TGen.

Anna MacDonald (AM): What inspired the development of the advanced TB test? Were there any particular motivators that got the project started?

David Engelthaler (DE): We had been developing a number of advanced technologies to understand how pathogens evolve in their environments and how they change between health and disease. Through discussions with a collaborator at UCSD, we realized that there was a problem with being able to accurately and quickly detect antibiotic resistance in TB, since:

- The TB bacteria takes so long to grow in the lab, so the current tests could take several weeks, and
- The TB bacteria lives as a "mixed population" in the lungs, that is, there are multiple independent populations of TB growing in the lung and some of these will become resistant before others, which causes confusion with other existing tests.

AM:  Could you give us an overview of how the test works?

DE: Our approach is to use highly multiplexed targeted sequencing to look at all known markers of resistance for all important TB drugs all at the same time. The method is essentially a combination of:

- PCR, a basic molecular tool to amplify up small pieces of targeted DNA region, and 
- DNA sequencing, in which we sequence the amplified targets to scan for the presence of important mutations.

We designed primers — short fragments of DNA to prime the amplification process in our regions of interest — for dozens of know gene regions that are involved in TB drug resistance. PCR and DNA sequencing had to be engineered to work together so we can amplify up all the targets at the same time and have a built in "barcode," which is essentially a short index sequence that is attached to each piece of amplified DNA. We do this so we can tell them apart during the sequencing process. The amplified DNA material can then be put into a DNA sequencer, and batched with dozens of samples.

The resulting sequence data is then automatically analyzed with a custom software package to provide a clinician-friendly report about the drug susceptibility of their patient's infection so they can best prescribe the right drugs.

AM: What makes the DeepChek®-TB test stand out from other TB tests?

DE: The DeepChek®-TB assay is one of only two tests that will be commercially available that takes this targeted sequencing approach for determining drug resistance. The technology behind the test was developed at TGen and has been published in a least 10 separate studies, with multiple collaborators in the U.S. and globally.

AM:  What have been the biggest challenges in developing the test?

DE: The biggest challenge has been in translating this advanced technology towards a cost-effective, easy-to-use tool that can be employed in different labs arounds the world. Our goal has been to shrink the number of steps needed, automate as much as possible and work with the various sequencing platforms that are on the market.  Our partnership with Advanced Biological Laboratories (ABL) is making this final step possible.

AM:  Are there any plans to develop similar tests for other infectious diseases?

DE: We already have at least a dozen different versions of this technology to tackle other critical pathogens and diseases.

We have a similar test that targets antibiotic resistance for the important healthcare acquired infections, such as MRSA, Klebsiella, CRE, and others. We have versions used for biothreat detection; versions for environmental testing of air and water; and multiple versions for important vector-borne disease pathogens; for example, mosquito viruses, such as West Nile Virus, and tick pathogens such as Lyme bacteria.

These are all currently for research use only, although we hope to find additional biotech partners to help get these assays ready for clinical use in the future.

David Engelthaler was speaking to Anna MacDonald, Science Writer for Technology Networks.