Tackling and tracking TB through DNA analysis
Find out how a multidisciplinary team of scientists came to create England's new way to identify how to fight and track TB outbreaks using DNA analysis.
Interviewees in order of appearance:
- Dr Nicola Fawcett: Clinical Research Fellow and a Doctor in Acute and General Medicine; Nicola studies antibiotic prescribing and the effects on antimicrobial resistance in the gut bacteria.
- Dr Jessica Hedge: Population Geneticist; Jessica studies how DNA analysis can be used to understand how bacteria evolve and develop drug resistance.
- Dr Timothy Walker: Academic Clinical Lecturer and Doctor in Microbiology/Infectious Diseases; Timothy studies how DNA analysis can be used to predict drug resistance, understand transmission of infections, and inform patient care.
- Professor Derrick Crook: Research Group Lead and Direct of the National Infection Service at Public Health England; Derrick has led the group in pioneering the use of DNA analysis from laboratory to patient care.
- Dr Dilrini de Silva: Bioinformatician; Dilrini designs and performs complex, large scale computational analyses of bacterial DNA to provide information on drug resistance and transmission of infections.
Dr Nicola Fawcett: So let's say the patient comes in with pneumonia, obviously we'll hear the patient's experience and see what's been going on, listen to their chest and do a chest X ray, and that will tell us that maybe there's a severe infection in the lungs, but it won't tell us what the cause of it is. So we'll know from previous experience that it's maybe one of a number of five or six suspects. And we'll treat the patient with antibiotics that would cover most of those suspects. But what we'll also do is do a blood test and we'll have the bacteria in the blood tests we can grow in a lab, and that will tell us which antibiotics are going to work. Now the research group uses an entirely new technique where they break open the bacteria and extract the DNA.
Dr Jessica Hedge: Tuberculosis in particular, is a slow growing bacterium. So it can take up to six weeks to grow each one individually to see whether it is resistant to any of those drugs and the benefit of performing whole genome sequencing is that you have your sequence very quickly within a matter of days and from that, you can work out which antibiotics it would be resistant to.
Dr Timothy Walker: So in the old world, you are doing a dozen different tests, each of which costs money. In the New World, you sequence the genome of the bacterium and from that, you derive all the information you need to answer all of the questions you want to ask. What species is it? Which other TB samples is it related to? Which drugs is it resistant to? And which will kill it? And it's just one test, and it costs about the same amount of money as one of the many other tests we currently use.
Prof Derrick Crook: It is extraordinary that this is immediately available, and even just 10 years ago, it might have taken me months, even years to get the complete picture.
Dr Dilrini De Silva: If we have DNA sequencing data available, once the sequencing run is done, we can process it through our bioinformatics workflows and be able to provide you all that information in a matter of hours.
Dr Jessica Hedge: In recent study, we achieved very high accuracy and also precision in predicting whether a particular TB sample is going to be resistant to a particular drug or not.
Prof Derrick Crook: Now we have past that comparative study, and we demonstrating the performance that we needed to have. Therefore, the decision was made to commit Public Health England to implementing it.
Dr Timothy Walker: Science is day after day of fairly menial grinding work, collecting data, cleaning it, making sense of it. Then every now and again, you get an extraordinary high when you look at the results and you see something new and you realise you're the first person in the world who's ever seen this.
Read more about the study (as well as the original paper) on the Modernising Medical Microbiology website.