Dr Zamin Iqbal studies the DNA of bacteria and parasites, and compares the genomes of individual pathogens to track the spread of antibiotic resistance. Pathogens accumulate small genetic changes over time, and by tracking these changes, it is possible to map the spread of an infection. This enables better surveillance of pathogen evolution, within a host, within a hospital and across the world.
Resistance to drugs in bacteria can be aquired by swapping genes between individual bacteria. Computer programs developed by Dr Iqbal enable doctors to predict which antibiotics will be met with drug resistance, enabling the selection of the right drug. His work also enables the tracking of an infection from patient to patient, as well as the tracking of the spread of an infection within a hospital.
Ultimately, medical research must translate into improved treatments for patients. At the Nuffield Department of Medicine, our researchers collaborate to develop better health care, improved quality of life, and enhanced preventative measures for all patients. Our findings in the laboratory are translated into changes in clinical practice, from bench to bedside.
Q: Can you tell us a bit about your research interests?
Zamin Iqbal: I work in computation and genetics. Every living organism inherits DNA in all of their cells from their parents, and in the process of inheriting it they do not get quite an exact copy, they get a few changes and we call these mutations. This sounds a little scary but it is just the raw material for evolution. My interests are in bacteria and parasites, organisms that essentially give you diseases. I study the nature of their DNA, and write what are essentially computer programs to compare the DNA of different organisms.
Q: What is the link between computation and genetics?
ZI: Maybe the right way to think about this is that DNA is a molecule: it is a long molecule made of an alphabet of just four smaller molecules which we call A, C, G and T for short. You can think of DNA as a long word. If I am interested in, say, how DNA affects properties of bacteria, how they resist drugs, or why you may be taller than I am, then what we want to do is compare those DNA 'words' with each other. That is the kind of thing you want to use a computer for. It makes those jobs much easier.
Q: Can you give us an example of an application for the sort of methods you use?
ZI: We have spent a lot of the last year looking at DNA of samples taken from people who are ill in the local hospital. What you can do, by looking at the DNA of viruses or bacteria, is determine the structure of the molecule and something about the properties. Bacteria can often be given the property of drug resistance by acquiring a gene from somebody else (another bacteria): they don’t just inherit genes from their parents but they swap DNA with their friends. You can look for the genes they have acquired and, if they are there, you can predict this bug is going to be drug resistant, so you shouldn’t use this drug.
Q: What are the most important lines of research that have developed in the last 5-10 years?
ZI: I think both the technology and the computer science of genetics have changed radically in the last ten years. The biggest change is improvements in the technology called genome sequencing, which basically means all the mechanics of being able to work out what the sequence of DNA 'word' is. We can now go and look at the genome of hundreds or thousands of humans, or tens of thousands of bacteria, and that means that we are now interested in a very detailed level of the differences between organisms, and how small changes even within one species can change the abilities of an organism.
Q: Why does this line of research matter and why should we fund it?
ZI: One of the things we hear a lot about in the news at the moment is the problem of the rise of antibiotic resistance. It is a confusing phrase: what it means is that bacteria on which drugs don’t work are becoming more and more common. There is a whole host of bacteria causing a huge number of different diseases that are now spreading and on which no drug works. At a very practical level, my methods are used and being tested in hospitals to be able to spot that at the point of treatment.
Q: How does your work fit into translational medicine within the department?
ZI: I work very closely with doctors, microbiologists, and infectious disease experts at the John Radcliffe Hospital. A lot of what I do focuses around trying to develop computer programs that not only will enable doctor to tell whether or not a drug is going to work for a patient, but also give an answer that they can interpret. You don’t need to be a computer genius to work them, you can actually practically use them in the NHS.