The use of next generation sequencing to measure the effects of antibiotics on resistance in the host microbiota

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Antimicrobial resistance is increasing worldwide, causing more serious and difficult to treat infections, and is of sufficient severity that the Chief Medical Officer has tabled it to be added to the national risk register. We face a future where infections become untreatable and previously routine procedures such as hip replacements and chemotherapy become too high risk to perform. Resistance is increasing both in the bacteria causing serious infection, but also in the 'good' bacteria in our gut which form part of our 'microbiome' - the community of microorganisms which share our body and are essential for daily function. The gut microbiome forms a reservoir of resistance genes which can be transmitted between different species of bacteria - including disease-causing strains, and cause them to become resistant too. It has been shown that resistance in the gut bacteria is associated with an increased likelihood of developing a resistant infection. Resistant bacteria can be acquired- from food sources (where there is high antibiotic use in farmed meat and aquaculture) from countries of high resistance prevalence (predominantly low-resource countries), and from healthcare institutions. By using antibiotics to treat infection, we are selecting for resistant organisms and increasing antimicrobial resistance.It has been shown that antibiotic use correlates with resistance on a population level, and based on this it is thought that by reducing overall antibiotic use we can reduce resistance. However reduction in antibiotic use has to be achieved safely and without putting patients at undue risk from undertreated infection, and there is not yet robust evidence that a reduction in antibiotic use in this way can provide a reduction in resistance.The long term aim of the project is to develop antibiotic treatment strategies able to reduce the development of resistance. To do this, we need to be able to measure and compare how much a particular antibiotic increases resistance. We also need to be able to understand what other factors lead to resistance. The bacteria colonising the gut are present in large numbers in faecal samples. Due to rapid advances in DNA sequencing technology we are able to measure resistance genes these bacteria by extracting bacterial DNA from faecal samples, and sequencing it in days, rather than months. I propose to pioneer and develop this Next-Generation Sequencing (NGS) technology to detect antibiotic resistance genes in faecal samples (measuring the gut ' resistome'). It has already been used to detect resistance in samples from the Human Microbiome Project, and the pattern of resistance was shown to follow country-wide antibiotic use. I will use it to assess the factors which lead to increased resistance in the gut bacteria, to try and find out where this resistance is being acquired from (food, travel, healthcare institutions). I will also use it to study the association between prior antibiotic use and resistance, including mode of delivery - there is evidence in mouse models that giving antibiotics orally may increase resistance in the gut compared to giving the same dose intravenously. I will then look at the dynamic effect of antibiotics by recruiting patients who will receive antibiotic therapy and analysing multiple faecal samples to see whether resistance returns to prior levels or is maintained. In this project I aim to identify which antibiotic strategies cause the least selection for antimicrobial resistance in the gut. This information will be used by clinicians to choose antibiotic strategies to take to clinical trials to show a reduction in resistance without risking undertreating infection, and to help decide which antibiotics to use to minimise the risk of future resistant infection to patients.