IRC Next Steps Plus: Ultra-Sensitive Enhanced NanoSensing of Anti-Microbial Resistance (u-Sense).

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Bacterial infection is an increasing problem, even in the developed world. Over the past 60 years antibiotics have been used to treat bacterial infections with good success. Treating a disease is much easier, and cheaper, if we can detect its presence early in the lifecycle. Detecting a bacterial disease requires specialist systems such as diagnostic instrumentation and diagnostic kits. As new strains of bacteria emerge scientists need to develop new kits to detect these new pathogens, a process which is very time consuming. The EPSRC i-sense IRC is a multidisciplinary collaboration that aims to speed up the time it takes to diagnose infectious disease and is developing a range of novel diagnostic technology for both bacteria and viruses. The IRC is currently seeking "Next Steps" Core funding to extend the lifetime of the IRC by creating an "i-sense2" IRC with the ultimate aim of becoming a sustainable Centre of Excellence.Recently, the effectiveness of antibiotics has begun to decline due the emergence of bacterial strains that are resistant to the commonly used, or even all, antibiotics. In order to effectively treat diseases caused by antibiotic resistant bacteria it is not enough to simply diagnose the identity of the bacterial species. It is also necessary to know whether the causative bacteria are resistant to the antibiotics that would usually be prescribed to the patient to treat the disease. Allied with the i sense2 Core IRC, and dependent upon the outcomes described in that proposal, this "Next Steps" Plus project, "u-Sense", aims to build on the success of the i-sense IRC, to develop a new type of diagnostic system that will not only detect whether a patient sample contains a particular type of harmful bacterium but will also determine rapidly which antibiotics the bacterium is resistant to. Detecting antibiotic resistance in bacteria is complicated as there are many ways in which the bacteria can modify its physiology to become resistant. In the u-Sense Plus project we will capitalise on the fact that bacterial antibiotic resistance is encoded in certain genes, or gene modifications, in the organism's genome. We will modify a novel bioinformatics system that has been developed as part of the i-sense IRC, termed IDRIS, so that is able to pinpoint the genetic features in bacteria that encode the antibiotic resistance traits, by searching through genomic sequences. The system will also generate the sequences necessary for the production of new diagnostic technologies to find these bacteria in future, without the need to carry out DNA sequencing. This new diagnostic technology will be based on a technique known as recombinase polymerase amplification (RPA) which is able to specifically amplify and detect the DNA sequences necessary to establish whether the organism is resistant to a given antibiotic. The format of the test will be in the form of a paper or plastic strip, much like a pregnancy test, to which the test sample is applied. To ensure that the system is sensitive enough to detect low numbers of resistant organisms we will investigate a novel method of detecting DNA that indicates resistance using a method called Surface-Enhanced Raman Scattering (SERS). SERS has the potential to detect rapidly and simultaneously, in a multiplexed format, a number of potential DNA sequences which are responsible for conferring resistance. While SERS normally requires expensive laboratory equipment for the test format, we will research and develop a miniaturised, cost-effective device that will ultimately allow the SERS detection system to be used outside of the laboratory in the hospital, GP surgery or even in the home. Overall, the project will result in a rapid, cost effective system that can be used in a variety of settings and ultimately promises to have a major impact on human health and disease management in developed and developing countries alike.