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

Lead Research Organisation: Newcastle University
Department Name: Institute of Cellular Medicine

Abstract

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.

Planned Impact

Antimicrobial resistance (AMR) occurs naturally due to genetic changes occurring in bacteria and is one of the world's greatest threats to healthcare. Millions of patients continue suffering following redundant or ineffective antibiotic treatment, hospitals are strained from longer-term stays or care, while billions of pounds are lost on an international scale due to antibiotics over- or mal-administration.

AMR is poorly identified, requiring labour- and time-intensive lab-based protocols. There are currently very few accurate technologies capable of rapidly identifying AMR bacterial strains. u-Sense introduces disruptive and innovative multiplexed systems designed for AMR detection. We will use a powerful computing system from Newcastle, called "IDRIS", to rapidly identity AMR strains from sequence data, create a integrated database of genetic information on antimicrobial resistant bacteria and rapidly design the DNA sequences necessary to develop rapid, non-sequencing based tests. By introducing a new, world-renowned research group at Strathclyde into the i-sense2 IRC, we will design and develop a multiplexed detection technology based on Raman scattering that will identify multiple, distinct biomarkers in one reading. This will be evaluated as a handheld device. u-Sense has enormous potential impact for academia and industry.

Academic Impact:
i) Current genetic profiling of AMR in bacteria is mostly based on cumbersome protocols (e.g. PCR/Sequencing). IDRIS presents a powerful computing and Cloud-based approach to identifying AMR genetic sequences from sequence data and designing the DNA necessary for rapid, non sequenced based, point of need sensors exploiting recombinase amplification technology.
ii) Raman spectroscopy is an exciting detection modality that hasn't been explored for its utility in bacterial screening against AMR, thus it is a disruptive technology. The research will be first-in-field and will elucidate potential avenues of translatable options for UK plc.
iii) This is a platform that can be re-engineered for other targets, supporting our potential for parallel and follow-on funding. This project greatly supports our goal of ensuring sustainability and creating a National Centre of Excellence.
iv) The career development of PDRAs is of high quality as they will be introduced to an extremely vibrant and multidisciplinary environment within the Core IRC. This will introduce new modalities (i.e. Raman spectroscopy and SERS analyses) within the consortium and maximize their potential for exploitation in detecting infectious diseases and AMR.

Industrial Impact:
The TLR level of the technologies proposed conform with the EPSRC remit. The activities in WP1 and outputs from the other WPs will shape potential Impact. Outcomes will be disseminated to interested industrial parties, such as those involved in the Core IRC investigate the AMR IP/patent landscape and market potential. Team members at Newcastle have already commissioned some limited market analysis in the bacterial diagnostics area and have discussed planning for a spin-out company. Strathclyde will use their experience in protecting IP (16 patents filed) and exploitation through licensing (> £150,000 in royalties accrued). Stevens has substantial experience in translation with 15 filed patents and is strongly supported by Imperial Innovations.

UK and Global Healthcare Impact:
The UK NHS is targeting high quality care with a focus on enhanced patient safety. We therefore foresee interest in rapid diagnosis and screening against AMR increasing. The information generated from u-Sense can impact healthcare research and organization on an international scale. Forecasting potential changes in antibiotic administration requires intensive feedback from healthcare leaders available within the Core IRC, and could result in significant and positive revisions of drug allocation, healthcare budgets, hospital costs and patient welfare.

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