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

即使在发达国家，细菌感染也是一个日益严重的问题。在过去的60年里，抗生素被用于治疗细菌感染，取得了很大的成功。如果我们能在生命周期的早期发现疾病的存在，治疗疾病就会容易得多，也便宜得多。检测细菌性疾病需要专门的系统，如诊断仪器和诊断试剂盒。随着新的细菌菌株的出现，科学家需要开发新的试剂盒来检测这些新的病原体，这一过程非常耗时。EPSRC i-sense IRC是一个多学科合作项目，旨在加快传染病诊断的时间，并正在开发一系列针对细菌和病毒的新型诊断技术。IRC目前正在寻求“下一步”核心资金，通过创建一个“i-sense2”IRC来延长IRC的生命周期，最终目标是成为一个可持续的卓越中心。最近，抗生素的有效性已经开始下降，由于细菌菌株的出现，这些菌株对常用的，甚至所有的抗生素都有抗药性。为了有效地治疗由耐药细菌引起的疾病，仅仅诊断细菌种类是不够的。同样有必要知道致病细菌是否对通常开给病人治疗疾病的抗生素有耐药性。“下一步”项目“u-Sense”与isense2 Core IRC合作，并依赖于该提案所描述的结果，旨在以i-sense IRC的成功为基础，开发一种新型诊断系统，不仅可以检测患者样本是否含有特定类型的有害细菌，还可以快速确定细菌对哪种抗生素具有耐药性。检测细菌的抗生素耐药性是很复杂的，因为细菌可以通过多种方式改变其生理机能来产生耐药性。在u-Sense Plus项目中，我们将利用细菌抗生素耐药性编码在生物体基因组中的某些基因或基因修饰中的事实。我们将修改一种新的生物信息学系统，该系统已被开发为i-sense IRC的一部分，称为IDRIS，以便能够通过搜索基因组序列来查明编码抗生素抗性性状的细菌的遗传特征。该系统还将产生必要的序列，以生产新的诊断技术，在未来发现这些细菌，而不需要进行DNA测序。这种新的诊断技术将基于一种被称为重组酶聚合酶扩增（RPA）的技术，这种技术能够特异性地扩增和检测DNA序列，以确定生物体是否对特定抗生素具有耐药性。测试的形式将是纸或塑料条的形式，很像怀孕测试，测试样本应用。为了确保该系统足够敏感，能够检测到少量的耐药生物，我们将研究一种检测DNA的新方法，该方法使用一种称为表面增强拉曼散射（SERS）的方法来指示耐药。SERS具有以多路复用格式快速同时检测负责赋予抗性的许多潜在DNA序列的潜力。虽然SERS通常需要昂贵的实验室设备进行测试格式，但我们将研究和开发一种小型化，具有成本效益的设备，最终使SERS检测系统能够在医院，全科医生手术甚至家庭的实验室之外使用。总的来说，该项目将产生一个快速、成本效益高的系统，可用于各种环境，并最终有望对发达国家和发展中国家的人类健康和疾病管理产生重大影响。

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.