OneAMR: a rapid, accurate, point-of-care platform for the detection and prevention of antimicrobial resistance (AMR)

抗菌素耐药性（AMR）是对公众健康的严重威胁，欧盟每年有2.5万人死于5种最常见的耐药性感染。抗生素耐药性是一个全球性问题，抗生素的过度使用加速了这一问题，如果不加以控制，它将使我们没有任何有效的药物来治疗感染。肺炎克雷伯菌（Klebsiella pneumoniae）是一种经常对所有抗生素具有耐药性的细菌，是医院获得性感染（如败血症和肺炎）的主要原因。与同一物种的非耐药菌株相比，耐药感染与住院时间更长、治疗费用增加以及患者预后更差有关。抗生素耐药性的威胁如此严重，以至于2014年设立了经度奖（Longitude Prize），奖金为1000万英镑，旨在发明一种廉价、准确、快速的即时检测方法（POCT），以帮助减少抗生素的使用。该奖项目前无人认领。为了治疗感染，医生需要知道它是由什么微生物引起的，以及什么样的抗生素对它有效。抗微生物药敏试验的金标准包括培养或培养微生物，以找到能阻止其生长的最低抗生素浓度，即最低抑制浓度（MIC）。这一过程在大型医院实验室中通常是自动化的，但仍然需要两天到几周的时间才能完成。医生会开一种广谱抗生素，然后观察是否有效。这意味着患者可能接受无效或不必要地选择耐药性的治疗。如果治疗是有针对性和快速的，它可以提高早期治疗的有效性，从而获得更好的结果，减少住院时间，减少临床环境中的耐药性。基因组测序可以在更短的时间内提供这些信息。这是通过对构成微生物基因组的DNA进行测序，并通过将其与已知序列数据库中的DNA进行比较来识别物种来完成的。通过与已知耐药基因和突变的数据库进行比较，可以尝试预测药物敏感性，这对于某些物种（如结核分枝杆菌）是准确的。对于一些病原体，很难预测耐药性，因为它是由我们无法预测的复杂基因型赋予的。较新的测序平台，如纳米孔测序，可以实时运行，可以在几分钟内识别细菌种类。这样的平台可能会给临床微生物学带来革命性的变化，但对于某些物种来说，仅凭基因组预测抗菌素耐药性的能力非常有限。该项目旨在结合基因组和对抗生素暴露的转录反应，以显着提高快速测试预测抗生素敏感性的能力。这种方法是通过将细菌细胞包裹在微滴中，并使用感兴趣的抗生素。在短时间暴露后，对同一细胞的基因组和转录组进行测序，并将基因组和转录组中包含的信息结合起来进行易感性预测。该项目的总体目标是开发一种能够分析血液和其他临床样本并在快速时间框架内提供准确结果的仪器。这是适合21世纪临床微生物学的传统培养方法。https://ecdc.europa.eu/sites/portal/files/media/en/publications/Publications/0909_TER_The_Bacterial_Challenge_Time_to_React.pdf2。https://longitudeprize.org/challenge

Antimicrobial resistance (AMR) is a serious threat to public health with 25,000 people a year in the EU dying from the five most common drug-resistant infections [1]. AMR is a global problem that has been accelerated by the overuse of antibiotics, if not brought under control it will leave us without any effective drugs to treat infections. One bacterial species, Klebsiella pneumoniae is frequently resistant to all antibiotics and is a major cause of hospital-acquired infections such as sepsis and pneumonia. Resistant infections are associated with longer hospital stays, increased costs of treatment and worse outcomes for patients when compared with non-resistant strains of the same species. So serious is the threat of AMR that in 2014 the Longitude Prize was created, a £10M challenge to invent a cheap, accurate and fast point-of-care test (POCT) that will help reduce the use of antibiotics [2], a prize that is currently unclaimed.In order to treat an infection a doctor needs to know what organism it is caused by and what antibiotics will be effective against it. The gold standard antimicrobial susceptibility testing involves growing or culturing the organism to find the lowest concentration of antibiotic that will stop it growing, a value known as the minimum inhibitory concentration (MIC). This process is often automated in large hospital laboratories but can still take between two days and several weeks to complete. Doctors will prescribe a broad-spectrum antibiotic and wait to see if it is effective. This means patients may receive treatment which is ineffective or that unnecessarily selects for resistance. If treatment is targeted and fast it can improve the effectiveness of the early therapy leading to better outcomes, reduced hospital stays and less resistance in the clinical environment.Genomic sequencing can help provide this information in much shorter time. This is done by sequencing the DNA which makes up the genomes of microbes and identifying the species by comparing it to those in a database of known sequences. By comparing to a database of known resistance genes and mutations, an attempt to predict drug sensitivity can be made, this is accurate for certain species such like Mycobacterium tuberculosis. For some pathogens it is very hard to predict resistance as it is conferred by complex genotypes that we cannot predict. Newer sequencing platforms such nanopore sequencing can run in real-time and can identify bacterial species in a matter of minutes. Such platforms could revolutionise clinical microbiology but for certain species the ability to predict AMR from just the genome is very limited. This project seeks to combine the genome and the transcriptional response to antibiotic exposure to dramatically improve the ability of rapid testing to predict antibiotic susceptibly.The way this will be done is by encapsulating bacterial cells within microdroplets with the antibiotic of interest. After a short exposure time the genome and transcriptome of the same cell are sequenced and the information contained in the genome and transcriptome are combined to make a prediction of susceptibility. The overall aims of this project are to develop an instrument which can analyse blood and other clinical samples and provide accurate results in a rapid timeframe. This is traditional culture suitable for 21st century clinical microbiology.1. https://ecdc.europa.eu/sites/portal/files/media/en/publications/Publications/0909_TER_The_Bacterial_Challenge_Time_to_React.pdf2. https://longitudeprize.org/challenge