Understanding mechanisms of antimicrobial resistance (AMR) in Streptococcus pneumoniae clinical isolates

肺炎链球菌，也称为肺炎，会引起侵袭性疾病，如肺炎和脑膜炎，每年导致数百万人死亡。为了在医院和诊所预防和治疗肺炎感染，患者被给予青霉素抗生素或非常类似的药物。这些药物可以杀死在患者体内生长的细菌，对抗感染，治愈个体。越来越多的青霉素耐药菌株正在世界各地出现，威胁着我们的治疗策略，并危及患者的预后。因此，迫切需要解决肺炎的青霉素耐药问题，以防止患者死亡。该项目将确定和表征耐药性的生物学基础，旨在找到使菌株对我们临床上常规使用的抗生素重新敏感的方法。要解决并最终预防肺炎中的青霉素耐药性，我们需要首先了解耐药性是如何发生的。这一理解对于结束一种非常熟悉的模式至关重要：一种新药发现导致耐药细菌，从而导致对更多药物的搜索。肺炎中的青霉素耐药性不是一步到位的，而是随着细菌一次一个地获得基因改变而逐渐出现。使用从患者身上分离的肺炎菌株，我们发现了一种正在产生抗生素耐药性的菌株，因此包含有限数量的基因变化。这种菌株是英国医院对肺炎青霉素耐药的典型模式，已经对这种药物表现出“低水平”抗药性。重要的是，同一类型的菌株是全球肺炎感染的罪魁祸首。因此，我们在这项研究中发现的细胞过程将普遍适用于世界各地的细菌谱系(相关菌株家族)。在初步工作中，我们已经通过基因组测序确定了这种菌株中的一些基因变化，但我们不知道这些变化中的哪些是支持青霉素耐药性的重要因素。我们的假设是，这些基因变化中的一个或多个导致了这种菌株对青霉素的低水平耐药性，这些变化是向肺炎杆菌对青霉素的高水平耐药性迈出的重要一步。为了验证我们的假设，我们将实施三种并行的鉴定方法，它们都是由下一代DNA测序提供支持的：一种全基因组图谱方法(TN-Seq)和两种相关的全基因组测序方法。这些方法将确定这些菌株抵抗青霉素治疗的重要因素，一旦确定，我们将开展进一步的工作，以了解这些新因素是如何发挥作用的。重要的是，我们的初步工作已经确定了一个新的耐药决定因素，我们将进行实验，以了解其在肺气肿细胞中的功能。我们的主要目标是使对青霉素具有低水平耐药性的临床分离株对青霉素治疗重新敏感，我们将在模拟临床患者治疗的模型感染系统中测试我们对耐药性的新理解。这项研究将帮助我们应对抗生素耐药感染的全球威胁，方法是找到确保药物在给患有致命肺炎链球菌疾病的患者时正常工作的方法。

The bacterium Streptococcus pneumoniae, also called pneumo, causes invasive diseases such as: pneumonia and meningitis, which lead to millions of deaths every year. To prevent and treat pneumo infections in hospitals and clinics, patients are given penicillin antibiotics, or drugs very similar to them. These drugs kill the bacteria growing inside the patient, combating the infection and curing the individual. Increasingly, strains resistant to penicillin are emerging across the world threatening our treatment strategies and jeopardising patient outcomes. Therefore, there is an urgent need to address penicillin resistance in pneumo to prevent patient deaths. This project will identify and characterise the biological underpinnings of resistance and aims to find way of re-sensitising strains to antibiotics we routinely use in clinics.To address, and ultimately prevent, penicillin resistance in pneumo we need to understand how resistance occurs in the first place. This understanding is vital to end an all too familiar pattern of: a new drug discovery leading to resistant bacteria, resulting in a search for yet more drugs.Penicillin resistance in pneumo does not occur in a single step, but emerges gradually as the bacterium acquires genetic alterations one at a time. Using pneumo strains isolated from patients, we have discovered a strain that is emerging on its journey towards antibiotic resistance and therefore contains a limited number of genetic changes. This strain is typical of the pattern of pneumo penicillin resistance in hospitals in the UK and already shows 'low-level' resistance to this drug. Importantly, strains of the same type are responsible for pneumo infections across the globe. Therefore cellular processes we discover in this study will be generally applicable to worldwide bacterial lineages (families of related strains). In preliminary work, we have already identified some of the genetic changes in this stain by genome sequencing, but we do not know which of these changes are important for underpinning the penicillin resistance. Our hypothesis is that one, or more, of these genetic changes is responsible for the 'low-level' resistance in this strain and these changes are an important step towards 'high-level' penicillin resistance in pneumo strains.To test our hypothesis, we will carry out three parallel identification methods all powered by next-generation DNA sequencing: a whole genome profiling method (Tn-Seq) and two related whole-genome sequencing methods. These methods will identify the factors that are important for the strains to resist penicillin treatment and, once identified, we will carry out further work to understand how these new factors function. Importantly, our preliminary work has already identified a new resistance determinant and we will carry out experiments to understand its function in the pneumo cell. Our primary aim is to re-sensitise the 'low-level' penicillin resistant clinical isolate to penicillin treatment and we will test our new understanding of resistance in a model infection system, which mimics treatment of patients in clinic. This research will help us tackle the global threat of antibiotic resistant infections, by finding ways to make sure drugs work properly when given to patients with deadly S. pneumoniae diseases.