Mechanisms of antimicrobial resistance in Helicobacter pylori

幽门螺杆菌是一种革兰氏阴性微需氧细菌，感染人类胃，导致消化性溃疡和胃癌。它是一种I类致癌细菌，是全球可预防癌症死亡的主要原因之一。由于抗生素耐药性的出现，幽门螺杆菌感染的治疗变得越来越困难，目前约有20%的一线治疗方法无法根除胃中的细菌。世界卫生组织最近将克拉霉素耐药幽门螺杆菌列为最优先考虑的抗生素耐药病原体之一，需要新的治疗方法。幽门螺杆菌是一种高度多态的细菌，具有很高的突变和重组率。世界各地的幽门螺杆菌基因组序列有很高的变异水平，甚至个别患者胃内的幽门螺杆菌基因类型也存在变异。幽门螺杆菌不是从受感染的患者身上常规培养出来进行抗生素敏感性测试的，因为它只能通过侵入性程序(内窥镜)恢复，而且它是一种生长缓慢、挑剔的微生物。有必要对目前流行的幽门螺杆菌菌株的抗生素敏感性谱进行更多的研究。将基因型与表型联系起来的研究将特别有益，因为它将使我们更好地了解幽门螺杆菌是如何对抗生素产生耐药性的。这些信息将来可能被用来帮助开发新的非侵入性诊断测试，为治疗和新的治疗提供信息。这个博士项目将包括以下部分或全部：-从人类临床病例中分离出的幽门螺杆菌的抗生素敏感性测试，并使用全基因组序列分析进行表型与基因的比较。-定向进化实验，在实验室中，我们将使幽门螺杆菌暴露于抗生素下，并分离出任何产生抗药性的菌落。然后，基因组序列和完整的比较基因组分析将确定已经形成的耐药性的机制。-使用基因组数据的分子模拟实验来预测抗生素耐药性的机制。-幽门螺杆菌分离株的纳米孔负离子测序，然后将这些数据与我们现有的Illumina MiSeq短读数据结合起来，产生高质量的、完整的杂交基因组组合。这些可以用来更详细地研究幽门螺杆菌的抗生素耐药基因，包括质粒分析。

Helicobacter pylori is a Gram negative, microaerophilic bacterium that infects the human stomach and causes peptic ulcers and gastric cancer. It is a bacterial class I carcinogen and is one of the leading causes of preventable cancer deaths worldwide. Treatment of H. pylori infection is becoming increasingly difficult due to the emergence of antibiotic resistance, and about 20% of first line H. pylori treatments now fail to eradicate the bacteria from the stomach. The World Health Organisation recently named clarithromycin resistant H. pylori as one of the highest priority antibiotic resistant pathogens for which new treatments are needed.H. pylori is a highly polymorphic bacterium, with high mutation and recombination rates. There are high levels of variation in H. pylori genome sequences across the world and even variation in H. pylori genotypes within individual patients' stomachs. H. pylori is not routinely cultured from infected patients for antibiotic susceptibility testing because it can only be recovered via an invasive procedure (endoscopy) and it is a slow-growing, fastidious organism. There is a need for more research into the antibiotic susceptibility profiles of currently circulating H. pylori strains. Research linking genotype to phenotype would be particularly beneficial because it would allow us to better understand how H. pylori becomes antibiotic resistant. This information could be used in the future to help develop new non-invasive diagnostic tests to inform treatment, and new treatments.This PhD project would include some or all of the following:- Antibiotic susceptibility testing of H. pylori isolates from human clinical cases and comparison of phenotype to genotype using whole genome sequence analysis.- Directed evolution experiments in which we would expose H. pylori to antibiotics in the lab and isolate any colonies that became resistant. Genome sequence and complete comparative genomics analyses would then determine the mechanisms of the resistance that has developed.- Molecular modelling experiments using genomic data to predict mechanisms of antibiotic resistance.- Nanopore MinION sequencing of H. pylori isolates then combination of this data with our existing Illumina MiSeq short read data to produce high quality, complete hybrid genome assemblies. These could then be used to study the antibiotic resistance genes of H. pylori in more detail, including plasmid analysis.