Mechanisms of antimicrobial resistance in Helicobacter pylori

幽门螺杆菌是一种革兰氏阴性、微需氧菌，感染人类胃并引起消化性溃疡和胃癌。它是一种细菌I类致癌物，是全球可预防癌症死亡的主要原因之一。H.由于抗生素耐药性的出现，pylori感染变得越来越困难，约20%的一线H.幽门螺杆菌的治疗现在不能根除胃中的细菌。世界卫生组织最近将耐克拉霉素的H。幽门螺杆菌作为最优先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性的细菌，具有高突变率和重组率。在H. pylori基因组序列，甚至H.幽门螺杆菌基因型在个别患者的胃。H.幽门螺旋杆菌不是常规地从感染患者中培养出来用于抗生素敏感性测试，因为它只能通过侵入性操作（内窥镜检查）来恢复，并且它是一种生长缓慢、挑剔的生物体。有必要对目前流行的H. pylori菌株。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H。pylori变得对抗生素有抗药性。这些信息可以在未来用于帮助开发新的非侵入性诊断测试，为治疗提供信息，以及新的治疗方法。从人类临床病例中分离的幽门螺杆菌，并使用全基因组序列分析比较表型与基因型。定向进化实验中，我们将暴露H。在实验室里用抗生素感染幽门螺杆菌，并隔离任何产生耐药性的菌落。然后，基因组序列和完整的比较基因组学分析将确定已经发展的抗性机制。使用基因组数据的分子建模实验来预测抗生素耐药性的机制。H. pylori分离物，然后将该数据与我们现有的Illumina MiSeq短读段数据组合以产生高质量的完整杂交基因组组装。这些结果可用于研究H. pylori，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.