Mechanisms of antimicrobial resistance in Helicobacter pylori

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.