A community-driven genomic investigation of Helicobacter pylori isolates from Indigenous communities in the Arctic of Canada.

• Main Author: Yarmie, Jeremiah
• Other Authors: Knox, Natalie (Medical Microbiology and Infectious Diseases) Graham, Morag (Medical Microbiology and Infectious Diseases), McClarty, Grant (Medical Microbiology and Infectious Diseases), Larcombe, Linda (Medical Microbiology and Infectious Diseases), Sparling, Richard (Microbiology)
• Format: Master Thesis
• Language: unknown
• Published: 2022
• Subjects: Helicobacter pylori; Bacterial genomics; Community-driven research; Aklavik; Arctic; Canada; Fort McPherson; Inuvik; Teslin
• Online Access: http://hdl.handle.net/1993/36166

Helicobacter pylori is a Gram-negative, flagellate, microaerophilic member of the Epsilonproteobacteria, with a spiral or curved bacilli morphology (Marshall and Warren 1984). The bacterium resides in the human stomach, and infections can span decades, often going undetected due to minor pathogenesis (Kusters et al. 2006). Infections frequency is higher in the Global South, and is associated with low socioeconomic status, education, remoteness, and inaccessibility to healthcare (Hooi et al. 2017; Bruce and Maaroos 2008). This infection is a public health concern because H. pylori infection increases the risk of adenocarcinoma of the gastric mucosa and gastric B-cell mucosal-associated lymphoid tissue (MALT) lymphoma, as well as peptic ulcer disease (Haley and Gaddy 2015). Indigenous communities in Canada experience increased rates of H. pylori infection, which is associated with poverty, crowded living conditions, and inaccessible health care. Infection is a concern for Indigenous communities given the bacterium's implication in the development of associated cancers, which is a severe health burden that too disproportionately affects Indigenous peoples. This project builds upon ongoing community-driven research by the Canadian North H. pylori (CANHelp) Working Group investigating the impact of H. pylori infection. In this research project we present the sequence H. pylori genomes of 57 CANHelp isolates sampled from the Western Canadian Arctic communities of Aklavik, Inuvik, Old Crow, Ross River, Teslin, and Fort McPherson and a comparator cohort of 73 southern Manitoban isolates. I developed and implemented a contamination detection pipeline to ensure only H. pylori sequence reads were used in genome assembly. The genomes were analyzed for their presence of: known markers associated with antimicrobial resistance to clarithromycin, metronidazole, levofloxacin, and amoxicillin; virulence factors like cagA, the cagPI, vacA, outer membrane proteins such as babA, and the Type I toxin-antitoxin system aapA1/isoA1; and ...