Helicobacter pylori (H.pylori) infection is etiologically associated with severe diseases including gastric cancer; but its pathogenicity is deeply shaped by the exceptional genomic diversification and geographic variation of the species. The clinical relevance of strains colonizing Africa is still debated. This study aimed to explore genomic features and virulence potentials of H. pylori KE21, a typical African strain isolated from a native Kenyan patient diagnosed with a gastric cancer. A high-quality circular genome assembly of 1,648,327 bp (1590 genes) obtained as a hybrid of Illumina Miseq short reads and Oxford Nanopore MinION long reads, clustered within hpAfrica1 population. This genome revealed a virulome and a mobilome encoding more than hundred features potentiating a successful colonization, persistent infection, and enhanced disease pathogenesis. Furthermore, through an experimental infection of gastric epithelial cell lines, strain KE21 showed the ability to promote interleukin-8 production and to induce cellular alterations resulting from the injection of a functional CagA oncogene protein into the cells. This study shows that strain KE21 is potentially virulent and can trigger oncogenic pathways in gastric epithelial cells. Expended genomic and clinical explorations are required to evaluate the epidemiological importance of H. pylori infection and its putative complications in the study population.

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Aim: This study sought to evaluate Pronto dry rapid urease® diagnostic test and compare its performance with culture. Study Design: Cross-sectional study. Place and Duration: From September 2017 to July 2018, across-sectional study was conducted at the Aga Khan University Hospital. Methodology: Patients attending endoscopy unit at the hospital were randomly sampled to provide gastric biopsy specimen. One specimen was tested for presence or absence of H. pylori using Pronto dry rapid urease® test and another specimen subjected to in vitro culture test which were then compared with histology reference results. Test validity and reliability was determined using Graph Pad Prism v5.01. Results: Of 274 study specimens, 121(44%) were positive for histology. Ninety-one (33%) of the study specimen were positive for culture compared to 147(54%) for Pronto dry rapid urease®. Pronto dry rapid urease® test had sensitivity of 100% (97.5%-100%) against 73.6% (64.8%-81.3%) for culture. Specificity was 96.1% (91.1%-98.7%) for Pronto dry rapid urease® compared to 35.3% (95% CI 24.1%-47.8%) for culture. Positive predictive value was 96.7% (92.5-98.9%) for Pronto dry rapid urease® compared to 97.8% (92.3%-99.7%) for culture. Negative predictive value was 100% (97%-100%) for Pronto dry rapid urease® against 82.5% (76.2%-87.7%) for culture. There was significant difference between both Pronto dry rapid urease® and culture test performance with histology in all validity measures, P< 0.001. On the other hand, there was no significant difference between Pronto dry rapid urease® and culture in all validity measures due to overlapping confidence intervals. Conclusion: Pronto dry rapid urease® out-performed culture in sensitivity and NPV. It would be the method of choice in H. pylori detection where histology is untenable and antimicrobial profiling which require culturing the bacterium is needless.