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.

Background Injecting drug use (IDU) is a key driver of the HIV epidemic particularly when individuals experience psychosocial conditions and risky sexual behavior in a syndemic manner. This study sets out to assess evidence of a syndemic pattern of psychosocial conditions (IDU, depression, intimate partner violence (IPV)) on one the hand and risky sexual behavior on the other while accounting for the socio-economic disadvantage among women who inject drugs (WWID) in low-income urban settings in Kenya. Methods Using a cross-sectional study design, this study recruited 306 WWIDs from two sites in Nairobi between January 2017 and July 2017. Multiple methodologies including descriptive analyses of co-occurrences of psychosocial conditions at the individual level, standard logistic regression analyses to examine relationships and interactions within and between psychosocial conditions and risky sexual behavior, and classification trees algorithm for predictive modeling via machine learning were employed. Results The prevalence of the psychosocial conditions was as follows: IDU, 88%; depression, 77.1%; and IPV, 84%. The prevalence of risky sexual behavior was 69.3%. IDU and depression were related to each other ( P < 0.05) and each of them with risky sexual behavior ( P < 0.05). The highest 2-way and 3-way co-occurrence of conditions were reported in IDU and depression (72%) and in IDU, depression, and risky sexual behavior (62%), respectively, indicating clustering of the conditions at the individual level. Further, each additional psychosocial condition (IDU and depression) was associated with sixfold odds ( P = 0.000) of having risky sexual behavior suggesting a dose-response relationship. Logistic regression analyses incorporating multiplicative interactive effects returned three significant variables ( P < 0.05): IDU*depression interaction effect, “Age when delivered the first child,” and “Income.” Classification tree modeling represented a 5-level interaction analysis with IDU and depression predicted to have the highest influence on risky sexual behavior. Conclusion Findings provide possible evidence of a syndemic pattern involving IDU, depression, and risky sexual behavior suggesting the need for an integrated approach to the implementation of harm reduction interventions among WWID in low-income urban settings in Kenya. This work highlights the need for further studies to authenticate the findings and to characterize pathways in the syndemic development in WWID.

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