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Despite the poor genomics research capacity in Africa, efforts have been made to empower African scientists to get involved in genomics research, particularly that involving African populations. As part of the Human Heredity and Health in Africa (H3Africa) Consortium, an initiative was set to make genomics research in Africa an African endeavor and was developed through funding from the United States' National Institutes of Health Common Fund and the Wellcome Trust. H3Africa is intended to encourage a contemporary research approach by African investigators and to stimulate the study of genomic and environmental determinants of common diseases. The goal of these endeavors is to improve the health of African populations. To build capacity for bioinformatics and genomics research, organizations such as the African Society for Bioinformatics and Computational Biology have been established. In this article, we discuss the current status of the bioinformatics infrastructure in Africa as well as the training challenges and opportunities. Key words: Africa, bioinformatics, genomics, Uganda. En dépit de la faible capacité en matière de recherche en génomique en Afrique, des efforts visant à habiliter les scientifiques africains à s'impliquer en recherche génomique, particulièrement celle visant des populations africaines, ont été faits. Le consortium 'Human Heredity and Health in Africa (H3Africa)' est une initiative visant à faire de la recherche génomique en Afrique un travail véritablement africain et il a été mis sur pied grâce à un financement conjoint du United States' National Institutes of Health Common Fund et du Wellcome Trust. H3Africa cherche à encourager l'emploi d'une approche contemporaine en recherche par des chercheurs africains et de stimuler l'étude des déterminants génomiques et environnementaux de maladies communes. Le but de ces efforts est d'améliorer la santé des populations africaines. Pour augmenter la capacité de recherche en matière de bioinformatique et de génomique, des organisations comme l'African Society for Bioinformatics and Computational Biology (Société africaine de bioinformatique et de biologie computationnelle) ont été mises sur pied. Dans cet article, les auteurs présentent l'état actuel de l'infrastructure bioinformatique en Afrique de même que les défis et opportunités en matière de formation. [Traduit par la Rédaction] Mots-clés: Afrique, bioinformatique, génomique, Uganda., Introduction Genomic technologies are developing at an unprecedented rate and continue to improve the potential to diagnose, treat, and elucidate the underpinnings of disease and health (Mulder et al. 2016). [...]

Background: Between January 2015 and July 2017, we investigated the frequency of carbapenem resistant Acinetobacter baumannii (CRAB) and carbapenem resistant Pseudomonas aeruginosa (CRPA) at the Mulago Hospital intensive care unit (ICU) in Kampala, Uganda. Carbapenemase production and carbapenemase gene carriage among CRAB and CRPA were determined; mobility potential of carbapenemase genes via horizontal gene transfer processes was also studied.Methods: Clinical specimens from 9269 patients were processed for isolation of CRAB and CRPA. Drug susceptibility testing was performed with the disk diffusion method. Carriage of carbapenemase genes and class 1 integrons was determined by PCR. Conjugation experiments that involved blaVIM positive CRAB/CRPA (donors) and sodium azide resistant Escherichia coli J53 (recipient) were performed.Results: The 9269 specimens processed yielded 1077 and 488 isolates of Acinetobacter baumannii and Pseudomonas aeruginosa, respectively. Of these, 2.7% (29/1077) and 7.4% (36/488) were confirmed to be CRAB and CRPA respectively, but 46 were available for analysis (21 CRAB and 25 CRPA). Majority of specimens yielding CRAB and CRPA were from the ICU (78%) while 20 and 2% were from the ENT (Ear Nose & Throat) Department and the Burns Unit, respectively. Carbapenemase assays performed with the MHT assay showed that 40 and 33% of CRPA and CRAB isolates respectively, were carbapenemase producers. Also, 72 and 48% of CRPA and CRAB isolates respectively, were metallo-beta-lactamase producers. All the carbapenemase producing isolates were multidrug resistant but susceptible to colistin. blaVIM was the most prevalent carbapenemase gene, and it was detected in all CRAB and CRPA isolates while blaOXA-23 and blaOXA-24 were detected in 29 and 24% of CRAB isolates, respectively. Co-carriage of blaOXA-23 and blaOXA-24 occurred in 14% of CRAB isolates. Moreover, 63% of the study isolates carried class 1 integrons; of these 31% successfully transferred blaVIM to E. coli J53.Conclusions: CRAB and CRPA prevalence at the Mulago Hospital ICU is relatively low but carbapenemase genes especially blaVIM and blaOXA-23 are prevalent among them. This requires strengthening of infection control practices to curb selection and transmission of these strains in the hospital. [ABSTRACT FROM AUTHOR]