Enhancing genomics and bioinformatics access in Africa: an imperative leap
Authors: Dickson Aruhomukama, Ronald Galiwango, Conor J Meehan, Benon Asiimwe
Journal: The Lancet Microbe (2024)

Despite the immense potential of genomics and bioinformatics in revolutionising public health in low-income countries (LICs) in Africa, their complete integration faces multiple obstacles. Among these obstacles, the scarcity of expertise, as underscored by Harris Onywera and colleagues, is notable.1Onywera H Ondoa P Nfii F et al.Boosting pathogen genomics and bioinformatics workforce in Africa.Lancet Infect Dis. 2023; (published online Sept 28)https://doi.org/10.1016/S1473-3099(23)00394-8PubMed Google Scholar Despite commendable efforts by institutions such as the Africa Centres for Disease Control and Prevention to offer genomics and bioinformatics training, especially for public health practitioners,1Onywera H Ondoa P Nfii F et al.Boosting pathogen genomics and bioinformatics workforce in Africa.Lancet Infect Dis. 2023; (published online Sept 28)https://doi.org/10.1016/S1473-3099(23)00394-8PubMed Google Scholar scarcity of expertise remains a great barrier to the integration of genomics and bioinformatics into public health systems.1Onywera H Ondoa P Nfii F et al.Boosting pathogen genomics and bioinformatics workforce in Africa.Lancet Infect Dis. 2023; (published online Sept 28)https://doi.org/10.1016/S1473-3099(23)00394-8PubMed Google Scholar Likewise, the profound yet tacit complexity inherent in the fields of genomics and bioinformatics further complicates their integration into public health systems. This inherent complexity undermines the development of a competent genomics and bioinformatics workforce in LICs in Africa.2Huang H Jörgensen C Stvilia B Genomics data curation roles, skills and perception of data quality.Libr Inf Sci Res. 2015; 37: 10-20Crossref Scopus (5) Google Scholar Addressing the inherent complexity of the fields of genomics and bioinformatics requires a decisive shift towards user-centred solutions—specifically, tools capable of navigating and overcoming the complexities of these fields.2Huang H Jörgensen C Stvilia B Genomics data curation roles, skills and perception of data quality.Libr Inf Sci Res. 2015; 37: 10-20Crossref Scopus (5) Google Scholar Simplifying these intricate domains through intuitive interfaces will empower non-technical experts, even without extensive prior training in genomics and bioinformatics, to meaningfully contribute to pathogen surveillance and to better inform public health.3Black A MacCannell DR Sibley TR Bedford T Ten recommendations for supporting open pathogen genomic analysis in public health.Nat Med. 2020; 26: 832-841Crossref PubMed Scopus (47) Google Scholar,4Pronyk PM de Alwis R Rockett R et al.Advancing pathogen genomics in resource-limited settings.Cell Genomics. 2023; 3100443Summary Full Text Full Text PDF PubMed Scopus (0) Google Scholar Prioritising user-centredness, accessibility, and adaptability tailored for LICs in Africa is pivotal to overcome the barriers posed by the scarcity of expertise and the complex nature of the genomics and bioinformatics domains. Envisioning a future in which genomics and bioinformatics tools become universally user-centred, accessible, and adaptable transcends the interface limitations to encompass proficient data analysis, interpretation, and reporting. This future envisions browser-based or non-browser-based interfaces that demand minimal technical proficiency, eventually revolutionising data analysis, interpretation, and reporting. Although these interfaces serve as essential tools, their true power lies in enabling non-technical experts not only to navigate the interfaces but also to analyse, interpret, and report from genomic data using bioinformatics tools. This comprehensive approach fosters a more inclusive and participative environment in pathogen surveillance to inform public health.4Pronyk PM de Alwis R Rockett R et al.Advancing pathogen genomics in resource-limited settings.Cell Genomics. 2023; 3100443Summary Full Text Full Text PDF PubMed Scopus (0) Google Scholar Further, this approach acknowledges that proficiency in data analysis, interpretation, and reporting is as crucial as user-centred, accessible, and adaptable interfaces for harnessing the full potential of genomics and bioinformatics in public health. Exploring the immense potential of genomics and bioinformatics to revolutionise public health in LICs in Africa requires the acknowledgment of the enduring health challenges that transcend sporadic events. These persistent concerns shape the landscape of public health, consistently impacting health-care systems, regardless of geographical boundaries or developmental stages. Such considerations extend beyond immediate crises toward more sustained threats that silently shape health frameworks. For instance, antimicrobial resistance (AMR) is a formidable and sustained public health threat that demands urgent attention.5Antimicrobial Resistance CollaboratorsGlobal burden of bacterial antimicrobial resistance in 2019: a systematic analysis.Lancet. 2022; 399: 629-655Summary Full Text Full Text PDF PubMed Scopus (3739) Google Scholar Unlike some infectious diseases, such as SARS-CoV-2, which might surge and wane,6Qasmieh SA Robertson MM Teasdale CA et al.The prevalence of SARS-CoV-2 infection and other public health outcomes during the BA.2/BA.2.12.1 surge, New York City, April–May 2022.Commun Med (Lond). 2023; 3: 92Crossref PubMed Google Scholar AMR poses an ongoing threat. The increase in AMR erodes the effectiveness of antibiotics, compromising the management of common infections.7Haney EF Hancock REW Addressing antibiotic failure—beyond genetically encoded antimicrobial resistance.Front Drug Discov. 2022; 2892975Crossref Google Scholar The pervasiveness of AMR spans continents and health-care settings, affecting both high-income countries and LICs.5Antimicrobial Resistance CollaboratorsGlobal burden of bacterial antimicrobial resistance in 2019: a systematic analysis.Lancet. 2022; 399: 629-655Summary Full Text Full Text PDF PubMed Scopus (3739) Google Scholar The high prevalence of AMR in health-care and community settings and in the environment necessitates a multi-sectoral and global approach.8McEwen SA Collignon PJ Antimicrobial resistance: a one health perspective.Microbiol Spectr. 2018; 6: 521-547Crossref Scopus (547) Google Scholar The overuse and misuse of antibiotics in human health and agriculture have increased the prevalence of AMR, compounding the urgency to optimise surveillance strategies.4Pronyk PM de Alwis R Rockett R et al.Advancing pathogen genomics in resource-limited settings.Cell Genomics. 2023; 3100443Summary Full Text Full Text PDF PubMed Scopus (0) Google Scholar Strengthening AMR surveillance is crucial to improve our understanding of the dynamics of resistant bacteria, to identify emerging patterns, and to guide effective treatment strategies. This concerted effort is essential not only to safeguard the efficacy of existing antibiotics but also to foster the development of new antibiotics. However, the complexity of AMR and its multifaceted nature necessitate comprehensive efforts, including coordinated and inclusive actions, beyond those of surveillance.9Mudenda S Chabalenge B Daka V et al.Global strategies to combat antimicrobial resistance: A one health perspective.Pharmacol Pharm. 2023; 14: 271-328Crossref Google Scholar These actions encompass various disciplines, involving both technical and non-technical experts. Hence, integrating genomics and bioinformatics for the detection and prediction of AMR can greatly improve surveillance and public health responses. Shifting focus on the challenge of AMR envisions an innovative health-care paradigm that harmonises genomics, bioinformatics, and multidisciplinary collaboration. For instance, both technical and non-technical experts can methodically collect diverse samples across different settings and swiftly use on-site frugal and less technically demanding sequencing technology, such as nanopore sequencing, to generate genomic data in near real-time.10Aruhomukama D Antimicrobial resistance data, frugal sequencing, and low-income countries in Africa.Lancet Infect Dis. 2022; 22: 933-934Summary Full Text Full Text PDF PubMed Scopus (0) Google Scholar The immediate integration of genomic data into an interface facilitates rapid analysis, interpretation, and reporting of actionable insights. Advancing genomics and bioinformatics in LICs in Africa demands a commitment to user-centredness, accessibility, and adaptability. The availability of user-centred, accessible, and adaptable tools and intuitive interfaces would represent a strategic leap, rather than a compromise. Simplifying the genomics and bioinformatics domains would ensure inclusivity, enabling meaningful contributions to pathogen surveillance to inform public health. As LICs in Africa move towards a healthier future, bridging the gap in accessibility to genomics and bioinformatics analyses is imperative. Bridging this gap necessitates not only addressing the scarcity of expertise and the inherent complexity of the field but also embraces a multi-sectoral approach to combat the most pressing public health threats, such as AMR. We declare no competing interests.