Leveraging genomic surveillance for public health: insights from Latin America

A Comment in The Lancet Microbe by Dickson Aruhomukama and colleagues1Aruhomukama D Galiwango R Meehan CJ Asiimwe B Enhancing genomics and bioinformatics access in Africa: an imperative leap.Lancet Microbe. 2024; 5: e410-e411Summary Full Text Full Text PDF PubMed Scopus (1) Google Scholar discusses the crucial role of genomics and bioinformatics in revolutionising public health in low-income countries in Africa, despite considerable barriers such as a shortage of expertise and the inherent complexity of these fields. The authors emphasise the need for user-centred, accessible, and adaptable tools to simplify these domains, thereby enabling non-technical experts to effectively contribute to pathogen surveillance and public health efforts. Furthermore, the authors suggest that intuitive interface development and reduced technical demands of genomics tools can enhance the integration of these technologies into public health systems. Overall, the authors advocate for a strategic commitment to make genomics and bioinformatics more accessible and less complex to fully harness their potential in addressing the ongoing and emerging health challenges in Africa. Latin America also faces similar challenges in terms of implementing these technologies. However, specific challenges that exist in Latin America should be considered for their potential implementation. Specifically, the region differs in terms of organisation, data generation, specialised institutions, and funding opportunities for implementing genomics and bioinformatics tools to address public health threats. Moreover, there are biases in university and public health infrastructures, and one of the most important challenges is the low level of English proficiency,2Education FirstEF English Proficiency Index.https://www.ef.com/wwen/epi/Date: 2023Date accessed: May 12, 2024Google Scholar which limits the implementation of genomics and bioinformatics tools primarily designed for an English-speaking audience. Unlike other regions such as Europe, the USA, and Africa, Latin American countries often encounter challenges related to scant funding and infrastructure for institutions that promote training in genomics and bioinformatics tools. The Pan American Health Organization (PAHO) serves as the supranational health agency that acts as a reference for adopting health policies in Latin America. Based on its experiences in genomic surveillance, PAHO is promoting PAHO Genomic Surveillance Regional Networks,3Pan American Health OrganizationPAHO Genomic Surveillance Regional Networks (PAHOGen).https://www.paho.org/en/pahogenDate: 2024Date accessed: May 20, 2024Google Scholar its first initiative on genomic surveillance regional networks, which aims to improve genomic surveillance of emerging pathogens in the Americas. This initiative supports efforts to improve laboratory sequencing capacity and generate timely data, contributing significantly to public health surveillance and response in the region. However, a summary of the surveillance objectives, capabilities, needs for technical cooperation, opportunities for integration with other networks, dissemination of information for response implementation, and involvement of universities as principal contributors in implementing genomics and bioinformatics is not available on its website. As scientists based in Latin America who have been working on genomics and bioinformatics for several years, we have encountered several challenges in their implementation. First, the high cost associated with accessing whole-genome sequencing is a major barrier, requiring substantial investment or access to funds, which are often non-existent or scarce. In our personal experience, we obtained whole-genome sequences through external collaborations with US institutions. The advances and advantages of Nanopore Sequencing could help us to implement these technologies in Latin America, considering that their cost of implementation is lower than that of other expensive technologies. The second aspect that limits the implementation of this technology is the deficiency in English language skills among many students and professionals, which hinders the learning and use of web-based tools for analysing genomic data, despite the considerable number of resources available online (eg, Galaxy, Center for Genomic Epidemiology, and Centre for Genomic Pathogen Surveillance) or command-line-based resources mainly in Python. The curricula for life science students in Latin America should quickly adopt genomics and bioinformatics. We suggest the development of courses in Spanish and Portuguese on teaching platforms such as Coursera or edX. The development of a body of professionals familiar with the basics of genomics and bioinformatics is essential. As noted previously,4Calero-Cáceres W Ortuño-Gutiérrez N Sunyoto T et al.Whole-genome sequencing for surveillance of antimicrobial resistance in Ecuador: present and future implications.Rev Panam Salud Pública. 2023; 47: e8Crossref PubMed Scopus (4) Google Scholar we recommend that the public health institutions in Latin America work more closely with academia. This collaboration will enable public health institutions to leverage academia’s experience in genomic analysis and bioinformatics as well as their engagement in the One Health approach to tackle public health challenges more effectively. We declare no competing interests. WCC would like to thank the Operative Unit of the Directorate of Research, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato for their funding of the project PFCIAB 39 (UTA-CONIN-2023-0294-R). JLB acknowledges the funding provided by the Generalitat de Catalunya through the Consolidated Research Group grant ICRA-ENV 2021 SGR 01282 and the funding from the CERCA program of the Catalan Government.