Associated organisationsAfrica Health Research Institute · Institut de Recherche pour le Developpement · KEMRI-Wellcome Trust Research Programme · National Health Laboratory Service · Oxford Clinical Research Unit - Vietnam · University of Liverpool · University of OxfordEurope PMC affiliations are not treated as award recipients or mapped locations.
Funding£4.4M
PeriodMay 2024 — May 2027
In plain English
AI plain-English summary
Eight research centres in Africa and Southeast Asia are scaling up their pandemic-built genomic surveillance systems to track three escalating infectious threats: dengue and chikungunya viruses, multidrug-resistant *Klebsiella pneumoniae*, and *Mycobacterium tuberculosis*. This matters because climate change is expanding the range of mosquito-borne viruses, while drug-resistant bacteria are outpacing current treatments. There is a critical shortage of genomic data from these regions, leaving health ministries blind to how these pathogens spread and evolve. Without that information, control measures—like antibiotic stewardship programmes or vector control campaigns—are designed in the dark. If the project succeeds, it will produce the first harmonised, cross-continental picture of how these infections move across borders. National health ministries will receive real-time data on transmission routes and drug-resistance patterns, enabling targeted interventions rather than blanket policies. The project also establishes a shared data standard (HL7 FHIR) across eight countries, making future genomic surveillance faster and cheaper to deploy. This is applied, operational research: it builds infrastructure that quietly underpins effective public health responses, from hospital antibiotic guidelines to national outbreak alerts.
View original technical description
Throughout the COVID-19 pandemic, the Africa Asia Programmes (AAPs), AHRI, KWTRP, MLW, MORU and OUCRU, and CIDRI-Africa (Discovery Platform), played a crucial role supporting Ministries of Health with diagnostics, genomic surveillance and real-time data to guide decision-making. We propose to now apply these established capacities to pathogens with an escalating infection burden in Africa and Southeast Asia, driven by climate change or the emergence of drug resistance, and for which there is a dearth of genomics data across Africa and Southeast Asia limiting effective action. The selected pathogens are: 1) the vector-borne dengue and chikungunya viruses; 2) multidrug- resistant Klebsiella pneumoniae; and 3) Mycobacterium tuberculosis. The proposed project will harmonise resources for archived and prospective sample collection and surveillance, whole-genome and targeted next-generation sequencing, metagenomics, bioinformatics, and the interoperability of genomic data and metadata across sites via the HL7 Fast Healthcare Interoperability Resources data standard. We aim to determine the national and international spread of these infections to inform national policy strategies for arboviruses control and antibiotic stewardship. The project will be managed via shared governance and oversight, enabling active engagement of the multidisciplinary teams with policy stakeholders across eight countries to accelerate translation of our findings to practice.
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