A global network of laboratories in Nigeria, India, Colombia, and the Philippines will begin routinely sequencing the DNA of bacterial pathogens to track the emergence and spread of drug-resistant infections. Antimicrobial resistance (AMR) is rising worldwide, but most low- and middle-income countries lack the genomic tools to detect dangerous new strains before they become widespread. Current surveillance relies on fragmented, often outdated methods that cannot distinguish between a local outbreak and a quietly expanding global threat. This project fills that gap by building permanent sequencing capacity in four strategically placed sentinel sites, each linked to existing public health networks. If successful, the network will create an early-warning system for high-risk clones and mobile resistance genes. Public health officials in each country will receive actionable data on which antibiotics are failing and which strains are spreading, enabling faster, more targeted responses. The open-access tools and reference databases will remain in place after the grant ends, allowing local teams to continue monitoring without external support. This is not fundamental science—it is a practical infrastructure project designed to make genomic surveillance a routine part of global infection control.
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The Sanger Institute has had a fundamental impact on our understanding of the biology of infectious disease since its inception. We have made significant steps in understanding the emergence and transmission of pathogens, and the mechanisms of acquisition and spread of antimicrobial resistance (AMR) through a series of global surveys in partnership with researchers in Africa, Asia, and South America. In collaboration with the Wellcome Trust Advanced Courses, we have also created and run capacity-building courses in pathogen genomics in all these regions. The Institute has placed the analysis of pathogen spread and AMR at the core of its strategic research plan. To enhance global reach, we established the Centre for Genomic Pathogen Surveillance (cGPS) as a vehicle for translating this research into public health benefit by the generation of open-access tools for the interpretation of local sequence data in a global context, and enacting pathogen and AMR surveillance through structured genomic surveys with partners in both HICs and LMICs. The Institute thus represents a convergence of cutting-edge basic science in pathogen genomics with the ability to translate this research into public health benefit on a global scale. The award of an NIHR-GHRU would enable the Institute to solidify and enhance our global network, and build a cohesive strategy by enabling and extending partnerships across this network for surveillance and public health. We would both build capacity in LMICs, complementing and enhancing existing surveillance of pathogens and AMR, and strengthen the cGPS surveillance hub, creating an intelligent surveillance network that will provide early warning of emerging pathogen and resistance threats. Building local genomics capacity in LMICs, and linking this to local surveillance networks, and on to a global system via open-source tools will build a solid platform to enable this capability to be maintained and strengthened beyond the lifetime of the grant. SCIENTIFIC STRATEGY The implementation of routine WGS of bacterial pathogens promises to transform epidemiological understanding on a global scale through the monitoring of the evolution, expansion and spread of high-risk clones (HRCs) and mobile AMR determinants. This vision is contingent on the construction of reference databases of circulating strains, combined with active surveillance through WGS to place new isolates in a regional, national and international context, using open-access tools accessible from anywhere on the planet. Here we propose to implement such a system through the provision of laboratory and bioinformatics capacity in four sentinel locations, each allied to public health networks and academic research institutes within strategically important countries. We will establish reference sequence databases of retrospectively collected contemporary isolates from a broad range of species to enable targeted prospective sequencing of isolates that exhibit properties of emerging high risk clones, or which have important antibiotic resistance patterns. The interpretation of this ongoing sampling in the context of the genetic background will provide actionable data for local, national and international policy-making. DESCRIPTION OF PLANNED PROGRAMME - Central Hub and National Units We will build upon existing expertise within cGPS (central hub) and the Sanger, and solidify existing and new capacity with a strategic focus on the utility of genomic data for global public health. In conjunction we will substantiate four regional sequencing Units to provide local capacity for analysis and research, and the generation of data to feed into global surveillance. Each site has developed or is developing a national programme of surveillance. Unit 1 – Dr Carlos, RITM, Phillipines Unit 2 - Dr Ravikumar, KIMS, Hospital and Research Centre, Bangalore, India Unit 3 – Dr Godoy, Tibaitata, Colombia Unit 4 – Dr Okeke, University of Ibadan, Nigeria
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