Title: NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance, Wellcome Trust Sanger Institute
Funder: Department of Health and Social Care

Abstract: 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 Local capacity will be built through a ‘sequencing package’ consisting of a genome sequencer, staff (bioinformatician and a sequencing technician) and costs for reagents and sequencing. The initial phase of the project focus on the setup and transfer of expertise in bioinformatics and data interpretation. The use of intuitive bioinformatics and web applications developed within cGPS will enable the ownership of interpretation at these local sites (see http://microreact.org and http://wgsa.net). Retrospective population structure The provision of contextual background population snapshots for key priority pathogens will be undertaken in conjunction with training and setup of National Units. Each site will identify a representative retrospective set of isolates from each species which will be shipped to the central hub during the initial setup of local facilities. Initial species will be based on WHO and local priority species: Escherichia coli, Klebsiella pneumoniae, Salmonella spp., Shigella spp. Neisseria gonorrhoeae, Acinetobacter baumannii, Staphylococcus aureus and Streptococcus pneumoniae Integrating with existing surveillance systems – Intelligent use of WGS Antibiotic resistance testing usually involves disk diffusion tests, often with data stored in laboratory information management systems for further use. One such example is WHONET (currently supported in over 2,300 laboratories in over 120 countries) for storing microbiology results. Alternative methods such as Vitek are used routinely for testing of panels of antibiotics with such data used to guide treatment strategies. These ‘antibiograms’ represent, across multiple geographic locations, a valuable resource within which to identify patterns of similarity as a proxy for clonal lineages. The monitoring of results from these methods, with centralisation of data, allows us to flag the emergence of novel antibiograms which can be used as a trigger for targeted WGS. Contextualising these lineages within a background population structure from retrospective sequencing, and the cumulative data from ongoing sequencing, will enable the identification of high risk clones, their risk assessment through prediction of resistance and virulence, production of rapid diagnostics (based on unique SNPs within the lineages) for local use, and mapping of their spread globally through the central hub. RESEARCH AGENDA AND EXPANSION OF NETWORK Each local site is currently engaged in the build up of national surveillance programmes utilising phenotypic antibiograms and WHONET and will develop independent research agendas based on local priorities: our aim is to enhance local capacity and expertise for this research. Central Hub research questions will be focussed on the utility of the network to inform on local and global spread of high-risk lineages, the undertaking of clonal risk mapping to provide data in formats that could be utilised for decision making, and the modelling of emergence and spread of novel lineages or mobile resistance determinants for risk prediction. Furthermore, we will seek to enhance and extend the reach of the local sites through integration with, and building upon, existing links and collaborations within The Sanger Institute and Wellcome research units. Short Term (Yrs 1 and 2) • Roll out of sequencing package at 4 sentinel locations • Training and installation of bioinformatics platforms at local sites • Retrospective sequencing of key pathogens at hub • Development of Standard Operating Procedures • Collective description of standardised panel of phenotypic tests • QA/QC testing for laboratory sequencing Medium Term (Yrs 2 and 3) • Combinatorial assessment of emerging lineages based on phenotypic data • Enhancing local research agenda using local WGS • Design of prospective sampling protocols and survey of key pathogens • Develop intelligent surveillance by building capacity in analysing prospectively collected data • Recruiting regionally for broader survey extending the reach of the National Units Long Term (Yrs 3 and 4) • Assessment and use of WGS for local and international surveillance • Cross-centre research projects • Further extend the reach of the network (with WHO) • Predictive use of data (transmission and clonal emergence) – Commissioned • Spatial risk modelling. • Sampling and analysis of global survey(s) Projects to be undertaken in years 1-2 1) Research capacity building and standardisation Local acquisition of equipment, staff, reagents and laboratory infrastructure and the embedded setup of National Units. Standardised protocols will be shared between Central hub and National Units for ongoing phenotypic testing through agreement of standard panels of antibiotics and data storage within WHONET. DNA extraction and WGS protocols developed across Units. Bioinformatics and local web applications for the processing and interpretation of data within a local context. 2) Population mapping and retrospective sequencing Isolates/DNAs will be shipped to Sanger for sequencing. Local sequencing of isolates will be undertaken in tandem with project 1 to define QC for sequencing and bioinformatics. Shared experience between sites and the central hub will and lead to definition of standard protocols / QC steps and data sharing and release protocols. Mapping of clones and will be undertaken through local instances of open bioinformatics tools. This will lead to a broad understanding of the background population of circulating strains within and between sites. Responsive Capacity The Central Hub and National Units will retain staff and sequencing capacity be called upon as required. Furthermore, the Sanger Infrastructure will be utilised to provide reactive, rapid sequencing turnaround and dissemination of information. Sanger has a track record in this area having previously used rapid sequencing to investigate local hospital outbreaks.

Lay abstract: The aim of our Global Health Research Unit is to provide actionable data derived from a global genomic surveillance network, that will inform patterns of antimicrobial resistance (AMR) and public health policies to control high-risk bacterial pathogens. We have partnered with strategically important sites in Asia (The Philippines and India), Africa (Nigeria) and South America (Colombia), to enhance capacity around whole genome sequencing (WGS) and its interpretation (bioinformatics), large scale sampling surveys, analytic methods and financial management – to enhance public health systems and responses in these countries and regions, while at the same time collecting and combining data from these and other networks to impact on AMR control at a global scale. The increasing prevalence of AMR threatens healthcare at every level and is now a major international threat to public health. Bacterial pathogens can evolve increased ability to transmit, cause disease and resist antibiotics. In order to deliver appropriate interventions we need systematic approaches for collecting and identifying AMR at a local level - and integrated systems to collate data to provide an international overview. This is particularly important in low and middle income countries (LMICs), which stand to benefit most from these interventions – and are key locations for the prevention of spread. Whole genome sequencing (WGS) of bacteria is transforming our ability to understand disease dynamics, enabling us to identify the genetic changes responsible for resistance, and compare this with the genomes of isolates from different individuals and locations to infer likely routes of spread. Data generated can be shared via online databases to provide clear, interpretable information to those that are responsible for taking action. The ongoing monitoring of bacterial populations requires the development of reference databases within a region, combined with ongoing sequencing to identify emerging strains at a national and international level. WGS combined with appropriate bioinformatics infrastructure promises a robust and rapid means of detection and assessment of risks associated with newly emerging bacterial clones, as well as monitoring their global spread, in a cost- effective manner. Our aim is to provide: Intelligent global surveillance of bacterial pathogens through appropriate sampling and analysis in sentinel surveillance sites within strategically relevant countries. Our specific objectives are to: Develop capacity for locally-led research projects in LMICs and sampling frameworks to address national public health and research needs; Provide actionable data at national and international levels to identify high-risk lineages of bacterial pathogens and determinants of antibiotic resistance, and open-access tools to understand their distribution and spread ; Provide resourcing and training for local capacity and expertise to ensure ownership of outputs and utility for action; Build a network of laboratories and experts across strategically important countries from which to expand to similar local contexts elsewhere.Each collaborating Unit has been chosen to represent a network of hospitals actively involved in the surveillance of AMR within each country. Expertise in interpretation through easy-to-use tools will enable each location to further develop local research agendas and to feed data into broader global monitoring of particular pathogens between sites.

Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING);2.4 SURVEILLANCE AND DISTRIBUTION
Health categories: INFECTION