NIHR Global Health Research Unit on Genomics and enabling data for Surveillance of Antimicrobial Resistance Antimicrobial resistant (AMR) bacterial infections are a rising global cause for concern. AMR is increasingly being predicted to significantly affect health and wellbeing on an international scale, and new technologies and greater understanding are required to reduce resistance to effective treatments. Monitoring how AMR progresses and increasing our understanding into how, when and where AMR emerges are essential to respond to the growing crisis and assess how effective local, national and international interventions are.  Whole Genome Sequencing (WGS) is a technology becoming more frequently used in public health communities and offers the ability to provide information at an individual level, as well as at a regional, national and international scale due to its digital nature. Using this surveillance combined with rapid data reporting, will strengthen the evidence base of research, which is crucial for public health decision makers and their capacity to respond. Progress is being made in technical support for practical uses. However, the remaining major problem is how to rapidly and routinely link data and its interpretation to provide the greatest value at all levels.

Our global multi-institutional partnership unit brings together established collaborations between the UK (Centre of Pathogen Genomic Surveillance -CGPS, Oxford University), Philippines (Research Institute for Tropical Medicine - RITM), Ibadan (University of Ibadan), India (KIMS Hospital and Research Centre) and Colombia (Colombian Agriculture Research Corporation AGROSAVIA) to continue to combat this growing problem. Capacity for WGS of AMR at each key site has been established or embedded into developing and existing national surveillance initiatives and has already helped outbreak detection and tracking of AMR populations. Building upon this foundation, the data landscape now needs to be put into use to guide public health policies and practices.

Through our partnerships we aim to reduce AMR bacterial infections through bettering WGS and surveillance across each site. Our main goals and objectives are detailed below.

The project will leave a legacy of engineering, data science and data driven surveillance by using WGS and achieving the highest value of the data on policy. It  will have a direct impact on patient lives and well-being and the prevention of infection at a very local level, with a strong focus on capacity building. Outputs will highly impact public health strategies for reducing the impact of AMR in our fight against infectious diseases and infection control to curb the threat of AMR. (1) Country Specific: To operationalise a data-driven WGS-enhanced surveillance model for priority AMR pathogens
i) Increase capacity at sentinel sites in Nigeria for WGS-enhanced surveillance to progress an emergent national public health surveillance system 
ii) Enhance detection and ceasing of hospital outbreaks in real-time by operationalising local and governmental stakeholder delivery in the Philippines
iii) Embed data-enhanced surveillance across OneHealth sectors with stakeholder reporting in Colombia
iv) Deliver reporting and enhanced surveillance for monitoring interventions (eg vaccines) in India
v) The UK will collaboratively develop, test and validate work packages with country sites and transfer capacity for data science/engineering while optimising additional technical support for WGS and training.

(2) Research: Deliver transformational capacity for data engineering, data-driven sampling strategies and technological advances in response to analysis of information architecture and stakeholder needs
i) Model national data landscapes across all countries to identify common practice, bottlenecks, and develop an architectural plan within which to enhance surveillance
ii) Develop a stakeholder landscape and reporting framework for key local, national and international infection prevention and antimicrobial policy questions.
iii) Transform the collection, linkage, interpretation and reporting of data to stakeholders via training and deployment of data science and engineering methods and tools.
iv) Develop a rational sampling framework for surveillance and targeted outbreak investigation through leveraging routinely collected laboratory AMR data to intelligently prioritise and maximise the value of WGS.
iv) Innovate novel solutions to enhance data and WGS driven surveillance for rollout in country and regionally.

(3) Implementation: Support regional networks in developing laboratory, bioinformatic, data and institutional capacity to build, maintain and sustain WGS-enhanced AMR surveillance.
i) Optimise and minituarise standardised laboratory process for microbiological and multiple sequencing technologies for operational use across surveillance networks
ii) Optimise and support local ownership of bioinformatics for assaying risk from genomic data and contextualising within the global landscape
iii) Transfer capacity and ownership of expertise in data science and engineering to equip networks to rapidly deploy data solutions and implement the delivery of research for action
iv) Enhance institutional financial and grant management to conduit practice and sustainability.

(4) Regional Centres of Excellence:  Create Regional Centres of Excellence linked to WHO for technical support and institutional capacity, building on previous genomic surveillance of AMR
(i) Enhance regional networks through engagement, training and transfer of expertise tailored to regional priorities
(ii) Work with national agencies, regional WHO offices and international agencies to deploy owned expertise regionally