UK wide One-health AMR Surveillance System, Discovery with Environmental System Exemplar

Description

Summary of the work Discovery for a UK wide One Health Surveillance system, a cross government programme for the analysis of antibiotic resistant across human, animal and environmental sources. Subject to agreement, Alpha, Beta and Live phases of the development of an exemplar system to enable real-time monitoring of environmental antimicrobial resistance reporting. Expected Contract Length 18 months (Total duration of all phases of project) Latest start date Monday 7 February 2022 Budget Range £1,000,000 (ex VAT) for all phases Why the Work is Being Done There is currently no routine monitoring of levels of resistant microbes at the organism or genetic level in the UK environment. Unless this threat is understood and interventions are put in place, treatments for many common human and animal infections will fail. Consequently, there is an urgent need for environmental surveillance and action to minimise the ongoing development and spread of antimicrobial resistance (AMR). This will be one of the first integrated AMR surveillance systems in the world and unique in its consideration of environmental AMR. We require the expertise of supplier with a proven track record of successful delivery to deliver an initial discovery phase to scope, initiate and set the strategy for OneHealth platform, linking in data sources from Environmental Agency, DEFRA, Food Standards Agency and National Laboratories programme, a new project aimed at linking cross-govt. data on one system. Problem to Be Solved A software platform is required to facilitate storage, processing, analysis, automation, comparison and publication/visualisation of AMR related data from human, animal and environmental sources. Data linkage pipelines will allow enrichment of datasets with information from matching records available via “big data” administrative collection such was the NHSD’s Hospital Episode Statistics. Environmental sampling and analysis data will be included, provided by the Environment Agency (including chemical and microbiological data) as well as clinical data from humans (including microbiological and molecular data) provided UKHSA. Information governance will be streamlined allowing users to submit single applications to obtain access to a host of datasets rather than have to make the same cases to each data owner separately. The system will be scalable, allowing datasets to grow and new ones to be added over time without degradation in system performance. The system will also allow users to build and deploy data dashboards, facilitating rapid dissemination of information. The work of this project is to perform Discovery for the UK wide One-Health System and subject to agreement the Alpha, Beta and Live phase will be to build an exemplar of the data and reporting component for the environmental data component. Who Are the Users Clinical, scientific and public health colleagues who are involved in environmental AMR surveillance, treatment of AMR in humans and animals as well as those who control infection and disease outbreaks in a range of medical settings. • Users need to be able to query the system in real-time to analyse trends in data as well as mapping of AMR disease across the UK • Users will be able to identify disease outbreaks using transmission data (Whole Genome Sequencing) • Users should be able to build and deploy dashboards – these should be configured to meet the user needs (using filters to transform and manipulate the data) • Users need to be able to query the system routinely or ad hoc Early Market Engagement None Work Already Done None Existing Team The successful supplier will be working mainly with a core project team, comprising: Project Manager, Epidemiological Lead, Project Support Officer, Architecture and Engineering Lead. The project has senior staff oversight and an Advisory Group of senior internal and external stakeholders. Current Phase Not started Skills & Experience • For Essential & Nice to Have skills/experience stating “recent experience” please provide the year of the project within your answer. Insert N/A in the corresponding response field for this guidance • Recent (within 3 years) and demonstrable experience of conducting the discovery phase relating to the use of digital solutions and technology, using data from large databases across the UK • Recent (within 3 years) and demonstrable experience of designing and implementing systems that perform data linkage between multiple data sources within different organisations • Recent (within 3 years) and demonstrable experience of applying the principles of user-centred design to the development of digital solutions for users that meet Accessibility standards level;AA of WCAG 2.1 • Recent (within 3 years) and demonstrable experience of designing systems to manage personally identifying information under General Data Protection Regulations (GDPR) • Recent (within 3 years) and demonstrable experience of designing systems able to work with high performance cluster computing • Recent (within 3 years) and demonstrable experience of delivering agile,discoveries & Beta phases to and/or on-behalf of Government Agencies meeting the Government Service Standard & technology code of conduct • Recent (within 3 years) demonstrable experience of developing strategies and project plans for new and innovative large-scale projects • Recent (within 3 years) demonstrable knowledge of appropriate data protection standards relevant to the sharing and linking of government data, both for policy/research and operational purposes • Recent (within 3 years) demonstrable experience of working effectively and collaboratively with multi-disciplinary client teams of policy, operational and analytical personnel Nice to Haves • Recent (within 3 years) experience of working with organisations, particularly relating to public health or disease surveillance. • Recent (within 3 years) experience of working with a range of users and stakeholders including scientific experts, technical and digital development team. • Recent (within 3 years) experience of working with interdisciplinary and cross-disciplinary project teams with varying experience of Agile methods • Recent (within 3 years) experience of exploring system architecture, hardware platform and open source software options to meet performance and scalability requirements. • Recent (within 3 years) experience of advanced methods for data linkage such as machine learning. • Recent (within 3 years) experience of working in a Linux environment. Work Location The work can be performed from any location and will be coordinated by UKHSA staff currently working remotely but may be based at UKHSA Colindale (London NW9) site. Work may be carried out from multiple locations, including the Supplier’s offices. Attendance at UKHSA Offices in London may be required for meetings. Supplier staff may be expected to be on-site at UKHSA locations to manage relationships with the project team, end-users and stakeholders from other organisations. For the Discovery phase, suppliers may have to travel within England and Wales to gather requirements from users and stakeholders. Working Arrangments The supplier will be expected to work using Scrum and all ceremonies will be open to the UKHSA project team, with a wider set of stakeholders expected to attend Show and Tells. The supplier will follow a 'one team' approach with the Project Manager and may include Scientific SMEs attending all daily stand-ups and participating fully in the work of the team. Security Clearance Not required Additional T&Cs None No. of Suppliers to Evaluate 5 Proposal Criteria • Proposed approach to conducting the Discovery phase of a public health big data linkage project including working within the constraints of existing organisational services and technologies (max score 10) • Proposed approach to applying the principles of user-centred design/user insights to assess the needs of scientific users for all phases of the project (max score 10) • Proposed approach to data analysis, transformation and migration (max score 15) • Proposed approach to working with information governance and system performance requirements for all phases of the project. (max score 15) • Proposed approach to conducting the Alpha, Beta and Live phases including open source solutions for linking and handling large volumes of data (max score 10) Cultural Fit Criteria • The shortlisted suppliers will be required demonstrate cultural fit through a presentation to a panel that should summarise their proposal for clarity and demonstrate how they propose to: • Work within the constraints of budgets and existing services and technologies already used within the programme (max score 5) • Demonstrate your approach to translating complex issues to different stakeholders including knowledge sharing and transfer to stakeholders throughout the duration of the project. (max score 5) • Provide details of how this contract may result in employment, training or education that may reduce the disability employment gap (max score 10) Payment Approach Capped time and materials Assessment Method • Case study • Presentation Evaluation Weighting Technical competence 60% Cultural fit 20% Price 20% Questions from Suppliers 1. Is there any intention of incorporating antimicrobial consumption data (either during the initial build or subsequently)? Yes, definitely will be a long term aim, questionable if it will be needed for the environmental exemplar 2. Are there specific drug-bug combinations of concern across the human, animal and environmental sectors? Yes there are, although often it is resistance to drugs of the same class or where resistance is strongly associated rather than the exact same drug being used in both humans and animals 3. If there are any drug-bug combinations of concern, is antimicrobial susceptibility data collected routinely across human, animal and environmental sectors? This needs to be determined in the discovery but in just the human health there is not a routine antibiogram generated. Different labs will test different panels of antibiotics possibly even using different methods and breakpoints to determine resistance 4. Is the UK One Health Report 2019 a good template for intended visualisations? It is a starting point but would want to consider this more during the discovery 5. Please can you confirm that the successful vendor will not be responsible for conducting data linkage?Have data fields required for linkage been identified and tested for linkage success rate? The application is likely to have to perform some data linkage of at least aggregate counts for example associating cases in humans and cases in the environment to the same lower layer super output areaThe discovery should determine what data items are already available for linkage and where these are inadequate recommend what needs to be added. 6. Please can you share any information on data structures for each of the databases to be included in the initial build of the One Health Surveillance System? These will be pinned down during Discovery 7. Has there been any consideration around the development of a simulated data so that researchers can explore the available data prior to submitted a request to gain access to the real data?Does the UKHSA have a panel of anticipated end users that can be approached to better understand user requirements? This is not possible. Previous experience of building a data system (ideally in a healthcare system) could be used as an example. There is not a panel that can be approached to better understand user requirements. 8. Is a solution to support efficient review of user requests to access the data required as part of this platform? No this is out of scope, but anticipated that the discovery will indicate that such a system would ultimately be required 9. Do you have a preference as to whether this platform is built on your infrastructure now, built on third party infrastructure and transferred to you at a suitable time, or rather it was built and managed outside of your infrastructure? Should be built on UKHSA infrastructure using technology we can support. Willing to consider other wise if compelling case can be made 10. Do you have any mandatory or preferred technology suppliers in regards to cloud, data engineering, data science and visualisation. No, further information will be provided to shortlisted suppliers. 11. The ‘Existing Team’ contains various roles that may echo supplier roles. The ‘Working Arrangements’ emphasise a ‘one team’ model and ‘attending all daily stand-ups and participating fully in the work of the team’. Is the customer looking for a supplier to provide embedded / assigned resources into an existing team and subject to UKHSA management /direction, or will the supplier be tasked on outcomes by the customer’s Product Owner? Expect the supplier will be tasked on outcomes by product owner but happy to explore other ways of working 12. In the ‘Existing Team’ section, there is mention of ‘Architecture and Engineering Lead’. Does the customer have a design pattern / criteria in mind? Are there any specific platforms (eg AWS / Azure) that are already determined? How much of the vision is already defined, versus needing to be defined by the new supplier? There is only the most high level vision defined and we are agnostic to platforms 13. Can the customer confirm if there is any relationship to other UKHSA platforms which support similar analytic work? Are there any specific technology constraints to consider and skills that are required of the new supplier? The platform will need to be able to talk to databases some in the cloud and others on prem in SQL clusters 14. There is mention of GDPR and Personal Data, however, there is specifically no requirement for Clearances. Please can the customer confirm if BPSS is required as a minimum? BPSS clearance is a requirement for UK based staff. BPSS does not apply to overseas suppliers therefore, overseas suppliers would need the equivalent and the onus is on the supplier to establish this. Please refer to the embedded link for rules for working outside the UK: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/714002/HMG_Baseline_Personnel_Security_Standard_-_May_2018.pdf 15. Can work be carried out offshore? Yes however, it is expected that any meetings and work will be conducted within normal UK working hours. Additionally, although we are currently remote working, there may be a need for face to face meetings during the lifetime of the contract and expenses would need to be met by the supplier.In addition, BPSS clearance is a requirement for UK based staff. BPSS does not apply to overseas suppliers therefore, overseas suppliers would need the equivalent and the onus is on the supplier to establish this. Please refer to the embedded link for rules for working outside the UK: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/714002/HMG_Baseline_Personnel_Security_Standard_-_May_2018.pdf 16. You request experience of delivering projects meeting the Government Service Standard and Technology Code of Practice. Will you accept evidence of the same to the Scottish Government Digital First Service Standards as a direct equivalent? Yes this is fine 17. Would you prefer multiple project examples as evidence for each required skill / experience or will you only mark the responses with reference to a single provided project example? Yes feel free to use as many examples as you wish 18. Has any pre-market engagement taken place with any other potential suppliers, either existing or non-existing UKHSA suppliers, around this opportunity? No 19. What are the material differences in the underlying requirements between this and the previous Unified Infection Dataset (UID) Systems Development project? UID is a linkage engine. This one health reporting system is more focused on reporting and visualisation of results rather than ad hoc linkage of patient records 20. Would the winning supplier of this work need to work closely with the successful provider for the previous UID project? No this would not be essential, the work is distinctly different 21. What is the relationship between this opportunity and the previous Unified Infection Dataset (UID) Systems Development project requirement? The two projects are not connected 22. Have any technology decisions already been made about the future direction for the development of the system and if so, what are they? No technology discussions have taken place.