Public-health agency to integrate Covid secondary infection data into national database

UKHSA looks to ‘automate and expand production of data’

Credit: Nick Youngson/Alpha Stock Images/CC BY-SA 3.0

The government’s public-health agency is to embark on a project to integrate into its national database information on co- and secondary infections affecting Covid-19 patients.

Co-infections include illnesses suffered concurrently with coronavirus – such as other respiratory conditions – while secondary infections are those that come in the wake of the virus, such as bacterial and fungal infections or pneumonia.

The UK Health Security Agency intends to bring data related to these infections into the national Unified Infection Dataset (UID) created last year. To support this process, the agency has signed a £242,110 contract with tech advisory firm PA Consulting.

During the first five weeks of a 13-week engagement, the company will be tasked with delivering a discovery phase, the aim of which is explore the current landscape of data sources and better “understand data input, data output and end-user requirements… and to review existing processes and code”, according to newly published commercial documents.

Once this exercise is complete – and following a two-week break over Christmas – PA will begin a secondary six-week phase of “onboarding” into the UID the relevant data sets on “bacterial, viral and fungal pathogens”, and then implementing automated processes allowing this data to flow into the system in future.

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The deal also covers the provision of “data validation and acceptance testing” services, as well as asking PA to help UKHSA “explore data pipeline memory optimisations” and “determine and optimise workflow scheduling”.

The public-health agency also requires the implement of Microsoft’s PowerBI analytics software to allow for “visualisation and exploration of co/secondary infection data”.

Finally, the consulting firm will be expected to provide “training of [the] UID UKHSA team to raise skill levels and increase knowledge of UID for advanced use cases and future development”.

Staff to be provided include front-end and back-end software developers, delivery leads, business-intelligence specialists, and data engineers. Depending on the services being provided and the seniority of the employee, day rates charged will range from £915 to £2,290. 

PA won the original contract, awarded in spring 2020, to develop the UID, the stated aim was to deliver “the automated linkage of several health surveillance ‘Big Data’ systems held by” UKHSA’s predecessor, Public Health England.

“There is no single national data set that gathers data on all clinically-significant infections with their corresponding antimicrobial susceptibilities, healthcare pre-exposure and clinical correlates,” the contract notice said. “Creating a link between national microbiological and clinical datasets will establish a Unified Infection Dataset. The UID will assist PHE strategies in executing its health protection function, including the investigation of incidents and outbreaks, and monitoring antimicrobial resistance. The epidemiological intelligence will allow us to identify potential targeted interventions and to assist in prioritising clinical and public health resources by monitoring long-term trends and assessing the impact of any outbreak or incident.”

It added: “Large surveillance datasets are stored separately by PHE on multiple servers and are not routinely linked. We cannot duplicate the stored data; therefore, we wish to create a virtual environment whereby we can perform linkage dynamically on an ad hoc basis and/or routinely, subject to end-user queries. The system will perform standard analysis of the linked data at a patient level. Information Governance must comply with strict organisational standards. An API will need to be developed to allow external users to access the data in the future.”

The system has now been launched, and PA has previously supported an on-boarding project for data related to healthcare-associated infections – such as so-called hospital superbugs MRSA and C. difficile – suffered by Covid-19 patients.

UKHSA was formed earlier this year and supersedes Public Health England. The newly created entity also incorporates the NHS Test and Trace programme, as well as the Joint Biosecurity Centre – a body set up by the government at the start of the coronavirus crisis to help inform pandemic response.


Sam Trendall

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