Case study: EMBL-EBI tool enables genomic outbreak surveillance for NHS Scotland

A new genomic analysis tool developed at EMBL-EBI, is helping NHS Scotland tackle antimicrobial resistance and improve outbreak response

Bacterial infections can spread quickly, especially in hospital settings or crowded communities, where vulnerable people are treated in close proximity and bacteria move between them. Antimicrobial-resistant infections are a growing threat, with over one million deaths attributable to AMR annually. Outbreaks caused by resistant strains can be difficult to control and treat.

Other bacterial infections, such as gonorrhoea, often cause no symptoms, making them even harder to detect and track. Cases of gonorrhoea are rising rapidly in the UK, and a new vaccine rollout across the UK aims to curb infections and slow its spread. Alongside the vaccine efforts, genomic surveillance – studying the DNA of these bacteria – can help track how the infection is spreading, and where interventions can stop outbreaks before they escalate.

One of the major challenges is that analysing bacterial genomes to spot outbreaks and transmission can be technically complex and time-consuming. Public health teams need tools that simplify the process, work across a range of bacteria, and produce results that are easy to interpret and act on.

Introducing PopPIPE

To meet this challenge, researchers at EMBL-EBI developed PopPIPE – the Population analysis PIPEline. PopPIPE is a user-friendly tool that clinicians and scientists can use to identify related bacterial samples, detect transmission events, and visualise the results.

“We designed our pipeline to be both rapid and reproducible, to create interactive visualisations, and so that it can easily be reconfigured and re-run on new datasets,” said John Lees, Group Leader at EMBL-EBI. “Perhaps most importantly, PopPIPE helps to make the many complex tools needed to run genomic epidemiology analyses accessible and efficient, opening up advanced analysis to users who may not have specialist bioinformatics expertise.”

Collaboration with the NHS in Scotland

In 2022, PopPIPE was used to investigate antibiotic-resistant bacterial infections across six hospital wards as part of a research collaboration between NHS Lothian and the University of St Andrews. Using this tool revealed clear transmission clusters and helped the team confirm suspected links between patients, as well as uncover new ones that had not been detected before. 

“PopPIPE significantly simplifies genomic epidemiology. It speeds up our outbreak response and improves accuracy, helping us manage infections more effectively,” said Martin McHugh, Principal Clinical Scientist at NHS Lothian. “It gives us a clearer picture of how infections are spreading and where we need to focus control measures.”

Encouraged by these results, the tool is now being evaluated for inclusion in the routine analysis pipeline managed by the Public Health Microbiology Bioinformatics team in Public Health Scotland. Initially, this will be piloted for the Enterococcus service, with gonorrhoea also earmarked for future evaluation. 

Gonorrhoea is a sexually transmitted infection (STI), which often spreads without symptoms, and presents different challenges for outbreak monitoring. PopPIPE is helping reveal how gonorrhoea strains move between cities and populations, providing a clearer picture of transmission dynamics and supporting better public health interventions. Other bacterial infections within the Public Health Microbiology portfolio will be evaluated in the future.

Impact and what’s next 

PopPIPE is designed to make advanced genomic analysis more accessible to a broad range of users. At Public Health Scotland, it is being integrated into national reference laboratory workflows and evaluated for use across multiple pathogens.

This collaboration demonstrates how bioinformatics tools can become part of routine public health practice when delivered through easy-to-use workflows. As sequencing becomes a routine component of infectious disease surveillance, bioinformatics tools such as this will play an increasingly important role in national and international health responses. 

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antimicrobial resistance, bioinformatics, case study, embl-ebi, genomics, lees, microbial systems, microbiology, research highlight