A University of Liverpool study has used advanced genetic and genomic techniques to offer a major step forward in understanding and diagnosing infectious intestinal diseases.
The large-scale study analysed more than 1,000 stool samples from people with diarrhoeal illness to harness two cutting edge tools.
Diarrhoea, a common symptom of infectious intestinal disease, affects an estimated 18 million people each year in the UK. However, despite its prevalence, traditional lab tests often fail to recognise its cause, especially when infections are caused by unidentifiable or emerging pathogens. This newly published study used metagenomic (DNA-based) and metatranscriptomic (gene or RNA-based) sequencing. Unlike traditional methods, these techniques do not rely on growing organisms in a lab. Instead, they detect and analyse the genetic material directly from patient samples.
Co-lead author, Dr Edward Cunningham-Oakes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool said: "This is the UK's largest study to compare traditional diagnostics with these next-generation tools. We not only found infections missed by standard tests, but we could see what the bugs were doing inside the gut-something standard diagnostics just can't show."
The work captures, for the first time, a comprehensive snapshot of the Salmonella gene expression directly from a human stool sample. The transcriptomic data provides new insights into how the bacteria survive and adapt after leaving the human gut. As Salmonella remains a priority diarrhoeal pathogen in the UK, the knowledge will be invaluable for helping scientists to target this dangerous pathogen.
The study's key findings highlight the power of RNA tests in detecting hidden infections-including elusive parasites and RNA viruses-while also identifying which genes are active during infection. Remarkably, RNA remained stable in stool samples even without preservatives, suggesting it is more robust than previously thought. Notably, the ratio of RNA to DNA helped differentiate true infections from harmless gut microbes. By combining both DNA and RNA data, researchers gained the clearest and most accurate picture of the infection process.
Co-lead Professor Alistair Darby, Co-Director of the University's Centre for Genomic Research said: "This study shows how genetic tools can revolutionise how we identify and understand intestinal infections. By understanding not just what's there, but what it's doing, we can improve public health responses, particularly around foodborne outbreaks."
The findings could significantly impact how diarrhoeal diseases are diagnosed, managed, and studied in the UK and beyond-especially in light of the growing need for rapid, accurate diagnostics that don't rely on outdated culturing methods.
The research also highlights the strategic role of Liverpool's Centre for Genomic Research (CGR) and the new Microbiome and Infectious Disease (MaID) initiative, which is part of the Liverpool City Region's Life Sciences Innovation Zone.
Professor Alistair Darby continued: "This is about more than diagnosing infections-it's about building a platform for innovation in healthcare. Our previous work has shown that healthcare professionals are open to this. By making our data open-access, we hope to help other researchers, NHS labs, and public health agencies build on our work."
Dr. Edward Cunningham-Oakes added: "Our results show that RNA, once thought too fragile to use in stool testing, can actually give us powerful insights into how infections work. That opens up new possibilities for diagnosing and treating these illnesses more effectively."
The research, led by scientists at the University of Liverpool, including Salmonella experts Dr Blanca Perez-Sepulveda and Professor Jay Hinton, was funded by the NIHR Health Protection Research Unit in Gastrointestinal Infections (HPRU-GI), a collaboration between the University of Liverpool, UK Health Security Agency, and other partners.
The paper, 'Enhancing Infectious Intestinal Disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples' was published in Genome Medicine (DOI: 10.1186/s13073-025-01478-w).
