New DNA Test Speeds Up Bacterial Infection Diagnosis

A new DNA sequencing technique that delivers faster and more accurate bacterial infection diagnoses could be implemented nationwide. The method, developed by the Medicines and Healthcare products Regulatory Agency (MHRA) in collaboration with the NHS, has been successfully tested in a pilot study across seven London hospitals. It offers quicker, targeted treatments and may help reduce hospital-acquired infections.

Traditional bacterial infection tests typically take around 7 days from sample collection. Some infections, such as tuberculosis, can take up to 8 weeks for a definitive diagnosis. These wait times can delay treatment and infection control efforts. 

Integrating long-read sequencing technology, such as nanopore sequencing, into routine diagnostics has the potential to enhance sensitivity and speed diagnostic times.

Amplicon-based sequencing techniques targeting the 16S ribosomal RNA gene (16S rRNA) are important for identifying bacterial pathogens, particularly in critical infections such as meningitis, pneumonia, osteo-articular infection, and sepsis when samples are culture-negative due to prior empiric antibiotic treatment. 

Most Hospitals Rely on Referral Laboratories

However, few NHS laboratories currently perform these tests, relying on unstandardised protocols with significant inter-laboratory discrepancies in assay performance and accuracy. The lack of commercially available quality assurance materials also makes it challenging to introduce and validate in-house 16S rRNA gene sequencing services. As a result, many hospitals opt to send samples to referral laboratories, increasing both costs and turnaround times.

A team of researchers from Barts Health NHS Trust in London, the National Measurement Laboratory, the University of Surrey, and the MHRA conducted a study to address these challenges. Their research, published in Frontiers in Cellular and Infection Microbiology, tested various nanopore sequencing approaches and preparation kits to create a reliable clinical testing framework for clinical implementation. 

New DNA Test Delivers Results in Two Days

The MHRA said that since 2024, the new DNA sequencing method has been used to analyse over 2000 patient samples across seven London hospitals. The technique was shown to accurately identify which bacteria are causing an infection, and which antibiotics will work best to treat it. 

The method is now being piloted to investigate and prevent hospital outbreaks caused by antibiotic-resistant ‘superbugs’. The MHRA is working to standardise the technology, to enable wider NHS adoption, with an ultimate goal of making rapid DNA sequencing a routine part of hospital diagnostics across the NHS.

Technology to Combat Antimicrobial Resistance

Health Minister Ashley Dalton praised the collaboration. “This groundbreaking use of the technology in hospitals will cut diagnosis times down from weeks to just 2 days” she said in a statement.

Dr Chrysi Sergaki, head of microbiome at the MHRA, said the agency would develop and provide reference materials to ensure that hospitals achieve “consistent, reliable, and accurate results they can trust”. Helping to detect antibiotic-resistant bacteria will be crucial in the fight against superbugs, she said.

Ian Butler, lead clinical scientist in medical microbiology at Barts Health, described the study as the first of its kind in the UK and among the first globally to clinically validate this sequencing technology.

The method has already been used to investigate a drug-resistant E. coli outbreak at Newham Hospital in November 2024, which affected 58 patients. By identifying how resistance spread between bacterial species, clinicians were able to improve patient care and prevent further transmission.

By analysing bacterial genetic material directly, we can detect even complex infections “more accurately, and much faster than traditional methods”, Butler said. “This means we can precisely diagnose the infection and identify the right treatment sooner — especially for critically ill patients.”

Dr Sheena Meredith is an established medical writer, editor, and consultant in healthcare communications, with extensive experience writing for medical professionals and the general public. She is qualified in medicine and in law and medical ethics.