Rapid DNA analysis supports infection diagnosis

Advances in DNA analysis are opening new pathways to detect and understand infections in animals.

An innovative approach to reading all the DNA in a clinical sample is enables scientists to identify bacteria present without the need for conventional, time-consuming culturing of bacteria in the lab.

This technique, known as metagenomic whole genome sequencing, is being used in research and clinical settings by researchers at the Roslin Institute and the Royal (Dick) School of Veterinary Studies, including treating patients at the School’s Hospital for Small Animals and Equine Hospital.

This approach can help diagnose infections more quickly and, sometimes, more accurately than with traditional methods, which typically rely on growing bacteria in the lab over several days to aid identification, and are not always conclusive.

The method extracts all genetic material directly from the sample and compares it to a reference database, to determine whether harmful bacteria are present. DNA can be read in real time, enabling bacteria to be identified within hours and appropriate antibiotics to be administered the same day.

Faster diagnosis supports targeted treatment, reducing the need for broad-spectrum antibiotics as a primary treatment, helping to limit the risk of antimicrobial resistance (AMR) developing in animals visiting veterinary clinics.

Faster answers

In some cases, rapid diagnosis could also reduce the need for prolonged isolation. 

New tools

Although widely explored in human healthcare, where the approach was developed earlier, the use of metagenomic sequencing in veterinary medicine is still emerging, with growing interest in its application to clinical cases.

The first research project to apply this approach in the School was designed to analyse bacterial DNA found in urine and skin samples from dogs with suspected infections.

This project aimed to detect a range of bacterial species commonly seen in clinical cases, helping vets to guide more targeted, effective treatment.

Expanding applications

Subsequent projects have built on this foundation to explore a wider range of applications. An ongoing project aims to demonstrate the use of rapid DNA analysis for diagnosing surgical site infections in cats and dogs.

Another project is seeking to adapt rapid DNA analysis for use in horses, focusing on infections that are difficult to diagnose using standard laboratory methods. 

Fast identification could be valuable for conditions such as joint infections affecting horses, where early treatment is critical.

Similar techniques are also being used to investigate broader questions in animal health. A study in rabbits combined DNA sequencing with traditional techniques to compare communities of microorganisms found in and upright-eared and lop-eared rabbits, as the latter are prone to ear infections.

The findings show that some animals naturally carry more bacteria than others, highlighting that sequencing results must be interpreted alongside the animal’s clinical signs, to distinguish whether disease is present.

Beyond diagnostics

Not all applications of rapid DNA sequencing are focused on real-time diagnosis of infection. Researchers are also exploring its use in areas such as cancer detection and retrospective analysis of disease.

An ongoing project aims to develop a liquid biopsy approach for canine cancers by analysing DNA in blood samples to distinguish between healthy dogs and those with tumours.

Other work is focused on developing methods to extract and sequence DNA from preserved tissue samples, enabling researchers to investigate historical cases and better understand the causes of past infections.

This could allow scientists to revisit unresolved cases, such as severe infections where the pathogen was never identified, and build a clearer picture of how diseases emerge and spread.

Researchers aim to refine rapid DNA sequencing methods for routine clinical use, including in smaller veterinary practices.

The original canine infection research project was supported by the Dogs Trust and published in Microbial Genomics. The ongoing equine and surgical site infection research projects are supported by the PetPlan Charitable Trust and the European College of Veterinary Surgeons Resident Research Grant, respectively. The rabbit research was published in Veterinary Dermatology.

Related links

Research publication – Canine bacterial infections

Research publication – Rabbit ear infections