A new lab at St Thomas’ Hospital has opened to test whether new nanopore-based DNA sequencing technology could support same day diagnosis of infections such as sepsis in NHS hospitals. The research at St Thomas’ Hospital in London will see if the technology could help clinicians prescribe the right antibiotics straight away, and ensure antibiotics are only prescribed when needed, with ongoing considerations around the reduction of spread of antibiotic resistance.
The NIHR Guy’s and St Thomas’ Biomedical Research Centre has opened a fully automated molecular lab with Oxford Nanopore Technology sequencers.
The DNA of pathogens can provide important information about their identity and their drug resistance. Scientists at St Thomas’ Hospital will test whether the sequencers can provide genetic results fast enough to allow doctors to reliably diagnose patients with bacterial infections in one day. They will then assess whether this could benefit patients by reducing the number of unnecessary antibiotic prescriptions, a major factor in the spread of antibiotic resistance.
Antibiotic resistance occurs when bacteria acquire genetic changes that make them resistant to antibiotic treatments. It is estimated that in the US and Europe, antimicrobial-resistant infections currently cause at least 50,000 deaths per year1. The problem is worsened by overprescribing of antibiotics when there is no bacterial infection. Currently, diagnosing infections can take between three to five days and doctors often need to give antibiotics while waiting for laboratory results.
The compact sequencers in the new lab have the potential to change this. They can analyse samples and produce DNA sequences in real time. These are then matched up to a library of bacterial sequences to show which infection a person has acquired, and what resistance genes are present. This would allow doctors to administer the most appropriate, targeted antibiotic to the patient to treat the infection.
The sequencers have been shown to identify pathogens and their drug resistance in many research studies. The new lab will assess the sequencers for accuracy and speed at scale in a diagnostic laboratory, and if successful will seek to translate this assessment to a clinical setting. The team will assess this by comparing the results from samples run through the sequencers, with the results from existing culture and sequencing methods. This is essential before they are used to make decisions on antibiotic treatment.
Dr Alka Saxena, Head of the Genomics Platform at the NIHR Biomedical Research Centre at Guy’s and St Thomas’ said:
“The speed at which this technology provides DNA sequence information is really exciting. But what we want to know is, can this technology process samples taken from patients quickly and accurately enough for clinical use?
“We are specifically looking at whether it can help doctors make better decisions about how they use antibiotics to treat infectious diseases. If the technology passes this crucial test, it has the potential to change the way we diagnose and treat patients with infection.”
Professor Jonathan Edgeworth, Director of the Centre for Clinical Infection and Diagnostics Research and Viapath Medical Director, said: “We are doing this research jointly from the start with front-line clinicians, research scientists and healthcare scientists to speed up the moving of scientific discovery and technological advance to the bed-side.
“We want to find out quickly whether Nanopore-based sequencing improves antibiotic treatment decisions on the wards, so that ultimately patients get faster targeted treatment of sepsis whilst also reducing exposure to unnecessary antibiotics so they don’t develop resistance to antibiotics. If our research shows that the technology can support faster diagnosis, we will then need to find a path through to routine use.”
The research will be conducted jointly by research scientists at Guy’s and St Thomas’ BRC and healthcare scientists at Viapath with the intention that, if it turns out to have patient benefit, Viapath will then deliver the diagnostic service for patient samples. Acquiring the technology was made possible by funding from the Department for Health and Social Care. The team expect results of the assessment to be available in the next year.