Researchers at the University of Cambridge have developed a new method to detect infectious variants of viruses or bacteria in humans, including those causing flu, COVID and tuberculosis.
The research, primarily funded by the European Research Council, allowed the researchers to develop a new method to rapidly detect emerging variants with antibiotic resistance.
The new method uses samples from infected humans to enable real-time monitoring of pathogens circulating in human populations.
It facilitates quick and automatic identification of vaccine-evading bugs and helps develop vaccines with more effective disease prevention.
University of Cambridge’s Department of Genetics professor, senior author of the report Henrik Salje said: “The approach will quickly show which variants of a pathogen are most worrying in terms of the potential to make people ill.
“If we see a rapid expansion of an antibiotic-resistant variant, then we could change the antibiotic that’s being prescribed to people infected by it, to try and limit the spread of that variant.
“This work has the potential to become an integral part of infectious disease surveillance systems around the world, and the insights it provides could completely change the way governments respond.”
The researchers used their new technique to analyse samples of Bordetella pertussis, the bacteria that causes whooping cough.
The new technology immediately identified three new variants circulating in the population that had been previously undetected.
Institut Pasteur National Reference Centre for whooping cough head professor Sylvain Brisse provided expertise on genomic analyses and epidemiology of Bordetella pertussis.
Researchers also used the new method to analyse samples of Mycobacterium tuberculosis, where it showed that two variants with resistance to antibiotics are spreading.
Sylvain Brisse said: “The novel method proves very timely for the agent of whooping cough, which warrants reinforced surveillance given its current comeback in many countries and the worrying emergence of antimicrobial resistant lineages.”
According to researchers, their work is an important part in the broader efforts to strengthen public health response to infectious disease.
The disease-causing bacteria and viruses are constantly evolving with underlying changes in their genetic make-up, to become faster at spreading between humans.
During the COVID pandemic, antibiotic resistance led to the emergence of new strains, including Omicron, which evolved from the original Wuhan strain.
The researchers said their new method could inform the choice of treatment for people who are infected and try to limit the spread of the disease.
By creating ‘family trees’, the new approach automatically identifies new variants based on genetic changes in the pathogen, and its spread in the human population.
Also, it can be used for a wide range of viruses and bacteria and requires only a small number of samples from infected people to reveal the variants circulating in a population.
The report’s first author Noémie Lefrancq said: “Our new method provides a way to show, surprisingly quickly, whether there are new transmissible variants of pathogens circulating in populations – and it can be used for a huge range of bacteria and viruses.
“We can even use it to start predicting how new variants are going to take over, which means decisions can quickly be made about how to respond.”
University of Cambridge’s Department of Veterinary Medicine researcher Julian Parkhill said: “Our method provides a completely objective way of spotting new strains of disease-causing bugs, by analysing their genetics and how they’re spreading in the population.”
