Researchers have devised a new way to identify more infectious disease outbreaks, including those causing flu, COVID, whooping cough and tuberculosis.
The new approach uses samples from infected humans to allow real-time monitoring of infectious disease outbreaks circulating in human populations and enable vaccine-evading bugs to be quickly and automatically identified. This could inform the development of vaccines that are more effective in preventing disease.
The approach can also quickly detect emerging variants with resistance to antibiotics. This could inform the choice of treatment for people who become infected – and try to limit the spread of the disease.
Constantly evolving to new threats
Infectious disease outbreaks are constantly evolving to be better and faster at spreading between us.
During the COVID pandemic, this led to the emergence of new strains: the original Wuhan strain spread rapidly but was later overtaken by other variants, including Omicron, which evolved from the original and was better at spreading.
Underlying this evolution are changes in the genetic makeup of the pathogens.
Pathogens evolve through genetic changes that make them better at spreading. Scientists are particularly worried about genetic changes that allow pathogens to evade our immune system and cause disease despite us being vaccinated against them.
Genetic sequencing detects new variants of infectious diseases
The new system uses genetic sequencing data to provide information on the genetic changes underlying the emergence of new variants of infectious diseases. This is important to help understand why different variants spread differently in human populations.
There are very few systems in place to keep watch for emerging variants of infectious diseases, apart from the established COVID and influenza surveillance programmes.
The technique is a major advance on existing approaches to infectious disease outbreaks, which has relied on groups of experts to decide when a circulating bacteria or virus has changed enough to be designated a new variant.
By creating ‘family trees’, the new approach identifies new variants automatically based on how much a pathogen has changed genetically and how easily it spreads in the human population – removing the need to convene experts to do this.
It can be used for a broad range of viruses and bacteria, and only a small number of samples taken from infected people are needed to reveal the variants circulating in a population. This makes it particularly valuable for resource-poor settings.
“Our new method provides a way to show, surprisingly quickly, whether there are new transmissible variants of pathogens circulating in populations. It can be used for a huge range of bacteria and viruses,” said Dr Noémie Lefrancq, first author of the report, who carried out the work at the University of Cambridge’s Department of Genetics.
Professor Julian Parkhill, a researcher in the University of Cambridge’s Department of Veterinary Medicine, added: “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.
“This means we can rapidly and effectively spot the emergence of new highly transmissible strains of infectious diseases.”
A timely technique in the infection control sector
The researchers used their new technique to analyse samples of Bordetella pertussis, the bacteria that causes whooping cough.
Several countries are currently experiencing their worst whooping cough outbreaks of the last 25 years. It immediately identified three new infectious disease outbreaks circulating in the population that had been previously undetected.
“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,” explained Professor Sylvain Brisse, Head of the National Reference Center for whooping cough at Institut Pasteur, who provided bioresources and expertise on Bordetella pertussis genomic analyses and epidemiology.
In a second test, they analysed samples of Mycobacterium tuberculosis, the bacteria that causes Tuberculosis. It showed that two variants with resistance to antibiotics are spreading.
Professor Henrik Salje from the University of Cambridge’s Department of Genetics and senior author of the report commented: “The approach will quickly show which variants of a pathogen are most worrying in terms of the potential to make people ill.
“This means a vaccine can be specifically targeted against these variants to make it as effective as possible.”
He concluded: “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.”
