New tool to fight infectious disease. Will the U.S. use it?
University of Cambridge
The new approach uses samples from infected humans to allow
real-time monitoring of pathogens 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.
It uses genetic sequencing data to provide information on
the genetic changes underlying the emergence of new variants. 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 programs. The technique is a major advance on the
existing approach to these diseases, 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.
The report is published in the journal Nature.
"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," said Dr Noémie Lefrancq, first author of the report, who carried
out the work at the University of Cambridge's Department of Genetics.
Lefrancq, who is now based at ETH Zurich, added: "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."
"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," said
Professor Julian Parkhill, a researcher in the University of Cambridge's
Department of Veterinary Medicine who was involved in the study.
Testing the technique
The researchers used their new technique to analyze samples
of Bordetella pertussis, the bacteria that causes whooping cough. Many
countries are currently experiencing their worst whooping cough outbreaks of
the last 25 years. It immediately identified three new variants 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," said 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.
"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," said Professor Henrik Salje in the University
of Cambridge's Department of Genetics, senior author of the report.
He added: "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."
The researchers say this work is an important piece in the
larger jigsaw of any public health response to infectious disease.
A constant threat
Bacteria and viruses that cause disease 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 were better at spreading. Underlying this
evolution are changes in the genetic make-up 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.
