The new algorithm is an advanced tool that can help develop probes to capture tracequantities of pathogens, both known and unknown from a wide variety of situations, likethe animal-to-human transmission of infections such as SARS-CoV-2 or monitorreservoirs in the environment for possible emerging pathogens.
To date most labs have bulk sequenced samples, a laborious and costly process thattypically requires scientists to tease out and then reassemble minute fragments ofspecific DNA, which are difficult to detect and often contaminated by the billions of otherorganisms in the same sample or environment.
Pathogens in clinical or wildlife settings samples of blood or saliva, for example, areparticularly challenging to isolate, since they can easily make up less than one one-millionth of a sample, especially in early stages of an infection, when concentrations arestill low and detection is most critical for patients.
Researchers successfully tested the probes on the entire family of coronaviruses,including SARS-CoV-2. The probes provide a shortcut by targeting, isolating andidentifying the DNA sequences – specifically and simultaneously – that are sharedamong related organisms, most often due to evolutionary history or ancestry.
“There are thousands of bacterial pathogens and being able to determine which one ispresent in a patient’s blood sample could lead to the correct treatment faster when timeis very important,” explains Zachery Dickson, lead author of the study and a graduatestudent in the Department of Biology.
“The probe makes identification much faster, meaning we could potentially save peoplewho might otherwise die,” he says.
Researchers also demonstrated the effectiveness of probes for capturing the incrediblywide array of pathogens associated with sepsis, a life-threatening and rapidlydeveloping condition that occurs when the body overreacts to an infection whichtypically starts in the lungs, urinary tract, skin or gastrointestinal tract.
“We currently need faster, cheaper and more succinct ways to detect pathogens inhuman and environmental samples that democratize the hunt and this pipeline doesexactly that,” says evolutionary geneticist Hendrik Poinar, a lead author on the studyand director of McMaster’s Ancient DNA Centre.
The discovery also holds promise for much broader applications for human health andscientific discovery, including the identification of intestinal parasites in ancient DNA,which could reveal new information on the evolution of catastrophic disease.
The process used to design the probes, a pipeline called HUBdesign or HierarchicalUnique Baits, is described in the journal Cell Reports Methods, published online today.