Researchers at McMaster University have developed a sophisticated new tool that could help provide early warning of rare and unknown viruses in the environment and identify potentially deadly bacterial pathogens which cause sepsis, among other uses.
Their findings are published in the journal Cell Reports Methods in a paper titled, “Probe design for simultaneous, targeted capture of diverse metagenomic targets.”
“A wide array of metagenomic research efforts are hampered by the same challenge: low concentrations of targets of interest combined with overwhelming amounts of background signal,” the researchers wrote.
“Although PCR or naive DNA capture can be used when there are a small number of organisms of interest, design challenges become untenable for large numbers of targets. We present HUBDesign, a bioinformatic pipeline that designs probes for targeted DNA capture, which leverages sequence homology to identify probe sets that maximize the breadth of coverage for targets while maintaining specificity.”
The new algorithm developed by researchers can help develop probes to capture trace quantities of pathogens, such as SARS-CoV-2 or monitor reservoirs in the environment for emerging pathogens.
Pathogens may be difficult to detect if they make up less than one one-millionth of a sample, especially in early stages of an infection. There is a need to better detect and isolate pathogens in natural settings. The researchers tested the probes on the entire family of coronaviruses, including SARS-CoV-2.
The probes provide a shortcut by targeting, isolating, and identifying the DNA sequences.
“There are thousands of bacterial pathogens and being able to determine which one is present in a patient’s blood sample could lead to the correct treatment faster when time is very important,” explained Zachery Dickson, lead author of the study and a graduate student in the department of biology.
“The probe makes identification much faster, meaning we could potentially save people who might otherwise die,” he added.
“We currently need faster, cheaper, and more succinct ways to detect pathogens in human and environmental samples that democratize the hunt and this pipeline does exactly that,” said evolutionary geneticist Hendrik Poinar, PhD, a lead author on the study and director of McMaster’s Ancient DNA Center.
The findings pave the way for broader applications for human health and scientific discovery, and can aid in the detection of pathogens associated with life-threatening conditions such as sepsis.