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McMaster University researchers have created a new tool that can help identify deadly bacteria pathogens and early warning signs of unknown viruses.
This algorithm can be used to develop advanced probes that capture trace amounts of pathogens from a variety of situations such as the animal-to human transmission of infections like SARS-CoV-2, or monitor environmental reservoirs for potential emerging pathogens.
Most labs have bulk sequenced their samples to date. This is a tedious and expensive process that often requires scientists to extract and then reassemble tiny fragments of DNA. These fragments can be difficult to detect, and are often contaminated by billions of organisms found in the same environment or sample.
It is difficult to isolate pathogens in wildlife or clinical settings. For example, samples of saliva or blood can make up as little as one millionth of a sample. This is especially true in the early stages of infection when patients are most vulnerable.
The probes were successfully tested on all coronaviruses including SARS-CoV-2. The probes allow for a quick way to identify, target, and isolate DNA sequences that are common among related organisms. This is often due to evolutionary history, or ancestry.
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.”Zachery Dickson, lead author of the study and graduate student, Department of Biology, McMaster University
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.”
Zachery Dickson, lead author of the study and graduate student, Department of Biology, McMaster University
He says, “The probe speeds up identification and could potentially save lives.”
Researchers also showed that probes can be used to capture the wide range of pathogens associated sepsis. This is a potentially life-threatening condition in which the body reacts too quickly to infection. It usually starts in the skin, lungs or gastrointestinal tract.
“We need more efficient, cost-effective and succinct methods to detect pathogens in humans and other environmental samples. This pipeline does just that,” said Hendrik Poinar (lead author of the study, and director McMaster’s Ancient DNA Centre).
This discovery has many other potential applications in human health and scientific discovery. It could include the identification of intestinal parasites within ancient DNA. This could provide new information about the evolution of severe disease.
The design process for the probes is described in the journal cell Reports: Methods. It was published online today.
Dickson, Z.W., et al. (2021) Probe design for simultaneous, targeted capture of diverse metagenomic targets. Cell Reports Methods. doi.org/10.1016/j.crmeth.2021.100069.