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Gene-editing technology used to identify Cryptosporidium

Australian researchers have been using a new method for identifying the presence of Cryptosporidium parvum in water samples, with the approach offering potential to significantly reduce time and cost of pathogen detection. 

UNSW Graduate School of Biomedical Engineering’s Professor Ewa Goldys and her team, including Professor Graham Vesey, Yi Li, Fei Deng and Tim Hall, have applied CRISPR technology to quickly and easily identify the harmful microorganisms.

Goldys said the research has shown that the CRISPR/Cas12a-based system can produce results in around 2.5 hours, much faster than usual microscopy-based testing.

“CRISPR is technology for gene editing, which was awarded a Nobel Prize in 2020. Not many people know that the same enzymes have been double-purposed for ultra-sensitive bacterial biochemical sensors, particularly for the detection of microorganisms,” Goldys said.

“Using this technology, we have been detecting water pathogens via surface proteins. These sensors are amazingly sensitive due to very finely attuned enzymes.”

The UNSW research has been focused on detecting Cryptosporidium, a microscopic parasite that can cause serious gastrointestinal disease, and is especially problematic in locations where water sources may be contaminated by animals.

“In reality, there only need to be a few Cryptosporidium cells present to cause severe gastrointestinal disease in the person who has consumed the water. People who are relatively healthy may experience illness, but for anyone who is immunocompromised, this can be fatal,” Goldys said.

“There are microscopy-based tests being done on these pathogens by water authorities, but this way of testing is a bit clunky. It can be difficult to find this pathogen by taking a small water sample, it requires human review under a microscope and it can take a long time and cost a lot of money.

“Using CRISPR, there is no need to peek under a microscope. We are able to do batch processing, assessing multiple samples at the same time, but with the same level of accuracy. This significantly reduces the need for microscopy, and the time and expense associated with it.”

Potential for detecting other pathogens

Goldys said CRISPR technology also has the potential to be developed further to improve detection of other bacteria and viruses, including possible identification of COVID-19 in samples.

“PCR [polymerase chain reaction] testing is commonly used to detect pathogens. But the challenge with PCR is that it can take quite some time for laboratory processing. In order to control the pandemic efficiently, we really need technology that is specific to the virus but able to give us fast answers,” Goldys said.

“CRISPR is actually able to provide this speed and accuracy.

“This could be a solution, not just for COVID-19 testing, but for every disease. There is a large spectrum of situations where rapid pathogen diagnostics would be very beneficial.”

Goldys said the application of CRISPR technology to pathogen detection is not an Australian first, but that the field is exciting and quickly expanding, and has the potential to transform the way harmful microorganisms are identified.

“We are not the first research group that have been applying CRISPR to detect different pathogens. There is such a huge scope of opportunities to apply this technology, the pockets of advancement are significant and are being followed by many researchers worldwide,” Goldys said.