Research in Action: Dr. Samir Patel

Cutting edge research at PHO’s laboratories: One-stop-shop for testing organisms

If you’re returning from abroad with a fever, your doctor will likely test you for malaria. You’ll give multiple blood samples at PHO’s laboratory, and if the results are inconclusive, you’ll face yet another round of tests.

Dr. Samir Patel, a clinical microbiologist at PHO, is fast-tracking this process with new technology. With one sample, he and his team at the PHO laboratories will be able to quickly and accurately diagnose a patient and recommend targeted treatment against any bacteria or virus.

“With this new technology we will be able to streamline the ordering of 30 different tests. One test will identify the pathogen–whether it’s dengue fever, West Nile virus, Chikungunya virus, or a new bacteria or virus,” said Patel, who is also a professor at U of T’s Department of Laboratory Medicine and Pathobiology.

Using this technology – called Next Generation Sequencing – currently in a validation phase, Patel takes a patient’s sample and analyzes its genetic code. His team then matches the code to a database of thousands of bacteria and viruses, interprets the complex data and provides a diagnosis.

Using this technology – called Next Generation Sequencing – currently in a validation phase, Patel takes a patient’s sample and analyzes its genetic code. His team then matches the code to a database of thousands of bacteria and viruses, interprets the complex data and provides a diagnosis.

“Our current tests can be expensive, time consuming and aren’t always accurate,” said Patel. “Next Generation Sequencing will revolutionize the microbiology field. With the information it provides we can fine-tune patient treatment.”

This technology will also remove the need for lengthy guesswork. For example, if an Ontario patient has a fever and a severe headache during the summer, doctors would normally test for West Nile virus. But those test results are frequently negative.

Instead of speculating, doctors will be able to let high-powered computers discover what’s in the sample.

“Dr. Patel’s work in pathogen discovery aims to deliver a one-stop-shop that can definitely determine the causative organisms in severe infections such as meningitis and encephalitis,” said Dr. Vanessa Allen, Chief of Medical Microbiology at PHO. “This has the potential to revolutionize the way we deliver microbiology diagnostics for improved patient care.”

Patel began using this technology for the Pathogen Discovery Program at PHO in 2012. The goal of the program is to diagnose difficult cases and to quickly and accurately identify bacteria and viruses that could cause an outbreak.

“Once the infection is confirmed, then the patient can be managed appropriately. This information can also be used to control the spread of disease; for example, a patient could be placed in an appropriate infection control setting. Or, if they are not infected, they can be taken off unnecessary antibiotics,” said Patel.

During an outbreak, Patel could also track the source of pathogens and their evolution. Others have used Next Generation Sequencing to identify and track specific strains of Ebola in West Africa.

“Should any outbreak occur in Ontario, we could test samples, identify the bacteria or virus that is causing the outbreak and track the spread using a systematic process,” said Patel. “We can also see how infectious a virus or bacteria is, and if similar strains are circulating through other parts of the world.”

Patel predicts that the technology, currently in use at the PHO laboratories, will be ready for clinicians to use for routine testing in a few years. But he sees the program as having broader implications than solely for clinicians. “Our hope is that this program will be used for routine clinical testing, but will also identify new or emerging viruses or bacteria. I see this as being a platform that will allow us to conduct surveillance across the province and allow us to determine what other pathogens are out there and what we need to study.”