Faster detection of dozens of dangerous pathogens possible

By Randy Shore, Vancouver Sun March 22, 2012

Water samples from all over B.C. are tested in the labs at BCCDC.

Photograph by: Geonome B.C. , [PNG Merlin Archive]

Scientists in B.C. are developing new tools that will cut the time needed for water testing from days to just hours and allow public safety officials to detect contamination in time to head off illness.
Researchers at the British Columbia Public Health Laboratories are designing a completely new approach to water testing using metagenomics, a way to detect the genetic signature of dozens of organisms all at the same time within hours of sampling.
Metagenomic testing done at the watershed rather than the tap could shorten the response time to contamination and allow public health officials to intervene in time to save people from being sickened, explained project co-leader Judith Isaac-Renton.
"The tools we have at our disposal are inadequate," said Isaac-Renton.
Rather than performing individual tests for suspected pathogens, a metagenomic tool would pulverize all the organisms in a water sample and analyze bits of genetic material in the resulting soup. Computer-driven pattern recognition software could then match the recognizable material, known as genetic markers or biomarkers, to the genetic codes of bacteria that are indicators of unhealthy water.
"We aren't so much looking for dangerous bugs, which is slow, inaccurate and too narrow, we are looking at the sig-nature of healthy water," Isaac-Renton explained.
Current testing regimes involve transporting water samples from all over the province to labs at the BC Centre for Disease Control where samples have to be cultured for one to two days to detect bacteria such as E. coli, the bug that sickened thousands and killed seven people in Walkerton, Ont., 12 years ago.
"It might take two days to get the samples and then an overnight delay to get the tests done," said Jennifer Gardy, a genome researcher at the BC Centre for Disease Control, a partner organization in the research project.
Heavy rains sometimes wash fecal contaminants from wild animals or farms into water-sheds, contaminants that can make their way to your tap in less than a day.
"By the time we come back to a community and say there was fecal contamination in their water, it's an event that has come and gone," she said. "We can say somebody pooped in your water - a couple of days ago."
A more sophisticated tool would be able to detect the presence of viruses and parasites that conventional testing regimes do not, as well as larger patterns in the population of organisms characteristic of both healthy and troubled watersheds.
Pathogens such as the diar-rhea-inducing protozoan cryptosporidium and the parasite toxoplasmosis found in cat feces are difficult to test for, but may cause serious illness in humans when they enter the water supply.
"We are missing a lot of key pathogens in our current testing regime," Gardy said.
There are 49 boil water advisories due to contamination in effect in the area served by Vancouver Coastal Health, the oldest one dating back to 1990. The $3.2-million project funded by Genome BC and Genome Canada will include development of a tool kit consisting of field-ready testing procedures that can be conducted on basic equipment common in labs all over the province and software that can be used to quickly detect the presence of unhealthy conditions.
Identifying the genetic signature of certain pathogens will also allow scientists to determine the source of the contamination. "If we know an E. coli is specific to cattle we can look upstream and find the farms and make sure they use less water in their manure runoffs or avoid using it after a heavy rainfall," she said.
rshore@vancouversun.com