Three days after heavy rainfall caused mass flooding in her Etobicoke home, Lois Thorne noticed mould.

 "You can see the watermarks...see how high the water was?," she told CBC’s Shannon Martin in the flood aftermath.

A few weeks post-flood, the watermarks are the least of her worries. Her home is now contaminated with E. coli.

One of the culprits that comes with flooding is toxic mould. And what started in the basement spread to her entire home.

Her house is likely not alone.

"In the last two weeks we've found at least 90-95 per cent homes we've inspected have had high levels of E. coli and bacteria associated with human waste," says private inspector Frank Haverkate of safeair.ca.

Haverkate swabbed the house after the floods and found the spread of the dangerous bacteria everywhere from door knobs to couches. No surface is spared - even if it looks clean and has been disinfected, danger could still persist.

Thorne has complained of a cough since the flooding.

Haverkate worries in the rush to repair flood damage homeowners like Thorne have not considered bacteria such as E. coli. And not all insurance companies and contractors test for it.

CBC News took samples of the mould and sent them to the lab to test for E. coli. One week later, the results are back, confirming E. coli bacteria all over the house, posing a significant health risk.

"The occupants of the home should consult their doctor, and stay out of the home until work is completed" to clean the entire house, not only in the basement but all upstairs, according to the report.

"Well that I will have to debate. I don’t have anywhere to go," says Thorne.

Cleaning a home of E. coli contamination is not a do-it-yourself endeavor, either. Specialists can charge $10-15 per square foot. For Thorne's home, that could be up to $20,000 in cleaning costs.