According to lead researcher Renata Picao, the "super bacteria" entered the city's waterways when sewage coming from local hospitals got channeled into the bay.
"We have been looking for 'super bacteria' in coastal waters during a one-year period in five beaches," Picao told CNN during a visit to her lab. "We found that the threats occur in coastal waters in a variety of concentrations and that they are strongly associated with pollution."
The samples were collected between 2013 and 2014. The superbug found was carbapenem-resistant Enterobacteriaceae, or CRE.
Picao said there is no reason to believe the levels have changed because raw sewage continues to flow into many waterways. She said the next step is to test the impact these bacteria can have when humans come in contact with them in coastal waters.
The news comes as Rio prepares to host hundreds of thousands of athletes and tourists during next month's Summer Olympics.
Among the beaches flagged were Flamengo and Botafogo, which border the bay where Olympic sailors are scheduled to compete.
"It's a nice sailing area but every time you get some water in your face, it feels like there's some alien enemy entering your face," German Paralympic sailor Heiko Kroger said during a recent visit to Rio. "I keep my nose and my lips closed."
Kroger believes the super bacteria may have caused a severe skin infection in one of his teammates during recent training.
'I don't take my children to these beaches'
Picao said she believes the city's fragile sanitation infrastructure is responsible for the presence of the super bacteria.
"This bacteria colonizes the intestine and it goes along with feces to the hospital sewage," Picao said. "We believe that hospital sewage goes into municipal sewage and gets to the Guanabara Bay or to other rivers and finally gets to the beach."
According to Rio's water utility, Cedae, the criteria established by the World Health Organization
have been followed.
"Fifty-one percent of the city's sewage is now treated," production director Edes de Oliveira told CNN. "Seven years ago it was only 11%." A new sewage plant that opened in May
in the western part of the city will serve about 430,000 residents.
When Rio made its bid to host the Summer Games back in 2009, it promised to clean up the polluted waterways and connect 80% of homes to the sewage system.
Despite concerns, neither Picao nor international Olympic authorities recommend moving the sailing venue.
"I wouldn't say to change the venues because we don't know the risks yet," Picao said. "We are making this alert because if athletes get infected there is a chance this bacteria is multiresistant and the physicians should know about this."
The other beaches that tested positive for the bacteria were Leblon and Ipanema, which are very popular among tourists and locals alike.
"I don't take my children to these beaches," Picao said. "We still need more studies to tell what would be the risk to human health of this exposure through the water."
Trouble ahead of Rio Olympics
The Rio Games are scheduled to begin on August 5, but with a month to go safety and financial issues continue to plague the international event.
An Australian athlete was mugged
close to her hotel, a local hospital designated for tourists was the scene of a fierce gun battle
and fears over the Zika virus have led several elite athletes to pull out.
Rio de Janeiro mayor Eduardo Paes
told CNN earlier this week the state was doing a terrible job in regard to security in the weeks before the Games. "It's completely failing at its work of policing and taking care of people," he said.
Paes on Tuesday told reporters that Rio was "far from being perfect," but that the city is being transformed for the event.
Carlos Arthur Nuzman, president of the Brazilian Olympic Committee, said Tuesday that the city was ready to start the Games.
"They will be a maximum success in this beautiful city of ours," Nuzman said.