Super bacteria is a form of bacteria that has grown resistant to antibiotics.
According to the Centres for Disease Control and Prevention, at least two million people become infected with this kind of bacteria each year, causing 23,000 deaths. It can prove fatal for 50 per cent of those afflicted.
Some doctors and scientists believe our dependence on antibiotics and antibacterial soaps is to blame for the development of drug-resistant bacteria.
The South American group's lead researcher, Renata Picao, said Rio's "super bacteria" made its way into the city's waterways through sewage from local hospitals, due to a lack of basic sanitation in the metropolitan area.
"We have been looking for super bacteria in coastal waters during a one-year period at five beaches," she told CNN. "We found that the threats occur in coastal waters in a variety of concentrations and that they are strongly associated with pollution."
She explained that intestinal bacteria was transported in patients' faeces to the hospital sewage, which then found its way into Guanabara Bay, to eventually get to the beach.
According to the report, the most amount of super bacteria was detected at Botafogo and Flamengo beaches, where sailors will compete in the Olympics. It was found in as much as 90 per cent of the water samples.
In Copacabana, where the triathlon and open-water swimming competitions will be held, 10 per cent of the water contained samples of the super bacteria.
Ipanema and Leblon, two beaches popular with locals and tourists alike, have also been affected at samples of 50 to 60 per cent.
Experts have likened it to competing in raw sewage.
When Rio bid on the games, they promised to clean up the bays and beaches. But the economy took a turn for the worse, and officials simply conceded that getting rid of all the pollutants was an impossible task by August.
As a result, their initial promise to reduce pollution by 80 per cent went to a best-case scenario of "over 50 per cent".
The mayor of Rio de Janeiro, Eudardo Paes, told CNN the state was doing a terrible job at getting the situation under control.
"It's completely failing at its work of policing and taking care of people," he said. However, he confirmed that the city was being transformed for the event despite being "far from perfect".
But the good news, according to experts, is that these superbugs can only really cause problems for those who are chronically ill with immunity problems.
Therefore, they may not pose a strong risk for athletes or healthy travellers.
WATER CONTAMINATION ISN'T RIO'S ONLY PROBLEM
It's not just the contaminated water that poses a threat to the Games.
Rio is fast running low on funds. Tickets sales are slow. The Zika virus is dominating headlines. An increase in police violence has left little confidence in public security. All of this, and the Olympic Games are just weeks away.
Authorities in the state of Rio are failing to combat the problem of police officers killing citizens in anti-crime operations.
Earlier this week, Human Rights Watch said a pattern of covering up police killings had thwarted efforts to curb violence in Rio's slums.
In a 109-page report, they said the state killed an average of almost two people per day last year, including many who were in custody, unarmed to trying to flee. The rate of deaths by police officers has been rising over the past three years.
Human rights groups have condemned the increasing use of force in slums and outlying areas.
According to the country's interim defence minister, Raul Jungmann, the country will increase the number of soldiers patrolling the streets in August to combat any violent activity.
The Zika virus is another issue plaguing the Games - one which has even prompted some athletes to stay home.
Last month, a group of 150 doctors, scientists and bioethicists even penned a letter to the World Health Organisation, urging that the Games be postponed or relocated due to the outbreak of the mosquito-borne virus.
"Currently, many athletes, delegations, and journalists are struggling with the decision of whether to participate in the Rio 2016 Games," the letter reads.
"We agree with the U.S. Centers for Disease Control recommendation that workers should consider delaying travel to areas with active Zika virus transmission".
Travellers have been warned to protect themselves from mosquito bites at all costs, suggesting long clothing, door screens and netting, and avoiding unprotected sex.
However, the World Health Organisation's emergency committee on Zika declared there was a "very low risk" of further international spread of the virus as a result of the Rio Games.
Of course, a flurry of warnings have preceded almost every city to host the Olympic Games. With Beijing, during the 2008 Summer Olympic Games, it was air pollution. The 2014 Sochi Winter Olympic Games faced accusations of too much sun and not enough hotel rooms.
But the super bacteria is just the latest in a string of problems hindering Brazil right now, leading some commentators to suggest that it could be the worst yet.
Not to mention, while more than 500,000 foreign visitors are expected to show up for the Games, not including the 10,500 athletes, few will actually come face to face with the real, poverty-stricken Rio, which is currently facing its worst recession since the 1930s.
He said more than 21,000 soldiers will assist civil and military police units to protect expressways, the Olympic Village and other Olympic routes in Rio de Janeiro.
