A study found that children with diarrhoea caused by the E.coli 0157 strain treated with antibiotics were 17 times more likely to develop a potentially fatal kidney disorder than those not given the drugs.
It starts with diarrhoea and vomiting and progresses to low urine output, a swollen abdomen and seizures.
The researchers at the University of Washington School of Medicine in Seattle published the findings of their study in the New England Journal of Medicine five weeks early because of fears about children's safety.
The E.coli bacteria is commonly found on the surface of raw hamburgers and several large outbreaks caused by contaminated burgers in the US in the early 1990s led to new federal government standards for cooking meat.
An outbreak of E. coli killed 21 people in central Scotland in 1996 and 1997.
The number of cases of E. coli poisoning has tripled in the UK over the last decade.
In about 15% of children who develop an E.coli infection, HUS appears soon after the onset of diarrhoea.
Infected
But the Seattle study looked at 71 children who were infected with the E.coli strain and found that HUS developed in more than half - five out of nine - children given antibiotics.
This compared to just five of 62 children not given antibiotics.
Lead researcher Dr Craig Wong said a link between HUS and antibiotic use was "strong and plausible".
He added: "We therefore advise against giving antibiotics to children who might be infected with E.coli 0157."
Antibiotics should only be given when stool tests show treatment with antibiotics will not increase the children's risk.
But resistance to antibiotics was not the cause of the problem, he said.
Dr Sarah O'Brien, head of the gastro-intestinal diseases section at the Public Health Laboratory Service in the UK, said the study's findings were "very important".
She said: "For some time we have had experimental evidence from work in the lab that treatment for people with E.coli 0157 could do more harm than good because of the potential to release toxins from inside the bacteria.
"For that reason we have always erred on the side of caution."
Most doctors would not be prescribing antibiotics for E.coli but those that were should now stop, she added.