Children treated with antibiotics before their second birthday are more likely to become obese later in their childhood, according to a new study.

US researchers looking at the impact of the common treatment for infections suggested that disruption of bacteria in the gut could have a longer term effect on children's metabolism and increase weight gain.

The group of American toddlers they followed were 26 per cent more likely to be diagnosed with childhood obesity if they had been prescribed an antibiotic, they found.

This weight gain risk increased with multiple treatments and researchers found a smaller impact from drugs taken to curb excessive stomach acid – which are rarely used in children in the UK.

Independent experts stressed there were limitations to the study which cannot rule out that other factors are affecting both weight and illnesses - unrelated to gut bacteria. For example, children from less well off backgrounds are more likely to be obese and to be exposed to cigarette smoke which can increase risks of infection.

But with childhood obesity and antibiotic overuse reaching crisis point in many developed nations they say the findings are worth further investigation.

The study, published in the journal Gut, set out to assess the use of antibiotics and antacid prescriptions in early childhood among those with a diagnosis of obesity.

Using the health records of more than 333,000 infants recorded into the US Military Health System database between 2006 and 2013 they found nearly three-quarters (72.4 per cent) had been prescribed an antibiotic.

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By age three 46,993 (14.1 per cent) children became obese, of whom 9,628 had not been prescribed any antibiotics or acid suppressants.

Because the study is observational it cannot establish cause but the authors wrote: “We found that outpatient prescriptions for antibiotics and acid-suppressing medications within the first two years of life are associated with the development of early childhood obesity.

“This association became stronger with prescriptions for more than one type of microbiota-altering medication.”

However children whose parents were below officer rank – a proxy for wealth and socioeconomic status – were also more likely to be obese and this could account for some of the risk.

Dr Max Davie, officer for health promotion for the Royal College of Paediatrics and Child Health, said: “Although this is reported as the largest study of its kind, it has got its limitations – it is observational and so you can’t establish cause, information about the mother’s weight, whether they smoked or had other underlying conditions aren’t available and there are complex links between the environment and obesity that need to be taken into account.

“That said, childhood obesity levels in the UK are at crisis point with one in three children overweight or obese by the time they leave primary school. We are also battling antibiotic resistance so any avoidable doses throughout the life-course would be beneficial to the cause. We therefore need to acknowledge these findings and would welcome further review."

Additional reporting by Press Association

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