The following study looked at this issue specifically (use of antibiotics causing type-1 diabetes) and found that it did not happen:
Denmark has a centralized records medical system, so it is possible to do studies where you look at all children in the country, and compare their antibiotics usage to their type-1 diabetes status. We could never do something like that here in the USA, but we can benefit from the studies done in other countries. This study was based on about 600,000 patients, and was just published recently (in 2009).
Here is about half of their abstract. I've removed the numbers, so that it reads better:
Use of any antibiotic was not associated with type 1 diabetes. Evaluation of type 1 diabetes risk according to number of courses of any antibiotic yielded no association between antibiotic use and type 1 diabetes. No specific class of antibiotics was associated with type 1 diabetes, no specific age of use was associated with type 1 diabetes, and no specific age at onset of type 1 diabetes was associated with antibiotics. In a large nationwide prospective study, no association between antibiotic use and type 1 diabetes was found among Danish children.I have not found any controlled clinical (human) studies which show that increased antibiotic use increases the chance of type-1 diabetes.
Joshua Levy
Blog: http://cureresearch4type1diabetes.blogspot.com
Web: http://joshualevy.pbworks.com/DiabetesCureReadyForHumanTrials