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The researchers think that repeated courses of antibiotics destroy the gut bacteria resulting in gut bacteria imbalance. From Red Orbit:

Antibiotic overuse could up diabetes risk, study says

Repeated use of some antibiotics could increase a person’s risk of developing type 2 diabetes, according to research published online Tuesday in the European Journal of Endocrinology. In the study, scientists from the University of Pennsylvania found that men and women who had ever been prescribed with at least two courses of specific types of antibiotics were more likely to eventually be diagnosed with type 2 diabetes than those who had taken no more than one.

The antibiotics used in the research came from one of four categories, according to LiveScience: penicillins, cephalosporins, quinolones and macrolides. The authors reviewed a database of UK patients, looking at the number of antibiotic prescriptions given to over 200,000 diabetic patients at least one year before those individuals were diagnosed with the condition...They found that the more courses of antibiotics that were prescribed to a person, the greater the risk that he or she would go on to develop the disease.

Patients who had been prescribed between two and five courses of penicillin increased their risk of diabetes by 8 percent, according to the Daily Mail, and the risk increased by 23 percent for those receiving more than five courses of the frequently used antibiotic versus the one- or no-course group.

Those who were given between two and five courses of quinolones, which are used to treat respiratory and urinary tract infections, had an increased diabetes risk of 15 percent, and those receiving more than five courses saw that risk shoot up by 37 percent. 

Those who were given just one course of antibiotics showed no such increase in diabetes risk, the researchers reported. Nor was there any link found between exposure to anti-virals and anti-fungals and diabetes risk. The reason for the association between frequent antibiotic use and the risk of diabetes is not clear, but may be related to a gut bacteria imbalance, they wrote.“Gut bacteria have been suggested to influence the mechanisms behind obesity, insulin resistance and diabetes in both animal and human models. Previous studies have shown that antibiotics can alter the digestive ecosystem,” added lead author Dr. Ben Boursi.