NSW Department of Primary Industries (NSW DPI) Immunology & Molecular Diagnostic Research Unit Team Leader, Dr James Chin, says it is commonly believed that each time an antibiotic is used only pathogens or disease-causing bacteria will be killed.

"Antibiotic use in hospitals is often perceived to be solely directed against only bad bacteria. In reality, antibiotics also act against entire microbial communities, including the good bacteria which can protect patients from pathogenic bacteria," he explained.

Antibiotics do not just eliminate bad bacteria, they also maintain a pool of antibiotic resistance genes within the microbial community of patients treated with antibiotics, said Dr Chin.

Using pigs as a model, Dr Chin and Dr Toni Chapman at NSW DPI's Elizabeth Macarthur Agricultural Institute have examined how E.coli bacteria - a common cause of diarrhoea in pigs and humans - respond to treatment by antibiotics.

Dr Chin told the 2007 Australian Society for Microbiology's annual conference in Adelaide that the current theory of antibiotic resistance is that the 'fittest' bacteria, that is, those carrying genes for resistance, are the most likely to survive.

"Because antibiotic treatment will never kill all bacteria, bad or good, there will always be a pool of antibiotic resistance bacteria that can potentially transfer resistance to incoming pathogens.," he explained. "It is important to identify the antimicrobial resistant gene pool in entire microbial communities before antibiotic treatment, said Dr Chin

He added that this has been tested with E. coli in pigs.