Hi,

Recent reasearch is showing now that, what we thought was "thrush" is actually the result of a Staph infection. When there are symptoms such as you describe - nipples that won't heal despite correct positioning, recurrent mastitis etc, your dr should always take a swab and have it cultured so that we know what we are dealing with.
There's every chance that this course of antibiotics will knock it on the head and you'll go on to breastfeed fine