Now some scientists believe genetics will be the new weapon in the fight, with doctors consulting bacterial genomes when treating disease.
This week a team at the Wellcome Trust Sanger Institute published a paper in the journal Science, which they say shows the first genetic picture of the evolutionary war between medicine and bacteria.
Bacterial genetics can be tricky. With humans, one person's DNA is passed on to their children, then to their children, and so on down the family tree.
Bacteria are altogether more frisky.
They pass DNA onto their descendants when they divide in two, but they also swap DNA with other bacteria, changing their genetic code.
It is like popping to the shop and changing eye colour with someone at the checkout.
This study has managed to tease out the differences between the two ways of passing on DNA in Streptococcus pneumoniae and draw its family tree.
