Gary Stix's article An Antibiotic Resistance Fighter (preview only) has a graphic on how a bacteria can undermine the effectiveness of antibiotics. I only reproduce the text here:
Rapid-fire mutations in Escherichia coli bacteria can undermine the effectiveness of ciprofloxacin (cipro), an antibiotic that is increasingly being prescribed by physicians.
1. Cipro's Action: Cipro usually harms bacteria by binding to an enzyme called gyrase and preventing it from functioning properly.
2. How Resistance Arises: Resistance is initiated when E. coli responds by generating single-stranded DNA. Individual molecules of another protein, RecA, the line up in a chain and attach to the single-stranded DNA. RecA facilitates cleavage of a regulatory protein, LexA. This change frees a set of formerly repressed genes to induce mutations elsewhere. The mutations end up blocking cipro's binding to gyrase, thereby preventing the drug from working.
3. A Possible Solution: Drugs that bound to LexA and prevented its cleavage - such as the hypothetical compound X detected here - would stall that sequence and thus could overcome resistance and restore effectiveness to the antibiotic.
The above mechanism was hypothesised and experiments were run to confirm this hypothesis by Romesberg, Cirz, Chin and others and the results were published on PLoS Biology.
An unexpected - and undesired - aside to the publication of the PLoS Biology paper emerged when the intelligent-design community embraced the results as confirmation of its unorthodox worldview. The frenzied mutations in Romesberg's experiments were not random, its members contend, but were set off under deliberate direction of the bacterium: "Life takes control of its fate. Living things are not passive participants of the interplay between stochastic events and envrionmental pressures," writes the pseudonymous Mike Gene on the website idthink.net, while adding, "That evolution may be under some form of intrinsic control is only a piece of the telelogical [design in nature] puzzle. But it is a significant piece, in that the ability to adapt, at least to these two antibiotics, is under control."