CHLORINE-RESISTANT PATHOGENS. “Some pathogens found in surface water are resistant to normal doses of chlorine but they are likely to be removed if appropriate treatment (e.g. fine filtration) is provided prior to chlorination.” Methods are slow to change. This is less about developing new resistance than the known variation in basal susceptibility to chlorine toxicity.
http://www.lboro.ac.uk/well/resources/fact-sheets/fact-sheets-htm/chlorination.htm