There are two main issues.  ...

There are two main issues.  Firstly the suspended solids level.  This can harbour high levels of bacteria, which are then protected against chlorine treatment.  Secondly the nitrogen content especially any free ammonia.  If that occurs, the chlorine reacts very quickly to form a range of chloramines, which only kill bacteria very slowly.  In clean water, 1 mg/L free chlorine kills 99.9% of bacteria in minutes.  Suspended solids impact the kill rate of chlorine.  I used autoclaved yeast to simulate dirty conditions and the chlorine levels required multiplied by 50 times in some experiments.  The other question to ask is what method are you using to detect E coli.  There are certain Bacilli which are able to grow on the selective media for coliforms and the way to differentiate them is to take a colony and carry out a Gram's stain on it.  They tend to show Gram positive although older cells may look Gram negative but they will show spores present in their cells.  E coli is Gram negative and does not produce spores.