Diesel "bug" is not an uncommon problem. The bug lives in the inversion layer between water and diesel fuel and will clog filters very quickly. If it gets as far as injectors then your in deep Sh.t! When the injector nozzle heats up during ignition, the bug turns to varnish and seizes the nozzle needle and your injectors are now destined for the scrap metal bin.
There are treatments available to kill the bugs, but by far the best approach is to remove your fuel tank, drain completely and wash out with the biocide that you would use to treat the bug. Drain ALL fuel lines and flush carefully with biocide. In all honesty I have actually used flexible rifle pull throughs to clean fuel lines!
Reassemble and full your system with clean fuel.To prevent reinfection, ensure you refill your fuel tank regularly but especially after a longish run. This is VERY important if you have Cummins or Detroit Diesel type unit injectors as the fuel returns to the fuel tank and warms the fuel in the tank. As the warm fuel contracts it draws cold air into the tanks, along with the moisture in the air. Over time the moisture builds up and hey presto, perfect conditions for the fuel bug.
If you have had an infection, and follow the above advice, I would strongly advise you to also dose your fuel tank (s) regularly with biocide to prevent reinfection, especially if you have bulk storage and/or you have vehicles that do not run often.
Don't bother asking your service station (Gas/petrol station) for advise, they will not have a clue what your talking about, and even if they do they will usually deny the existence of the bug as they want to avoid any liability.