You may have to put filter in filter assembly before autoclavIng. Years ago, I was analyzing total and fecal coliform, fecal strep. I used Millipore filters, filtering apparatus. Millipore had a disinfecting system apparatus that used UV light. It was expensive, so I made one that had two UV lights in a wooden box, lined with stainless steel for reflection. These lights produce direct UV light and ozone too. I was filtering stream water, diluted as needed with specially prepared sterilized and buffered filter water. There was sometimes some non-countable colonies (unsure If gram negative), so I do not know if that was from water sample or filter. But some water samples or just pure dilution water did not have any colonies, so contamination did not appear to be a problem. If suggestions obtained do not work, I would discuss issue with an analytical chemist or microbiologist, or perhaps support services at Millipore Corp. If you can find a local lab that runs similar samples, you might ask for help or volunteer some time to work and observe their techniques, equipment and processing of samples.