I am assuming you had a big contamination if you had to go through such extremes but I don't know the particulars or where you think the contamination came from. So, I would first make sure your biological safety cabinets are working and that your incubators are functioning properly. For your incubators, I would have extra sets of shelves and water pans. I would autoclave one set and exchange every week or so. Water pans should be autoclaved and then use sterile water and add a fungal inhibitor. Use disposable pipets and a clean pipette aid for adding media to dishes. I would also recommend using disposable lab coats and gloves along with a sticky mat at the door. These are some suggestions that may help. To test for contamination some some people will use open Trypticase Soy Yeast agar plates (TSY Plates) without antibiotics. Place them in areas of the cell culture room. Leave them open for a hour then incubate at 37C in a bacterial incubator. I hope this helps.