I know that guinea pig urine (OK, Cashews) has traces of E-coli and other nasty bacteria in it (found while searching for something causing his illness) ... to be honest, I'm sure my waste isn't a paddling pool of joy so I wouldn't be too worried about what your pigs can pass to you.
Problems with bacteria only really exist if your immune system becomes compromised - in which case you'd be in hospital (JOY!) or if you decide to rub your hand in your pigs cage and then suck on it while watching Eastenders. You need large quantities to affect the kid and yourself and I doubt that'd happen unless you were being ridiculous. It's there. It'll be on your mind but it's hardly a threat. Get one of those hand-sanitiser squishy things if you're worried and don't let the cage get to the stage where it stinks of ammonia (which you shouldn't do anyway)