Unfortunately, we are left with little more than speculation at this point. That said:
As a writer, I can follow a narrative thread and recognized the foreshadowing of the conversation with Rick and his son over the naming of the pig and her state of health. This conversation appears innocent enough but will serve as a sign of hidden infection in the group.
We see Patrick, sick, fevered, coughing with flu-like symptoms, dare we say "swine flu-like" symptoms. The foreshadowing is after Rick noticing the dead pig after he returns from his harrowing event with Clara.
Everything going wrong...
Adding insult to injury, the foraging party returns after losing one of their own, it appears the "30 days without an Incident" period is ended both from without and now from within, as Patrick succumbs sweaty, fevered, barely coherent (coughing over the shower water...didn't anyone notice his increased coughing? Where does he live that no one noticed this?) and dying in the shower, inside the compound with no gates between him and many potential victims...
Beyond the Fourth Wall
Honestly, seeing that he was likely added in the off-season, picked up from outside of the normal and safe populations of Woodbury, how he got infected was less important THAN he got infected and there were no protocols to notice this. Curiously enough we haven't seen much in the way of infection in the series. I would think with all of the dead lying about, disease should be much more of a player than it has so far.
In a world where everyone is infected with the Zombie virus, a health survey on a daily basis, checking for infections, scratches, colds and flu symptoms, as well as a watch set on anyone who is sick (or extremely old) should be a mandatory thing.
But if they did this, they would not be on television. This is not a show about people doing the right things, but how under stress, they can make simple mistakes with long lasting repercussions.