I believe that most any bacteria would come from the outside of the egg. Even if it were true that the egg yolk is infected the lime juice is so acidic it would kill the bacteria or parasite eggs. Lemon and Lime juice is acidic but helps our body to be alkaline.
I add lemon juice to my water every day to kill any bacteria or parasite eggs that get into me. I love a hot lemon tonic in the morning with a dash of stevia... This is just one of the things that I do, every day, to create a unwelcome envirement for parasites!