Cook the eggs, or like Kkrista123said; scrambled eggs.
It has to be thouroughly cooked and then it is fine. Don't chuck them down raw like an 80's dude-getting-in-shape-eye-of-the-tiger movie, and no runny yokes.
In some country's some vets have shots for ducks that makes them immune for salmonella. Over here if you want to sell your eggs or the meat you háve to get it. I still haven't found one that comes over for only a handfull of ducks though...unfortunately. But maybe where you live it is possible.
For the rest;
Like WanneBehillbilly said; try to handle everything hygenic. Wash your coop, your hands, your eggs, etc. (and raw fruits and vegetables by the way...people tend to forget that it is not just a 'meat-thing'.)
Thoroughly cook till the yoke is also cooked.
IF you want to have runny yokes; most of the time IF it has salmonella ánd it works out bad for you; you will have stuff running out of two ways of your body (like a short stomach flue). This is something most people cán survive. Do not feed non-thouroughly cooked/baked eggs to children, pregnant women, elderly, sick people, or anything that might have a less strong immune system.