When asked what is the typical pathogen associated with poultry most of my students will answer Salmonella but there is another pathogen that is also likely to cause illness in customers, Campylobacter. This bacteria is found primarily in poultry; chicken, duck, turkey and game birds are all effected. It is found in healthy poultry stocks, in some cattle and sheep, dogs and it has even been found on farmyard flies. It does not effect poultry but can cause some reproductive problems for cattle. From 20 - 100% of chicken have it in their systems. Even free ranged poultry and wild birds will have it regularly. It is found more typically in industrialized countries but it may or may not have anything to do with modern farming techniques. It is also easily spread through wild populations.
The bacteria, more specifically Campylobacter jejuni, is a major cause of intestinal distress in humans. Estimates are from 2 - 4,000,000 people are effected each year in the U.S. The disease causes gastroenteridis and includes symtoms such as diarrhea and vomiting and lasts about a week. Typical home diagnosis is "stomache flu". The bacteria takes about two or three days to incubate so tracing its source may be difficult.
So what can be done? Cooking to proper temperature, 165 F according to USDA guidlines, will destroy it. Storing meats appropriately with poultry on the bottom shelves or seperate from other meats, washing all contact surfaces properly, possibly using seperate cutting boards are all ways to prevent contamination.
It is estimated that about a 400 - 500 bacteria count is needed to bring on symtoms in some people. For others it is higher depending on the digestive health of the person. It is not typically lethal with few deaths occuring and only in those who have a compromised immune system.
Now the stinky part, Campylobacter is spread primarly through fecal matter. Animals raised in close quarters may be more likely to have it but free ranged poultry populations are very likely to have it too. Many chefs today like to cook duck to less than 165F, so be sure to rinse the exterior and sear the duck well to reduce risk. Ducks are defeathered and then dipped in parrafin to remove very fine down feathers. This may help to reduce risk but if they are eviscerated poorly there could still be problems. Fresher poultry is less likely to have a high bacteria count and keeping poultry very cold is also important. http://www.fda.gov/Food/FoodSafety/FoodborneIllness/FoodborneIllnessFoodbornePathogensNaturalToxins/BadBugBook/ucm070024.htm