After the salmonella scare last year there were a lot of proponents of backyard chickens that were saying that such things only happen in filthy commercial facilities and that somehow backyard birds were magically immune to such things because they are well cared for.
If your birds run around outside, if you have rodents, if you have flies, if you have wild birds that enter your coop or share feed with your birds, if you have cats that commingle with your birds and defecate near them, if there are times of the year when conditions in your coop/run are rather damp, then an argument could be made that eggs from backyard flocks are even more susceptible to contamination from salmonella than those from conventional large-scale production systems.