my answer about your question , the sample should be taken from tissues of the morbid birds recently or from fecal samples , and the quantity of sample about 1 gram are sufficient to isolate the Salmonella and E.coli .
Simple statistics will tell you probabilities for detection at different prevalences of target organism and sample numbers. Single sample size usually is 10-25 g for meat/skin. We used around 10g chicken neck-skin for slaughtered chicken hanging on the chain-line. Search Danish reports for describtion of sock sampling flock status. As I recall this has proven much better than fecal swabs and other single bird sampling.