Stool cultures present a unique challenge in the microbiology laboratory because of the diversity of the normal flora of the human gut.
Within any stool culture, dozens of different organisms may be present with different significance. In fact, a large number of pediatric cases of diarrhea are caused by viruses that are no longer tested by culture, but have been replaced by molecular techniques. The ability of PCR to specifically target these pathogens independent of in vitro growth greatly reduces the chances of missing common causes of GI illnesses. It also increases our ability to positively ID which organism caused the illness.