After a quick search it looks like the mainstream explanation is that people were just getting sick for "unknown reasons" before being able to test cheaply enough for e coli:

>"The sudden debut of E. coli O157:H7 in the 1980s made many people wonder how it had come to be. Was it the monstrous product of the modern food industry? Tarr and his colleagues analyzed the genome of the bacteria to estimate its time of origin. “These organisms have been around for 7,000 years,” says Tarr. It’s possible that E. coli O157:H7 and other pathogenic strains caused outbreaks for centuries before microbiologists could identify them as the cause."

http://www.newsweek.com/e-coli-rise-superbacteria-67931