Escherichia coli is a normal inhabitant of the healthy gut, but is also an important and widespread human and animal pathogen. E. coli has been associated with human infections including diarrhea, urinary tract infections, and meningitis. E. coli are designated into pathogenic variants (pathovars, also known as pathotypes) based largely on molecular markers associated with specific disease presentations. Many of these biomarkers are present on mobile genetic elements, which provide difficulties in accurate identification and surveillance of these pathogens.