Sources of E. coli
Where does E. coli come from?
E. coli O157:H7 bacteria and other pathogenic E. coli mostly live in the intestines of cattle, but E. coli bacteria have also been found in the intestines of chickens, deer, sheep, and pigs. [1, 35]
A 2003 study on the prevalence of E. coli O157:H7 in livestock at 29 county and three large state agricultural fairs in the United States found that E. coli O157:H7 could be isolated from 13.8% of beef cattle, 5.9% of dairy cattle, 3.6% of pigs, 5.2% of sheep, and 2.8% of goats.  Over 7% of pest fly pools also tested positive for E. coli O157:H7.  Shiga toxin-producing E. coli does not make the animals that carry it ill.  The animals are merely the reservoir for the bacteria. 
According to a study published in 2011, an estimated 93,094 illnesses are due to domestically acquired E. coli O157:H7 each year in the United States.  Estimates of foodborne-acquired O157:H7 cases result in 2,138 hospitalizations and 20 deaths annually. 
What makes E. coli O157:H7 remarkably dangerous is its very low infectious dose, and how relatively difficult it is to kill these bacteria. [4, 27] “E. coli O157:H7 in ground beef that is only slightly undercooked can result in infection.”  As few as 20 organisms may be sufficient to infect a person and, as a result, possibly kill them.  And unlike generic E. coli, the O157:H7 serotype multiplies at temperatures up to 44 Fahrenheit, survives freezing and thawing, is heat-resistant, grows at temperatures up to 111 F, resists drying, and can survive exposure to acidic environments. [27, 28] And, finally, to make it even more of a threat, E. coli O157:H7 bacteria are easily transmitted by person-to-person contact. [4, 13]
Trace-back and source identification
E. coli O157:H7 and other non-O157 STEC are now routinely “fingerprinted” as part of surveillance of foodborne disease.  This surveillance was first initiated in response to the major outbreak of E. coli O157:H7 infections in 1993. As described by the CDC on the PulseNet website:
In 1993, a large outbreak of foodborne illness caused by the bacterium Escherichia coli O157:H7 occurred in the western United States. In this outbreak, scientists at CDC performed DNA "fingerprinting" by pulsed-field gel electrophoresis (PFGE) and determined that the strain of E. coli O157:H7 found in patients had the same PFGE pattern as the strain found in hamburger patties served at a large chain of regional fast food restaurants. Prompt recognition of this outbreak and its cause may have prevented an estimated 800 illnesses. As a result, CDC developed standardized PFGE methods and in collaboration with the Association of Public Health Laboratories (APHL), created PulseNet so that scientists at public health laboratories throughout the country could rapidly compare the PFGE patterns of bacteria isolated from ill persons and determine whether they are similar.
When a sample is taken from food that is contaminated with bacteria, such as E. coli O157:H7, Listeria, Salmonella, or Campylobacter, the sample is tested (or cultured) to obtain and identify the bacterial isolate.  Similarly, if a person consumes contaminated food, and becomes infected as a result, a stool sample can be cultured to obtain and identify the bacterial isolate. These bacterial isolates are then broken down into component parts to create a DNA “fingerprint.” [52, 53] The “fingerprint” can then be compared and matched up to the “fingerprint” of isolates from other persons who consumed the contaminated food.  When “fingerprints” match, the match is proof that the contaminated food was the source of the illness.
The process of obtaining the DNA “fingerprint” is called Pulse Field Gel Electrophoresis (PFGE).  The PFGE technique is used to separate the DNA of the bacterial isolate into smaller pieces. The DNA is placed in a flat gel matrix of agarose, a polysaccharide obtained from agar, and exposed to an alternating electric field. [52, 53] Individual pieces of DNA, or bands, will migrate across the gel, creating a bar code-like pattern unique to each strain.  By performing the procedure, scientists can identify hundreds of strains of E. coli O157:H7 as well as strains of Listeria, Salmonella, and Campylobacter.