How will the source of the E. coli outbreak linked to Chipotle be identified?

An E. coli outbreak linked to Chipotle restaurants in Oregon and Washington state has resulted in at least 22 people falling sick including 8 who have been hospitalized. Health department officials in both states along with the Centers for Disease Control and the Food and Drug Administration are investigating the outbreak, whose source is still unknown. GENeS asked scientists to comment on how the source of food poisoning outbreaks are identified.


Dr. Michael Doyle, Regents Professor of Food Microbiology,Director, Center for Food Safety, Department of Food Science & Technology, University of Georgia (webpage):

Expertise: bacterial food borne pathogens, methods to reduce pathogens on produce, meat, and poultry.

“The normal practice in these cases is to invite the CDC to lead the investigation. Sometimes the FDA and USDA could also be involved. Typically there are epidemiological studies conducted using standard questionnaires to identify the vehicle that caused the outbreak. This involves case control studies that take into account the food consumption history of individuals who were affected and those that were not. If a food item is identified as having a statistically significant association with causing the illness, the investigation will focus on that that item.

“Depending upon what the vehicle is, the federal agency that has oversight of that particular food item will have jurisdiction over the trace back. If its meat, poultry or processed eggs, that organization would be United States Department of Agriculture (USDA). If it is anything else like produce, it would be the Food and Drug Administration (FDA).

“Trace back techniques have gotten so good that it may be possible to trace the source of the contamination back to not only the processor but also the grower. The other thing that is new to this process and could help trace back is the use of whole genome sequencing of the outbreak bacteria for which the CDC and FDA are developing databases. For E. coli the complete genome information of outbreak strains is expected to be available in the next few years but the FDA and CDC may have enough information in their existing database to match the strain of E. coli to a particular source.”


Dr. Chobi DebRoy, Clinical Professor, Department of Veterinary and Biomedical Sciences, Director, E. coli Reference Center, The Pennsylvania State University (webpage):

Expertise: pathogenic E. coli, diagnostics, whole genome sequencing. Dr DebRoy is the Director of the E. coli Reference Center, one of the largest repositories for E. coli isolates and a major diagnostic laboratory in North America.

“The FDA will be now investigating the source of the E. coli strain that may have caused the outbreak. While most of the outbreak of illnesses are caused by Shiga toxin producing E. coli strain O157:H7, in 2012 the FDA Food Safety and Inspection Service included six other strains of E. coli as adulterants in meat. These are O26, O45, O103, O111, O121 and O145. All these strains produce Shiga toxins that are essential for the bacteria to be pathogenic. The FDA will isolate E. coli from produce and other food materials that have been consumed and then identify the strain by established molecular methods. To determine the strain that may have caused the outbreak, E. coli isolated from victims of the outbreak and from the food consumed have to match genetically. If they match and show 98-100% identity statistically, they will be able to identify the source of the infection. DNA sequencing of the whole E. coli genomes have been also used for tracking sources of contamination by FDA.

“The molecular method generally takes at least 18- 24 hours just to isolate and confirm the bacterial strain as E. coli. However, to determine the source it will take longer, since they have to test hundreds, if not thousands of samples, for the bacteria and compare the strains.”


Declared interests (see GENeS register of interests policy):

No interests declared.



FDA Investigating Outbreak of E. coli Infections‘ U.S. Food and Drug Administration notification posted on October 31, 2015.

Please feel free to leave your comments below, but be aware that by doing so you agree to our Terms & Conditions.