General Mills logoIn February 2016, federal food safety officials began their investigation into a widespread E. coli outbreak, which eventually led to the recall of over 30 million pounds of General Mills flour. The outbreak has been linked to General Mills’ flour processing plant in Kansas City, Missouri.

To date, Food and Drug Administration (FDA) officials, along with officials within China’s Centre for Food Safety, state that the investigation is ongoing. Through the use of cutting-edge laboratory technology and intensive research, officials were eventually able to track down the root cause of the contamination.

Following is an examination of the background, investigation, and outcome of the ongoing E. coli outbreak linked to General Mills.


When federal officials identified the E. coli outbreak in February, 14 cases had been reported to food safety officials. Eventually, the strain of bacteria was discovered: Shiga toxin-producing Escherichia coli O121 (STEC O121), or E. coli O121. The samples were collected from individuals who were stricken with the illness in both Arizona and Oklahoma.

E. coli
Image courtesy NIAID | Flickr

There are various strains of E. coli, many of which are essential to normal digestion, residing within the intestines of most mammals. Other strains, including E. coli O121, cause illness to occur. This was the strain discovered within samples of people who became ill in this particular case.

Certain strains of E. coli produce the Shiga toxin, which is often called Shiga toxin-producing Escherichia coli O121, or STEC O121. The strains can also be referred to as Verocytotoxin-producing E. coli (VTEC) or enterohemorrhagic E. coli (EHEC). When food outbreaks occur within the United States, they are generally of the O157 strain, which is the most ubiquitous type of STEC within North America.

E. coli O121 is a pathogenic variety of E. coli that can cause severe illness. Common symptoms include severe intestinal bleeding or hemorrhage. Without prompt treatment, hemolytic uremic syndrome may develop, which can result in kidney failure. Other symptoms may include stomach cramps, diarrhea (which is frequently bloody), fever (which is rare) and vomiting. Symptoms of E. coli O121 generally range in duration from three to four days, with recovery taking place within five to seven days.


Soon after the official classification of this case as an “outbreak,” food safety officials within the CDC and the FDA intensified their investigation. The stimulus for this action was the discovery by PulseNet—CDC’s national and regional network that tracks foodborne infections—confirming that an outbreak existed.

According to one investigator, “Based on preliminary information we had about a potential link, calls with General Mills began in late April.” After officials identified the outbreak in February, with 14 cases, some asked: why the delay?

The simple answer is that certain variations of E. coli are more difficult to detect than others. In this instance, the origin was the strain O121, a more difficult form of E. coli to detect than more common strains, such as E. coli O157. After initial lab testing for the presence of bacteria, the FDA determined the strain to be “non-O157,” requiring the use of Whole Genome Sequencing (WGS).

Whole Genome Sequencing and GenomeTrakr

WGS is the latest tool to be used in foodborne outbreak investigations. While a detailed breakdown of WGS is beyond the scope of this post, it can be broken down into simplified terms, states Dr. Eric Brown, director of the Division of Microbiology at the Center for Food Safety and Applied Nutrition:

Image courtesy NIAID | Flickr

“Think of Salmonella, for instance, as a tribe of many thousands of subtly different pathogens…(WGS) helps us to crack the genetic code. A pathogen can evolve very quickly and begin to acquire unique genetic signatures (that) identify it as coming from a particular region.”

Once the laboratory has the derived genomic data, it is uploaded to a global database called GenomeTrakr. The database contains WGS information on over 50,000 strains of bacteria, which are called isolates.

Through rigorous investigation requiring the use of WGS and GenomeTrakr, FDA officials were able to isolate STEC O121 from samples of General Mills flour collected from homes of ill people in Arizona and Oklahoma.” WGS and GenomeTrakr information deduced the likely source of the outbreak to be one location: a General Mills facility in Kansas City, Missouri.


To date, the CDC reports that 42 people from 21 states have been infected with the outbreak strain STEC O121. Of those 42 individuals, 11 needed to be hospitalized. None of them developed kidney failure, and no deaths have been reported.

General Mills has expanded its recall to include three varieties of flour products. More than 30 million pounds of flour is being recalled, according to the latest estimates. General Mills has posted advisory and cautionary information related to the outbreak on its website,