Inadequate traceability measures and protections for confidential corporate information complicated and delayed the investigation of a 2016-17 Salmonella outbreak linked to ground beef, making it virtually impossible for government to warn the public or suggest a recall.

However, analysis of the deadly outbreak also showed the importance of high-tech laboratory advances such as DNA fingerprinting of pathogens, according to a research report on the 21-state Salmonella Newport outbreak recently posted by the Centers for Disease Control and Prevention.

“This investigation emphasizes the utility of (whole genome sequencing) WGS during outbreak investigations and identifies the need for improvements in traceability from the consumer to the farm,” the 22-person research team reported. 

“… tracing back cows at slaughter/processing establishments to the farm from which they originated was problematic because cows were not systematically tracked from farm to slaughter/processing establishments.”

For their analysis, the scientists reviewed data from the Salmonella Newport outbreak, which sickened at least 106 people, with 42 hospitalizations and one death. The outbreak illnesses began in October 2016 and continued through July 2017. 

During the outbreak, epidemiologists and other public health investigators found several indicators that pointed to contaminated beef from slaughtered dairy cattle. Laboratory tests confirmed the outbreak strain of Salmonella Newport in a sample of ground beef from an outbreak victim’s home, as well as in four New Mexico dairy cows. 

The outbreak strain was also confirmed in a sample of fecal matter from a New Mexico dairy cow that investigators collected at a Texas slaughterhouse. Federal officials determined the specific New Mexico dairy farm that sold the animal for slaughter.

However, officials from the USDA’s Food Safety and Inspection Service could not name that farm or report to the public whether the other three infected dairy cows had come from it.

“Because of confidentiality practices, officials were not able to identify the farm or farms of origin for the dairy cows associated with the other three samples or whether the four dairy cows were associated with a single farm,” according to the research report. “… This investigation identified the outbreak strain only in samples from dairy cattle from New Mexico.”

The outbreak investigation included traceback from 11 victims’ shopper loyalty cards and grocery store receipts. Those records showed about 20 ground beef suppliers belonging to at least 10 corporations. The victims’ purchase records showed the ground beef had come from at least a dozen slaughterhouses operated by three companies.

A complex and less than transparent supply chain for beef, particularly ground beef, contributes to the possibility for outbreaks and difficulties for those who investigate them, the researchers concluded.

“Foodborne outbreak investigations could be enhanced by improvements in the traceability of cows from their originating farms or sale barns, through slaughter and processing establishments, to ground beef sold to consumers,” according to the report.

The inclusion of dairy cows in the beef supply is also problematic, the scientists reported.

While most ground beef in the United States is produced from beef cattle, 18 percent is produced from dairy cows. Dairies sell their cows for beef production through sale barns and directly to slaughterhouses when the cows grow old or if their milk production is insufficient. 

Differences in dairy operations and beef operations likely increase the chance of contamination of beef products in general and specifically during in the 2016-17 outbreak, according to the food safety researchers.

“One possible explanation is that dairy cows carrying a high Salmonella load that overwhelmed antimicrobial interventions could have gone to multiple slaughter/processing establishments, resulting in contamination of multiple brands and lots of ground beef,” according to the research report.