“During the relevant production period, all such tests were negative,” Fairbank Farms said in written answers to questions from The Times.

Image A meat display at Costco, which requires independent E. coli testing by its grinding facility. Credit... Justin Sullivan/Getty Images

However, the company added on Thursday that it was re-evaluating its testing procedures. “In addition to those controls, Fairbank is evaluating the addition of another firewall such as additional testing of incoming product,” the company said.

Asked about the move by Trader Joe’s to terminate its relationship, the company said: “We respect each retailer’s right to select their suppliers. And any retailer may dictate a quality assurance protocol for their suppliers to follow to protect their customers. Our finished product testing protocol is the most stringent in the industry and that continues to be a selling point with our customers.”

The United States Department of Agriculture, which banned the deadly E. coli strain known as 0157:H7 in 1994, has encouraged  but does not require  meat companies to test their products for the pathogen. In the absence of such a rule, meat companies have adopted varied practices.

But in recent weeks, a growing number of meat industry officials have said they endorse trim testing by grinders despite resistance by slaughterhouses and some trade groups. Grinders typically use trimmings from multiple suppliers, these food safety experts say, and only ingredient testing, when it uncovers E. coli, enables grinders to identify the slaughterhouse that shipped the contaminated trim.

“The raw material sampling really helps you do the trace back needed to go back to someone and say, ‘I don’t know what’s going on, you’ve controlled this for a long time, what’s changed?’ ” said Dr. David M. Theno, a consultant who became a food safety officer at Jack in the Box after the fast food chain’s deadly outbreak of E. coli in 1992, which prompted the government ban on 0157:H7.

Dr. Theno, who retired last year, said he worked with Costco and AFA Foods’ predecessor company to devise new safety systems, and he confirmed previous statements by AFA Foods officials that they started testing trim at their grinding facilities, like Costco did, but then stopped when slaughterhouses balked at selling them trim.