SALINAS VALLEY, Calif. -- Six weeks after a deadly E. coli outbreak, supermarkets are laying down the law, telling farmers in the Salinas Valley they have until mid-December to come up with new rules to prevent contamination.

E. coli in bagged spinach led to three deaths and hundreds of illnesses in September.

NBC stations across the country joined NBC11 News in an investigation to test bagged produce to measure the safety of American produce.

Salinas Valley produce giant Natural Selections Foods, the company at the center of the outbreak, gave NBC11 News exclusive access to their facility for a behind-the-scenes look at the packaging process.

Health experts said the E. coli bacteria from cow manure was tracked, probably by wild animals, into spinach fields and that E. coli-tainted spinach passed undetected through Natural Selection Foods in San Juan Bautista.

NBC stations across the country collected more than 100 samples of bagged produce -- of all kinds and several brands -- from store shelves.

The bags were then packed and shipped to a laboratory in Chicago, where they were tested for E. coli and other potentially dangerous contaminants.

The testing was done twice to make sure the results were accurate.

The results showed the produce was clean.

The Centers for Disease Control in Atlanta estimates more than 70 million people fall victim to some sort of food-borne illness every year.

MORE: NBC11 Answers E. coli Questions

Drew Starbird, food safety expert at Santa Clara University, said many of those illnesses go unreported. Starbird also said many of them are brief and many of the contaminations and originate in restaurants and the home.

"I think this particular event is going to really stimulate some significant changes in good agriculture practices and in government regulation of the fresh produce industry," said Starbird.

The changes are in full motion at Natural Selection Foods

"We are truly sorry for anybody who got sick for a product that we packed," said Charles Sweat, chief operating officer for Natural Selection Foods.

"It was absolutely gut-wrenching for us as a company, all of our employees, to think that there was a product that we packed that could have been contaminated and made people sick. It was an absolute emotional rollercoaster," said Sweat.

A representative from Natural Selection Foods showed NBC11 News the measures the company has in place in order to keep their products contaminant-free.

"We are truly sorry for anybody who got sick for a product that we packed." - Charles Sweat, CEO, Natural Selection Food

Employees and visitors must wear protective clothing, including a mock and rubber gloves. Everyone's hands and feet are disinfected before they enter the plant.

There are high-tech sorting devices that use lasers to separate individual leaves for the slightest imperfection.

There are also complex cleaning systems where the product is washed three different times before moving on to the next step in the packaging process.

Even with those measures, something got through the system and people got sick.

"We could have taken the status quo approach and said it's an isolated case, but we're not a status quo company. So, we brought in some of the best microbiologists in the country to educate us about this bacteria," Sweat told NBC11 News.

The company's test approach resulted in a technique learned from the beef industry called Test and Hold.

Every shipment that now comes into Natural Selection Foods is sampled and doesn't go any further until it tests clean.

Since starting the Test and Hold program last month, the company said contaminants have been discovered and product has been destroyed.

But, the question remains: Will the changes be enough to stop another outbreak like the one the industry experienced this fall, or will the produce industry and the American people once again have to learn from experience?