From the first reports of a salmonella outbreak this spring, it took a full 89 days before jalapeño and serrano peppers correctly came under suspicion as the culprit. During that period, as more than 1,440 victims trickled in to hospitals, federal officials struggled to trace the source of the outbreak, erroneously singling out tomatoes for weeks before homing in on peppers. No sooner had that outbreak tapered off than the high-end Whole Foods Market was forced to launch a massive recall of E. coli-infested ground beef.

The incidents prompted renewed calls for reform and stricter oversight of food safety. Some lawmakers are even suggesting stripping the Food and Drug Administration and the U.S. Department of Agriculture of their inspection duties and giving them to a new agency. Yet the FDA in particular has long been starved of funding and understaffed. Its workload, meanwhile, is rapidly expanding as the global food chain grows larger, more complicated, and less transparent, all of which adds to the agency's already overcrowded plate.

Congress is under pressure to take up major food-safety legislation this fall that would offer sweeping proposals for regulatory change. The country's appetite for reform, however, is likely to collide with an uncomfortable reality: The responsibility for food safety, as it works today, lies heavily in private hands. Even as bacterial outbreaks have become more high-profile and the financial fallout from recalls more severe, the government has been handing off many food-safety responsibilities to industry. Food safety today is a business—and a booming one at that.

For most Americans, however, the FDA is still the public face of food safety. It was created in 1906 amid the fervid response to Upton Sinclair's The Jungle, which exposed unsanitary conditions in meatpacking factories. Today, the duties are split. The USDA handles meat, and the FDA takes care of pretty much everything else. But in reality, oversight of farms and food plants has gradually changed hands. A pivotal moment came in the mid-1990s, after 21 people in Connecticut and Illinois were hospitalized during a huge lettuce-related outbreak of E. coli that was ultimately tied back to a grower in California. In response to this and other incidents, federal officials worked with academics and industry to come up with a set of voluntary guidelines to avoid future outbreaks.

Inspections. The move spawned a whole new cottage industry of third-party companies calling themselves "food-safety consultants." Practically every major food manufacturer today—from Kraft to Costco—hires experts to check out the ingredients that are entering its facilities.

In some ways, this represents a huge step forward. Even with an engorged budget, the FDA couldn't begin to get inspectors into all the factories, processing plants, distribution centers, warehouses, and packing plants in the country to check them for problems. Right now, the agency focuses on juices and seafood, because those two products have a higher risk of going bad. Indeed, it would cost the FDA more than $3.5 billion to inspect every one of the roughly 250,000 domestic and foreign food facilities just once, a recent Government Accountability Office report found. Industry insiders say the FDA is lucky if it gets to the same facility once every three years.

But the new model has also created some alarming potential gaps. For one thing, there's no certification system for these third-party inspectors. Critics worry that retailers hire these companies not only to ensure food quality but also as a defense mechanism to help protect their public image in case something goes wrong. "These audits are like icing on the cake of litigation," says Bill Marler, the attorney who represented more than 100 victims in the 1993 E. coli outbreak case linked to the Jack in the Box fast-food chain. "Every major manufacturer does them, and every manufacturer pays no attention to them."

There are other potential troubles, too. Tomato and spinach growers are audited heavily because they've had so many problems in the past, but other crops, such as broccoli and cauliflower, are scrutinized less. "Retailers aren't demanding it," says Trevor Suslow, a food-safety expert at the University of California-Davis. Many growers, he adds, "are living in a continuing state of denial about whether they should be doing anything." And there's also the concern that these efforts could, perversely, be making food less safe. In some cases, experts say, a grower will have to pay for audits from six or seven companies just to satisfy the demands of all of its different buyers. The overlapping attention might help eliminate problems, but it's also costly. For slaughter facilities squeezed by rising costs, cutting out E. coli tests has been one of their money-saving tactics, as recent raids have revealed.

The price tag is important. With new technology, companies can do all sorts of wild—if at times unsettling—things to keep food free of bacteria. For one thing, they can zap it with radiation. The government approved irradiated meat in 1997, and regulators last month gave the nod to leafy vegetables like lettuce and spinach. But irradiation is still controversial. Advocacy groups say it ruins taste and destroys nutrients, and consumer fears about irradiation have limited its adoption. More broadly, companies with effective new products—be they oxidizing sprays, viral cocktails, or microbe detectors—often struggle to find buyers, because of either costs or public concerns.

Biotech companies, for example, are working on another promising technology that food companies prefer not to talk about—bacteriophages, which are naturally occurring viruses that kill certain bacteria, including E. coli and Listeria. One company, Intralytix, received FDA approval in 2006 to sell its "phage cocktail" as an additive to ready-to-eat meats like hot dogs and deli turkey, which are more prone to factory contamination. It's now used by at least one commercially available smoked salmon brand. But don't look for it on many labels. Intralytix CEO John Vazzana says that food companies are interested, but they get cold feet about having to put a disclaimer on their hot-dog or deli-meat packaging that would alert consumers about the little guys inside. (Some are bypassing the rules by removing the viruses before packaging.)

Little enforcement. Whether it's new technology or inspectors-for-hire, private-sector remedies can go only so far. Voluntary inspection guidelines clearly have their shortcomings. They didn't prevent the 2006 outbreak of E. coli involving spinach that claimed five lives and caused more than $350 million of damage. To win back consumers, the Western Growers Association, which represents California and Arizona produce farmers, spent much of 2007 working with the federal government to overhaul its guidelines. Under the new agreement, state agriculture officials are being trained to do inspections, and more scientific sanitation standards have been adopted. Observers say these moves could help, but enforcement and penalties are limited. Though many growers choose to participate, they are not required to by law.

If Congress takes up food safety this fall, it will most likely focus on efforts to improve the response time to outbreaks, perhaps by adopting a national trace-back program to locate contaminated food more quickly. It also might push the Centers for Disease Control and Prevention, the agency responsible for tracking down the source of an outbreak, to do a better job of sharing information with the FDA.

But these reforms are just one side of the coin. The other half, the prevention part, will depend on bringing order to the sprawling mosaic that is the global food chain. Today, about 80 percent of the nation's seafood and slightly less than half its fresh fruits are imported from overseas. But the FDA inspects only about 1 percent. Private auditors must be part of the answer, says Christine Humphrey, a former FDA field investigator. The challenge is to make sure they're qualified. She points to medical devices as a possible guide. In the late 1990s, regulators couldn't work fast enough to approve new devices. To eliminate the waiting list without lowering standards, the FDA began certifying third-party companies. "The results have been phenomenal," she says.