On a late June morning, thousands of newborn chicks in a West Virginia chicken house huddled together for warmth, forming a fuzzy, moving yellow carpet.

Over the next two months, these chicks pecked at the dirt, nibbled on pellets, grew up. They were packed into crates, trucked to a slaughterhouse, cut into parts and sent to a distribution center for shipment to supermarkets and restaurants.

At every step along the way, some of those chickens were infected with salmonella, a pathogen that lives in the intestinal tracts of birds and other animals and can easily spread. Invisible, tasteless and odorless, it doesn’t make the chickens sick. But transferred to humans, it can lead to salmonellosis — an infection that causes diarrhea, fever and stomach cramps, and, in severe cases, can spread from the intestines to the bloodstream.

It sickens an estimated 1 million people annually, and is the most commonly reported foodborne illness. The incidence of salmonella infection has remained stubbornly high even as foodborne illnesses have been dropping over the past 15 years. Included among those that have declined is listeria, although that pathogen has been implicated in the current deadly outbreak of infections from cantaloupe traced to a farm in Colorado. More than 70 people in 18 states have gotten ill so far, and at least 15 have died.

A look at how the nation’s food safety system operates in the case of salmonella-infected poultry shows how a combination of industry practices and gaps in government oversight results in a fractured effort that leaves the ultimate responsibility for safe food with the consumer.

The farm

Food safety experts and poultry scientists say that salmonella control must start on the farm, but federal food safety inspectors never set foot there. The Agriculture Department’s Food Safety and Inspection Service lacks the legal authority to test for salmonella on farms or to require farmers to have a food safety plan.

As a result, attempts to prevent salmonella are done voluntarily by farmers or because poultry processing companies ask them to — leading to a patchwork of efforts, some of which work better than others.

For instance, vaccinating the hens used in breeding can reduce — but not eliminate — the incidence of salmonella in their offspring, researchers found by testing chickens before slaughter.

While vaccination has been on the rise over the past two years, the practice has not been widely embraced by the poultry industry, largely because of its cost and varied efficacy. Among those breeding operations that do vaccinate their birds, the number of doses given and the strains of salmonella that are targeted vary widely.

Live birds are almost never tested for salmonella. And because the bacteria do not make the birds sick, they show no signs of being infected.

As a result, farmers don’t know whether their chicks have salmonella — and, if they do, how widespread the infection is — or whether their interventions have been effective.

This moves the onus of killing the pathogen later down the line.

Transport to the slaughterhouse can weaken a chicken’s immune system, increasing salmonella levels in its gut. USDA researcher Marcos Rostagno noted that overcrowding, extreme temperatures, food and water deprivation, rough handling and even just the normal motions of a truck lumbering down a highway can produce stress, allowing salmonella to thrive.

And once salmonella bacteria enter a processing plant, poultry experts say, it’s difficult to get them out.

The slaughterhouse

At every step along the way, there are opportunities for salmonella contamination to spread and opportunities to prevent it. USDA requires every processing plant to have a food safety plan — a list of points in the production process where dangers can arise and how the company plans to control them. But companies decide how extensive the interventions are.

On its Web site, USDA lists the names and locations of slaughter plants where salmonella has been detected in more than 10 percent of the poultry tested by the agency. Since the end of 2007, the list has included nine of Tyson Foods’ 33 broiler plants and six of Pilgrim’s 26 plants that were operating as of August (but no Perdue plant). Together, the country’s three largest poultry producers — Tyson is No. 1, followed by Pilgrim and Perdue — account for about half of the 38 billion pounds of chicken produced in the United States each year.

In addition to its Georgetown, Del., processing plant, Perdue gave News21 a tour of one of its hatcheries and a feed mill, along with a farm with which it has a contract.

At the Georgetown plant, brushes, treated water and antimicrobial rinses are constantly monitored throughout the line, and Perdue tests birds for salmonella throughout the week at various stages of the process. Contamination can vary from flock to flock and season to season, said Bruce Stewart-Brown, the company’s vice president of food safety and quality.

The key to killing salmonella is being vigilant in maintaining proper temperature, pH level and chemical concentration of the water as well as keeping a close eye on other controls. For example, if the flow of fresh water in the scalder is not managed properly, each carcass will be rinsed by dirty water, exposing it to cross contamination.

Stan Bailey, a retired USDA microbiologist, said that during his career, he noticed that some companies worked harder than others on food safety. “I think different people have different attitudes on how much they’re willing to spend,” he said.

And no matter how much salmonella USDA finds in raw meat, it cannot be kept off the market.

Looking back

That wasn’t always the case — or at least it wasn’t the intent.

In 1998, USDA told meat and poultry processors they would be shut down if their salmonella contamination level exceeded 20 percent — then the industry’s average — for three consecutive tests. Production would halt. Money would be lost. And a plant would have to fix the problem before it could reopen.

A Texas-based meat company sued. The company, Supreme Beef Processors, said USDA had no legal authority to shut it down after it failed three salmonella tests over eight months.

The courts agreed. In 2001, a federal appeals court upheld a lower court’s decision accepting the company’s argument that, because salmonella is naturally occurring, the government cannot close a plant due to salmonella contamination.

Elsa Murano, USDA’s undersecretary for food safety at the time, told News21 that the agency still has the power to close plants for failing to follow their own food safety plans, and she said that salmonella testing is just one indicator the agency uses to measure companies’ performance.

Efforts in Congress to give the performance standards teeth have stagnated.

Following the court decision, Sen. Tom Harkin (D-Iowa) introduced legislation to give USDA the legal authority to shut down plants that repeatedly violate performance standards. Senate Republicans voted as a bloc to kill it, joined by two Democrats.

Harkin then made repeated efforts to advance legislation known as Kevin’s Law — in memory of a Colorado toddler who died in 2001 after eating a hamburger contaminated with E. coli O157:H7 — but the measures never got out of committee. Similar bills on the House side sputtered as well.

Some of the ideas in Kevin’s Law were included in the Food Safety Modernization Act, signed into law in January. It gives inspectors from the U.S. Food and Drug Administration the authority to order recalls and shut down processors that repeatedly sell contaminated produce, eggs or other non-meat products. But the new law doesn’t apply to USDA and the meat processors it oversees.

Despite USDA’s lack of enforcement muscle, in July it tightened its performance standards for poultry slaughterhouses for the first time. Under the new standard, no more than 7.5 percent of a plant’s raw chickens can test positive for salmonella bacteria — down from 20 percent previously and in line with the industry’s recent average.

As an incentive to comply, plants that don’t meet USDA’s standards are posted online.

But the tests sample whole carcasses before the birds are cut into pieces, when further cross contamination can happen.

This helps explain why the USDA’s salmonella contamination rate of 7.5 percent in slaughter plants is lower than what the FDA has found in retail stores. In 2009, FDA tests showed that 21 percent of the chicken breasts it sampled from grocery stores were contaminated with salmonella.

“The chickens walk into the slaughterhouse with salmonella on board and they leave with salmonella on board,” said Robert Tauxe, deputy director of the Division of Foodborne, Waterborne and Environmental Diseases at the Centers for Disease Control and Prevention.

And it still has opportunities to spread.

To market

Heat is the main danger.

A 2007 industry study found unsafe temperatures in 30 percent of food transports between processors and distribution centers, and in 15 percent of food transports between distribution centers and retail stores.

Here again, the government isn’t really checking. Federal regulation of food transport has been shared and tossed around among various agencies over the past half-century and hasn’t always taken food safety into account.

The regulation of food transportation is “a little bit of a no man’s land,”said Sarah Klein, staff attorney at the Center for Science in the Public Interest, a consumer advocacy group.

To reduce the risk from salmonella, USDA says poultry should be cooked to 165 F, as measured by a meat thermometer. To prevent cross contamination during food preparation, people should wash their hands with soap and warm water for 20 seconds before and after handling raw poultry or other foods; and they should wash cutting boards, utensils and countertops with hot, soapy water or a bleach solution after cutting raw poultry or other meats.

But half of American consumers do not use food thermometers, 40 percent don’t separate raw from ready-to-eat foods, and almost half use the same cutting boards for raw poultry and produce, according to a 2011 survey by the International Food Information Council Foundation, a public education group based in the District.

The survey found that most people felt that the government and food manufacturers share responsibility.

“Food that comes into your home contaminated — not your fault,” said Klein. “The food shouldn’t have been contaminated in the first place.”

News21 reporter Robyne McCullough contributed to this article.

This article was produced as part of the Knight-Carnegie News21 program, a  national university reporting project headquartered at the Walter Cronkite School of Journalism and Mass Communication at Arizona State University. The reporters conducted their research as fellows at the University of Maryland in College Park.