It was 7 a.m. on Independence Day when a doctor told Rose and Roger Porter Jr. that their daughter could die within hours. For nearly a week, Mikayla, 10, had suffered intensifying bouts of fever, diarrhea and stabbing stomach pains.
That morning, the Porters rushed her to a clinic where a doctor called for a helicopter to airlift her to a major medical center.
The gravity of the girl’s illness was remarkable given its commonplace source. She had gotten food poisoning at a pig roast from meat her parents had bought at a local butcher in McKenna, Wash., and spit-roasted, as recommended, for 13 hours.
Mikayla was one of nearly 200 people reported ill in the summer of 2015 in Washington State from tainted pork — victims of the fastest-growing salmonella variant in the United States, a strain that is particularly dangerous because it is resistant to antibiotics.
What followed was an exhaustive detective hunt by public health authorities that was crippled by weak, loophole-ridden laws and regulations — and ultimately blocked by farm owners who would not let investigators onto their property and by their politically powerful allies in the pork industry.
The surge in drug-resistant infections is one of the world’s most ominous health threats, and public health authorities say one of the biggest causes is farmers who dose millions of pigs, cows and chickens with antibiotics to keep them healthy — sometimes in crowded conditions before slaughter.
[Read our other stories in our series on drug resistance, Deadly Germs, Lost Cures.)
Overuse of the drugs has allowed germs to develop defenses to survive. Drug-resistant infections in animals are spreading to people, jeopardizing the effectiveness of drugs that have provided quick cures for a vast range of ailments and helped lengthen human lives over much of the past century.
But public health investigators at times have been unable to obtain even the most basic information about practices on farms. Livestock industry executives sit on federal Agriculture Department advisory committees, pour money into political campaigns and have had a seat at the table in drafting regulations for the industry, helping to ensure that access to farms is generally at the owners’ discretion.
Dr. Parthapratim Basu, a former chief veterinarian of the Agriculture Department’s Food Safety and Inspection Service, said the pork industry regularly thwarted access to information on antibiotic use.
“When it comes to power, no one dares to stand up to the pork industry,” he said, “not even the U.S. government.”
A reconstruction of the Washington outbreak provides a rare look into how these forces play out. The New York Times reviewed government documents, medical records and emails of scientists and public health officials, as well as conducted interviews with victims, investigators, industry executives and others involved.
Those industry officials argued in documents and interviews that farmers needed protection against regulators and scientists who could unfairly harm their business by blaming it for a food-poisoning outbreak when the science was complex and salmonella endemic in livestock. The tension mirrors a broader distrust in agriculture and other business about the intention of federal regulators and other government overseers.
“Have you ever heard of the phrase, ‘I’m from the government, I’m here to help you’ — and you know they’re going to screw you?” said David J. Hofer, the secretary-treasurer of the Midway Hutterite Colony, a religious community that runs a hog farm in Conrad, Mont. Mr. Hofer said he was one of the farmers who objected to the farm inspections during the outbreak.
“They might have public health in mind, but they don’t care if in the process they break you.”
In the end, Mikayla Porter survived, but the threat of the infection that nearly killed her continues — not least because investigators still lack access to essential data.
A Danger Grows
There are 2,500 different types of salmonella. The one that infected Mikayla is called 4,5,12:i-minus. It first showed up in the late 1980s in Portugal, and then in Spain, Thailand, Taiwan, Switzerland and Italy. In the United States, infections it causes have risen 35 percent over the past decade, while the overall rate of salmonella infections has stayed constant.
The strain typically resists four major antibiotics: ampicillin, streptomycin, sulfisoxazole and tetracycline.
“We can see resistance is really increasing,” said Dr. Robert V. Tauxe, director of the division of food-borne, waterborne and environmental diseases at the Centers for Disease Control and Prevention.
This particularly virulent strain of salmonella is just one of a growing number of drug-resistant germs that put farm families, and meat eaters generally, at risk.
A study in Iowa found that workers on pig farms were six times more likely to carry multidrug-resistant staph infections, notably MRSA. A study in North Carolina found that children of pig workers were twice as likely to carry MRSA than children whose parents didn’t work in a swine operation.
Those germs can also wind up on pork sold to consumers. An analysis of government data by the Environmental Working Group, a research organization, found that 71 percent of pork chops at supermarkets in the United States carried resistant bacteria, second only to ground turkey, at 79 percent.
Like many outbreaks of resistant infections, the salmonella variant that sickened Mikayla is usually so widely dispersed that the C.D.C. has had a hard time tracking it.
But in the Washington outbreak, the infection was new to the region, and tests revealed the bug had the same genetic profile in patients, creating ideal conditions for scientific detective work.
“This was our real opportunity,” said Allison Brown, a C.D.C. epidemiologist. “Everything lined up.”
A Celebration Turns Dire
The Porter family had invited friends and neighbors to the pig roast to celebrate a major life change: In three days, they would be moving to Costa Rica.
But the day after the roast, Mikayla felt sick, and by 4:30 a.m. the following morning, she had diarrhea so severe that her parents took her to the emergency room.
There, a doctor said she had a stomach bug, assuring them it would pass and approving her to travel. Her parents also felt sick, but not as seriously, and they flew to Costa Rica as planned.
After arriving, Mikayla got much worse, excreting mucus and blood. She lay in agony on the couch, the family dogs sitting beside her protectively.
A doctor at BeachSide Clinic near Tamarindo, the town where the family had rented a house, prescribed the antibiotic azithromycin, medical records show. It did not work.
The family returned to the clinic the next day. That is when Dr. Andrea Messeguer told Mikayla’s parents their daughter could die, and helped arrange the airlift to Hospital CIMA in the capital, San José.
There, doctors determined that Mikayla had a systemic infection. She received intravenous hydration and antibiotics.
Tests came back from the national lab showing the drug-resistant salmonella strain.
Back in Washington, many others were also getting sick.
On July 19, Nicholas Guzley Jr., a police officer, ate pork at a restaurant in Seattle, and at 2 a.m. threw up in the shower. The medical ordeal that followed was so excruciating — vomiting, diarrhea, bleeding, a fever of 103.9 degrees, dehydration and multiple hospital visits — that he said it was worse than a near-death experience in 2003 when he had been hit by a truck.
“If you stack up all the pain from all the injuries, this blew it away,” he said.
On July 23, the head of Washington’s Department of Health sent out an alert, warning that 56 people had fallen ill and publicizing an investigation into the outbreak by the state’s health and agriculture agencies, coordinating with the C.D.C. The Washington State epidemiologist, Dr. Scott Lindquist, took the lead.
On July 27, a restaurant had its permit suspended for food safety violations, including failure to keep its food hot enough. Multiple restaurants were identified as possible sources of tainted pork, along with several pig roasts.
Dr. Lindquist and his team discovered that many of the infected roast pigs had come from a slaughterhouse called Kapowsin Meats. Tests of 11 samples taken from slaughter tables, knives, hacksaws, transport trucks and other spots showed that eight were positive for the resistant strain.
At Kapowsin, the state investigators spoke to the federal official responsible for inspecting the slaughterhouse, who suggested that they look for the farms where the tainted pork had come from.
The Heart of an Outbreak
Records obtained by the state showed that many of the pigs supplied to Kapowsin originated on industrial farms in neighboring Montana.
On Aug. 13, state records noted that the investigative team — including the C.D.C. and the federal Agriculture Department — was in touch with officials in Montana to discuss gaining access to the farms.
Determining where the outbreak originated would have allowed the team to trace other possibly infected pork, recall it and advise the owners on how to change their practices.
But such investigations are extremely sensitive because the publicity can be bad for business, and because the law protects farmers in such situations. Over all, the government has little authority to collect data on farms.
“We have people in the slaughterhouses every day, all day long,” said Paul Kieker, the acting food safety administrator at the Agriculture Department. “We don’t have a lot of jurisdiction on farms.”
The Food and Drug Administration is charged with collecting antibiotic use data. But farms are not required to provide it, and only do so voluntarily.
As a result, the federal government has no information about the antibiotics used on a particular farm and no way to document the role of the drugs in accelerating resistance.
“I haven’t been on a farm for years,” said Tara Smith, a professor at Kent State University and an expert on the connection between resistance and livestock. “They’ve closed their doors to research and sampling.”
Investigators Are Turned Away
Dr. Lindquist, the epidemiologist leading the investigation of the Washington outbreak, pleaded with Montana’s health agency to help him gain access to the farms that had supplied the Kapowsin slaughterhouse.
In a memo to state officials, he told them that such infections were increasing rapidly and that “on-farm investigations will help us better understand the ecology of salmonella” and “prevent future human illnesses.”
Days later, he received a phone call from Dr. Liz Wagstrom, the chief veterinarian for the National Pork Producers Council, a group that lobbies on behalf of the livestock industry. Its campaign donations to congressional candidates have more than doubled in the past decade, to $2 million in 2018, according to the Center for Responsive Politics.
Dr. Wagstrom sought to find out what Dr. Lindquist had learned in his investigation and what he was saying to the media, he said, recalling the conversation. He said she was worried the pig farms might be unfairly tarnished, arguing that salmonella was common on farms, so an investigation wouldn’t prove anything, even if the infection was detected.
In an interview, Dr. Wagstrom said she was concerned that farm visit wouldn’t yield valuable information. “What would you learn that could positively impact public health?”
The industry soon became more involved. Officials from the National Pork Board joined regular crisis conference calls during the investigation, along with numerous state and federal health and agriculture officials.
The board is a group of pork industry executives whose members are elected by the industry and then appointed by the secretary of agriculture, cementing a tight bond between business and government.
Dr. Lindquist initially welcomed the executives’ presence, given their expertise, though he did not know who had initially invited them.
Rules With Big Loopholes
That same year, F.D.A. guidelines went into effect that were supposed to enable the tracking of antibiotics on farms. They required farms to obtain prescriptions from veterinarians to dispense antibiotics, and only to animals sick or at risk of illness. The guidelines said that farms must stop using antibiotics as “growth promoters.”
But the rules have loopholes, which were highlighted a year earlier when officials from the F.D.A., C.D.C., the Agriculture Department and the Pew Charitable Trusts met at the University of Tennessee. The group heard from Thomas Van Boeckel, an expert in statistical modeling and antibiotic resistance who was then at Princeton.
Dr. Van Boeckel told the group that he could build maps showing changing levels of antibiotic use on farms and compare them with changing levels of resistance.
To do so, he said, he needed data sets by region or, better yet, by farm.
“I was told there was a single data point per year, literally,” he said.
That data point: Around 33 million pounds of medically important antibiotics, a 26 percent increase from 2009, were sold in the United States for farm use. The figure, collected from sales data by the F.D.A., was the sum total of the information they were able to provide him.
Dr. Van Boeckel told the group that without more specific information, he couldn’t do any real measurement.
“They said: Yeah, that’s going to be challenging.”
As the end of August neared, Mikayla Porter had stabilized, but in Washington State, the salmonella caseload continued to grow.
On Aug. 26, Kapowsin agreed to cease operations, in cooperation with the state. The next day, there was a recall of 523,380 pounds of its pork products.
At the same time, the Montana Pork Producers Council wrote to the Washington health agency, saying it was “clear that there is little to no value in conducting on-farm investigations,” and that investigators should focus on slaughterhouses.
Anne Miller, the council’s executive director, said she did not appreciate that the researchers were coming at a time of crisis. “The trick to getting good information is get research before you get to that situation,” she said. “Why hadn’t this been done prior?”
She spoke to pork producers in the state, and some expressed concern about being unfairly blamed for the outbreak, worried that government officials seeking information on their farms could unfairly tarnish their image and business.
Mr. Hofer, of the farm in Conrad, said in a phone interview that he objected strongly to the investigation.
“I was animated about that,” he said. “Let’s say they found something — it probably would have screwed up some other markets we had.”
Mr. Hofer said his farm provided pigs to Kapowsin but did not know if the sales had overlapped with the outbreak. He said it was clear to him that the slaughterhouse was to blame. “There was salmonella all over that plant.”
On Aug. 28, the National Pork Producers Council sent Washington State a follow-up letter concurring with Ms. Miller.
“I know that you do not want any inadvertent negative consequences to farms as a result of this proposed on-farm sampling,” Dr. Wagstrom wrote in the letter.
Ms. Miller and others in the industry said farms could provide voluntary information on antibiotic use, but they have taken a hard line on government access because of fears that individual farms would be singled out for a complex problem with multiple causes.
The position stuns some scientists.
“So let’s not do anything to give anyone a bad reputation, including any bad behavior?” asked Dr. James Johnson, a professor at the University in Minnesota and an expert in resistant infections. “The people who stand to benefit from having everyone remain ignorant are the ones who protest the loudest.”
That September, Dr. Lindquist still hoped his team would get the go-ahead to take samples from the five farms thought to have been possible sources for the outbreak, but it never came.
“I don’t know even to this day why this got stymied,” he said.
He said he did not know that Ms. Miller, the head of the Montana Pork Council, had contacted the farms and been told they would not permit a visit from researchers.
The farms officially declined, through her, to comment for this story.
By Sept. 22, the case load had hit 178 known infections, with 29 people hospitalized, but the outbreak was petering out. The investigation ended, Dr. Lindquist said, “with a whimper.”
“During the outbreak, I heard from restaurants, patients, the slaughterhouse, the U.S.D.A., F.D.A., the Department of Agriculture in Washington and Montana, the health department in Montana and the health department in Washington State,” Dr. Lindquist said. “I did not hear from the farms.”