The sample is still undergoing analysis. The bacteria were detected May 27, nearly three months after the first discovery of the gene in a pig sample.
On Wednesday, USDA officials said the most recent pig sample came from a slaughterhouse in Illinois. The first sample came from a slaughterhouse in South Carolina.
The same gene, mcr-1, also was identified last month in an E. coli strain from a 49-year-old Pennsylvania woman with no recent travel outside the country. That marked the first time the colistin-resistant strain had been found in a person in the United States, raising alarms among health officials and infectious-disease experts tracking its appearance in Asia, Europe and Canada.
Each of the three U.S. cases involves different strains of E. coli. The latest animal case suggests the gene is already circulating through multiple routes here.
"Mounting evidence suggests the mcr-1 gene is circulating within the United States," said Patrick McGann, one of the Defense Department researchers who identified the gene in the patient in Pennsylvania. "Our sample was in a woman with no recent travel history, the pig samples are from slaughterhouses in the USA, and [the] strains are all different."
But the sources have yet to be identified, McGann said.
U.S. officials have been looking for the gene since its emergence in pigs and people in China was reported late last year. There have since been dozens more reports in animals and people on three continents. The number of positive cases in animals is about 20 times that in humans, so researchers say it's not that surprising that two pig samples have tested positive in the United States.
Public health officials' biggest fear is that the gene will spread to bacteria that are now susceptible only to colistin. In all three cases here, the gene was carried on a plasmid, a mobile piece of DNA that easily can transfer the gene to other bacteria. That would result in a kind of super-superbug, invincible to every life-saving antibiotic available.
Appearing before a congressional hearing Tuesday on antibiotic resistance, a top expert at the Centers for Disease Control and Prevention said it is essential to slow the spread of resistant bacteria.
"Antibiotic resistance is perhaps the single most important infectious disease threat of our time," Beth Bell, who heads prevention and control of a wide range of infectious diseases at the CDC, said in her written statement.
"The identification of the mcr-1 gene vividly illustrates the domestic and global challenges of antibiotic resistance," she told members of the House Energy and Commerce subcommittee on oversight and investigations. The gene was first identified last November "and in less than six months, it has been found in a human and two animals in the U.S."
According to Bell, the investigation by the agency and the Pennsylvania health department into the woman's case is currently focused on identifying and screening contacts she had at home and while a hospital patient to determine whether any might carry bacteria with the mcr-1 gene. The patient was treated at a military outpatient facility in Pennsylvania, and the antibiotic-resistant strain of bacteria was found in her urine.
The patient was treated with other types of antibiotics and is fine, officials have said. Bell said the CDC has been able to verify that the patient no longer has the bacteria in her urine.
A national surveillance system that includes the CDC, USDA and the Food and Drug Administration has analyzed more than 55,000 bacterial samples collected from food animals, retail meats and people. None has contained the gene.
As part of that effort, the USDA's Agricultural Research Service has been looking through 2,000 intestinal samples from cattle, hogs, turkeys and chickens; about 1,300 samples have already been evaluated. That's how scientists detected the antibiotic-resistant bacteria in the first pig sample on March 3. It took several more weeks of testing to determine its particular characteristics, the spokeswoman said.
Department officials didn't publicly disclose their finding until May 26, the day that Defense Department researchers published a paper outlining how they found the gene in the Pennsylvania patient.