The old-fashioned way of testing for MRSA is to plop a sample taken from a person or animal into a dish filled with antibiotics. If the bacteria survives and grows, it has a gene that renders it immune to the drugs. If it dies, then it is a susceptible breed of S. aureus and can be treated with standard antibiotics.
The newer, genetic tests for MRSA are quicker and largely automated, and with their costs quickly coming down, they have been poised to take the place of the culture tests. "Generally, these are incredibly accurate," Holmes said of the genetic tests.
But the new strain indicates that it might be time for a revision of the genetic screening tests—and to not be so hasty to move away from the culture-based tests. A patient with this strain of MRSA tested with the genetic test would be wrongly diagnosed as having a more treatable S. aureus infection and likely given drugs that would prove ineffective.
The gene that evaded the state-of-the-art genetic tests is a remodeled version of the known resistance gene mecA. After sequencing the new strain's genome, however, the researchers found that its mecA gene was only about 60 percent the same as the known version. With so many different base pairs than the target gene, the tests were not catching it—a miss that Holmes equates to searching a digitized text document for a term but spelling it wrong in the search window, thus returning a null result.
In the investigation, 11 of the samples that turned out to be antibiotic-resistant did not have either the old or the new mecA gene, which has Holmes and his team wondering what it is that is making these strains resistant. They are currently sequencing the genomes of these types to try to find out.
The appearance of drug-resistant bacteria of many kinds in humans in recent decades has largely been attributed to the over- and misuse of antibiotics in people. When drugs are not taken to the end of their course or are used for non-bacterial infections such as viral infections, they can kill off weaker bacteria, prompting the stronger ones to survive and propagate. And some can eventually become immune to the drugs entirely.
The situation in the livestock industry has been described in similar terms. In many confined feeding operations, animals are given prophylactic antimicrobials as a matter of course to stave off any infections before they start.
Dairy farmers in the U.K. use antimicrobials to treat the common udder infection mastitis. Holmes explains that farmers are under great pressure to keep their herds healthy despite high production demands. "The majority of farmers are under tremendous financial pressure," he said. "When you drive your cows hard, you get more mastitis." And when their cows get this infection a farmer will naturally want to "use the best tool that they have in their armory to treat those cows."
That the newly described MRSA strain was also found in people in Denmark raised questions for some, given that the country has been at the forefront of reducing antibiotic use in livestock. But because the first isolate from a human in Denmark was from 1975, the strain has been in existence for some time—through some of the high years of antibiotic use in farm animals.
Is antibiotic use in livestock directly responsible for this new strain? "I don't think that can be resolved with this study," Smith says. And the study authors note that with their data they cannot prove that the use of antimicrobials on farms led directly to the development of this new resistant strain. But the correlation has been established in other studies. "It is clear that use of antibiotics in adult dairy cows and other food-producing animals does contribute to increased antimicrobial resistance," concluded the authors of a March review paper published in Foodborne Pathogens and Diseases.
By looking at the limited data they have from their first study, Holmes said the prevalence of this strain "appears to be rising at the moment." He and his team will spend part of the summer sampling more farms and hospitals throughout the U.K. to get a better picture of the strain's prevalence.
Could this strain also be lurking in the U.S.? "I would guess that it is," Smith says. "If we turn over some rocks, I would guess that we would find it." In Denmark, samples from each case of MRSA are collected, providing researchers with a comprehensive view of the disease landscape, but in the U.S. testing is more sporadic.
The new find highlights the need for more widespread testing and a detective hunt to find out where and when this strain emerged, Smith says. And the revelation that dairy herds can carry MRSA also underscores the importance of proper hygiene and animal care, Holmes noted.