FDA clears test for genetic markers of antibiotic resistance

The US Food and Drug Administration (FDA) yesterday approved a new test that will enable hospitals to quickly identify bacteria that are resistant to the strongest class of antibiotics.

In a news release, the FDA said it has cleared for marketing the Xpert Carba-R Assay, a test that checks patient specimens for the presence of five different genetic markers associated with bacteria that are resistant to carbapenem antibiotics, which are widely used in healthcare facilities to treat severe infections.

Carbapenem-resistant Enterobacteriaceae, or CRE, is a family of 70 different kinds of bacteria that have become increasingly prevalent in US hospitals and are considered a major public health threat by the Centers for Disease Control and Prevention (CDC).

As the FDA explains, current methods to test for the presence of CRE involve growing bacteria from fecal material in cultures, then testing the bacteria for antimicrobial susceptibility, a process that can take up to 4 days. The Xpert Carba-R Assay can detect the genes associated with carbapenemase—the enzyme produced by CRE that disables carbapenem antibiotics—in less than an hour, according to a press release from Cepheid, the company that manufactures the test.

"By using a specimen taken directly from a patient to test for the presence of genetic markers, hospitals can more quickly identify these dangerous bacteria resistant to certain antibiotics," Alberto Gutierrez, PhD, director of the FDA's Office of In Vitro Diagnostics and Radiological Health, said in the FDA news release.

A dangerous superbug

According to the CDC, CRE primarily affect patients in acute and long-term healthcare settings who are being treated for other conditions. They are more likely to affect patients with compromised immune systems, patients whose care requires devices like ventilators or catheters, and patients taking long courses of antibiotics.

Because CRE are resistant to commonly used antibiotics, and in some cases are completely resistant to all available antibiotics, they are associated with high mortality rates.

In a March 2013 Vital Signs report, the CDC estimated that CRE germs kill up to half of the patient who get bloodstream infections from them. That report also indicated that 4% of US hospitals—and about 18% of long-term acute care hospitals—had at least one patient with a CRE infection.

In December 2015, the CDC warned about the emergence of a new strain of CRE that carries enzymes coated with mobile pieces of DNA known as plasmids that deactivate carbapenem antibiotics. This strain of CRE has the potential to spread rapidly because the plasmids can be easily copied and transferred to other types of bacteria in the human body.

Limitations of the test

The FDA decision to approve the test was based on the results of two clinical trials. One study, which used rectal swabs from 755 patients in hospitals and long-term care facilities, compared the results of the new test with results from reference cultures.

In the other study, designed to test the clinical performance of the Xpert Carba-R Assay, 432 rectal swabs were prepared with specific concentrations of bacteria containing the genes detected by the test. In both studies, the new test performed similarly to the culture method.

But the FDA also cautioned that the new test should not replace the standard modes of testing for CRE. That's because the Xpert Carba-R Assay tests only for the most prevalent genes associated with carbapenem resistance and does not detect the bacteria themselves, nor does it detect all types of carbapenemase genes. As a result, the FDA recommends that labs use the test in conjunction with standard bacterial cultures.

See also:

Jun 29 FDA news release

Jun 29 Cepheid news release

March 2013 CDC Vital Signs report

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