A visualization of how the antibiotic resistance test works. Credit: Caltech

A new test developed by Caltech researchers may help stem the tide of antibiotic-resistant bacteria by giving medical professionals a sneak peek into how bacteria will react to a specific antibiotic.

Overuse and misuse of the prescription drugs are driving the rise of antibiotic-resistant bacteria and multi-drug resistant bacteria, or superbugs. Part of the misuse is due to the fact that doctors often skip first-line antibiotics, like methicillin or amoxicillin, in favor of prescribing stronger, second-line antibiotics like ciprofloxacin—in the fear that the afflicting bacteria will already be resistant to the first-line. While this practice increases the chances that treatment will be effective, it also increases the chances that bacteria will become resistant to second-line antibiotics as well.

But, the newly developed Caltech test could solve this problem by letting a doctor know if their patient’s infection is resistant to a particular antibiotic in 30 minutes, rather than the two to three days it takes currently.

“The [current] tests are so slow," says Rustem Ismagilov, director of the Jacobs Institute for Molecular Engineering for Medicine, and a co-author on the paper describing the test method that was published yesterday in Science Translational Medicine. "We can change the world with a rapid test like this. We can change the way antibiotics are prescribed."

The test works like this: a sample of urine is collected from a patient and divided into two part. One part is exposed to an antibiotic for 15 minutes, while the other incubates without antibiotics. The bacteria from each sample are then lysed to release their cellular contents, which are run through a process that combines a detection chemistry technique called digital real-time loop-mediated isothermal amplification, or dLAMP, with a device called a SlipChip (previously developed of Ismagilov and his Caltech colleagues). This combination replicates specific DNA markers so they can be imaged and individually counted as discrete fluorescent spots appearing on the chip.

According to the researchers, the test operates on the principle that typical bacteria will replicate their DNA less well in an antibiotic solution, resulting in the presence of fewer DNA markers. However, if the bacteria are resistant to the antibiotic, their DNA replication will go unhampered and the test will reveal similar numbers of DNA markers in both the treated and untreated solutions.

To test their device, Ismagilov and his team collected 54 samples of urine from patients with urinary tract infections, one of the most common bacterial infections in humans. When executed on the chip, test results had a 95 percent match with those obtained using the current gold standard, which involves sending the sample to a test lab for a two to three-day analysis. The 95 percent accuracy of Ismagilov’s test was achieved within 30 minutes.

Ismagilov and co-author Nathan Schoepp told Caltech they plan to begin running the test on other types of infectious bacteria to see how well it performs. They also hope to tweak the testing procedures to work with blood samples. Blood infections are more difficult to test because the bacteria are present in much lower numbers than they are in urine, but such a test could help reduce mortality from blood-borne infections.