Testing for Antibiotic Resistance

Finding the Deadly One in a Million

Humanity is on the frontlines of a battlefield. Or at least, that is how David Weiss, PhD, associate professor in infectious diseases, likes to think of it. Weiss is leading the campaign to make sure humanity never sees a “post-antibiotic world.” His lab is dedicated to studying and detecting heteroresistance, a mechanism that allows some bacteria to escape antibiotic treatment.

It’s like Star Wars, he explains, as we are surrounded by “these tiny little organisms we can’t see with our naked eye, [organisms that] can wreak such havoc.” When penicillin was discovered in 1928, it seemed as if humanity’s new weapon would wipe out disease. And for decades, it did. But now, antibiotics are starting to lose their effectiveness. Bacteria are learning how to outsmart medications, a phenomenon called antibiotic resistance. According to the CDC, more than 2 million cases of antibiotic-resistant bacteria occur each year in the United States, leading to over 23,000 deaths per year. And the totals are mounting.

“It’s a big deal if we think about what the world was like before antibiotics,” Weiss says, “If there were no antibiotics to treat an infection, would we still go out to ride our bikes and risk infection or injury?” But because of individuals like Weiss, currently the director of the Emory Antibiotic Resistance Center, “We’re not going to get to that bad point because we’re making a lot of headway.”

Bacteria
Bacteria graphic

The story begins in the hallways of any modern hospital. When a patient comes in with a severe infection, doctors take a sample and send it to the lab for analysis. Different strains of bacteria have developed resistance to certain antibiotics, but not to others. Whether or not treatment is successful depends on choosing the right antibiotic. At the lab, researchers test the sample to help the clinician select an appropriate antibiotic for treatment. If the sample displays one or more resistance characteristics, the doctor may elect to prescribe colistin, generally considered the last line of defense against a bacterial infection.

Unfortunately, the resistance analysis isn’t always correct. Currently, researchers and clinicians rely on a commercial diagnostic product called the Etest to check for antibiotic resistance. The results of the Etest often vary, especially in the case of determining colistin resistance. In some cases, erroneous results lead doctors to prescribe colistin or other antibiotics that ultimately don’t cure patients. This wastes valuable time before a more suitable antibiotic is chosen and prescribed. Scientists and clinicians alike do not understand why the Etest results vary, but Weiss believes he has found an answer: it is not sensitive enough.

When a patient has a bacterial infection, millions of bacterial cells multiply in that patient’s body and generally, either all of these cells are resistant to a certain antibiotic, or none of them are. However, Weiss focuses his research on a phenomenon called heteroresistance. This means that, in some cases, almost all bacterial cells in a given population will be susceptible to a certain antibiotic. But hidden in the crowd are a few individual cells, perhaps one in a million, that are resistant to an antibiotic. If an infection is heteroresistant, a last-line antibiotic like colistin will be able to kill a majority of the bacteria, but a small subset survive the treatment, and continue to thrive and repopulate within the patient, and are now completely resistant to colistin.

Weiss has developed a test that is sensitive enough to detect these one-in-a-million bacteria. This test still utilizes the Etest, but uses a special cell media to ensure greater sensitivity and the ability to detect the heteroresistant subpopulations. Heteroresistance can be turned off or on in any given bacterium and has no clear genetic underpinning. This new culture medium is able to identify the individual bacterial cells that display heteroresistance, and raise the red flag to lab workers.

David Weiss, PhD
D. Weiss photo

Weiss's new media to detect heteroresistance can be added to the arsenal of antibiotic-resistance tests already used in hospital diagnostic labs. If an infection is discovered to be heteroresistant to colistin, doctors will know ahead of time that colistin will not successfully treat the infection, and instead, may select an antibiotic (or combination of antibiotics) that increases the odds of success. As an added benefit, reducing reliance on last-line antibiotics like colistin helps to avoid bacteria developing further levels of antibiotic resistance. Prescribing an antibiotic that won’t work is the equivalent of showing one’s hand of cards to another player; it allows bacteria the opportunity to peek at doctors’ plans and develop a counterattack.

The new media has already demonstrated success by detecting previously unrecognized heteroresistance in a Klebsiella pneumoniae clinical isolate. Klebsiella infections can have a 40-50% mortality rate if not treated properly. Once the new technology is implemented in labs, doctors can identify and treat this and other antibiotic-resistant infections more effectively.

Weiss knows however, that bacteria are resourceful. For every obstacle they've ever faced, “bacteria have figured out a way to do it.” In this battle, Weiss is trying to keep one step ahead.