By Deborah Borfitz 

May 18, 2023 | A new antimicrobial susceptibility testing (AST) method developed by scientists at the University of California, Santa Barbara, resolves the longstanding conflict between what the gold-standard assay says will work and actual patient outcomes when it comes to selecting antibiotics. The alternative AST protocol reveals that antibiotics already widely available on the market—including azithromycin (Z-Pak), the second most commonly prescribed antibiotic in 2022—can cure superbugs but aren’t used because they’re rejected by the testing approach universally embraced for the past 50 years.   

This astonishing news was showcased in a study recently published in Cell Reports Medicine (DOI: 10.1016/j.xcrm.2023.101023). “The main point is people are not Petri plates, and that’s why antibiotics fail,” according to Michael Mahan, Ph.D., professor of microbiology at the UC Santa Barbara, who helped lead the study. 

Since 2015, Mahan has been advocating for antibiotic testing under conditions that simulate the body. Here, he and his team showed their novel approach not only identified antibiotics that predicted a change in susceptibility crossing a clinical breakpoint used to classify patient isolates as susceptible (S) or resistant (R)—but proved it in over 25 animal models of sepsis. 

This was no easy task. Pathogens that sicken and kill humans don’t necessarily behave the same way in mice, and infections and treatments have different routes of delivery. But this is a specialty of Mahan’s lab, which has spent serious money making the case for the adoption of new practices and the unlearning of old and outmoded knowledge. 

Findings of the study, which involved screening more than 500 antibiotic-bacteria combinations, suggest that the gold-standard in vitro test is incorrect about 15% of the time, says Mahan. Most physicians are already aware of its flaws, which is why they so often go “off-menu” to prescribe antibiotics based on their clinical experience. 

But every major hospital in the U.S. now has an antibiotic stewardship committee endeavoring to ensure optimal patient care and avoid the selection for antibiotic resistant strains, he notes. Doctors wanting to prescribe an antibiotic that’s not at the top of the recommendation list must justify the decision. 

Dire Situation 

AST quantifies the minimum inhibitory concentration of antibiotics inhibiting growth of a bacterium, and physicians focus on the drugs falling in the S (okay to use) or R (not okay) categories, explains Mahan. “Time to antibiotics” is the number one determinant for treatment success, so getting it right matters. 

In the wait time for AST results, physicians will often prescribe a broad-spectrum antibiotic to sick patients. If they don’t get better on that drug cocktail, the list provides a backup plan—if enough of the bacteria can be isolated, he says. In about half of blood samples from very sick sepsis patients, “we can’t [even] get a bug.” 

Some patients hospitalized with multidrug-resistant infections have “perished unnecessarily” simply because the right antibiotic wasn’t administered, he says. “It is happening every day... [and] it is not a small number.” 

For superbugs that are considered resistant to every known antibiotic, the situation is dire. Out of sheer desperation, patients are sometimes treated with last-resort drugs developed back in 1940s that are effective but highly toxic (e.g., colistin).  

Antibiotic testing in cell culture medium represents “new hope in a battle [against antimicrobial resistance] we are not winning,” Mahan stresses. “It’s not going to solve everything; people are still going to get sick, and people are still going to die... [but] we think this is the tip of the iceberg. We’re still perfecting this test,” which will ultimately be used on both urine (e.g., for urinary tract infections) as well as blood samples.  

Improved Prescribing 

“The new test needed to be substantially better than the gold-standard test because a marginal improvement would not change clinical practices that have been in place for more than half a century,” says Mahan. 

The time and cost involved with doing the tests are identical and, when they agree with each other produce “nearly perfect prediction of clinical outcome,” he reports. This should give physicians confidence that they’re doing the right thing. “When the tests don’t agree, we show that (predictive accuracy) is markedly in favor of the new test.” 

Patient case studies support the results of this work. Several rejected antibiotics have effectively treated superbugs in humans—specifically, β-lactams for refractory bacteremia caused by methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus, azithromycin monotherapy for multidrug-resistant P. aeruginosa, and azithromycin/piperacillin-tazobactam combination therapy for CRE (carbapenem-resistant Enterobacterales) Achromobacter xylosoxidans. 

The discovery that drugs in today’s toolbox are more useful than previously imagined is why the new test will improve the way new antibiotics are prescribed, used, and discovered, says Mahan. “Anyone can use this. We have made this freely available to all; there’s no patent protection.” 

There’s also no learning curve. The only difference between the old and new tests is that tissue culture media is used, which is commercially available everywhere, he continues. The standard test instead uses Mueller–Hinton broth developed in 1941 to grow Neisseria gonorrhea, and it fails to consider the environmental conditions in the body that enable bacteria to outwit antibiotics by, for example, changing their surface to prevent antibiotic entry.   

The imperfect correlation between recommended antibiotics and clinical observations over the years has given rise to the “90–60” rule, which holds that infections caused by isolates defined as “susceptible” respond well to therapy in 90% of cases, whereas infections caused by isolates defined as “resistant” respond well in 60% of cases. 

The implications of all this in the fight against antimicrobial resistance are significant, says Mahan, given that it takes 10 to 15 years at a cost of $1.7 billion to bring a new drug to market. “Reevaluation of existing antibiotics may be of far greater benefit,” especially since 95% of antibiotic research is being done by small and woefully under-funded biotech companies and most of them have never made a product.  

For big pharma, sales for a given antibiotic are less than $50 million annually relative to the enormous cost of developing a single agent, he says. “It’s a no-win situation. You either must charge more or subsidize the pharmaceutical companies since they have basically abandoned antibiotic research because it is fiscally untenable.” 

Adoption of the new AST approach might not be entirely welcome news to the few companies that have made a capital investment in an antibiotic if it is revealed to have limited effectiveness, he says. However, the ubiquitous Z-Pak—which has been generic since 2005—has emerged as a clear winner. “It scores very low on the gold-standard test for MRSA and thus is not [up to now] prescribed for this indication.” 

Sepsis and Human Testing 

Sepsis not only has an unreasonably high 30% mortality rate, Mahan says, even if patients survive, retrospective studies have shown they have an “irreversibly shortened” lifespan since the condition causes massive inflammation and clotting throughout the body. And many survivors have cognitive decline. 

For hospitals, sepsis is also incredibly expensive to treat, he continues. This is because death results from multiple organs being deprived of oxygen. This occurs because of blood clotting throughout the body—termed disseminated intravascular coagulation (DIC)—or “death is coming” in physician vernacular.  Also, blood vessels become very leaky, causing a catastrophic drop in blood pressure. Hospitals routinely use a sequential organ failure assessment score (SOFA) to track this deadly cascade of events, and those tests are costly.  

A human subjects protocol allowing use of the new AST approach in selective cases is undergoing approval at Santa Barbara Cottage Hospital, Mahan reports. Treatment for patients in sepsis that are not responding to their standard antibiotic regimen will now also include antibiotics recommended by the new test, termed adjunctive therapy. 

If researchers succeed in demonstrating that the addition of new AST improves patient outcomes, as Mahan fully expects will happen, they will have moved the test a step closer to the day when it theoretically replaces the gold-standard test for antibiotic susceptibility. The change will undoubtedly happen, he says, because the new test requires no change in instrumentation or procedures and promises significant cost and life savings.