Oliver Schacht, PhD

The battle against COVID-19 has become increasingly complex with the emergence of two major phenomena: the rise of secondary bacterial co-infections and the novel SARS-CoV-2 mutation hot spots, making individual diagnosis and treatment a more difficult task for front line health workers. Among these newer concerns, one holds a distinct sense of familiarity as the global health community was fighting it long before the COVID-19 pandemic reared its head – antibiotic resistance. 

Antibiotic resistant “superbugs” infect 

2.8 million people and kill over 35,000 in the U.S.

 warn that it could ultimately lead to more COVID-19–related deaths. Standard antibiotics are no match for these superbugs. One reported case of a woman in her seventies who had contracted a bacterial infection after breaking her femur was diagnosed with a carbapenem-resistant Enterobacteriaceae (CRE) superbug that was 

resistant to all 26 types of antibiotics available in the U.S. to treat infection

. After two weeks in the hospital, the patient died, revealing just how difficult it is to fight antibiotic resistance and bringing into question how much more challenging this battle will be as it accompanies the COVID-19 pandemic. 

Physicians need an arsenal of diagnostic tools to evaluate beyond just the presence of SARS-CoV-2; they also need to be able to identify superbugs where there is suspicion of microbial co-infections in order to effectively provide an individualized treatment plan for each patient. Just as we saw speedy innovation bring us SARS-CoV-2 testing, rapid diagnostics for antibiotic resistance markers are emerging to help the medical community narrow in on these concerns.

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SARS-CoV-2’s role in fueling antibiotic resistance

SARS-CoV-2 directly attacks a patient’s respiratory system, making it difficult for the individual to breathe. For mild cases, a dry cough may be present, but for the more severe cases that require hospitalization, shortness of breath and acute respiratory distress syndrome may cause the patient to require a more invasive intervention such as a ventilator. 

Longer stays in hospitals and use of invasive procedures such as ventilators can put patients at risk for developing antibiotic resistant secondary infections and further complicate their course of treatment. Many healthcare facilities are ill-equipped to address these superbugs, primarily because the antibiotic resources capable of eliminating these pathogens are cost-prohibitive and in short-supply due to the dwindling pipeline of antibiotic innovation. 

As a result, doctors have to use their best judgement to instead determine which course of readily available and affordable antibiotics may be the most effective for each individual patient. Inappropriate, or inadequate, selection could lead to extended suffering and even death, making it a high-stakes decision that has to be made quickly with little to no information on the exact cause of the underlying issue. 

A simple solution, and one that would be less of a gamble, is to utilize readily available rapid molecular diagnostics to determine what is causing the illness and what antibiotics the patient may be resistant to, prior to administering the antibiotics. Unfortunately for many physicians, it can take days before the test results from standard microbiology culture are returned, and they simply can’t wait that long to prescribe treatment since this virus and secondary infections both develop and progress in a quick manner.

Better treatment begins with earlier diagnostic evaluation

To effectively treat a patient, particularly one that has been hospitalized and is at greater risk for developing a super infection, incorporating rapid molecular diagnostic testing can be both clinically valuable and life-saving, allowing for earlier evaluation of the patient for these concerns and providing the physician with actionable results in a matter of just a few hours rather than days. Already today there are FDA-cleared diagnostic technologies for lower respiratory tract infections such as pneumonia, e.g. the LRT aspirate and BAL panels that quickly analyze antibiotic resistant pathogens and identify bacterial co-infections in under five hours. Faster access to such test results takes the guesswork out of diagnosis and treatment, particularly when it comes to antibiotics. 

Simultaneously performing these rapid molecular diagnostic tests at the same time that SARS-CoV-2 tests are administered in high-risk patients is key to catching these superbugs early, minimizing transmission and establishing appropriate infection control measures. Rapid identification of bacterial co-infections and antibiotic-resistant pathogens can help physicians determine if a patient is likely to spread a superbug on to others. A study observing the 2004 SARS outbreak found that 

76% of infections were acquired in healthcare facilities

 and hospitalized patients with bacterial infections were sources of super-spreading, with one patient capable of infecting upwards of 10 additional individuals.  

Physicians need rapid diagnostics for more than just the SARS-CoV-2 virus and fortunately there are a few FDA-cleared tests for lower respiratory co-infections such as pneumonia capable of identifying antibiotic resistance markers that can easily be integrated into initial COVID-19 testing algorithms. With faster insights, physicians can more effectively and proactively address the growing superbug risk before it too becomes a pandemic.  

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Rapid molecular diagnostic testing can be both clinically valuable and life-saving.

Author | Oliver Schacht, PhD

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