Guest Column | May 11, 2020

Using Broader Diagnostics To Detect Bacterial Co-Infections And Drug Resistance In COVID-19 Patients

By Oliver Schacht, Ph.D., OpGen

COVID 19 Coronavirus

Rapid diagnostic technologies that aid in the detection and management of COVID-19 cases play an essential role in delivering quick, targeted treatment to slow down transmission and flatten the curve. During the initial pandemic response, testing was focused only on SARS-CoV-2 virus detection, but as this public health concern evolves, a broader arsenal of tests may need to be considered to detect other health threats that can go undetected or develop as a consequence of secondary infections in COVID-19 hospitalized patients.

Shedding Light On Hidden Infections

The vast majority of deaths during viral disease outbreaks are from secondary drug-resistant bacterial infections. This was the case in the 1918 influenza pandemic as well as in the 2009 H1N1 pandemic where 29-55 percent of deaths were attributed to secondary infections, and COVID-19 seems to be headed in a similar direction.

It’s unfortunately common for patients to develop bacterial infections, such as pneumonia and sepsis, while hospitalized for other indications. COVID-19 is no exception; those who are hospitalized for COVID-19 are most vulnerable to these dangerous co-infections. It’s estimated that one in seven COVID-19 patients will develop a secondary bacterial infection while hospitalized. And this risk is exacerbated when these critically ill patients require ventilation.

Without rapid and reliable diagnostic tools such as highly multiplexed molecular syndromic panels that deliver results on a broad range of bacterial pathogens and antimicrobial resistance genes, detection of important bacterial infections may go unnoticed or diagnosis may be delayed, thus resulting in delayed treatment and a cascade of unintended and detrimental clinical and economic consequences. Among co-infected respiratory pathogens detected in SARS-CoV-2 positive patients, Mycoplasma pneumoniae (23 percent) and Legionella pneumophila (20 percent) have been reported (Xing et al., 2020). Acinetobacter baumannii, highly resistant to antibiotics, and Klebsiella pneumoniae also have been reported (Chen et al., 2020). Other cases of co-infections have presented concerns as well. For instance, it is difficult to differentiate Pneumocystis pneumonia (PCP) from COVID-19 based on symptoms and imaging, and the detection of Pneumocystis cysts or trophozoites in respiratory specimens by routine microbiological methods has limitations. Yet, both diseases are severely life-threatening.

Healthcare workers are moving at a rapid pace to care for a high volume of COVID-19 patients but, in doing so, considering the possibility of bacterial co-infections and related risks should also be evaluated in the context of the patients’ clinical status.

Crafting An Effective And Responsible Treatment Plan

Another risk among hospitalized COVID-19 patients is the development of superinfections, often caused by antimicrobial resistant pathogens transmitted within a facility. A recent study of SARS-CoV-2-infected adults admitted to Wuhan, China hospitals found that 10 percent-20 percent of patients developed superinfections during treatment. These bacterial and fungal drug-resistant infections, found in the observed COVID-19 patients, came from pathogens called out on the CDC’s 2019 list of antibiotic resistance threats.

Often, clinicians will treat a patient suspected of having an infection with broad spectrum antibiotics or even administer these treatments empirically during a hospital stay. Additional reports out of China have found that COVID-19 patients are no exception to this practice – in Chinese hospitals, 80 percent-100 percent of patients with severe COVID-19 were treated with antibiotics. However, without a complete understanding of the patient’s condition, this practice can lead to the development or exacerbation of drug-resistant infections, which can spread rapidly to other vulnerable patients in the same facility.

The good news is that rapid, FDA-cleared molecular diagnostic panels are readily available that detect a broad range of bacteria and resistance genes with only two minutes of hands-on time. These panels provide doctors with results in hours, rather than days, empowering them to deliver timely and targeted antibiotic treatment. In some patients, this might mean deescalating the use of broad-spectrum antibiotics to prevent the development of drug-resistance. In others, these results can help doctors pinpoint the most-effective antibiotic based on the patient’s diagnosis. Both scenarios enhance antibiotic stewardship, with the ultimate goal of lowering the risk of drug-resistant infection and preserving crucial antibiotic resources for when they’re needed most. With broader COVID-19 patient diagnostics in hand, doctors can act fast to isolate and properly treat co-infected patients to prevent further transmission and shorten the time spent in critical care.

As healthcare workers around the world strive to provide the best possible care amid the pandemic, rapid diagnostic testing should be expanded beyond identifying COVID-19 to alert clinicians of the presence of potential co-infections and antimicrobial-resistant pathogens that may negatively impact patient outcomes or lead to secondary outbreaks if left unaddressed. Even during the fast-paced outbreak response, clinicians owe it to themselves and their patients to incorporate readily available diagnostic platforms. With these solutions, they can better understand patient cases and treat those under their care efficiently and responsibly.

About The Author

Oliver Schacht is the CEO of OpGen, Inc., a pioneering bioinformatics and genomic analysis company providing complete solutions for patients, hospitals, and network-wide infection prevention and treatment.