Q&A: Using faster diagnostics to treat COVID-19 patients Special

Posted Nov 2, 2020 by Tim Sandle
COVID-19 patients are increasingly susceptible to co-infections such as pneumonia and Staphylococcus - many of which display similar symptoms to COVID-19. What are the options for patients and can new diagnostics help?
File photo: Deborah Cannon of the Special Pathogens Branch as she processes SARS specimens.
File photo: Deborah Cannon of the Special Pathogens Branch as she processes SARS specimens.
CDC/ Media / Anthony Sanchez
While testing is available to identify and rule out these solutions but they often take days, leading to treatments that accelerate the issues. There are, however, new solutions, such as tests of faster speed (results within 5 hours) and greater efficacy. Such technologies can more precisely identify key markers in patients.
To understand more about this topic, Digital Journal spoke with Oliver Schacht, CEO of OpGen about how rapid diagnostics technologies are evolving to quickly identify pathogens and more effectively guide precise treatments for COVID-19 patients.
Digital Journal: How easy is it to identify pathogens with conventional technology?
Oliver Schacht: Conventional microbiological culture testing has been the cornerstone of bacterial and fungal pathogen identification and the foundation of understanding the link between microorganisms and infectious diseases for the past 130 years. The procedure uses enrichment in selective media and cultivation to identify microorganisms. The method is relatively inexpensive in materials costs; however, it requires a skilled microbiologist, it is laborious and time-consuming, and results can take up to several days, thereby delaying the identification and understanding of the confirmed pathogen and leaving clinicians no choice but to treat empirically with broad-spectrum antibiotics in the meantime.
Other limitations include the fact that some organisms may not be easily detectable by conventional culture methods; growth may be impacted by prior treatment with antibiotics, and some organisms do not grow at all in culture. Also, only a fraction of organisms can be successfully cultured in a polymicrobial sample due mostly to various factors such as fastidious growth requirements, non-viable organisms or inhibition of pathogenic organisms. These factors make accurate diagnosis and treatment of infections a challenge. Furthermore, delayed appropriate therapy has been shown to be associated with longer duration of antibiotic therapy, contributing to increased antibiotic resistance as well as longer hospital stays and higher mortality rates.
DJ: How can rapid diagnostics help?
Schacht: Rapid diagnostics can increase the speed and array of pathogens tested, helping clinicians and researchers gain valuable information earlier on in the treatment process. Conventional culture was traditionally considered to be the gold standard and cost-effective, making it the more obvious choice. Now, however, emerging molecular diagnostic technologies have evolved as multiplex panels, which can test for more than 40 or so different pathogens and antibiotic resistance markers in mere hours instead of days, allowing this information to be considered before treatment is administered.
These diagnostics are important to identify the etiological pathogen and differentiate between viral and bacterial infections, to identify the antimicrobial resistances, and to find out which antimicrobial agent should be used in treatment decisions. These multiplex molecular panels may be able to identify underlying infection causes that conventional cultures may not test for or miss, such as legionella bacteria. Studies on these emerging diagnostics are also showing a high degree of clinical sensitivity and efficacy in optimizing antimicrobial selection and utilization and patient outcomes when coupled with antimicrobial stewardship programs.
A transmission electron micrograph of SARS-CoV-2 virus particles
A transmission electron micrograph of SARS-CoV-2 virus particles
Handout, National Institute of Allergy and Infectious Diseases/AFP/File
DJ: Which technologies are optimal for the SARS-CoV-2 virus?
Schacht:Real-time reverse transcription polymerase chain reaction (RT-PCR) has been and continues to remain the optimal technology for diagnosis of SARS-CoV-2 infection, generally performed on nasopharyngeal or oropharyngeal swab specimens. However, RNA extraction constitutes a major bottleneck in current testing. SARS-CoV-2 kits that deploy extraction-free modalities, such as our CE-marked SARS-CoV-2 Kit with PCR-Compatible Universal Lysis Buffer (PULB) , allow labs to circumvent the need for extraction equipment and extraction kits/reagents. This can help provide operational and workflow efficiencies, reduce time to results to approximately one hour and realize cost savings.
DJ: Which other co-infection pathogens present an additional risk with someone showing COVID-19 symptoms?
Schacht:Diagnosis and management of severe COVID-19 is challenging because the signs and symptoms are similar to that of bacterial pneumonia, presenting the complex dilemma of whether the patient has COVID-19 or bacterial pneumonia. Consequently, COVID-19 infection, especially in hospitalized patients, is a well-established predisposing factor for secondary bacterial pneumonia, meaning that the patient may in fact have a bacterial pneumonia co-infection. A study released earlier this year from the Karolinska Institute found that 25% of hospitalized COVID-19 patients in the ICU have a bacterial co-infection. Bacterial co-infections, such as pneumonia and sepsis, are on the rise in COVID-19 patients and pose a substantial risk to their prognosis.
DJ: How can diagnostics assist here?
Schacht:Current estimates suggest that nearly 80% of the patients admitted in the ICU with COVID-19 receive antibiotics. Antibiotic therapy in the absence of etiological diagnosis of infection has both clinical and public health implications. By deploying fast and comprehensive molecular diagnostic panels that rapidly detect and identify bacterial and fungal pathogens and antibiotic resistance markers, it is possible to make appropriate treatment decisions and administer effective antibiotics where warranted and reduce transmission risks if they are in a hospital or healthcare facility. Rapid molecular diagnostics also make it possible to pinpoint drug-resistant pathogens and help to improve patient outcomes, especially amidst the COVID-19 pandemic and the upcoming flu season.
DJ: How can such data be used to advance public health?
Schacht:Data from these molecular diagnostics can help advance public health in two key areas. First, as we’ve mentioned, is minimizing the spread of deadly co-infections and antibiotic resistance among hospitalized patients. Having access to which pathogens and antibiotic resistance markers are present within hours can help reduce transmission rates from patient to patient.
In addition to faster treatments and reduced transmission risks for patients, new diagnostic and bioinformatics technologies enable to better track and predict antimicrobial resistance. This technology is currently available and being tested across hospital networks in states like New York, to detect, track and manage AMR threats in an attempt to avoid outbreaks and enhance infection control. In addition, with advancements in AI-powered NGS technology, there is future potential for molecular antibiotic susceptibility testing directly from patient samples, again in only a few hours, making these AI-powered bioinformatics technologies a promising solution for understanding both the broader and individualized picture of public health.