Pneumonia has been around for centuries and remains a major cause of morbidity, mortality, and healthcare expense today.

The most commonly used method for identifying respiratory pathogens in pneumonia - bacterial culture - was first developed in the 1880s. Though there have been many breakthroughs in our treatment of pneumonia - such as antibiotics and mechanical ventilation - our clinical identification of respiratory pathogens still relies on the time-consuming culture-based techniques. In response, The National Institute of Allergy and Infectious Diseases (NIAID) has expressed a critical need for rapid, accurate identification of pathogens in pneumonia. 

Leading the team that is stepping up to the plate is Robert Dickson, MD, an Associate Director of MCIRCC and an Assistant Professor in the Division of Pulmonary and Critical Care Medicine. His work as principal investigator of Rapid Pathogen Identification in Pneumonia Using Real-time Metagenomics and Ultrasensitive PCR has the potential to transform the way pneumonia is diagnosed, and was recently awarded $428,875 in NIAID R21 funding over two years.

Pneumonia is a 21st century problem that we are still diagnosing with 19th century tools,” says Dickson. “This study aims to change that.

The project utilizes ultrasensitive PCR detection techniques for quantifying lung bacteria, as well as a new-to-market palm-sized DNA sequencer called the  MinIon (developed by Oxford Nanopore Technologies, Oxford, UK) for real-time pathogen identification. 

This powerful combination could potentially tell clinicians which bacteria are present in the lungs (“who’s there?”) as well as the total bacterial burden (“how much?”) in less than four hours, and for less than $100. In addition, clinicians may also be able to use bacterial genetic information to rapidly determine antibiotic resistance and optimal antibiotic selection. Current culture-based techniques require 24-72 hours to provide this information.

“For the past decade, the University of Michigan has been a field-leader in the study of the microbiome, using bacterial gene sequencing to study the bacterial communities in our bodies. But until recently, these molecular techniques were too slow, expensive, and labor-intensive for clinical use,” explains Dr. Dickson. “Our study team has recently shown that by using recent advances in these DNA-based techniques, we can identify the pathogens that cause lung infections within hours rather than days or weeks.” 

Dickson partnered with Scott VanEpps, MD, PhD from Emergency Medicine and Biomedical Engineering, John Erb-Downward, PhD from Pulmonary and Critical Care Medicine and Duane Newton, PhD from Pathology and the Clinical Microbiology Laboratory to bring together a powerhouse of clinical diagnostics and research expertise.

By accelerating the identification of respiratory pathogens, optimizing administration of appropriate antibiotics, and minimizing unneeded antibiotic use, Dickson and his team will improve the treatment of lung infections creating a timeless win for tackling pneumonia.