Rapid Diagnostic Testing for Infective Endocarditis and Myocarditis Using Nanopore Targeted Sequencing

ABSTRACT Background Infective endocarditis (IE) and myocarditis are serious heart diseases that can lead to life‐threatening complications. These illnesses can have infectious origins, including viral, bacterial, or fungal pathogens. Traditional detection methods, such as culture‐based methods, have limited ability to detect causative pathogens because of antibiotic use and the difficulty in cultivating intracellular and fastidious bacteria as well as viruses. In clinical settings, rapid diagnostics for pathogen identification are essential for timely treatment and appropriate antimicrobial therapy. Methods We successfully developed a method based on nanopore targeted sequencing (NTS) with pathogen‐specific panels for testing myocarditis and IE. As part of this pilot study, a sample‐to‐results protocol was developed with an optimized in‐house pipeline and bioinformatics analysis solution. Results The performance of NTS met our expectations for sensitivity, specificity, and turnaround time. The pathogen‐specific panel testing was accomplished in a 10‐h turnaround time, achieving a detection limit of 20 copies/test for the IE target panel and 10 copies/test for the myocarditis target panel. NTS achieved a clinical performance of 85.0% sensitivity and 96.3% specificity compared with culture testing methods, using 74 clinical specimens from patients (53 male, 21 female) associated with IE. Conclusions The rapid turnaround time of NTS is advantageous for managing acute infections, such as IE and myocarditis. NTS is a powerful tool for rapidly diagnosing infections in IE and myocarditis with significant potential for broader clinical applications.