Clinical Test Comparison for Improved Diagnosis of Mucormycosis

Abstract

Abstract Mucormycosis is a rapidly progressive and invasive fungal infection caused by members of the order Mucorales. Proper treatment relies on a timely diagnosis. However, traditional fungal culture takes several days to weeks and has low sensitivity for recovering Mucorales, as these organisms are sensitive to specimen preparation, including tissue homogenization, and low storage temperatures. More rapid and sensitive diagnostic methods are needed to promptly detect infection. Our laboratory previously developed a real-time PCR assay that detects the most common genera associated with mucormycosis to help improve diagnosis. The assay was analytically validated for a variety of specimen types including serum, tissue (both fresh and FFPE), respiratory secretions and body fluids. Little is known about the agreement between our laboratory developed PCR and other detection methods such as culture or sequencing. We reviewed 6 years of laboratory data to assess overall PCR positivity rate, positivity rate across sample types, and agreement with culture and/or pan-fungal sequencing. We also calculated turnaround time to results to gauge the diagnostic value of Mucorales PCR. Test comparisons with fungal culture and/or pan-fungal sequencing were performed if testing was ordered within 30 days of each other. In our study, we reviewed 3,804 total PCR orders for 2,195 patients. The overall positivity rate of Mucorales PCR orders was 3.81% and varied among different sample types, with fresh tissue and body fluid having the highest positivity rates (18.11% total tissue (33.3% lung tissue) and 10.94% all body fluid (12.5% pleural fluid)) and sputum and CSF having the lowest positivity rates (<1% positivity for both). In a cohort of 428 patients with fungal culture and/or sequencing also performed, 29 patients tested positive for Mucorales by at least one method. PCR detected Mucorales on average 7.83 days sooner than fungal culture (average time to positive result: 3.65 vs. 11.47 days). In patients with culture- or sequencing-confirmed Mucorales infection, PCR had a 100% agreement when comparing shared samples from the same source and collection time. Mucorales PCR was also able to detect infection in 10 (34.5%) other patients who were culture-negative for Mucorales. Our findings suggest that PCR could be a valuable diagnostic tool for suspected mucormycosis, especially tissue invasive disease. PCR increased case detection by 34.5% with a faster turnaround time than culture with lesser cost than sequencing. The main limitation of our study was lack of access to patient information to assess pretest probability of Mucormycosis.