Mucorales PCR for the rapid diagnosis of mucormycosis: 6 years of testing in a national reference laboratory and tertiary hospital

ABSTRACT Mucormycosis is an invasive mold disease (IMD) caused by fungi in the order Mucorales. Early initiation of active antifungal therapy is critical for optimal outcomes, and molecular diagnostics can speed up the time to critical results. We reviewed 6 years of Mucorales polymerase chain reaction (PCR) testing to assess agreement with culture, histopathology, and/or pan-fungal sequencing across different specimen types. Medical record review was also performed to adjudicate cases of suspected IMD from our institution. A total of 5,779 PCRs and 2,017 fungal cultures from the same patients were performed during the study period. PCR results were issued approximately 7 days sooner than Mucorales-positive cultures. The overall PCR positivity rate was 2.9%. Sinus and other fresh tissue specimens had the highest diagnostic yield (23.8% and 19.4% PCR positive, respectively). PCR cycle thresholds (Cts) were significantly earlier for culture-positive specimens and for tissue versus other sample types, while serum had the latest Cts (all comparisons P < 0.005). Among 315 specimens with shared testing, PCR detected all culture- or sequencing-positive samples ( n = 13), and negative percent agreement across methods was high (97.3%). Twenty-one cases of proven/probable mucormycosis were identified from our hospitals; 67% had at least one positive PCR. False-negative PCRs came from serum ( n = 6) or cerebrospinal fluid ( n = 1), while false positives were rare (PCR specificity: 99%). In conclusion, Mucorales PCR is a useful adjunct to routine testing for suspected IMD, given its relatively rapid turnaround time and high specificity. Testing should ideally be performed using fresh tissue from the primary site of infection when possible. IMPORTANCE This work addresses a critical gap in the diagnosis of mucormycosis, a rapidly progressive and frequently fatal invasive mold disease for which timely, accurate laboratory confirmation is essential but often difficult to achieve. By evaluating over 6 years of real-world Mucorales polymerase chain reaction (PCR) testing in a national reference laboratory and tertiary-care setting, this study provides robust evidence that targeted PCR offers substantially faster turnaround times than culture while maintaining high specificity across multiple specimen types. The findings underscore the diagnostic value of molecular testing, particularly from fresh tissue obtained at the site of infection, and highlight important limitations of serum testing that can inform optimal test utilization. In the context of increasing mucormycosis incidence, absence of reliable antigen-based diagnostics, and the need for early antifungal therapy, these data support the incorporation of Mucorales PCR as a complementary tool to conventional methods.