Universal digital high-resolution melting for the detection of pulmonary mold infections

J Clin Microbiol. 2024 Jun 12;62(6):e0147623. doi: 10.1128/jcm.01476-23. Epub 2024 May 2.

Abstract

Invasive mold infections (IMIs) are associated with high morbidity, particularly in immunocompromised patients, with mortality rates between 40% and 80%. Early initiation of appropriate antifungal therapy can substantially improve outcomes, yet early diagnosis remains difficult to establish and often requires multidisciplinary teams evaluating clinical and radiological findings plus supportive mycological findings. Universal digital high-resolution melting (U-dHRM) analysis may enable rapid and robust diagnoses of IMI. A universal fungal assay was developed for U-dHRM and used to generate a database of melt curve signatures for 19 clinically relevant fungal pathogens. A machine learning algorithm (ML) was trained to automatically classify these pathogen curves and detect novel melt curves. Performance was assessed on 73 clinical bronchoalveolar lavage samples from patients suspected of IMI. Novel curves were identified by micropipetting U-dHRM reactions and Sanger sequencing amplicons. U-dHRM achieved 97% overall fungal organism identification accuracy and a turnaround time of ~4 hrs. U-dHRM detected pathogenic molds (Aspergillus, Mucorales, Lomentospora, and Fusarium) in 73% of 30 samples classified as IMI, including mixed infections. Specificity was optimized by requiring the number of pathogenic mold curves detected in a sample to be >8 and a sample volume to be 1 mL, which resulted in 100% specificity in 21 at-risk patients without IMI. U-dHRM showed promise as a separate or combination diagnostic approach to standard mycological tests. U-dHRM's speed, ability to simultaneously identify and quantify clinically relevant mold pathogens in polymicrobial samples, and detect emerging opportunistic pathogens may aid treatment decisions, improving patient outcomes.

Importance: Improvements in diagnostics for invasive mold infections are urgently needed. This work presents a new molecular detection approach that addresses technical and workflow challenges to provide fast pathogen detection, identification, and quantification that could inform treatment to improve patient outcomes.

Keywords: HRM; IMI; dPCR; machine learning.

Publication types

  • Evaluation Study

MeSH terms

  • Bronchoalveolar Lavage Fluid / microbiology
  • Fungi* / classification
  • Fungi* / genetics
  • Fungi* / isolation & purification
  • Humans
  • Invasive Fungal Infections / diagnosis
  • Invasive Fungal Infections / microbiology
  • Lung Diseases, Fungal* / diagnosis
  • Lung Diseases, Fungal* / microbiology
  • Machine Learning
  • Molecular Diagnostic Techniques / methods
  • Sensitivity and Specificity*
  • Transition Temperature