TY - JOUR
T1 - NGS-based Aspergillus detection in plasma and lung lavage of children with invasive pulmonary aspergillosis
AU - Wesdorp, Emmy
AU - Rotte, Laura
AU - Chen, Li-Ting
AU - Jager, Myrthe
AU - Besselink, Nicolle
AU - Vermeulen, Carlo
AU - Hagen, Ferry
AU - van der Bruggen, Tjomme
AU - Lindemans, Caroline
AU - Wolfs, Tom
AU - Bont, Louis
AU - de Ridder, Jeroen
N1 - Publisher Copyright:
© The Author(s) 2025.
PY - 2025/3/17
Y1 - 2025/3/17
N2 - In immunocompromised pediatric patients, diagnosing invasive pulmonary aspergillosis (IPA) poses a significant challenge. Next-Generation Sequencing (NGS) shows promise for detecting fungal DNA but lacks standardization. This study aims to advance towards clinical evaluation of liquid biopsy NGS for Aspergillus detection, through an evaluation of wet-lab procedures and computational analysis. Our findings support using both CHM13v2.0 and GRCh38.p14 in host-read mapping to reduce fungal false-positives. We demonstrate the sensitivity of our custom kraken2 database, cRE.21, in detecting Aspergillus species. Additionally, cell-free DNA sequencing shows superior performance to whole-cell DNA sequencing by recovering higher fractions of fungal DNA in lung fluid (bronchoalveolar lavage [BAL] fluid) and plasma samples from pediatric patients with probable IPA. In a proof-of-principle, A. fumigatus was identified in 5 out of 7 BAL fluid samples and 3 out of 5 plasma samples. This optimized workflow can advance fungal-NGS research and represents a step towards enhancing diagnostic certainty by enabling more sensitive and accurate species-level diagnosis of IPA in immunocompromised patients.
AB - In immunocompromised pediatric patients, diagnosing invasive pulmonary aspergillosis (IPA) poses a significant challenge. Next-Generation Sequencing (NGS) shows promise for detecting fungal DNA but lacks standardization. This study aims to advance towards clinical evaluation of liquid biopsy NGS for Aspergillus detection, through an evaluation of wet-lab procedures and computational analysis. Our findings support using both CHM13v2.0 and GRCh38.p14 in host-read mapping to reduce fungal false-positives. We demonstrate the sensitivity of our custom kraken2 database, cRE.21, in detecting Aspergillus species. Additionally, cell-free DNA sequencing shows superior performance to whole-cell DNA sequencing by recovering higher fractions of fungal DNA in lung fluid (bronchoalveolar lavage [BAL] fluid) and plasma samples from pediatric patients with probable IPA. In a proof-of-principle, A. fumigatus was identified in 5 out of 7 BAL fluid samples and 3 out of 5 plasma samples. This optimized workflow can advance fungal-NGS research and represents a step towards enhancing diagnostic certainty by enabling more sensitive and accurate species-level diagnosis of IPA in immunocompromised patients.
U2 - 10.1038/s41525-025-00482-8
DO - 10.1038/s41525-025-00482-8
M3 - Article
C2 - 40097415
VL - 10
JO - npj Genomic Medicine
JF - npj Genomic Medicine
IS - 1
M1 - 24
ER -