NGS-based Aspergillus detection in plasma and lung lavage of children with invasive pulmonary aspergillosis

Emmy Wesdorp; Laura Rotte; Li-Ting Chen; Myrthe Jager; Nicolle Besselink; Carlo Vermeulen; Ferry Hagen; Tjomme van der Bruggen; Caroline Lindemans; Tom Wolfs; Louis Bont; Jeroen de Ridder

doi:10.1038/s41525-025-00482-8

NGS-based Aspergillus detection in plasma and lung lavage of children with invasive pulmonary aspergillosis

Emmy Wesdorp, Laura Rotte, Li-Ting Chen, Myrthe Jager, Nicolle Besselink, Carlo Vermeulen, Ferry Hagen, Tjomme van der Bruggen, Caroline Lindemans, Tom Wolfs, Louis Bont, Jeroen de Ridder

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

Samenvatting

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.

Originele taal-2	Engels
Pagina's (van-tot)	24
Tijdschrift	NPJ genomic medicine
Volume	10
Nummer van het tijdschrift	1
DOI's	https://doi.org/10.1038/s41525-025-00482-8
Status	Gepubliceerd - 17 mrt. 2025

Toegang tot document

10.1038/s41525-025-00482-8

Citeer dit

@article{fbafe65d172742a98c3b2306de96db9f,

title = "NGS-based Aspergillus detection in plasma and lung lavage of children with invasive pulmonary aspergillosis",

abstract = "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.",

author = "Emmy Wesdorp and Laura Rotte and Li-Ting Chen and Myrthe Jager and Nicolle Besselink and Carlo Vermeulen and Ferry Hagen and {van der Bruggen}, Tjomme and Caroline Lindemans and Tom Wolfs and Louis Bont and {de Ridder}, Jeroen",

note = "{\textcopyright} 2025. The Author(s).",

year = "2025",

month = mar,

day = "17",

doi = "10.1038/s41525-025-00482-8",

language = "English",

volume = "10",

pages = "24",

number = "1",

}

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

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

SN - 2056-7944

VL - 10

SP - 24

JO - NPJ genomic medicine

JF - NPJ genomic medicine

IS - 1

ER -