Cell-free DNA next-generation sequencing successfully detects infectious pathogens in pediatric oncology and hematopoietic stem cell transplant patients at risk for invasive fungal disease

Amy E. Armstrong, Jenna Rossoff, Desiree Hollemon, David K. Hong, William J Muller, Sonali Chaudhury*

*Corresponding author for this work

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background: We sought to determine if next-generation sequencing (NGS) of microbial cell-free DNA (cfDNA) in plasma would detect pathogens in pediatric patients at risk for invasive fungal disease (IFD). Procedures: Pediatric hematology, oncology, and stem cell transplant patients deemed at risk for new IFD had blood samples drawn at three time-points separated by 1-month intervals. The primary outcome measure was detection of fungal pathogens compared to standard clinical testing. Secondary outcomes included identification of other infectious pathogens, relationship to European Organization for Research and Treatment of Cancer's Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases’ Mycoses Study Group (EORTC/MSG) guidelines, and assessment of antifungal therapy. Results: NGS identified fungal pathogens in seven of 40 at-risk patients for IFD and results were identical in four of six proven cases, including Aspergillus fumigatus by lung biopsy, Candida albicans by blood or pancreatic pseudocyst cultures, and Rhizopus delemar by skin biopsy. Rhizopus oryzae identified on skin biopsy and A. fumigatus isolated on day 27 of 28 of culture from lung biopsy were not detected by cfDNA NGS, possibly due to lack of bloodstream penetration and questionable pathogenicity, respectively. Numerous DNA viruses were detected in patients with prolonged febrile neutropenia or abnormal imaging. Extended antifungal therapy was used in 73% of patients. Follow-up cfDNA sequencing in patients who were positive at enrollment was negative at 1 and 2 months. Conclusions: cfDNA NGS detected fungal pathogens from blood confirming its potential to guide treatment decisions in pediatric patients at risk for IFD and limit excessive empiric antifungal use. Future studies are needed to better understand the sensitivity and specificity of this approach.

Original languageEnglish (US)
Article numbere27734
JournalPediatric Blood and Cancer
Volume66
Issue number7
DOIs
StatePublished - Jul 1 2019

Fingerprint

Mycoses
Hematopoietic Stem Cells
Pediatrics
Transplants
DNA
Biopsy
Rhizopus
Aspergillus fumigatus
National Institute of Allergy and Infectious Diseases (U.S.)
Pancreatic Pseudocyst
Febrile Neutropenia
Sodium Glutamate
Lung
Skin
DNA Viruses
Hematology
Therapeutics
Candida albicans
DNA Sequence Analysis
Virulence

Keywords

  • cell-free DNA
  • fungal disease
  • pediatric oncology
  • pediatric stem cell transplantation

ASJC Scopus subject areas

  • Pediatrics, Perinatology, and Child Health
  • Hematology
  • Oncology

Cite this

@article{99ebdfa32f6d4d68bd1971f62021e716,
title = "Cell-free DNA next-generation sequencing successfully detects infectious pathogens in pediatric oncology and hematopoietic stem cell transplant patients at risk for invasive fungal disease",
abstract = "Background: We sought to determine if next-generation sequencing (NGS) of microbial cell-free DNA (cfDNA) in plasma would detect pathogens in pediatric patients at risk for invasive fungal disease (IFD). Procedures: Pediatric hematology, oncology, and stem cell transplant patients deemed at risk for new IFD had blood samples drawn at three time-points separated by 1-month intervals. The primary outcome measure was detection of fungal pathogens compared to standard clinical testing. Secondary outcomes included identification of other infectious pathogens, relationship to European Organization for Research and Treatment of Cancer's Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases’ Mycoses Study Group (EORTC/MSG) guidelines, and assessment of antifungal therapy. Results: NGS identified fungal pathogens in seven of 40 at-risk patients for IFD and results were identical in four of six proven cases, including Aspergillus fumigatus by lung biopsy, Candida albicans by blood or pancreatic pseudocyst cultures, and Rhizopus delemar by skin biopsy. Rhizopus oryzae identified on skin biopsy and A. fumigatus isolated on day 27 of 28 of culture from lung biopsy were not detected by cfDNA NGS, possibly due to lack of bloodstream penetration and questionable pathogenicity, respectively. Numerous DNA viruses were detected in patients with prolonged febrile neutropenia or abnormal imaging. Extended antifungal therapy was used in 73{\%} of patients. Follow-up cfDNA sequencing in patients who were positive at enrollment was negative at 1 and 2 months. Conclusions: cfDNA NGS detected fungal pathogens from blood confirming its potential to guide treatment decisions in pediatric patients at risk for IFD and limit excessive empiric antifungal use. Future studies are needed to better understand the sensitivity and specificity of this approach.",
keywords = "cell-free DNA, fungal disease, pediatric oncology, pediatric stem cell transplantation",
author = "Armstrong, {Amy E.} and Jenna Rossoff and Desiree Hollemon and Hong, {David K.} and Muller, {William J} and Sonali Chaudhury",
year = "2019",
month = "7",
day = "1",
doi = "10.1002/pbc.27734",
language = "English (US)",
volume = "66",
journal = "Pediatric Blood and Cancer",
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T1 - Cell-free DNA next-generation sequencing successfully detects infectious pathogens in pediatric oncology and hematopoietic stem cell transplant patients at risk for invasive fungal disease

AU - Armstrong, Amy E.

AU - Rossoff, Jenna

AU - Hollemon, Desiree

AU - Hong, David K.

AU - Muller, William J

AU - Chaudhury, Sonali

PY - 2019/7/1

Y1 - 2019/7/1

N2 - Background: We sought to determine if next-generation sequencing (NGS) of microbial cell-free DNA (cfDNA) in plasma would detect pathogens in pediatric patients at risk for invasive fungal disease (IFD). Procedures: Pediatric hematology, oncology, and stem cell transplant patients deemed at risk for new IFD had blood samples drawn at three time-points separated by 1-month intervals. The primary outcome measure was detection of fungal pathogens compared to standard clinical testing. Secondary outcomes included identification of other infectious pathogens, relationship to European Organization for Research and Treatment of Cancer's Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases’ Mycoses Study Group (EORTC/MSG) guidelines, and assessment of antifungal therapy. Results: NGS identified fungal pathogens in seven of 40 at-risk patients for IFD and results were identical in four of six proven cases, including Aspergillus fumigatus by lung biopsy, Candida albicans by blood or pancreatic pseudocyst cultures, and Rhizopus delemar by skin biopsy. Rhizopus oryzae identified on skin biopsy and A. fumigatus isolated on day 27 of 28 of culture from lung biopsy were not detected by cfDNA NGS, possibly due to lack of bloodstream penetration and questionable pathogenicity, respectively. Numerous DNA viruses were detected in patients with prolonged febrile neutropenia or abnormal imaging. Extended antifungal therapy was used in 73% of patients. Follow-up cfDNA sequencing in patients who were positive at enrollment was negative at 1 and 2 months. Conclusions: cfDNA NGS detected fungal pathogens from blood confirming its potential to guide treatment decisions in pediatric patients at risk for IFD and limit excessive empiric antifungal use. Future studies are needed to better understand the sensitivity and specificity of this approach.

AB - Background: We sought to determine if next-generation sequencing (NGS) of microbial cell-free DNA (cfDNA) in plasma would detect pathogens in pediatric patients at risk for invasive fungal disease (IFD). Procedures: Pediatric hematology, oncology, and stem cell transplant patients deemed at risk for new IFD had blood samples drawn at three time-points separated by 1-month intervals. The primary outcome measure was detection of fungal pathogens compared to standard clinical testing. Secondary outcomes included identification of other infectious pathogens, relationship to European Organization for Research and Treatment of Cancer's Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases’ Mycoses Study Group (EORTC/MSG) guidelines, and assessment of antifungal therapy. Results: NGS identified fungal pathogens in seven of 40 at-risk patients for IFD and results were identical in four of six proven cases, including Aspergillus fumigatus by lung biopsy, Candida albicans by blood or pancreatic pseudocyst cultures, and Rhizopus delemar by skin biopsy. Rhizopus oryzae identified on skin biopsy and A. fumigatus isolated on day 27 of 28 of culture from lung biopsy were not detected by cfDNA NGS, possibly due to lack of bloodstream penetration and questionable pathogenicity, respectively. Numerous DNA viruses were detected in patients with prolonged febrile neutropenia or abnormal imaging. Extended antifungal therapy was used in 73% of patients. Follow-up cfDNA sequencing in patients who were positive at enrollment was negative at 1 and 2 months. Conclusions: cfDNA NGS detected fungal pathogens from blood confirming its potential to guide treatment decisions in pediatric patients at risk for IFD and limit excessive empiric antifungal use. Future studies are needed to better understand the sensitivity and specificity of this approach.

KW - cell-free DNA

KW - fungal disease

KW - pediatric oncology

KW - pediatric stem cell transplantation

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JO - Pediatric Blood and Cancer

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SN - 1545-5009

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