ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2019
Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers, 1 of them a synthesis that pooled it.
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Who cites it
91 citing papers in PubMed, 1 synthesis or guideline pooled it, 151 citations in OpenAlex.
- Application of Metagenomic Next-Generation Sequencing inFrontiers in medicine · 2022Pooled it
- Clinical impact of metagenomic next-generation sequencing for pathogen identification and guided therapy in pediatric intensive care unit patients with severe pulmonary infections.Microbiology spectrum · 2026Article
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- Real-world pathogen spectrum, clinical actionability, and host correlates of first-time mNGS testing in hospitalized patients with hematologic diseases.Frontiers in cellular and infection microbiology · 2026Article
- Diagnosis of Paralytic Rabies by Metagenomics Next-Generation Sequencing: A Case Report and Review of the Literature.Veterinary medicine and science · 2026Review
- Research progress on the current status of respiratory pathogen infections and their detection methods.Frontiers in microbiology · 2026Review
- Application of metagenomic next-generation sequencing in children with pneumonia of unknown etiology.Frontiers in cellular and infection microbiology · 2026Article
- Bronchoalveolar Lavage Microbiota in Critically Ill Patients with Aspiration Pneumonia: An Exploratory Comparison with Community-Acquired Pneumonia and Analysis ofInfection and drug resistance · 2026Article
- The complexity of invasive fungal diseases in the intensive care unit: evaluation of metagenomic next-generation sequencing.Frontiers in cellular and infection microbiology · 2026Article
- Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.NPJ biofilms and microbiomes · 2025Article
- Pathogen Detection in Spinal Infections: Next-Generation Sequencing Versus Conventional Microbiological Methods.Current medical science · 2025Article
- Evaluation of High-Throughput Gene Chip Array for Enhanced Diagnosis of Bone and Joint Infections: A Comparative Analysis with mNGS and Conventional Culture Methods.Infection and drug resistance · 2025Article
- A retrospective analysis comparing metagenomic next-generation sequencing with conventional microbiology testing for the identification of pathogens in patients with severe infections.Frontiers in cellular and infection microbiology · 2025Article
- BALF metagenomic next-generation sequencing for the diagnosis of pulmonary mycobacterial infection in persons with HIV: a retrospective, diagnostic accuracy study.Frontiers in microbiology · 2025Article
- Affinity of Malassezia and Other Yeasts for Pulmonary Lipids.Mycopathologia · 2024Article
- Review
- Epidemiology of Diffuse Alveolar Hemorrhage in Pediatric Allogeneic Hematopoietic Cell Transplantation Recipients.Transplantation and cellular therapy · 2024Article
- Advantages of metagenomic next-generation sequencing in the management of ANCA-associated vasculitis patients with suspected pulmonary infection as a rule-out tool.BMC pulmonary medicine · 2024Article
- The clinical application value of multi-site mNGS detection of patients with sepsis in intensive care units.BMC infectious diseases · 2024Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors at 6 institutions in 1 country.
Funding
Abstract
backgroundDespite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next-generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children.
methodsWe collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children's hospitals from 2014-2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort.
resultsWe identified a rich cross-domain pulmonary microbiome that contained bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33-0.72 vs median, 0.96; IQR, 0.94-0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001).
conclusionsAn optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.
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