ArticleJournal of clinical microbiology2022
Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens.
Article in Journal of clinical microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to 2 registered trials, which are not on this map. Cited by 131 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Detection of Pathogen and Antibiotic Resistance Genes by Targeted Next-Generation Sequencing Compared With Metagenomic Next-Generation Sequencing in ICU Patients.
Pneumonia Direct Pilot
Who cites it
131 citing papers in PubMed, 188 citations in OpenAlex.
- INHALE WP3, a multicentre, open-label, pragmatic randomised controlled trial assessing the impact of rapid, ICU-based, syndromic PCR, versus standard-of-care on antibiotic stewardship and clinical outcomes in hospital-acquired and ventilator-associated pneumonia.Intensive care medicine · 2025Trial
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.Microbiology spectrum · 2026Article
- Label-free Raman spectroscopic imaging enables high-content molecular phenotyping of respiratory diseases from bronchoalveolar lavage fluid.Journal of translational medicine · 2026Article
- Molecular Diagnostics of Infectious Diseases.Yonago acta medica · 2026Review
- Research progress on detection technologies for Mycoplasma pneumoniae.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Review
- Application of targeted next-generation sequencing in children with community-acquired pneumonia.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Application of targeted next-generation sequencing in the etiological diagnosis of peritoneal dialysis-associated peritonitis: a single-center prospective cohort study.International urology and nephrology · 2026Article
- Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis.Respiratory research · 2026Article
- Application of BALF combined with tNGS for detecting Chlamydia psittaci in resource-limited areas: lessons learned from the 2025 temporally associated case series investigation.BMC infectious diseases · 2026Article
- Epidemiological and pathogen characteristics of symptomatic male reproductive tract infections in Hunan province: retrospective study.Scientific reports · 2026Article
- Quantitative interpretation models for targeted next-generation sequencing in lower respiratory tract infections: a multicenter prospective study.Respiratory research · 2026Article
- Next-generation sequencing of cell-free microbial DNA in blood samples of critically ill children: a single-center experience.Molecular and cellular pediatrics · 2026Article
- Evaluating Seqstant LiveGene Analysis in real-time assessment of metagenomic next-generation sequencing (mNGS) data from respiratory samples.Infection · 2026Article
- Bordetella pertussis re-emergence - NGS-based RPTM analysis reveals the atypical clinical features of children.BMC infectious diseases · 2026Article
- Impact of Metagenomic Next-Generation Sequencing on Antibiotic Management in Pediatric Patients.Medicina (Kaunas, Lithuania) · 2026Article
- Evaluation of diagnostic performance of comprehensive respiratory virus panel: comparison of next-generation-sequencing to real-time polymerase chain reaction for detection of respiratory viruses.Annals of clinical microbiology and antimicrobials · 2026Article
- Amplicon-based sequencing as a diagnostic tool for severe pneumonia in the ICU.Scientific reports · 2026Article
- Clinical impact of targeted next-generation sequencing in paediatric pneumonia management: a real-world study evaluating diagnostic concordance and antimicrobial stewardship across multiple specimen types.Italian journal of pediatrics · 2026Article
- A novel targeted hybrid capture-NGS assay for sensitive detection of multiplex respiratory pathogens.Microbiology spectrum · 2026Article
71 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) workflows applied to bronchoalveolar lavage (BAL) fluid specimens could enhance the detection of respiratory pathogens, although optimal approaches are not defined. This study evaluated the performance of the Respiratory Pathogen ID/AMR (RPIP) kit (Illumina, Inc.) with automated Explify bioinformatic analysis (IDbyDNA, Inc.), a targeted NGS workflow enriching specific pathogen sequences and antimicrobial resistance (AMR) markers, and a complementary untargeted metagenomic workflow with in-house bioinformatic analysis. Compared to a composite clinical standard consisting of provider-ordered microbiology testing, chart review, and orthogonal testing, both workflows demonstrated similar performances. The overall agreement for the RPIP targeted workflow was 65.6% (95% confidence interval, 59.2 to 71.5%), with a positive percent agreement (PPA) of 45.9% (36.8 to 55.2%) and a negative percent agreement (NPA) of 85.7% (78.1 to 91.5%). The overall accuracy for the metagenomic workflow was 67.1% (60.9 to 72.9%), with a PPA of 56.6% (47.3 to 65.5%) and an NPA of 77.2% (68.9 to 84.1%). The approaches revealed pathogens undetected by provider-ordered testing (Ureaplasma parvum, Tropheryma whipplei, severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], rhinovirus, and cytomegalovirus [CMV]), although not all pathogens detected by provider-ordered testing were identified by the NGS workflows. The RPIP targeted workflow required more time and reagents for library preparation but streamlined bioinformatic analysis, whereas the metagenomic assay was less demanding technically but required complex bioinformatic analysis. The results from both workflows were interpreted utilizing standardized criteria, which is necessary to avoid reporting nonpathogenic organisms. The RPIP targeted workflow identified AMR markers associated with phenotypic resistance in some bacteria but incorrectly identified
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.