ArticleGenome medicine2021
Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units.
Article in Genome medicine, 2021. 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 34 papers.
What it found
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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.
Pneumonia Direct Pilot
Monitoring of Antimicrobial Resistance Based on Metagenomics Analyses in Pneumonia Patients: a Genomic Epidemiology Study
Who cites it
34 citing papers in PubMed, 63 citations in OpenAlex.
- Trial
- Bronchoalveolar Lavage Metagenomic Sequencing in the Early Post-Lung Transplantation Period: A Pilot Comparison with Microbiologic Culture.medRxiv : the preprint server for health sciences · 2026Article
- Microbiome Profiling Reveals Prognostic Heterogeneity inmedRxiv : the preprint server for health sciences · 2026Article
- Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pneumonia in Patients With Cancer.Cancer medicine · 2026Article
- Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid pathogen and antimicrobial resistance detection.npj antimicrobials and resistance · 2026Review
- Microplastics enhance the risk of cross-genus dissemination of carbapenemase resistance plasmids in ICU patients.Frontiers in cellular and infection microbiology · 2026Article
- Article
- Host DNA depletion assisted metagenomic sequencing of bronchoalveolar lavage fluids for diagnosis of pulmonary tuberculosis.Annals of clinical microbiology and antimicrobials · 2025Article
- The drainome: longitudinal metagenomic characterization of wastewater from hospital ward sinks to characterize the microbiome and resistome and to assess the effects of decontamination interventions.The Journal of hospital infection · 2024Article
- Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia.Nature communications · 2024Article
- MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.Briefings in bioinformatics · 2024Article
- Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.Genome medicine · 2024Article
- PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting.Communications biology · 2024Article
- Clinical application and evaluation of metagenomic next-generation sequencing in pathogen detection for suspected central nervous system infections.Scientific reports · 2024Article
- Unified metagenomic method for rapid detection of microorganisms in clinical samples.Communications medicine · 2024Article
- Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection.BMC medical genomics · 2024Article
- Routine Metagenomics Service for ICU Patients with Respiratory Infection.American journal of respiratory and critical care medicine · 2024Article
- Applicability of Bronchoalveolar Lavage Fluid and Plasma Metagenomic Next-Generation Sequencing Assays in the Diagnosis of Pneumonia.Open forum infectious diseases · 2024Article
- Application of Host-Depleted Nanopore Metagenomic Sequencing in the Clinical Detection of Pathogens in Pigs and Cats.Animals : an open access journal from MDPI · 2023Article
- Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana.Nature microbiology · 2023Article
Corrections and comments
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Authors and funding
22 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundClinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity.
methodsCMg using nanopore sequencing was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave.
resultsAn 8-h CMg workflow was 92% sensitive (95% CI, 75-99%) and 82% specific (95% CI, 57-96%) for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of β-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from 4 positive and 39 negative samples. Molecular typing using 24-h sequencing data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak involving 14 patients across three ICUs.
conclusionCMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg.
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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.