ArticleScientific reports2020
Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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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.
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Who cites it
18 citing papers in PubMed.
- Bridging the gap:Gut microbes · 2026Review
- Microbial spectrum and antimicrobial resistance are associated with outcomes after endoscopic ultrasound-guided therapy of pancreatic fluid collections.Scientific reports · 2026Article
- Rapid Identification of Infections Directly from Isolates and Clinical Specimens with the MasSpec Pen Technology.bioRxiv : the preprint server for biology · 2026Article
- Comparative diagnostic evaluation of real-time PCR and culture for detecting pathogens in podiatric wound infections.Microbiology spectrum · 2026Article
- Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens.Gut pathogens · 2025Article
- Universal, untargeted detection of bacteria in tissues using metabolomics workflows.Nature communications · 2025Article
- Pathogen-pathogen interactions during co-infections.The ISME journal · 2025Review
- The dawn of ethnomicrobiology: an interdisciplinary research field on interactions between humans and microorganisms.Journal of ethnobiology and ethnomedicine · 2024Review
- In vitro evaluation of the effect of transport medium, temperature, and time on the recovery ofJDS communications · 2023Article
- Bartonella spp. Infections Identified by Molecular Methods, United States.Emerging infectious diseases · 2023Review
- Antibiotic Resistance in Patients with Cystic Fibrosis: Past, Present, and Future.Antibiotics (Basel, Switzerland) · 2023Review
- The clinical utility of Nanopore 16S rRNA gene sequencing for direct bacterial identification in normally sterile body fluids.Frontiers in microbiology · 2023Article
- In vitro virulence activity of Pseudomonas aeruginosa, enhanced by either Acinetobacter baumannii or Enterococcus faecium through the polymicrobial interactions.Archives of microbiology · 2022Article
- Next-generation sequencing as an advanced supplementary tool for the diagnosis of pathogens in lower respiratory tract infections: An observational trial in Xi'an, China.Biomedical reports · 2022Article
- Comparison of Strategies for Isolating Anaerobic Bacteria from the Porcine Intestine.Applied and environmental microbiology · 2021Article
- A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation.Nature communications · 2021Observational
- Clinical Implications of Polymicrobial Synergism Effects on Antimicrobial Susceptibility.Pathogens (Basel, Switzerland) · 2021Review
- Using Plate-Wash PCR and High-Throughput Sequencing to Measure Cultivated Diversity for Natural Product Discovery Efforts.Frontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Optimal clinical decision-making depends on identification of clinically relevant organisms present in a sample. Standard microbiological culture may fail to identify unusual or fastidious organisms and can misrepresent relative abundance of sample constituents. Culture-independent methods have improved our ability to deconvolute polymicrobial patient samples. We used next-generation 16S rRNA gene sequencing (NGS16S) to determine how often cultivatable organisms in complex polymicrobial samples are not reported by standard culture. Twenty consecutive bronchoalveolar lavage (BAL) samples were plated to standard and additional media; bacteria were identified by NGS16S analysis of DNA extracted directly from samples or from washed culture plates. 96% of organisms identified were cultivable, but only 21% were reported by standard culture, indicating that standard work-up provides an incomplete assessment of microbial constituents. Direct NGS16S correlated well with standard culture, identifying the same predominant organism in 50% of samples. When predominant organisms differed, NGS16S most often detected anaerobes, whose growth is unsupported by standard culture conditions for this specimen. NGS16S identified more organisms per sample and allowed identification of fastidious organisms, while culture was better at capturing organisms when bacterial load was low, and allowed incidental recovery of non-bacterial pathogens. Molecular and culture-based methods together detect more organisms than either method alone.
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