ArticleMicrobial genomics2021
Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a
Article in Microbial genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed, 29 citations in OpenAlex.
- Evolution of foodborne disease surveillance in China: A 32-year journey from monitoring to early warning.One health (Amsterdam, Netherlands) · 2026Article
- Application of mNGS in traceability investigation of foodborne disease outbreaks caused byFrontiers in microbiology · 2026Article
- Article
- Enhancing infectious intestinal disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples.Genome medicine · 2025Article
- Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce.Foods (Basel, Switzerland) · 2025Article
- Whole-genome sequencing and metagenomics reveal diversity and prevalence ofMicrobiology spectrum · 2025Article
- Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing: a case study on fluoroquinolone resistance.Frontiers in microbiology · 2025Article
- Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.Scientific data · 2024Article
- Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling.Frontiers in microbiology · 2024Article
- Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria.BMC genomics · 2023Article
- Integrated molecular approaches for fermented food microbiome research.FEMS microbiology reviews · 2023Review
- Restriction Endonuclease-Based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing.Applied and environmental microbiology · 2023Article
- mStrain: strain-level identification ofBioinformatics advances · 2023Article
- bettercallsal: better calling ofFrontiers in microbiology · 2023Article
- Making microbial genomics work for clinical and public health microbiology.Microbial genomics · 2022Article
- Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies.Frontiers in microbiology · 2021Article
- Genomic Surveillance of Foodborne Pathogens: Advances and Obstacles.Journal of public health management and practice : JPHMPArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Food-borne outbreak investigation currently relies on the time-consuming and challenging bacterial isolation from food, to be able to link food-derived strains to more easily obtained isolates from infected people. When no food isolate can be obtained, the source of the outbreak cannot be unambiguously determined. Shotgun metagenomics approaches applied to the food samples could circumvent this need for isolation from the suspected source, but require downstream strain-level data analysis to be able to accurately link to the human isolate. Until now, this approach has not yet been applied outside research settings to analyse real food-borne outbreak samples. In September 2019, a
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.