ArticleBMC bioinformatics2024
Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets.
Article in BMC bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Perseus: lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes.Bioinformatics (Oxford, England) · 2026Article
- Viral Metagenomic Analysis of Bat Fly Pupae.Pathogens (Basel, Switzerland) · 2026Article
- Comprehensive Evaluation of Safety and Probiotic Potential of Lactiplantibacillus plantarum HY7715 Isolated from Korean kimchi.Probiotics and antimicrobial proteins · 2026Article
- Ocular community state types reveal distinct microbial compositions among microbiomes with implications for trachoma control.bioRxiv : the preprint server for biology · 2026Article
- Pathogen detection in central nervous system infections: moving metagenomic sequencing closer to clinical practice.BMC infectious diseases · 2026Article
- Oral and plasma microbiome in the context of acute febrile illness.medRxiv : the preprint server for health sciences · 2026Article
- Filtering for truth: high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN).BMC genomics · 2026Article
- Spatial and temporal patterns of public transit aerobiomes.Microbiome · 2026Article
- Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.BMC microbiology · 2026Article
- Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.PLoS computational biology · 2026Article
- Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.Antibiotics (Basel, Switzerland) · 2025Review
- Detection ofFood chemistry. Molecular sciences · 2025Article
- Genomic GC bias correction improves species abundance estimation from metagenomic data.Nature communications · 2025Article
- Optimization of 16S RNA Sequencing and Evaluation of Metagenomic Analysis with Kraken 2 and KrakenUniq.Diagnostics (Basel, Switzerland) · 2025Article
- Detection of parasites in food and water matrices by shotgun metagenomics: A narrative review.Food and waterborne parasitology · 2025Review
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3 authors.
Funding
Abstract
backgroundCulture-independent diagnostic tests are gaining popularity as tools for detecting pathogens in food. Shotgun sequencing holds substantial promise for food testing as it provides abundant information on microbial communities, but the challenge is in analyzing large and complex sequencing datasets with a high degree of both sensitivity and specificity. Falsely classifying sequencing reads as originating from pathogens can lead to unnecessary food recalls or production shutdowns, while low sensitivity resulting in false negatives could lead to preventable illness.
resultsWe used simulated and published shotgun sequencing datasets containing Salmonella-derived reads to explore the appearance and mitigation of false positive results using the popular taxonomic annotation softwares Kraken2 and Metaphlan4. Using default parameters, Kraken2 is sensitive but prone to false positives, while Metaphlan4 is more specific but unable to detect Salmonella at low abundance. We then developed a bioinformatic pipeline for identifying and removing reads falsely identified as Salmonella by Kraken2 while retaining high sensitivity. Carefully considering software parameters and database choices is essential to avoiding false positive sample calls. With well-chosen parameters plus additional steps to confirm the taxonomic origin of reads, it is possible to detect pathogens with very high specificity and sensitivity.
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