ArticleBMC research notes2012
Using metagenomic analyses to estimate the consequences of enrichment bias for pathogen detection.
Article in BMC research notes, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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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.
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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
23 citing papers in PubMed, 58 citations in OpenAlex.
- Breaking the culture habit: Complementing culture-based veterinary diagnostics with metagenomic data -A case study of feline and canine skin infections.BMC veterinary research · 2026Article
- Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.Microbiome · 2025Article
- A metagenomic analysis coupled with oligotrophic enrichment approach for detecting specified microorganisms in potable groundwater samples.Frontiers in microbiology · 2025Article
- PathogenDx DetectX Combined Demonstrates Equivalent Performance in Comparison to Four AOAC Certified Methods for the Detection of Aspergillus Species, Salmonella Species, and STEC in Dried Hemp Flower.Journal of AOAC International · 2023Article
- Surveillance of Listeria monocytogenes: Early Detection, Population Dynamics, and Quasimetagenomic Sequencing during Selective Enrichment.Applied and environmental microbiology · 2021Article
- Determination of Antimicrobial Resistance Patterns in Salmonella from Commercial Poultry as Influenced by Microbiological Culture and Antimicrobial Susceptibility Testing Methods.Microorganisms · 2021Article
- Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads.BMC genomics · 2021Article
- Article
- STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.The Lancet. Infectious diseases · 2020Review
- Optimization of a Method for the Concentration of Genetic Material in Bacterial and Fungal Communities on Fresh Apple Peel Surfaces.Microorganisms · 2020Article
- Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples.Applied and environmental microbiology · 2018Article
- Molecular Identification of Bacteria in Intra-abdominal Abscesses Using Deep Sequencing.Open forum infectious diseases · 2018Article
- Listeria monocytogenes Strains Underrepresented during Selective Enrichment with an ISO Method Might Dominate during Passage through Simulated Gastric Fluid andApplied and environmental microbiology · 2016Article
- Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak.BMC microbiology · 2016Article
- Mungo bean sprout microbiome and changes associated with culture based enrichment protocols used in detection of Gram-negative foodborne pathogens.Microbiome · 2016Article
- Recent and emerging innovations in Salmonella detection: a food and environmental perspective.Microbial biotechnology · 2016Review
- Early Recovery ofFrontiers in microbiology · 2016Article
- Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing.BMC microbiology · 2015Article
- The impact of systemic and copper pesticide applications on the phyllosphere microflora of tomatoes.Journal of the science of food and agriculture · 2015Article
- Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases?Methods in molecular biology (Clifton, N.J.) · 2015Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEnriching environmental samples to increase the probability of detection has been standard practice throughout the history of microbiology. However, by its very nature, the process of enrichment creates a biased sample that may have unintended consequences for surveillance or resolving a pathogenic outbreak. With the advent of next-generation sequencing and metagenomic approaches, the possibility now exists to quantify enrichment bias at an unprecedented taxonomic breadth.
findingsWe investigated differences in taxonomic profiles of three enriched and unenriched tomato phyllosphere samples taken from three different tomato fields (n = 18). 16S rRNA gene meteganomes were created for each of the 18 samples using 454/Roche's pyrosequencing platform, resulting in a total of 165,259 sequences. Significantly different taxonomic profiles and abundances at a number of taxonomic levels were observed between the two treatments. Although as many as 28 putative Salmonella sequences were detected in enriched samples, there was no significant difference in the abundance of Salmonella between enriched and unenriched treatments.
conclusionsOur results illustrate that the process of enriching greatly alters the taxonomic profile of an environmental sample beyond that of the target organism. We also found evidence suggesting that enrichment may not increase the probability of detecting a target. In conclusion, our results further emphasize the need to develop metagenomics as a validated culture independent method for pathogen detection.
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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.