ArticleMicrobiome2017
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.
Article in Microbiome, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 100 citations in OpenAlex.
- Article
- RAmpSim: a thermodynamic simulator for hybridization capture in metagenomic sequencing.Bioinformatics (Oxford, England) · 2026Article
- Early-life development of the microbiome and resistome in antibiotic-naïve dairy calves.Microbiology spectrum · 2026Article
- Article
- Different DNA input amounts and library preparation kits yield comparable resistome characterization using target-enriched metagenomic sequencing.Frontiers in microbiology · 2026Article
- Targeted probe capture metagenomics-enabled surveillance of multidrug-resistant organisms and antimicrobial resistance genes in post-handwashing areas of public washrooms.Environmental microbiome · 2025Article
- Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples.Molecular biology and evolution · 2025Article
- Methods, applications, and computational challenges in bait capture enrichment.Cell reports methods · 2025Review
- Hybridization capture sequencing formBio · 2025Article
- OLTA: Optimizing bait seLection for TArgeted sequencing.Bioinformatics (Oxford, England) · 2025Article
- Article
- Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.ISME communications · 2025Article
- Enriching the future of public health microbiology with hybridization bait capture.Clinical microbiology reviews · 2024Review
- The gut microbiome and resistome of yellow perch (One health (Amsterdam, Netherlands) · 2024Article
- Factors impacting target-enriched long-read sequencing of resistomes and mobilomes.Genome research · 2024Article
- The TELCoMB Protocol for High-Sensitivity Detection of ARG-MGE Colocalizations in Complex Microbial Communities.Current protocols · 2024Article
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools.BMC microbiology · 2024Article
- Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era.Nature reviews. Microbiology · 2024Review
- Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves.Animal microbiome · 2023Article
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Authors and funding
15 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundShotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias.
resultsThe use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins.
conclusionsThese results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.
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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.