ArticleMicrobiome2018
In-depth resistome analysis by targeted metagenomics.
Article in Microbiome, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- Ceftriaxone and Cefotaxime Have Similar Effects on the Intestinal Microbiota in Human Volunteers Treated by Standard-Dose Regimens.Antimicrobial agents and chemotherapy · 2019Trial
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- Coccidiosis prevention strategies shape the microbiome, resistome and mobilome composition in the broiler gut.Animal microbiome · 2026Article
- The gut resistome as a potential determinant of immunotherapy response: antibiotics, immunometabolism, and precision oncology.Frontiers in microbiology · 2026Review
- Antibiotic use in Chilean salmon aquaculture: antimicrobial resistance, sustainability, and One Health implications.Frontiers in microbiology · 2026Review
- Gut microbiome dysbiosis and functional alterations inGut microbes reports · 2026Article
- Microbial interactions as the key to understanding and controlling environmental spread of antibiotic resistance genes.npj antimicrobials and resistance · 2025Article
- Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.BMC medical genomics · 2025Article
- Methods, applications, and computational challenges in bait capture enrichment.Cell reports methods · 2025Review
- Article
- Mitigating antimicrobial resistance by innovative solutions in AI (MARISA): a modified James Lind Alliance analysis.npj antimicrobials and resistance · 2025Article
- Veterinary Clinics as Reservoirs forAntibiotics (Basel, Switzerland) · 2025Review
- CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment.Applied and environmental microbiology · 2025Article
- Evaluating methods for genome sequencing ofMicrobial genomics · 2025Article
- Detection of rare plasmid hosts using a targeted Hi-C approach.ISME communications · 2025Article
- Enriching the future of public health microbiology with hybridization bait capture.Clinical microbiology reviews · 2024Review
- Associations between acquired antimicrobial resistance genes in the upper respiratory tract and livestock farm exposures: a case-control study in COPD and non-COPD individuals.The Journal of antimicrobial chemotherapy · 2024Article
- Factors impacting target-enriched long-read sequencing of resistomes and mobilomes.Genome research · 2024Article
- The Staphylococcus aureus-antagonizing human nasal commensal Staphylococcus lugdunensis depends on siderophore piracy.Microbiome · 2024Article
- Monitoring of Pseudomonas aeruginosa mutational resistome dynamics using an enrichment panel for direct sequencing of clinical samples.EBioMedicine · 2024Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
backgroundAntimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype. Here, we describe a novel strategy that combines targeted metagenomics using last generation in-solution capture platforms, with novel bioinformatics tools to establish a standardized framework that allows both quantitative and qualitative analyses of resistomes.
methodsWe developed ResCap, a targeted sequence capture platform based on SeqCapEZ (NimbleGene) technology, which includes probes for 8667 canonical resistance genes (7963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), and 2517 relaxase genes (plasmid markers) and 78,600 genes homologous to the previous identified targets (47,806 for antibiotics and 30,794 for biocides or metals). Its performance was compared with metagenomic shotgun sequencing (MSS) for 17 fecal samples (9 humans, 8 swine). ResCap significantly improves MSS to detect "gene abundance" (from 2.0 to 83.2%) and "gene diversity" (26 versus 14.9 genes unequivocally detected per sample per million of reads; the number of reads unequivocally mapped increasing up to 300-fold by using ResCap), which were calculated using novel bioinformatic tools. ResCap also facilitated the analysis of novel genes potentially involved in the resistance to antibiotics, metals, biocides, or any combination thereof.
conclusionsResCap, the first targeted sequence capture, specifically developed to analyze resistomes, greatly enhances the sensitivity and specificity of available metagenomic methods and offers the possibility to analyze genes related to the selection and transfer of antimicrobial resistance (biocides, heavy metals, plasmids). The model opens the possibility to study other complex microbial systems in which minority populations play a relevant role.
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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.