ArticleNucleic acids research2023
MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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Who cites it
125 citing papers in PubMed.
- Mass azithromycin distribution and antibiotic resistance in the gut and nasopharynx: a cluster-randomized trial.Nature medicine · 2026Trial
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- Artificial intelligence catalyzes antimicrobial peptide design.Synthetic and systems biotechnology · 2027Review
- First human isolation ofNew microbes and new infections · 2026Article
- Phage-ICE tandems facilitate bacterial adaptation and antimicrobial resistance spread.Science advances · 2026Article
- Characterization of the gut microbiome and resistome of piglets supplemented with low, moderate, and high concentrations of zinc oxide.Microbiology spectrum · 2026Article
- Comparative evaluation of three high-molecular-weight DNA extraction kits for Oxford Nanopore sequencing ofMicrobiology spectrum · 2026Article
- Subclinical Mastitis and Antibiotic Exposure Reshape the Milk Bacteriome, Resistome, and Metabolic Functional Profiles in Dairy Cows.MicrobiologyOpen · 2026Article
- Exploring the Oral Resistome: From Metagenomics to Precision Oral Health.Microorganisms · 2026Review
- Integrated qPCR and Shotgun Metagenomics for Surveillance of Antimicrobial Resistance in Municipal Wastewater from Central Italy.Antibiotics (Basel, Switzerland) · 2026Article
- Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.Antibiotics (Basel, Switzerland) · 2026Review
- Genome features and antimicrobial resistance ofMicrobiology spectrum · 2026Article
- Article
- Seasonal Restructuring of Microbial Communities and Resistomes in the Shitalakshya River, Bangladesh Revealed by Shotgun Metagenomics.MicrobiologyOpen · 2026Article
- Pangenomic and genomic plasticity analyses of the genus Rickettsia.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Article
- Profiling the gut resistome to unlock antimicrobial resistance biology and inform clinical risk.Nature communications · 2026Review
- Comprehensive Phenotypic and Genomic Study for Understanding the Variability in Susceptibility of Listeria monocytogenes to AMPs and Bacteriocins.Probiotics and antimicrobial proteins · 2026Article
- Phenotypic and genomic insights into Stenotrophomonas sepilia SMBL8: metabolic versatility, antibiotic resistance and pathogenic potential.World journal of microbiology & biotechnology · 2026Article
- Responsible Use of Large Language Models in Microbial Genomics and Bioinformatics: A Life-Science Framework for Reliability, Reproducibility, and Risk-Aware Interpretation.Life (Basel, Switzerland) · 2026Review
65 more citing papers are in PubMed but not listed here.
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11 authors.
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Abstract
Antimicrobial resistance (AMR) is considered a critical threat to public health, and genomic/metagenomic investigations featuring high-throughput analysis of sequence data are increasingly common and important. We previously introduced MEGARes, a comprehensive AMR database with an acyclic hierarchical annotation structure that facilitates high-throughput computational analysis, as well as AMR++, a customized bioinformatic pipeline specifically designed to use MEGARes in high-throughput analysis for characterizing AMR genes (ARGs) in metagenomic sequence data. Here, we present MEGARes v3.0, a comprehensive database of published ARG sequences for antimicrobial drugs, biocides, and metals, and AMR++ v3.0, an update to our customized bioinformatic pipeline for high-throughput analysis of metagenomic data (available at MEGLab.org). Database annotations have been expanded to include information regarding specific genomic locations for single-nucleotide polymorphisms (SNPs) and insertions and/or deletions (indels) when required by specific ARGs for resistance expression, and the updated AMR++ pipeline uses this information to check for presence of resistance-conferring genetic variants in metagenomic sequenced reads. This new information encompasses 337 ARGs, whose resistance-conferring variants could not previously be confirmed in such a manner. In MEGARes 3.0, the nodes of the acyclic hierarchical ontology include 4 antimicrobial compound types, 59 resistance classes, 233 mechanisms and 1448 gene groups that classify the 8733 accessions.
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