ArticleScientific reports2020
Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 81 citations in OpenAlex.
- Comparative evaluation of three high-molecular-weight DNA extraction kits for Oxford Nanopore sequencing ofMicrobiology spectrum · 2026Article
- A WGS workflow for identifying genetically modified and foodborne-pathogenicFood chemistry. Molecular sciences · 2026Article
- Review
- High-risk clonal expansion of IMP-producingAntimicrobial agents and chemotherapy · 2025Article
- Sample Preparation for Multi-Omics Analysis: Considerations and Guidance for Identifying the Ideal Workflow.Proteomics · 2025Review
- Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art.Frontiers in genetics · 2025Review
- Sequencing Strategy to Ensure Accurate Plasmid Assembly.ACS synthetic biology · 2024Article
- Characterization of acquired β-lactamases inMicrobiology spectrum · 2024Article
- A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome.Microbiome · 2024Article
- Sequencing Strategy to Ensure Accurate Plasmid Assembly.bioRxiv : the preprint server for biology · 2024Article
- Unraveling metagenomics through long-read sequencing: a comprehensive review.Journal of translational medicine · 2024Review
- Synsor: a tool for alignment-free detection of engineered DNA sequences.Frontiers in bioengineering and biotechnology · 2024Article
- Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements.PeerJ · 2024Article
- Identification of plasmids in avian-associated Escherichia coli using nanopore and illumina sequencing.BMC genomics · 2023Article
- Illuminating the Genomic Landscape ofMicroorganisms · 2023Article
- Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria.BMC genomics · 2023Article
- Long read genome assemblers struggle with small plasmids.Microbial genomics · 2023Article
- Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements.Scientific reports · 2023Article
- Whole-genome sequence analysis of clinically isolated carbapenem resistant Escherichia coli from Iran.BMC microbiology · 2023Article
- Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems.Environmental microbiome · 2023Article
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Antimicrobial resistance (AMR) is a major public health threat. Plasmids are able to transfer AMR genes among bacterial isolates. Whole genome sequencing (WGS) is a powerful tool to monitor AMR determinants. However, plasmids are difficult to reconstruct from WGS data. This study aimed to improve the characterization, including the localization of AMR genes using short and long read WGS strategies. We used a genetically modified (GM) Bacillus subtilis isolated as unexpected contamination in a feed additive, and therefore considered unauthorized (RASFF 2014.1249), as a case study. In GM organisms, AMR genes are used as selection markers. Because of the concern of spread of these AMR genes when present on mobile genetic elements, it is crucial to characterize their location. Our approach resulted in an assembly of one chromosome and one plasmid, each with several AMR determinants of which five are against critically important antibiotics. Interestingly, we found several plasmids, containing AMR genes, integrated in the chromosome in a repetitive region of at least 53 kb. Our findings would have been impossible using short reads only. We illustrated the added value of long read sequencing in addressing the challenges of plasmid reconstruction within the context of evaluating the risk of AMR spread.
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