ArticleMicrobial genomics2018
MinION nanopore sequencing identifies the position and structure of bacterial antibiotic resistance determinants in a multidrug-resistant strain of enteroaggregative Escherichia coli.
Article in Microbial genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Molecular insights into antimicrobial resistance in human bacterial pathogens: mechanisms, resistance genes, and translational diagnostic applications.Frontiers in microbiology · 2026Review
- Microbiology and epidemiology of enteroaggregativeJournal of medical microbiology · 2025Article
- Genomic insights into the spread of vancomycin- and tigecycline-resistant Enterococcus faecium ST117.Annals of clinical microbiology and antimicrobials · 2025Article
- Decoding the genome and epigenome of avianFrontiers in veterinary science · 2025Article
- Utility of hybrid whole genome sequencing in assessing potential nosocomial VIM transmission.Antimicrobial stewardship & healthcare epidemiology : ASHE · 2024Article
- Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria.Diagnostics (Basel, Switzerland) · 2023Review
- The impact of applying various de novo assembly and correction tools on the identification of genome characterization, drug resistance, and virulence factors of clinical isolates using ONT sequencing.BMC biotechnology · 2023Article
- Prevalence and molecular characteristics of polymyxin-resistantFrontiers in cellular and infection microbiology · 2023Article
- Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouringMicrobial genomics · 2022Article
- Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidalMicrobial genomics · 2022Article
- Article
- Antibiotic resistance in plant growth promoting bacteria: A comprehensive review and future perspectives to mitigate potential gene invasion risks.Frontiers in microbiology · 2022Review
- Use of Nanopore Sequencing to Characterise the Genomic Architecture of Mobile Genetic Elements EncodingFrontiers in microbiology · 2022Article
- Identification of isolated or mixed strains from long reads: a challenge met onMicrobial genomics · 2021Article
- Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs.Genome biology · 2021Article
- Emergence of carbapenem-resistantJournal of medical microbiology · 2021Article
- Rapid Methods for Antimicrobial Resistance Diagnostics.Antibiotics (Basel, Switzerland) · 2021Review
- A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing.F1000Research · 2021Article
- Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing.BMC genomics · 2020Article
- Nanopore sequencing reveals genomic map of CTX-M-type extended-spectrum β-lactamases carried by Escherichia coli strains isolated from blue mussels (Mytilus edulis) in Norway.BMC microbiology · 2020Article
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4 authors.
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Abstract
The aim of this study was to use single-molecule, nanopore sequencing to explore the genomic environment of the resistance determinants in a multidrug-resistant (MDR) strain of enteroaggregative Escherichia coli serotype O51 : H30, sequence type (ST) 38. Sequencing was performed on the MinION Flow cell MIN-106 R9.4. Nanopore raw FAST5 reads were base-called using Albacore v1.2.1, converted to FASTA and FASTQ formats using Poretools v0.6.0, and assembled using Unicycler v0.4.2, combining the long-read sequencing data with short-read data produced by Illumina sequencing. The genome was interrogated against an antimicrobial resistance (AMR) gene reference database using blast. The majority of the 12 AMR determinants identified were clustered together on the chromosome at three separate locations flanked by integrases and/or insertion elements [region 1 -catA, blaOXA-1, aac(6')-Ib-cr, tetA and blaCTX-M-15; region 2 - dfrA1 and aadA1; region 3 - catA, blaTEM-1, tetA and sul2]. AMR determinants located outside these three regions were a chromosomally encoded blaCMY-16, mutations in gyrA and parC, and two plasmid-encoded AMR determinants, blaOXA-181 and qnrS1 located on the same IncX3 plasmid. Long-read analysis of whole genome sequencing data identified mobile genetic elements on which AMR determinants were located and revealed the combination of different AMR determinants co-located on the same mobile element. These data contribute to a better understanding of the transmission of co-located AMR determinants in MDR E. coli causing gastrointestinal and extra-intestinal infections.
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