ArticleMicrobial genomics2026
Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate.
Article in Microbial genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed.
- Genomic surveillance of multidrug-resistant Enterobacterales in a long-term care facility in Northern Italy based on a point prevalence screening.Scientific reports · 2026Article
- Evolutionary dynamics of the multidrug-resistantMicrobial genomics · 2026Article
- AI in variant analysis: fast track to genetic diagnoses.Human genetics · 2026Review
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole bacterial genome sequence reconstruction using Oxford Nanopore Technologies ('Nanopore') long-read-only sequencing may offer a lower-cost, higher-throughput alternative for pathogen surveillance to 'hybrid' assembly with recent improvements in Nanopore sequencing accuracy. We evaluated the accuracy, including plasmid reconstruction, of Nanopore long-read-only genome assemblies of Enterobacterales. We sequenced 92 genomes from clinical Enterobacterales isolates, collected in England under a national surveillance programme, with long-read Nanopore (R10.4.1, Dorado v5.0.0 super-high-accuracy basecalled) and short-read Illumina (NovaSeq) sequencing approaches. Genomes were assembled using three long-read-only (Flye, Hybracter long and Autocycler) and three hybrid assemblers (Hybracter hybrid, Unicycler normal and bold). Three polishing modalities (Medaka v2 with subsampled or un-subsampled long-reads; Polypolish+Pypolca with short-reads) were investigated. Autocycler circularised the most chromosomes [87/92 (95%)]. Plasmid sequence reconstruction was comparable among all assemblers except Flye, all recovering 90-96% of plasmids, although the 'ground truth' was uncertain. Flye performed worse than other assemblers on almost all metrics. Autocycler+Medaka (un-subsampled long-reads) was the most accurate long-read-only assembler/polisher combination, comparable to hybrid assemblies [median 0 (IQR: 0-0) single nucleotide variants (SNVs) and 0 (IQR: 0-1) insertions/deletions (indels) per genome; median quality value/
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