Sergio Arredondo-Alonso1,2, Anna K Pöntinen1, François Cléon3, Rebecca A Gladstone1, Anita C Schürch4, Pål J Johnsen3, Ørjan Samuelsen3,5, Jukka Corander1,2,6. 1. Department of Biostatistics, University of Oslo, 0317, Oslo, Norway. 2. Parasites and Microbes, Wellcome Sanger Institute, Cambridgeshire CB10 1RQ, UK. 3. Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway. 4. Department of Medical Microbiology, UMC Utrecht, 3584 CX, Utrecht, the Netherlands. 5. Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038, Tromsø, Norway. 6. Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, 02130, Espoo, Helsinki, Finland.
Abstract
BACKGROUND: Bacterial whole-genome sequencing based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits those contiguous sequences to be unambiguously bridged into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose an isolate selection strategy that optimizes a representative selection of isolates for long-read sequencing considering as input large-scale bacterial collections. RESULTS: Despite an uneven distribution of long reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98), which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library. CONCLUSIONS: The proposed long-read isolate selection ensures the completion of bacterial genomes that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.
BACKGROUND: Bacterial whole-genome sequencing based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits those contiguous sequences to be unambiguously bridged into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose an isolate selection strategy that optimizes a representative selection of isolates for long-read sequencing considering as input large-scale bacterial collections. RESULTS: Despite an uneven distribution of long reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98), which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library. CONCLUSIONS: The proposed long-read isolate selection ensures the completion of bacterial genomes that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.
Authors: Claudio U Köser; Matthew T G Holden; Matthew J Ellington; Edward J P Cartwright; Nicholas M Brown; Amanda L Ogilvy-Stuart; Li Yang Hsu; Claire Chewapreecha; Nicholas J Croucher; Simon R Harris; Mandy Sanders; Mark C Enright; Gordon Dougan; Stephen D Bentley; Julian Parkhill; Louise J Fraser; Jason R Betley; Ole B Schulz-Trieglaff; Geoffrey P Smith; Sharon J Peacock Journal: N Engl J Med Date: 2012-06-14 Impact factor: 91.245
Authors: Sergio Arredondo-Alonso; Anna K Pöntinen; François Cléon; Rebecca A Gladstone; Anita C Schürch; Pål J Johnsen; Ørjan Samuelsen; Jukka Corander Journal: Gigascience Date: 2021-12-09 Impact factor: 6.524