Complete Genome Sequence of Francisella tularensis Live Vaccine Strain NR-28537 (BEI Master Cell Bank)

Player, Robert A.; Verratti, Kathleen; Grady, Sarah L.; Beck, Linda; Goodwin, Bruce G.; Earnhart, Christopher G.; Sozhamannan, Shanmuga

doi:10.1128/mra.01248-20

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“…While single strains have been sequenced using nanopore technology for F. tularensis [ 39 ] and hybrid assemblies were used to support Ba. anthracis genotyping [ 24 ], to the authors’ knowledge no systematic comparison of Illumina and ONT sequencing for Ba.…”

Section: Introductionmentioning

confidence: 99%

Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis

et al. 2023

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Background Bacterial epidemiology needs to understand the spread and dissemination of strains in a One Health context. This is important for highly pathogenic bacteria such as Bacillus anthracis, Brucella species, and Francisella tularensis. Whole genome sequencing (WGS) has paved the way for genetic marker detection and high-resolution genotyping. While such tasks are established for Illumina short-read sequencing, Oxford Nanopore Technology (ONT) long-read sequencing has yet to be evaluated for such highly pathogenic bacteria with little genomic variations between strains. In this study, three independent sequencing runs were performed using Illumina, ONT flow cell version 9.4.1, and 10.4 for six strains of each of Ba. anthracis, Br. suis and F. tularensis. Data from ONT sequencing alone, Illumina sequencing alone and two hybrid assembly approaches were compared. Results As previously shown, ONT produces ultra-long reads, while Illumina produces short reads with higher sequencing accuracy. Flow cell version 10.4 improved sequencing accuracy over version 9.4.1. The correct (sub-)species were inferred from all tested technologies, individually. Moreover, the sets of genetic markers for virulence, were almost identical for the respective species. The long reads of ONT allowed to assemble not only chromosomes of all species to near closure, but also virulence plasmids of Ba. anthracis. Assemblies based on nanopore data alone, Illumina data alone, and both hybrid assemblies correctly detected canonical (sub-)clades for Ba. anthracis and F. tularensis as well as multilocus sequence types for Br. suis. For F. tularensis, high-resolution genotyping using core-genome MLST (cgMLST) and core-genome Single-Nucleotide-Polymorphism (cgSNP) typing produced highly comparable results between data from Illumina and both ONT flow cell versions. For Ba. anthracis, only data from flow cell version 10.4 produced similar results to Illumina for both high-resolution typing methods. However, for Br. suis, high-resolution genotyping yielded larger differences comparing Illumina data to data from both ONT flow cell versions. Conclusions In summary, combining data from ONT and Illumina for high-resolution genotyping might be feasible for F. tularensis and Ba. anthracis, but not yet for Br. suis. The ongoing improvement of nanopore technology and subsequent data analysis may facilitate high-resolution genotyping for all bacteria with highly stable genomes in future.

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Section: Introductionmentioning

confidence: 99%

Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis

et al. 2023

View full text Add to dashboard Cite

show abstract

Complete Genome Sequence of Francisella tularensis Live Vaccine Strain NR-28537 (BEI Master Cell Bank)

Abstract: The genome of Francisella tularensis live vaccine strain NR-28537 was sequenced by a hybrid approach utilizing an Oxford Nanopore Technologies R9 flow cell and an Illumina MiSeq platform. De novo assembly of the resulting long and short reads produced a single-contig whole-genome sequence.

Cited by 1 publication

References 10 publications

Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis

Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis

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