Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

GigaScience

Samuel S Minot³  C Nicole Rosenzweig²  Dana R Kadavy³  Kristen L Willis¹  Alvin T Liem²  Elizabeth J Corriveau²  Jamie L Haas³  Andy Kilianski² 

[1] Defense Threat Reduction Agency, 8725 John J Kingman Rd Stop 6201, Ft. Belvoir 22060-6201, VA, USA;Edgewood Chemical Biological Center, 5183 Black Hawk Rd Bldg E3150 Rm 324, Aberdeen Proving Ground 21010, MD, USA;Signature Science, LLC, 8329 N. MoPac Expressway, Austin 78759, TX, USA

关键词: Long-read sequencing;    Whole genome sequencing;    Escherichia coli;    Poxvirus;    Pathogen detection;    Amplicon;    Nanopore;    NGS;    Oxford Nanopore;    MinION™;   

Others  :  1141407
DOI  :  10.1186/s13742-015-0051-z

 received in 2014-12-24, accepted in 2015-02-27,  发布年份 2015

【 摘 要 】

Background

The MinION™ nanopore sequencer was recently released to a community of alpha-testers for evaluation using a variety of sequencing applications. Recent reports have tested the ability of the MinION™ to act as a whole genome sequencer and have demonstrated that nanopore sequencing has tremendous potential utility. However, the current nanopore technology still has limitations with respect to error-rate, and this is problematic when attempting to assemble whole genomes without secondary rounds of sequencing to correct errors. In this study, we tested the ability of the MinION™ nanopore sequencer to accurately identify and differentiate bacterial and viral samples via directed sequencing of characteristic genes shared broadly across a target clade.

Results

Using a 6 hour sequencing run time, sufficient data were generated to identify an E. coli sample down to the species level from 16S rDNA amplicons. Three poxviruses (cowpox, vaccinia-MVA, and vaccinia-Lister) were identified and differentiated down to the strain level, despite over 98% identity between the vaccinia strains. The ability to differentiate strains by amplicon sequencing on the MinION™ was accomplished despite an observed per-base error rate of approximately 30%.

Conclusions

While nanopore sequencing, using the MinION™ platform from Oxford Nanopore in particular, continues to mature into a commercially available technology, practical uses are sought for the current versions of the technology. This study offers evidence of the utility of amplicon sequencing by demonstrating that the current versions of MinION™ technology can accurately identify and differentiate both viral and bacterial species present within biological samples via amplicon sequencing.

【 授权许可】

   
2015 Kilianski et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

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