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MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

Nature Biotechnology volume 33, pages 296–300 (2015)Cite this article

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Abstract

Short-read, high-throughput sequencing technology cannot identify the chromosomal position of repetitive insertion sequences that typically flank horizontally acquired genes such as bacterial virulence genes and antibiotic resistance genes. The MinION nanopore sequencer can produce long sequencing reads on a device similar in size to a USB memory stick. Here we apply a MinION sequencer to resolve the structure and chromosomal insertion site of a composite antibiotic resistance island in Salmonella Typhi Haplotype 58. Nanopore sequencing data from a single 18-h run was used to create a scaffold for an assembly generated from short-read Illumina data. Our results demonstrate the potential of the MinION device in clinical laboratories to fully characterize the epidemic spread of bacterial pathogens.

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Figure 1
Figure 2: Genetic organization of the S. Typhi chromosomal resistance island.
Figure 3: Comparison of the S. Typhi chromosomal resistance island with two closely related plasmids.

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European Nucleotide Archive

NCBI Reference Sequence

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Acknowledgements

M. Day (Salmonella Reference Unit, Public Health England) for antibiotic susceptibility tests. J.O'G. and J.W. were funded by the University of East Anglia. We would like to thank Oxford Nanopore Technologies Ltd. for including us in the MinION Access Programme. We would also like to thank L. Nederbragt for a thorough review and contributions toward the presentation of Figure 1.

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Author notes

  1. Philip M Ashton and Satheesh Nair: These authors contributed equally to this work.

Authors and Affiliations

  1. Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK.,

    Philip M Ashton, Satheesh Nair & Tim Dallman

  2. Department of Biomedical Sciences, University of Sassari, Sassari, Italy

    Salvatore Rubino

  3. Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia

    Salvatore Rubino

  4. National Reference Centre for Salmonellae and other Enterics, Robert Koch Institute, Wernigerode, Germany

    Wolfgang Rabsch

  5. Norwich Medical School, University of East Anglia, Norwich, UK

    Solomon Mwaigwisya, John Wain & Justin O'Grady

Authors
  1. Philip M Ashton
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Contributions

P.M.A., S.N., T.D., J.W. and J.O'G. conceived the study, performed the analysis and wrote the first draft of the manuscript. J.O'G. and S.M. performed the MinION sequencing. P.M.A. and T.D. performed the bioinformatics analysis. S.N. performed the PCR analysis and coordinated the Illumina sequencing. P.M.A., T.D., S.R., W.R., J.W. and J.O'G. analyzed the resistance island structure and insertion site and devised the figures. All authors contributed to editing and data analysis of the final manuscript.

Corresponding authors

Correspondence to Tim Dallman or Justin O'Grady.

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Competing interests

J.O'G. is a participant of Oxford Nanopore's MinION Access Programme (MAP) and received the MinION device and flowcells used for this study free of charge.

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Supplementary Figures 1–5, Supplementary Tables 1–3 (PDF 345 kb)

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Ashton, P., Nair, S., Dallman, T. et al. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 33, 296–300 (2015). https://doi.org/10.1038/nbt.3103

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