Improved characterisation of MRSA transmission using within-host bacterial sequence diversity

M. D. Hall, M. T.G. Holden, P. Srisomang, W. Mahavanakul, V. Wuthiekanun, D. Limmathurotsakul, K. Fountain, J. Parkhill, E. K. Nickerson, S. J. Peacock, C. Fraser

Research output: Contribution to journalArticle

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) transmission in the hospital setting has been a frequent subject of investigation using bacterial genomes, but previous approaches have not yet fully utilised the extra deductive power provided when multiple pathogen samples are acquired from each host. Here, we use a large dataset of MRSA sequences from multiply-sampled patients to reconstruct colonisation of individuals in a high-transmission setting in a hospital in Thailand. We reconstructed transmission trees for MRSA. We also investigated transmission between anatomical sites on the same individual, finding that this either occurs repeatedly or involves a wide transmission bottleneck. We examined the between-subject bottleneck, finding a wide range in the amount of diversity transmitted. Finally, we compared our approach to the simpler method of identifying transmission pairs using single nucleotide polymorphism (SNP) counts. This suggested that the optimum threshold for identifying a pair is 39 SNPs, if sensitivities and specificities are equally weighted.

Original languageEnglish
JournaleLife
Volume8
Early online date8 Oct 2019
DOIs
Publication statusE-pub ahead of print - 8 Oct 2019

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Hall, M. D., Holden, M. T. G., Srisomang, P., Mahavanakul, W., Wuthiekanun, V., Limmathurotsakul, D., ... Fraser, C. (2019). Improved characterisation of MRSA transmission using within-host bacterial sequence diversity. eLife, 8. https://doi.org/10.7554/eLife.46402

Improved characterisation of MRSA transmission using within-host bacterial sequence diversity. / Hall, M. D.; Holden, M. T.G.; Srisomang, P.; Mahavanakul, W.; Wuthiekanun, V.; Limmathurotsakul, D.; Fountain, K.; Parkhill, J.; Nickerson, E. K.; Peacock, S. J.; Fraser, C.

In: eLife, Vol. 8, 08.10.2019.

Research output: Contribution to journalArticle

Hall, MD, Holden, MTG, Srisomang, P, Mahavanakul, W, Wuthiekanun, V, Limmathurotsakul, D, Fountain, K, Parkhill, J, Nickerson, EK, Peacock, SJ & Fraser, C 2019, 'Improved characterisation of MRSA transmission using within-host bacterial sequence diversity', eLife, vol. 8. https://doi.org/10.7554/eLife.46402
Hall MD, Holden MTG, Srisomang P, Mahavanakul W, Wuthiekanun V, Limmathurotsakul D et al. Improved characterisation of MRSA transmission using within-host bacterial sequence diversity. eLife. 2019 Oct 8;8. https://doi.org/10.7554/eLife.46402
Hall, M. D. ; Holden, M. T.G. ; Srisomang, P. ; Mahavanakul, W. ; Wuthiekanun, V. ; Limmathurotsakul, D. ; Fountain, K. ; Parkhill, J. ; Nickerson, E. K. ; Peacock, S. J. ; Fraser, C. / Improved characterisation of MRSA transmission using within-host bacterial sequence diversity. In: eLife. 2019 ; Vol. 8.
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