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

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Matthew D Hall, Matthew TG Holden, Pramot Srisomang, Weera Mahavanakul, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Kay Fountain, Julian Parkhill, Emma K Nickerson, Sharon J Peacock, Christophe Fraser

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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.
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Original languageEnglish
Article numbere46402
JournaleLife
Volume8
Early online date8 Oct 2019
DOIs
Publication statusE-pub ahead of print - 8 Oct 2019

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