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

Published version
Peer-reviewed

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Authors

Srisomang, Pramot 
Mahavanakul, Weera 
Wuthiekanun, Vanaporn 

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 used 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 considerable variation 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.

Description

Keywords

MRSA, epidemiology, global health, hospital infections, human, molecular epidemiology, Adult, Child, Computational Biology, Cross Infection, DNA, Bacterial, Disease Outbreaks, Genetic Variation, Genome, Bacterial, Humans, Methicillin-Resistant Staphylococcus aureus, Phylogeny, Polymorphism, Single Nucleotide, Staphylococcal Infections, Thailand, Whole Genome Sequencing

Journal Title

Elife

Conference Name

Journal ISSN

2050-084X
2050-084X

Volume Title

8

Publisher

eLife Sciences Publications, Ltd
Sponsorship
Medical Research Council (G1000803)
Wellcome (098051) Chief Scientist Office (SIRN10) Wellcome (106698/Z/14/Z) Medical Research Council (G1000803) European Research Council (PBDR-339251)