Research

Bayesian identification of bacterial strains from sequencing data


Reference:

Sankar, A., Malone, B., Bayliss, S., Pascoe, B., Méric, G., Hitchings, M. D., Sheppard, S. K., Feil, E. J., Corander, J. and Honkela, A., 2016. Bayesian identification of bacterial strains from sequencing data. Microbial Genomics, 2 (08).

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    Official URL:

    https://doi.org/10.1099/mgen.0.000075

    Abstract

    Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is important to accurately identify the presence and estimate relative abundances of the target organisms from short sequence reads obtained from a sample. This task is particularly challenging when the set of interest includes very closely related organisms, such as different strains of pathogenic bacteria, which can vary considerably in terms of virulence, resistance and spread. Using advanced Bayesian statistical modelling and computation techniques we introduce a novel pipeline for bacterial identification that is shown to outperform the currently leading pipeline for this purpose. Our approach enables fast and accurate sequence-based identification of bacterial strains while using only modest computational resources. Hence it provides a useful tool for a wide spectrum of applications, including rapid clinical diagnostics to distinguish among closely related strains causing nosocomial infections. The software implementation is available at https://github.com/PROBIC/BIB

    Details

    Item Type Articles
    CreatorsSankar, A., Malone, B., Bayliss, S., Pascoe, B., Méric, G., Hitchings, M. D., Sheppard, S. K., Feil, E. J., Corander, J. and Honkela, A.
    DOI10.1099/mgen.0.000075
    Uncontrolled Keywordspathogenic bacteria,strain identification,staphylococcus aureus,probabilistic modelling
    DepartmentsFaculty of Science > Biology & Biochemistry
    Research CentresCentre for Mathematical Biology
    EPSRC Centre for Doctoral Training in Statistical Mathematics (SAMBa)
    Milner Centre for Evolution
    RefereedYes
    StatusPublished
    ID Code53429
    Additional Information16 pages, 7 figures

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