A transcriptomic approach to identify novel drug efflux pumps in bacteria

Liping Li, Sasha G. Tetu, Ian T. Paulsen, Karl A. Hassan*

*Corresponding author for this work

    Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

    8 Citations (Scopus)


    The core genomes of most bacterial species include a large number of genes encoding putative efflux pumps. The functional roles of most of these pumps are unknown, however, they are often under tight regulatory control and expressed in response to their substrates. Therefore, one way to identify pumps that function in antimicrobial resistance is to examine the transcriptional responses of efflux pump genes to antimicrobial shock. By conducting complete transcriptomic experiments following antimicrobial shock treatments, it may be possible to identify novel drug efflux pumps encoded in bacterial genomes. In this chapter we describe a complete workflow for conducting transcriptomic analyses by RNA sequencing, to determine transcriptional changes in bacteria responding to antimicrobials.
    Original languageEnglish
    Title of host publicationBacterial multidrug exporters
    Subtitle of host publicationmethods and protocols
    EditorsAkihito Yamaguchi, Kunihiko Nishino
    Place of PublicationNew York, NY
    PublisherHumana Press Inc.
    Number of pages15
    ISBN (Electronic)9781493974542
    ISBN (Print)9781493974528
    Publication statusPublished - 2018

    Publication series

    NameMethods in molecular bioogy
    PublisherHumana Press
    ISSN (Print)1064-3745
    ISSN (Electronic)1940-6029


    • multidrug efflux
    • drug resistance
    • transcriptomics
    • RNA-Seq
    • gene expression


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