A Transcriptomic Approach to Identify Novel Drug Efflux Pumps in Bacteria

  • Liping Li
  • Sasha G. Tetu
  • Ian T. Paulsen
  • Karl A. Hassan
Part of the Methods in Molecular Biology book series (MIMB, volume 1700)


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.

Key words

Multidrug efflux Drug resistance Transcriptomics RNA-Seq Gene expression 



This work was supported by a Macquarie University International Research Excellence Scholarship to L.L., an Australian Research Council Discovery Early Career Research Fellowship to S.G.T. (DE150100009), an Australian National Health and Medical Research Council Project Grant to I.T.P. and K.A.H. (1060895), and a Macquarie University Research Development Grant to K.A.H. (9201401563).


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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Liping Li
    • 1
  • Sasha G. Tetu
    • 1
  • Ian T. Paulsen
    • 1
  • Karl A. Hassan
    • 2
  1. 1.Department of Chemistry and Biomolecular SciencesMacquarie UniversitySydneyAustralia
  2. 2.Department of Chemistry and Biomolecular SciencesMacquarie UniversityNorth RydeAustralia

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