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

5 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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