Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin

Amy K. Cain*, Christine J. Boinett, Lars Barquist, Janina Dordel, Maria Fookes, Matthew Mayho, Matthew J. Ellington, David Goulding, Derek Pickard, Ryan R. Wick, Kathryn E. Holt, Julian Parkhill, Nicholas R. Thomson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Citations (Scopus)


Colistin remains one of the few antibiotics effective against multi-drug resistant (MDR) hospital pathogens, such as Klebsiella pneumoniae. Yet resistance to this last-line drug is rapidly increasing. Characterized mechanisms of colR in K. pneumoniae are largely due to chromosomal mutations in two-component regulators, although a plasmid-mediated colR mechanism has recently been uncovered. However, the effects of intrinsic colistin resistance are yet to be characterized on a whole-genome level. Here, we used a genomics-based approach to understand the mechanisms of adaptive colR acquisition in K. pneumoniae. In controlled directed-evolution experiments we observed two distinct paths to colistin resistance acquisition. Whole genome sequencing identified mutations in two colistin resistance genes: in the known colR regulator phoQ which became fixed in the population and resulted in a single amino acid change, and unstable minority variants in the recently described two-component sensor crrB. Through RNAseq and microscopy, we reveal the broad range of effects that colistin exposure has on the cell. This study is the first to use genomics to identify a population of minority variants with mutations in a colR gene in K. pneumoniae.

Original languageEnglish
Article number9868
JournalScientific Reports
Issue number1
Publication statusPublished - 1 Dec 2018

Bibliographical note

Funding Information:
We would like to thank and acknowledge Thamarai Schneiders for her kind gift of the Ecl8 strain. This work was supported by the Wellcome Trust grant number WT098051. The salaries of AKC and CJB were supported by the Medical Research Council [grant number G1100100/1] and MJE is supported by Public Health England. LB is supported by a research fellowship from the Alexander von Humboldt Stiftung/Foundation. KEH is supported by the NHMRC of Australia (Fellowship #1061409).

Publisher Copyright:
© 2018 The Author(s).


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