Evolution of colistin resistance in the klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics

Axel B. Janssen; Dennis J. Doorduijn; Grant Mills; Malbert R.C. Rogers; Marc J.M. Bonten; Suzan H.M. Rooijakkers; Rob J.L. Willems; Jose A. Bengoechea; Willem van Schaik

doi:10.1128/AAC.01958-20

Evolution of colistin resistance in the klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics

Axel B. Janssen, Dennis J. Doorduijn, Grant Mills, Malbert R.C. Rogers, Marc J.M. Bonten, Suzan H.M. Rooijakkers, Rob J.L. Willems, Jose A. Bengoechea, Willem van Schaik^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

15 Citations (Scopus)

Abstract

The increasing prevalence of multidrug-resistant Klebsiella pneumoniae has led to a resurgence in the use of colistin as a last-resort drug. Colistin is a cationic antibiotic that selectively acts on Gram-negative bacteria through electrostatic interactions with anionic phosphate groups of the lipid A moiety of lipopolysaccharides (LPSs). Colistin resistance in K. pneumoniae is mediated through loss of these phosphate groups, their modification by cationic groups, and by the hydroxylation of acyl groups of lipid A. Here, we study the in vitro evolutionary trajectories toward colistin resistance in four clinical K. pneumoniae complex strains and their impact on fitness and virulence characteristics. Through population sequencing during in vitro evolution, we found that colistin resistance develops through a combination of single nucleotide polymorphisms, insertions and deletions, and the integration of insertion sequence elements, affecting genes associated with LPS biosynthesis and modification and capsule structures. Colistin resistance decreased the maximum growth rate of one K. pneumoniae sensu stricto strain, but not those of the other three K. pneumoniae complex strains. Colistin-resistant strains had lipid A modified through hydroxylation, palmitoylation, and L-Ara4N addition. K. pneumoniae sensu stricto strains exhibited cross-resistance to LL-37, in contrast to the Klebsiella variicola subsp. variicola strain. Virulence, as determined in a Caenorhabditis elegans survival assay, was increased in two colistin-resistant strains. Our study suggests that nosocomial K. pneumoniae complex strains can rapidly develop colistin resistance through diverse evolutionary trajectories upon exposure to colistin. This effectively shortens the life span of this last-resort antibiotic for the treatment of infections with multidrug-resistant Klebsiella.

Original language	English
Article number	e01958-20
Number of pages	15
Journal	Antimicrobial Agents and Chemotherapy
Volume	65
Issue number	1
Early online date	16 Dec 2020
DOIs	https://doi.org/10.1128/AAC.01958-20
Publication status	Published - Jan 2021

Bibliographical note

Funding Information:
W.v.S. was funded by the Netherlands Organisation for Scientific Research through a Vidi grant (grant no. 917.13.357) and a Royal Society Wolfson Research Merit Award (grant no. WM160092). Work in the laboratory of J.A.B. was supported by the Biotechnology and Biological Sciences Research Council BBSRC, (grant no. BB/N00700X/1, BB/P020194/1, and BB/P006078/1) and a Queen’s University Belfast start-up grant. S.H.M.R. was funded by an ERC Starting grant (grant no. 639209-ComBact). The funders had no role in study design, data collection and interpretation, the decision to submit the work for publication, or manuscript preparation. The authors have declared that no competing interests exist.

Publisher Copyright:
© 2020 American Society for Microbiology. All Rights Reserved.

Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.

Keywords

Antibiotic resistance
Colistin
Evolution
Klebsiella
Virulence

ASJC Scopus subject areas

Pharmacology
Pharmacology (medical)
Infectious Diseases

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Cite this

Janssen, A. B., Doorduijn, D. J., Mills, G., Rogers, M. R. C., Bonten, M. J. M., Rooijakkers, S. H. M., Willems, R. J. L., Bengoechea, J. A., & van Schaik, W. (2021). Evolution of colistin resistance in the klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics. Antimicrobial Agents and Chemotherapy, 65(1), Article e01958-20. https://doi.org/10.1128/AAC.01958-20

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title = "Evolution of colistin resistance in the klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics",

abstract = "The increasing prevalence of multidrug-resistant Klebsiella pneumoniae has led to a resurgence in the use of colistin as a last-resort drug. Colistin is a cationic antibiotic that selectively acts on Gram-negative bacteria through electrostatic interactions with anionic phosphate groups of the lipid A moiety of lipopolysaccharides (LPSs). Colistin resistance in K. pneumoniae is mediated through loss of these phosphate groups, their modification by cationic groups, and by the hydroxylation of acyl groups of lipid A. Here, we study the in vitro evolutionary trajectories toward colistin resistance in four clinical K. pneumoniae complex strains and their impact on fitness and virulence characteristics. Through population sequencing during in vitro evolution, we found that colistin resistance develops through a combination of single nucleotide polymorphisms, insertions and deletions, and the integration of insertion sequence elements, affecting genes associated with LPS biosynthesis and modification and capsule structures. Colistin resistance decreased the maximum growth rate of one K. pneumoniae sensu stricto strain, but not those of the other three K. pneumoniae complex strains. Colistin-resistant strains had lipid A modified through hydroxylation, palmitoylation, and L-Ara4N addition. K. pneumoniae sensu stricto strains exhibited cross-resistance to LL-37, in contrast to the Klebsiella variicola subsp. variicola strain. Virulence, as determined in a Caenorhabditis elegans survival assay, was increased in two colistin-resistant strains. Our study suggests that nosocomial K. pneumoniae complex strains can rapidly develop colistin resistance through diverse evolutionary trajectories upon exposure to colistin. This effectively shortens the life span of this last-resort antibiotic for the treatment of infections with multidrug-resistant Klebsiella.",

keywords = "Antibiotic resistance, Colistin, Evolution, Klebsiella, Virulence",

author = "Janssen, {Axel B.} and Doorduijn, {Dennis J.} and Grant Mills and Rogers, {Malbert R.C.} and Bonten, {Marc J.M.} and Rooijakkers, {Suzan H.M.} and Willems, {Rob J.L.} and Bengoechea, {Jose A.} and {van Schaik}, Willem",

note = "Funding Information: W.v.S. was funded by the Netherlands Organisation for Scientific Research through a Vidi grant (grant no. 917.13.357) and a Royal Society Wolfson Research Merit Award (grant no. WM160092). Work in the laboratory of J.A.B. was supported by the Biotechnology and Biological Sciences Research Council BBSRC, (grant no. BB/N00700X/1, BB/P020194/1, and BB/P006078/1) and a Queen{\textquoteright}s University Belfast start-up grant. S.H.M.R. was funded by an ERC Starting grant (grant no. 639209-ComBact). The funders had no role in study design, data collection and interpretation, the decision to submit the work for publication, or manuscript preparation. The authors have declared that no competing interests exist. Publisher Copyright: {\textcopyright} 2020 American Society for Microbiology. All Rights Reserved. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",

year = "2021",

month = jan,

doi = "10.1128/AAC.01958-20",

language = "English",

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journal = "Antimicrobial Agents and Chemotherapy",

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Janssen, AB, Doorduijn, DJ, Mills, G, Rogers, MRC, Bonten, MJM, Rooijakkers, SHM, Willems, RJL, Bengoechea, JA & van Schaik, W 2021, 'Evolution of colistin resistance in the klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics', Antimicrobial Agents and Chemotherapy, vol. 65, no. 1, e01958-20. https://doi.org/10.1128/AAC.01958-20

Evolution of colistin resistance in the klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics. / Janssen, Axel B.; Doorduijn, Dennis J.; Mills, Grant et al.
In: Antimicrobial Agents and Chemotherapy, Vol. 65, No. 1, e01958-20, 01.2021.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Evolution of colistin resistance in the klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics

AU - Janssen, Axel B.

AU - Doorduijn, Dennis J.

AU - Mills, Grant

AU - Rogers, Malbert R.C.

AU - Bonten, Marc J.M.

AU - Rooijakkers, Suzan H.M.

AU - Willems, Rob J.L.

AU - Bengoechea, Jose A.

AU - van Schaik, Willem

N1 - Funding Information: W.v.S. was funded by the Netherlands Organisation for Scientific Research through a Vidi grant (grant no. 917.13.357) and a Royal Society Wolfson Research Merit Award (grant no. WM160092). Work in the laboratory of J.A.B. was supported by the Biotechnology and Biological Sciences Research Council BBSRC, (grant no. BB/N00700X/1, BB/P020194/1, and BB/P006078/1) and a Queen’s University Belfast start-up grant. S.H.M.R. was funded by an ERC Starting grant (grant no. 639209-ComBact). The funders had no role in study design, data collection and interpretation, the decision to submit the work for publication, or manuscript preparation. The authors have declared that no competing interests exist. Publisher Copyright: © 2020 American Society for Microbiology. All Rights Reserved. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2021/1

Y1 - 2021/1

N2 - The increasing prevalence of multidrug-resistant Klebsiella pneumoniae has led to a resurgence in the use of colistin as a last-resort drug. Colistin is a cationic antibiotic that selectively acts on Gram-negative bacteria through electrostatic interactions with anionic phosphate groups of the lipid A moiety of lipopolysaccharides (LPSs). Colistin resistance in K. pneumoniae is mediated through loss of these phosphate groups, their modification by cationic groups, and by the hydroxylation of acyl groups of lipid A. Here, we study the in vitro evolutionary trajectories toward colistin resistance in four clinical K. pneumoniae complex strains and their impact on fitness and virulence characteristics. Through population sequencing during in vitro evolution, we found that colistin resistance develops through a combination of single nucleotide polymorphisms, insertions and deletions, and the integration of insertion sequence elements, affecting genes associated with LPS biosynthesis and modification and capsule structures. Colistin resistance decreased the maximum growth rate of one K. pneumoniae sensu stricto strain, but not those of the other three K. pneumoniae complex strains. Colistin-resistant strains had lipid A modified through hydroxylation, palmitoylation, and L-Ara4N addition. K. pneumoniae sensu stricto strains exhibited cross-resistance to LL-37, in contrast to the Klebsiella variicola subsp. variicola strain. Virulence, as determined in a Caenorhabditis elegans survival assay, was increased in two colistin-resistant strains. Our study suggests that nosocomial K. pneumoniae complex strains can rapidly develop colistin resistance through diverse evolutionary trajectories upon exposure to colistin. This effectively shortens the life span of this last-resort antibiotic for the treatment of infections with multidrug-resistant Klebsiella.

AB - The increasing prevalence of multidrug-resistant Klebsiella pneumoniae has led to a resurgence in the use of colistin as a last-resort drug. Colistin is a cationic antibiotic that selectively acts on Gram-negative bacteria through electrostatic interactions with anionic phosphate groups of the lipid A moiety of lipopolysaccharides (LPSs). Colistin resistance in K. pneumoniae is mediated through loss of these phosphate groups, their modification by cationic groups, and by the hydroxylation of acyl groups of lipid A. Here, we study the in vitro evolutionary trajectories toward colistin resistance in four clinical K. pneumoniae complex strains and their impact on fitness and virulence characteristics. Through population sequencing during in vitro evolution, we found that colistin resistance develops through a combination of single nucleotide polymorphisms, insertions and deletions, and the integration of insertion sequence elements, affecting genes associated with LPS biosynthesis and modification and capsule structures. Colistin resistance decreased the maximum growth rate of one K. pneumoniae sensu stricto strain, but not those of the other three K. pneumoniae complex strains. Colistin-resistant strains had lipid A modified through hydroxylation, palmitoylation, and L-Ara4N addition. K. pneumoniae sensu stricto strains exhibited cross-resistance to LL-37, in contrast to the Klebsiella variicola subsp. variicola strain. Virulence, as determined in a Caenorhabditis elegans survival assay, was increased in two colistin-resistant strains. Our study suggests that nosocomial K. pneumoniae complex strains can rapidly develop colistin resistance through diverse evolutionary trajectories upon exposure to colistin. This effectively shortens the life span of this last-resort antibiotic for the treatment of infections with multidrug-resistant Klebsiella.

KW - Antibiotic resistance

KW - Colistin

KW - Evolution

KW - Klebsiella

KW - Virulence

U2 - 10.1128/AAC.01958-20

DO - 10.1128/AAC.01958-20

M3 - Article

C2 - 33139278

AN - SCOPUS:85098644684

SN - 0066-4804

VL - 65

JO - Antimicrobial Agents and Chemotherapy

JF - Antimicrobial Agents and Chemotherapy

IS - 1

M1 - e01958-20

ER -

Evolution of colistin resistance in the klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

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