Prediction of fluoroquinolone susceptibility directly from whole-genome sequence data by using liquid chromatography-tandem mass spectrometry to identify mutant genotypes

Wan Ahmad Kamil Wan Nur Ismah; Yuiko Takebayashi; Jacqueline Findlay; Kate J. Heesom; Juan Carlos Jiménez-Castellanos; Jay Zhang; Lee Graham; Karen Bowker; O. Martin Williams; Alasdair P. MacGowan; Matthew B. Avison

doi:10.1128/AAC.01814-17

Prediction of fluoroquinolone susceptibility directly from whole-genome sequence data by using liquid chromatography-tandem mass spectrometry to identify mutant genotypes

Wan Ahmad Kamil Wan Nur Ismah, Yuiko Takebayashi, Jacqueline Findlay, Kate J. Heesom, Juan Carlos Jiménez-Castellanos, Jay Zhang, Lee Graham, Karen Bowker, O. Martin Williams, Alasdair P. MacGowan, Matthew B. Avison^*

^*Corresponding author for this work

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

12 Citations (Scopus)

Abstract

Fluoroquinolone resistance in Gram-negative bacteria is multifactorial, involving target site mutations, reductions in fluoroquinolone entry due to reduced porin production, increased fluoroquinolone efflux, enzymes that modify fluoroquinolones, and Qnr, a DNA mimic that protects the drug target from fluoroquinolone binding. Here we report a comprehensive analysis, using transformation and in vitro mutant selection, of the relative importance of each of these mechanisms for fluoroquinolone nonsusceptibility using Klebsiella pneumoniae as a model system. Our improved biological understanding was then used to generate 47 rules that can predict fluoroquinolone susceptibility in K. pneumoniae clinical isolates. Key to the success of this predictive process was the use of liquid chromatography-tandem mass spectrometry to measure the abundance of proteins in extracts of cultured bacteria, identifying which sequence variants seen in the whole-genome sequence data were functionally important in the context of fluoroquinolone susceptibility.

Original language	English
Article number	e01814-17
Journal	Antimicrobial Agents and Chemotherapy
Volume	62
Issue number	3
DOIs	https://doi.org/10.1128/AAC.01814-17
Publication status	Published - Mar 2018
Externally published	Yes

Bibliographical note

Funding Information:
Genome sequencing was provided by MicrobesNG (http://www.microbesng.uk/), which is supported by the BBSRC (grant number BB/L024209/1). This work was funded by grant MR/N013646/1 to M.B.A., A.P.M., O.M.W. and K.J.H. and grant NE/N01961X/1 to M.B.A. and A.P.M. from the Antimicrobial Resistance Cross Council Initiative supported by the seven research councils. W.A.K.W.N.I. was funded by a postgraduate scholarship from the Malaysian Ministry of Education. J.-C.J.-C. was funded by a postgraduate scholarship from CONACyT, Mexico.

Funding Information:
Genome sequencing was provided by MicrobesNG (http://www.microbesng.uk/), which is supported by the BBSRC (grant number BB/L024209/1). This work was funded by grant MR/N013646/1 to M.B.A., A.P.M., O.M.W. and K.J.H. and grant NE/N01961X/1 to M.B.A. and A.P.M. from the Antimicrobial Resistance Cross Council Initiative supported by the seven research councils. W.A.K.W.N.I. was funded by a postgraduate scholarship from the Malaysian Ministry of Education. J.-C.J.-C. was funded by a postgraduate scholarship from CONACyT, Mexico. We have no transparency declarations.

Publisher Copyright:
Copyright © 2018 American Society for Microbiology. All Rights Reserved.

Keywords

Antibiotic resistance
Klebsiella pneumoniae
Susceptibility testing

UN SDGs

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

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10.1128/AAC.01814-17

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Ismah, W. A. K. W. N., Takebayashi, Y., Findlay, J., Heesom, K. J., Jiménez-Castellanos, J. C., Zhang, J., Graham, L., Bowker, K., Williams, O. M., MacGowan, A. P., & Avison, M. B. (2018). Prediction of fluoroquinolone susceptibility directly from whole-genome sequence data by using liquid chromatography-tandem mass spectrometry to identify mutant genotypes. Antimicrobial Agents and Chemotherapy, 62(3), [e01814-17]. https://doi.org/10.1128/AAC.01814-17

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title = "Prediction of fluoroquinolone susceptibility directly from whole-genome sequence data by using liquid chromatography-tandem mass spectrometry to identify mutant genotypes",

abstract = "Fluoroquinolone resistance in Gram-negative bacteria is multifactorial, involving target site mutations, reductions in fluoroquinolone entry due to reduced porin production, increased fluoroquinolone efflux, enzymes that modify fluoroquinolones, and Qnr, a DNA mimic that protects the drug target from fluoroquinolone binding. Here we report a comprehensive analysis, using transformation and in vitro mutant selection, of the relative importance of each of these mechanisms for fluoroquinolone nonsusceptibility using Klebsiella pneumoniae as a model system. Our improved biological understanding was then used to generate 47 rules that can predict fluoroquinolone susceptibility in K. pneumoniae clinical isolates. Key to the success of this predictive process was the use of liquid chromatography-tandem mass spectrometry to measure the abundance of proteins in extracts of cultured bacteria, identifying which sequence variants seen in the whole-genome sequence data were functionally important in the context of fluoroquinolone susceptibility.",

keywords = "Antibiotic resistance, Klebsiella pneumoniae, Susceptibility testing",

author = "Ismah, {Wan Ahmad Kamil Wan Nur} and Yuiko Takebayashi and Jacqueline Findlay and Heesom, {Kate J.} and Jim{\'e}nez-Castellanos, {Juan Carlos} and Jay Zhang and Lee Graham and Karen Bowker and Williams, {O. Martin} and MacGowan, {Alasdair P.} and Avison, {Matthew B.}",

note = "Funding Information: Genome sequencing was provided by MicrobesNG (http://www.microbesng.uk/), which is supported by the BBSRC (grant number BB/L024209/1). This work was funded by grant MR/N013646/1 to M.B.A., A.P.M., O.M.W. and K.J.H. and grant NE/N01961X/1 to M.B.A. and A.P.M. from the Antimicrobial Resistance Cross Council Initiative supported by the seven research councils. W.A.K.W.N.I. was funded by a postgraduate scholarship from the Malaysian Ministry of Education. J.-C.J.-C. was funded by a postgraduate scholarship from CONACyT, Mexico. Funding Information: Genome sequencing was provided by MicrobesNG (http://www.microbesng.uk/), which is supported by the BBSRC (grant number BB/L024209/1). This work was funded by grant MR/N013646/1 to M.B.A., A.P.M., O.M.W. and K.J.H. and grant NE/N01961X/1 to M.B.A. and A.P.M. from the Antimicrobial Resistance Cross Council Initiative supported by the seven research councils. W.A.K.W.N.I. was funded by a postgraduate scholarship from the Malaysian Ministry of Education. J.-C.J.-C. was funded by a postgraduate scholarship from CONACyT, Mexico. We have no transparency declarations. Publisher Copyright: Copyright {\textcopyright} 2018 American Society for Microbiology. All Rights Reserved.",

year = "2018",

month = mar,

doi = "10.1128/AAC.01814-17",

language = "English",

volume = "62",

journal = "Antimicrobial Agents and Chemotherapy",

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Ismah, WAKWN, Takebayashi, Y, Findlay, J, Heesom, KJ, Jiménez-Castellanos, JC, Zhang, J, Graham, L, Bowker, K, Williams, OM, MacGowan, AP & Avison, MB 2018, 'Prediction of fluoroquinolone susceptibility directly from whole-genome sequence data by using liquid chromatography-tandem mass spectrometry to identify mutant genotypes', Antimicrobial Agents and Chemotherapy, vol. 62, no. 3, e01814-17. https://doi.org/10.1128/AAC.01814-17

Prediction of fluoroquinolone susceptibility directly from whole-genome sequence data by using liquid chromatography-tandem mass spectrometry to identify mutant genotypes. / Ismah, Wan Ahmad Kamil Wan Nur; Takebayashi, Yuiko; Findlay, Jacqueline et al.

In: Antimicrobial Agents and Chemotherapy, Vol. 62, No. 3, e01814-17, 03.2018.

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

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AU - Takebayashi, Yuiko

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AU - Heesom, Kate J.

AU - Jiménez-Castellanos, Juan Carlos

AU - Zhang, Jay

AU - Graham, Lee

AU - Bowker, Karen

AU - Williams, O. Martin

AU - MacGowan, Alasdair P.

AU - Avison, Matthew B.

N1 - Funding Information: Genome sequencing was provided by MicrobesNG (http://www.microbesng.uk/), which is supported by the BBSRC (grant number BB/L024209/1). This work was funded by grant MR/N013646/1 to M.B.A., A.P.M., O.M.W. and K.J.H. and grant NE/N01961X/1 to M.B.A. and A.P.M. from the Antimicrobial Resistance Cross Council Initiative supported by the seven research councils. W.A.K.W.N.I. was funded by a postgraduate scholarship from the Malaysian Ministry of Education. J.-C.J.-C. was funded by a postgraduate scholarship from CONACyT, Mexico. Funding Information: Genome sequencing was provided by MicrobesNG (http://www.microbesng.uk/), which is supported by the BBSRC (grant number BB/L024209/1). This work was funded by grant MR/N013646/1 to M.B.A., A.P.M., O.M.W. and K.J.H. and grant NE/N01961X/1 to M.B.A. and A.P.M. from the Antimicrobial Resistance Cross Council Initiative supported by the seven research councils. W.A.K.W.N.I. was funded by a postgraduate scholarship from the Malaysian Ministry of Education. J.-C.J.-C. was funded by a postgraduate scholarship from CONACyT, Mexico. We have no transparency declarations. Publisher Copyright: Copyright © 2018 American Society for Microbiology. All Rights Reserved.

PY - 2018/3

Y1 - 2018/3

N2 - Fluoroquinolone resistance in Gram-negative bacteria is multifactorial, involving target site mutations, reductions in fluoroquinolone entry due to reduced porin production, increased fluoroquinolone efflux, enzymes that modify fluoroquinolones, and Qnr, a DNA mimic that protects the drug target from fluoroquinolone binding. Here we report a comprehensive analysis, using transformation and in vitro mutant selection, of the relative importance of each of these mechanisms for fluoroquinolone nonsusceptibility using Klebsiella pneumoniae as a model system. Our improved biological understanding was then used to generate 47 rules that can predict fluoroquinolone susceptibility in K. pneumoniae clinical isolates. Key to the success of this predictive process was the use of liquid chromatography-tandem mass spectrometry to measure the abundance of proteins in extracts of cultured bacteria, identifying which sequence variants seen in the whole-genome sequence data were functionally important in the context of fluoroquinolone susceptibility.

AB - Fluoroquinolone resistance in Gram-negative bacteria is multifactorial, involving target site mutations, reductions in fluoroquinolone entry due to reduced porin production, increased fluoroquinolone efflux, enzymes that modify fluoroquinolones, and Qnr, a DNA mimic that protects the drug target from fluoroquinolone binding. Here we report a comprehensive analysis, using transformation and in vitro mutant selection, of the relative importance of each of these mechanisms for fluoroquinolone nonsusceptibility using Klebsiella pneumoniae as a model system. Our improved biological understanding was then used to generate 47 rules that can predict fluoroquinolone susceptibility in K. pneumoniae clinical isolates. Key to the success of this predictive process was the use of liquid chromatography-tandem mass spectrometry to measure the abundance of proteins in extracts of cultured bacteria, identifying which sequence variants seen in the whole-genome sequence data were functionally important in the context of fluoroquinolone susceptibility.

KW - Antibiotic resistance

KW - Klebsiella pneumoniae

KW - Susceptibility testing

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U2 - 10.1128/AAC.01814-17

DO - 10.1128/AAC.01814-17

M3 - Article

C2 - 29263066

AN - SCOPUS:85042386024

SN - 0066-4804

VL - 62

JO - Antimicrobial Agents and Chemotherapy

JF - Antimicrobial Agents and Chemotherapy

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M1 - e01814-17

ER -

Prediction of fluoroquinolone susceptibility directly from whole-genome sequence data by using liquid chromatography-tandem mass spectrometry to identify mutant genotypes

Abstract

Bibliographical note

Keywords

UN SDGs

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