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A workflow for bacterial metabolic fingerprinting and lipid profiling: application to Ciprofloxacin challenged Escherichia coli

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Abstract

The field of lipidomics focuses upon the non-targeted analysis of lipid composition, the process of which follows similar routines to those applied in conventional metabolic profiling, however lipidomics differs with respect to the sample preparation steps and chosen analytical platform applied to the sample analysis. Conventionally, lipidomics has applied analytical techniques such as direct infusion mass spectrometry and more recently reverse phase liquid chromatography–mass spectrometry, for the detection of mono-, di-, and tri-acyl glycerols, phospholipids, and other complex lipophilic species such as sterols. The field is rapidly expanding, especially with respect to the clinical sciences where it is known that changes of lipid composition, especially phospholipids, are commonly associated with many disease processes. As a proof of principle study, a small number of Escherichia coli isolates were selected on the basis of their sensitivity to a second generation fluoroquinolone antibiotic, known as Ciprofloxacin (E. coli isolates 161 and 171, non-ST131 isolates, which are resistant and sensitive respectively: E. coli isolates 160 and 173, ST131 sequence isolates which are resistant and susceptible respectively). It has been proposed that Ciprofloxacin may be a surface active drug that interacts at the surface-water interface of the phospholipid bi-layer where the head groups reside. Further, antibiotic resistance through intracellular exclusion is known to result in remodelling of the phospholipid membrane. Therefore, to study the effects of Ciprofloxacin on both susceptible and resistant bacterial strains, lipid profiling would present an informative approach. Control and antibiotic challenged cultures for each of the isolates were compared for changes in metabolite and lipid composition as detected by FT-IR spectroscopy and RP-UHPLC–MS, and appraised with a variety of chemometric data analysis approaches. The developed bacterial lipidomics workflow was deemed to be highly reproducible (with respect to the employed technical and analytical routines) and led to the detection of a large array of lipid classes as well as highlighting a range of significant lipid alterations that differed in regulation between susceptible and resistant E. coli isolates.

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Acknowledgments

JWA, AV, YX, and RG would like to acknowledge CR-UK for current research funding. HR thanks The Saudi Ministry of higher education and King Saud University for funding. EC and RG are grateful to the EU Commonsense (http://www.fp7projectcommonsense.eu/) project (Grant 261809) financed by the European Commission under the 7th Framework Programme for Research and Technological Development.

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Authors and Affiliations

  1. Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK

    J. William Allwood, Haitham AlRabiah, Elon Correa, Andrew Vaughan, Yun Xu & Royston Goodacre

  2. Microbiology and Virology Unit, School of Translational Medicine, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PL, UK

    Mathew Upton

  3. Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK

    Royston Goodacre

  4. School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK

    J. William Allwood

  5. School of Biomedical and Healthcare Sciences, Plymouth University, Drake Circus, Plymouth, PL4 8AA, UK

    Mathew Upton

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  1. J. William Allwood
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Correspondence to J. William Allwood.

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J. William Allwood and Haitham AlRabiah have contributed equally to this publication.

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Allwood, J.W., AlRabiah, H., Correa, E. et al. A workflow for bacterial metabolic fingerprinting and lipid profiling: application to Ciprofloxacin challenged Escherichia coli . Metabolomics 11, 438–453 (2015). https://doi.org/10.1007/s11306-014-0674-6

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