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High-throughput analysis of lipidomic phenotypes of methicillin-resistant Staphylococcus aureus by coupling in situ 96-well cultivation and HILIC-ion mobility-mass spectrometry

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Abstract

Antimicrobial resistance is a major threat to human health as resistant pathogens spread globally, and the development of new antimicrobials is slow. Since many antimicrobials function by targeting cell wall and membrane components, high-throughput lipidomics for bacterial phenotyping is of high interest for researchers to unveil lipid-mediated pathways when dealing with a large number of lab-selected or clinical strains. However, current practice for lipidomic analysis requires the cultivation of bacteria on a large scale, which does not replicate the growth conditions for high-throughput bioassays that are normally carried out in 96-well plates, such as susceptibility tests, growth curve measurements, and biofilm quantitation. Analysis of bacteria grown under the same condition as other bioassays would better inform the differences in susceptibility and other biological metrics. In this work, a high-throughput method for cultivation and lipidomic analysis of antimicrobial-resistant bacteria was developed for standard 96-well plates exemplified by methicillin-resistant Staphylococcus aureus (MRSA). By combining a 30-mm liquid chromatography (LC) column with ion mobility (IM) separation, elution time could be dramatically shortened to 3.6 min for a single LC run without losing major lipid features. Peak capacity was largely rescued by the addition of the IM dimension. Through multi-linear calibration, the deviation of retention time can be limited to within 5%, making database-based automatic lipid identification feasible. This high-throughput method was further validated by characterizing the lipidomic phenotypes of antimicrobial-resistant mutants derived from the MRSA strain, W308, grown in a 96-well plate.

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Funding

This work was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award number R01AI136979.

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  1. Dylan H. Ross

    Present address: Biological Sciences Division, Pacific Northwest National Laboratory, WA, 99352, Richland, USA

Authors and Affiliations

  1. Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA

    Rutan Zhang, Amy Li, Dylan H. Ross & Libin Xu

  2. Department of Pharmacy, University of Washington, Seattle, WA, 98195, USA

    Nate K. Ashford & Brian J. Werth

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Contributions

L. Xu and R. Zhang contributed to the study conception and design. Material preparation, data collection, and analysis were performed by R. Zhang, N.K. Ashford, A. Li, and D.H. Ross. The first draft of the manuscript was written by R. Zhang with contributions from L. Xu and B.J. Werth. All authors read and approved the final manuscript.

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Correspondence to Libin Xu.

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Zhang, R., Ashford, N.K., Li, A. et al. High-throughput analysis of lipidomic phenotypes of methicillin-resistant Staphylococcus aureus by coupling in situ 96-well cultivation and HILIC-ion mobility-mass spectrometry. Anal Bioanal Chem 415, 6191–6199 (2023). https://doi.org/10.1007/s00216-023-04890-6

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