Integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin–rifampicin combination against Pseudomonas aeruginosa
Abstract Background Understanding the mechanism of antimicrobial action is critical for improving antibiotic therapy. For the first time, we integrated correlative metabolomics and transcriptomics of Pseudomonas aeruginosa to elucidate the mechanism of synergistic killing of polymyxin–rifampicin com...
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| Format: | Article |
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BMC
2022-10-01
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| Series: | Journal of Biomedical Science |
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| Online Access: | https://doi.org/10.1186/s12929-022-00874-3 |
| _version_ | 1797991621973770240 |
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| author | Mohd Hafidz Mahamad Maifiah Yan Zhu Brian T. Tsuji Darren J. Creek Tony Velkov Jian Li |
| author_facet | Mohd Hafidz Mahamad Maifiah Yan Zhu Brian T. Tsuji Darren J. Creek Tony Velkov Jian Li |
| author_sort | Mohd Hafidz Mahamad Maifiah |
| collection | DOAJ |
| description | Abstract Background Understanding the mechanism of antimicrobial action is critical for improving antibiotic therapy. For the first time, we integrated correlative metabolomics and transcriptomics of Pseudomonas aeruginosa to elucidate the mechanism of synergistic killing of polymyxin–rifampicin combination. Methods Liquid chromatography-mass spectrometry and RNA-seq analyses were conducted to identify the significant changes in the metabolome and transcriptome of P. aeruginosa PAO1 after exposure to polymyxin B (1 mg/L) and rifampicin (2 mg/L) alone, or in combination over 24 h. A genome-scale metabolic network was employed for integrative analysis. Results In the first 4-h treatment, polymyxin B monotherapy induced significant lipid perturbations, predominantly to fatty acids and glycerophospholipids, indicating a substantial disorganization of the bacterial outer membrane. Expression of ParRS, a two-component regulatory system involved in polymyxin resistance, was increased by polymyxin B alone. Rifampicin alone caused marginal metabolic perturbations but significantly affected gene expression at 24 h. The combination decreased the gene expression of quorum sensing regulated virulence factors at 1 h (e.g. key genes involved in phenazine biosynthesis, secretion system and biofilm formation); and increased the expression of peptidoglycan biosynthesis genes at 4 h. Notably, the combination caused substantial accumulation of nucleotides and amino acids that last at least 4 h, indicating that bacterial cells were in a state of metabolic arrest. Conclusion This study underscores the substantial potential of integrative systems pharmacology to determine mechanisms of synergistic bacterial killing by antibiotic combinations, which will help optimize their use in patients. Graphical Abstract |
| first_indexed | 2024-04-11T08:53:47Z |
| format | Article |
| id | doaj.art-52a39e3a3dae40c08de9d292fc297724 |
| institution | Directory Open Access Journal |
| issn | 1423-0127 |
| language | English |
| last_indexed | 2024-04-11T08:53:47Z |
| publishDate | 2022-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Biomedical Science |
| spelling | doaj.art-52a39e3a3dae40c08de9d292fc2977242022-12-22T04:33:20ZengBMCJournal of Biomedical Science1423-01272022-10-0129111910.1186/s12929-022-00874-3Integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin–rifampicin combination against Pseudomonas aeruginosaMohd Hafidz Mahamad Maifiah0Yan Zhu1Brian T. Tsuji2Darren J. Creek3Tony Velkov4Jian Li5Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash UniversityInfection Program and Department of Microbiology, Monash Biomedicine Discovery Institute, Monash UniversityDepartment of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at BuffaloDrug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash UniversityDepartment of Biochemistry and Pharmacology, University of MelbourneInfection Program and Department of Microbiology, Monash Biomedicine Discovery Institute, Monash UniversityAbstract Background Understanding the mechanism of antimicrobial action is critical for improving antibiotic therapy. For the first time, we integrated correlative metabolomics and transcriptomics of Pseudomonas aeruginosa to elucidate the mechanism of synergistic killing of polymyxin–rifampicin combination. Methods Liquid chromatography-mass spectrometry and RNA-seq analyses were conducted to identify the significant changes in the metabolome and transcriptome of P. aeruginosa PAO1 after exposure to polymyxin B (1 mg/L) and rifampicin (2 mg/L) alone, or in combination over 24 h. A genome-scale metabolic network was employed for integrative analysis. Results In the first 4-h treatment, polymyxin B monotherapy induced significant lipid perturbations, predominantly to fatty acids and glycerophospholipids, indicating a substantial disorganization of the bacterial outer membrane. Expression of ParRS, a two-component regulatory system involved in polymyxin resistance, was increased by polymyxin B alone. Rifampicin alone caused marginal metabolic perturbations but significantly affected gene expression at 24 h. The combination decreased the gene expression of quorum sensing regulated virulence factors at 1 h (e.g. key genes involved in phenazine biosynthesis, secretion system and biofilm formation); and increased the expression of peptidoglycan biosynthesis genes at 4 h. Notably, the combination caused substantial accumulation of nucleotides and amino acids that last at least 4 h, indicating that bacterial cells were in a state of metabolic arrest. Conclusion This study underscores the substantial potential of integrative systems pharmacology to determine mechanisms of synergistic bacterial killing by antibiotic combinations, which will help optimize their use in patients. Graphical Abstracthttps://doi.org/10.1186/s12929-022-00874-3Gram-negative bacteriaAntibiotic resistanceCombination therapySystems pharmacologyColistinGenome-scale metabolic modeling |
| spellingShingle | Mohd Hafidz Mahamad Maifiah Yan Zhu Brian T. Tsuji Darren J. Creek Tony Velkov Jian Li Integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin–rifampicin combination against Pseudomonas aeruginosa Journal of Biomedical Science Gram-negative bacteria Antibiotic resistance Combination therapy Systems pharmacology Colistin Genome-scale metabolic modeling |
| title | Integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin–rifampicin combination against Pseudomonas aeruginosa |
| title_full | Integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin–rifampicin combination against Pseudomonas aeruginosa |
| title_fullStr | Integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin–rifampicin combination against Pseudomonas aeruginosa |
| title_full_unstemmed | Integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin–rifampicin combination against Pseudomonas aeruginosa |
| title_short | Integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin–rifampicin combination against Pseudomonas aeruginosa |
| title_sort | integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin rifampicin combination against pseudomonas aeruginosa |
| topic | Gram-negative bacteria Antibiotic resistance Combination therapy Systems pharmacology Colistin Genome-scale metabolic modeling |
| url | https://doi.org/10.1186/s12929-022-00874-3 |
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