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Nang SC, Lu J, Yu HH, Wickremasinghe H, Azad MAK, Han M, Zhao J, Rao G, Bergen PJ, Velkov T, Sherry N, McCarthy DT, Aslam S, Schooley RT, Howden BP, Barr JJ, Zhu Y, Li J. Phage resistance in Klebsiella pneumoniae and bidirectional effects impacting antibiotic susceptibility. Clin Microbiol Infect 2024; 30:787-794. [PMID: 38522841 DOI: 10.1016/j.cmi.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
OBJECTIVES Bacteriophage (phage) therapy is a promising anti-infective option to combat antimicrobial resistance. However, the clinical utilization of phage therapy has been severely compromised by the potential emergence of phage resistance. Although certain phage resistance mechanisms can restore bacterial susceptibility to certain antibiotics, a lack of knowledge of phage resistance mechanisms hinders optimal use of phages and their combination with antibiotics. METHODS Genome-wide transposon screening was performed with a mutant library of Klebsiella pneumoniae MKP103 to identify phage pKMKP103_1-resistant mutants. Phage-resistant phenotypes were evaluated by time-kill kinetics and efficiency of plating assays. Phage resistance mechanisms were investigated with adsorption, one-step growth, and mutation frequency assays. Antibiotic susceptibility was determined with broth microdilution and population analysis profiles. RESULTS We observed a repertoire of phage resistance mechanisms in K pneumoniae, such as disruption of phage binding (fhuA::Tn and tonB::Tn), extension of the phage latent period (mnmE::Tn and rpoN::Tn), and increased mutation frequency (mutS::Tn and mutL::Tn). Notably, in contrast to the prevailing view that phage resistance re-sensitizes antibiotic-resistant bacteria, we observed a bidirectional steering effect on bacterial antibiotic susceptibility. Specifically, rpoN::Tn increased susceptibility to colistin while mutS::Tn and mutL::Tn increased resistance to rifampicin and colistin. DISCUSSION Our findings demonstrate that K pneumoniae employs multiple strategies to overcome phage infection, which may result in enhanced or reduced antibiotic susceptibility. Mechanism-guided phage steering should be incorporated into phage therapy to better inform clinical decisions on phage-antibiotic combinations.
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Affiliation(s)
- Sue C Nang
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jing Lu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Heidi H Yu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hasini Wickremasinghe
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Mohammad A K Azad
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Meiling Han
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jinxin Zhao
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Gauri Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Phillip J Bergen
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Tony Velkov
- Biomedicine Discovery Institute, Department of Pharmacology, Monash University, Clayton, Victoria, Australia
| | - Norelle Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David T McCarthy
- Department of Civil Engineering, Monash University, Clayton, Victoria, Australia
| | - Saima Aslam
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Robert T Schooley
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Yan Zhu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jian Li
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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Bril’kov MS, Stenbakk V, Jakubec M, Vasskog T, Kristoffersen T, Cavanagh JP, Ericson JU, Isaksson J, Flaten GE. Bacterial extracellular vesicles: towards realistic models for bacterial membranes in molecular interaction studies by surface plasmon resonance. Front Mol Biosci 2023; 10:1277963. [PMID: 38152113 PMCID: PMC10751319 DOI: 10.3389/fmolb.2023.1277963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/01/2023] [Indexed: 12/29/2023] Open
Abstract
One way to mitigate the ongoing antimicrobial resistance crisis is to discover and develop new classes of antibiotics. As all antibiotics at some point need to either cross or just interact with the bacterial membrane, there is a need for representative models of bacterial membranes and efficient methods to characterize the interactions with novel molecules -both to generate new knowledge and to screen compound libraries. Since the bacterial cell envelope is a complex assembly of lipids, lipopolysaccharides, membrane proteins and other components, constructing relevant synthetic liposome-based models of the membrane is both difficult and expensive. We here propose to let the bacteria do the hard work for us. Bacterial extracellular vesicles (bEVs) are naturally secreted by Gram-negative and Gram-positive bacteria, playing a role in communication between bacteria, as virulence factors, molecular transport or being a part of the antimicrobial resistance mechanism. bEVs consist of the bacterial outer membrane and thus inherit many components and properties of the native outer cell envelope. In this work, we have isolated and characterized bEVs from one Escherichia coli mutant and three clinical strains of the ESKAPE pathogens Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa. The bEVs were shown to be representative models for the bacterial membrane in terms of lipid composition with speciesstrain specific variations. The bEVs were further used to probe the interactions between bEV and antimicrobial peptides (AMPs) as model compounds by Surface Plasmon Resonance (SPR) and provide proof-of-principle that bEVs can be used as an easily accessible and highly realistic model for the bacterial surface in interaction studies. This further enables direct monitoring of the effect induced by antibiotics, or the response to host-pathogen interactions.
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Affiliation(s)
- Maxim S. Bril’kov
- Drug Transport and Delivery Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Victoria Stenbakk
- Drug Transport and Delivery Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Martin Jakubec
- Chemical Synthesis and Analysis Research Group, Department of Chemistry, Faculty of Natural Sciences and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Terje Vasskog
- Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Tone Kristoffersen
- Chemical Synthesis and Analysis Research Group, Department of Chemistry, Faculty of Natural Sciences and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Jorunn Pauline Cavanagh
- Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Johanna U. Ericson
- Research Group for Host Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Johan Isaksson
- Chemical Synthesis and Analysis Research Group, Department of Chemistry, Faculty of Natural Sciences and Technology, UiT the Arctic University of Norway, Tromsø, Norway
- Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Gøril Eide Flaten
- Drug Transport and Delivery Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
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Krishnan ST, Winkler D, Creek D, Anderson D, Kirana C, Maddern GJ, Fenix K, Hauben E, Rudd D, Voelcker NH. Staging of colorectal cancer using lipid biomarkers and machine learning. Metabolomics 2023; 19:84. [PMID: 37731020 PMCID: PMC10511619 DOI: 10.1007/s11306-023-02049-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/07/2023] [Indexed: 09/22/2023]
Abstract
INTRODUCTION Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide. Alteration in lipid metabolism and chemokine expression are considered hallmark characteristics of malignant progression and metastasis of CRC. Validated diagnostic and prognostic biomarkers are urgently needed to define molecular heterogeneous CRC clinical stages and subtypes, as liver dominant metastasis has poor survival outcomes. OBJECTIVES The aim of this study was to integrate lipid changes, concentrations of chemokines, such as platelet factor 4 and interleukin 8, and gene marker status measured in plasma samples, with clinical features from patients at different CRC stages or who had progressed to stage-IV colorectal liver metastasis (CLM). METHODS High-resolution liquid chromatography-mass spectrometry (HR-LC-MS) was used to determine the levels of candidate lipid biomarkers in each CRC patient's preoperative plasma samples and combined with chemokine, gene and clinical data. Machine learning models were then trained using known clinical outcomes to select biomarker combinations that best classify CRC stage and group. RESULTS Bayesian neural net and multilinear regression-machine learning identified candidate biomarkers that classify CRC (stages I-III), CLM patients and control subjects (cancer-free or patients with polyps/diverticulitis), showing that integrating specific lipid signatures and chemokines (platelet factor-4 and interluken-8; IL-8) can improve prognostic accuracy. Gene marker status could contribute to disease prediction, but requires ubiquitous testing in clinical cohorts. CONCLUSION Our findings demonstrate that correlating multiple disease related features with lipid changes could improve CRC prognosis. The identified signatures could be used as reference biomarkers to predict CRC prognosis and classify stages, and monitor therapeutic intervention.
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Affiliation(s)
- Sanduru Thamarai Krishnan
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6DX, UK
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, 151 Wellington Road, Clayton, VIC, 3168, Australia
| | - David Winkler
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, 3086, Australia
- School of Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2QL, UK
| | - Darren Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
- Monash Proteomics and Metabolomics Facility, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Dovile Anderson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
- Monash Proteomics and Metabolomics Facility, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Chandra Kirana
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Woodville, SA, 5011, Australia
| | - Guy J Maddern
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Woodville, SA, 5011, Australia
| | - Kevin Fenix
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Woodville, SA, 5011, Australia
| | - Ehud Hauben
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Woodville, SA, 5011, Australia
| | - David Rudd
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, 151 Wellington Road, Clayton, VIC, 3168, Australia.
| | - Nicolas Hans Voelcker
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, 151 Wellington Road, Clayton, VIC, 3168, Australia.
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Clayton, VIC, 3168, Australia.
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Lu J, Han M, Yu HH, Bergen PJ, Liu Y, Zhao J, Wickremasinghe H, Jiang X, Hu Y, Du H, Zhu Y, Velkov T. Lipid A Modification and Metabolic Adaptation in Polymyxin-Resistant, New Delhi Metallo-β-Lactamase-Producing Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0085223. [PMID: 37432123 PMCID: PMC10433984 DOI: 10.1128/spectrum.00852-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/12/2023] [Indexed: 07/12/2023] Open
Abstract
Polymyxins are last-line antibiotics employed against multidrug-resistant (MDR) Klebsiella pneumoniae. Worryingly, polymyxin resistance is rapidly on the rise globally. Polymyxins initially target lipid A of lipopolysaccharides (LPSs) in the cell outer membrane (OM), causing disorganization and cell lysis. While most studies focus on how genetic variations confer polymyxin resistance, the mechanisms of membrane remodeling and metabolic changes in polymyxin-resistant strains remain unclear, thus hampering the development of effective therapies to treat severe K. pneumoniae infections. In the present study, lipid A profiling, OM lipidomics, genomics, and metabolomics were integrated to elucidate the global mechanisms of polymyxin resistance and metabolic adaptation in a polymyxin-resistant strain (strain S01R; MIC of >128 mg/L) obtained from K. pneumoniae strain S01, a polymyxin-susceptible (MIC of 2 mg/L), New Delhi metallo-β-lactamase (NDM)-producing MDR clinical isolate. Genomic analysis revealed a novel in-frame deletion at position V258 of PhoQ in S01R, potentially leading to lipid A modification with 4-amino-4-deoxy-l-arabinose (L-Ara4N) despite the absence of polymyxin B. Comparative metabolomic analysis revealed slightly elevated levels of energy production and amino acid metabolism in S01R compared to their levels in S01. Exposure to polymyxin B (4 mg/L for S01 and 512 mg/L for S01R) substantially altered energy, nucleotide, and amino acid metabolism and resulted in greater accumulation of lipids in both strains. Furthermore, the change induced by polymyxin B treatment was dramatic at both 1 and 4 h in S01 but only significant at 4 h in S01R. Overall, profound metabolic adaptation was observed in S01R following polymyxin B treatment. These findings contribute to our understanding of polymyxin resistance mechanisms in problematic NDM-producing K. pneumoniae strains and may facilitate the discovery of novel therapeutic targets. IMPORTANCE Antimicrobial resistance (AMR) is a major threat to global health. The emergence of resistance to the polymyxins that are the last line of defense in so-called Gram-negative "superbugs" has further increased the urgency to develop novel therapies. There are frequent outbreaks of K. pneumoniae infections in hospitals being reported, and polymyxin usage is increasing remarkably. Importantly, the polymyxin-resistant K. pneumoniae strains are imposing more severe consequences to health systems. Using metabolomics, lipid A profiling, and outer membrane lipidomics, our findings reveal (i) changes in the pentose phosphate pathway and amino acid and nucleotide metabolism in a susceptible strain following polymyxin treatment and (ii) how cellular metabolism, lipid A modification, and outer membrane remodeling were altered in K. pneumoniae following the acquisition of polymyxin resistance. Our study provides, for the first time, mechanistic insights into metabolic responses to polymyxin treatment in a multidrug-resistant, NDM-producing K. pneumoniae clinical isolate with acquired polymyxin resistance. Overall, these results will assist in identifying new therapeutic targets to combat and prevent polymyxin resistance.
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Affiliation(s)
- Jing Lu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Meiling Han
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Heidi H. Yu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Phillip J. Bergen
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yiyun Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jinxin Zhao
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Hasini Wickremasinghe
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Xukai Jiang
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yang Hu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Haiyan Du
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yan Zhu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Tony Velkov
- Department of Pharmacology, The Faculty of Medicine Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
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Boness HVM, de Sá HC, Dos Santos EKP, Canuto GAB. Sample Preparation in Microbial Metabolomics: Advances and Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:149-183. [PMID: 37843809 DOI: 10.1007/978-3-031-41741-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Microbial metabolomics has gained significant interest as it reflects the physiological state of microorganisms. Due to the great variability of biological organisms, in terms of physicochemical characteristics and variable range of concentration of metabolites, the choice of sample preparation methods is a crucial step in the metabolomics workflow and will reflect on the quality and reliability of the results generated. The procedures applied to the preparation of microbial samples will vary according to the type of microorganism studied, the metabolomics approach (untargeted or targeted), and the analytical platform of choice. This chapter aims to provide an overview of the sample preparation workflow for microbial metabolomics, highlighting the pre-analytical factors associated with cultivation, harvesting, metabolic quenching, and extraction. Discussions focus on obtaining intracellular and extracellular metabolites. Finally, we introduced advanced sample preparation methods based on automated systems.
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Affiliation(s)
- Heiter V M Boness
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Hanna C de Sá
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Emile K P Dos Santos
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Gisele A B Canuto
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil.
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Hasan CM, Pottenger S, Green AE, Cox AA, White JS, Jones T, Winstanley C, Kadioglu A, Wright MH, Neill DR, Fothergill JL. Pseudomonas aeruginosa utilizes the host-derived polyamine spermidine to facilitate antimicrobial tolerance. JCI Insight 2022; 7:158879. [PMID: 36194492 PMCID: PMC9746822 DOI: 10.1172/jci.insight.158879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 09/27/2022] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa undergoes diversification during infection of the cystic fibrosis (CF) lung. Understanding these changes requires model systems that capture the complexity of the CF lung environment. We previously identified loss-of-function mutations in the 2-component regulatory system sensor kinase gene pmrB in P. aeruginosa from CF lung infections and from experimental infection of mice. Here, we demonstrate that, while such mutations lowered in vitro minimum inhibitory concentrations for multiple antimicrobial classes, this was not reflected in increased antibiotic susceptibility in vivo. Loss of PmrB impaired aminoarabinose modification of LPS, increasing the negative charge of the outer membrane and promoting uptake of cationic antimicrobials. However, in vivo, this could be offset by increased membrane binding of other positively charged molecules present in lungs. The polyamine spermidine readily coated the surface of PmrB-deficient P. aeruginosa, reducing susceptibility to antibiotics that rely on charge differences to bind the outer membrane and increasing biofilm formation. Spermidine was elevated in lungs during P. aeruginosa infection in mice and during episodes of antimicrobial treatment in people with CF. These findings highlight the need to study antimicrobial resistance under clinically relevant environmental conditions. Microbial mutations carrying fitness costs in vitro may be advantageous during infection, where host resources can be utilized.
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Affiliation(s)
- Chowdhury M. Hasan
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Sian Pottenger
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Angharad E. Green
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Adrienne A. Cox
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Jack S. White
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Trevor Jones
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Craig Winstanley
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Megan H. Wright
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Daniel R. Neill
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Joanne L. Fothergill
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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Mahamad Maifiah MH, Zhu Y, Tsuji BT, Creek DJ, Velkov T, Li J. Integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin-rifampicin combination against Pseudomonas aeruginosa. J Biomed Sci 2022; 29:89. [PMID: 36310165 PMCID: PMC9618192 DOI: 10.1186/s12929-022-00874-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
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.
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Affiliation(s)
- Mohd Hafidz Mahamad Maifiah
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
- International Institute for Halal Research and Training, International Islamic University Malaysia, 50728, Kuala Lumpur, Malaysia
| | - Yan Zhu
- Infection Program and Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Brian T Tsuji
- Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Tony Velkov
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Jian Li
- Infection Program and Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.
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Constitutive Phenotypic Modification of Lipid A in Clinical Acinetobacter baumannii Isolates. Microbiol Spectr 2022; 10:e0129522. [PMID: 35861511 PMCID: PMC9431647 DOI: 10.1128/spectrum.01295-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The degree of polymyxin B (PMB) resistance was measured in 40 clinical Acinetobacter baumannii isolates obtained from health care facilities. All of the tested isolates possessed a multidrug-resistant (MDR) phenotype against four classes of antibiotics (meropenem, doxycycline, gentamicin, and erythromycin), except for PMB. The blaOXA-23 gene was detected throughout the genetic analysis and experimental assay, indicating that all of the MDR strains were carbapenem-resistant A. baumannii strains. Multilocus sequence typing-based genotyping revealed that nine selected strains belonged to the international clone II lineage. When matrix-assisted laser desorption ionization–time of flight mass spectrometry was performed, intrinsic lipid A modification by phosphoethanolamine (PEtN) incorporation was noticeable only in the PMB-resistant (PMBR) strains. However, the presence of hexa- and penta-acylated lipid A due to the loss of the laurate (C12) acyl chain was noted in all PMB-susceptible strains but not in the PMBR strains. The reduction of negative surface charges in the PMBR strains was assessed by zeta potential analysis. Fluorescence imaging using dansyl-PMB revealed that, in the PMBR strains, PMB was less likely to bind to the cell surface. IMPORTANCE The widespread presence of MDR pathogens, including A. baumannii, is causing serious hospital-acquired infections worldwide. Extensive surveillance of MDR clinical A. baumannii isolates has been conducted, but the underlying mechanisms for their development of MDR phenotypes are often neglected. Either lipid A modification or loss of lipopolysaccharide in Gram-negative bacteria leads to PMBR phenotypes. The prevalence of intrinsic lipid A modification in PMBR clinical strains was attributed to high levels of basal expression of pmrC and eptA-1. Our findings suggest that new therapeutic strategies are warranted to combat MDR pathogens due to the emergence of many PMBR clinical strains.
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Nitrite Promotes ROS Production to Potentiate Cefoperazone-Sulbactam-Mediated Elimination to Lab-Evolved and Clinical-Evolved Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0232721. [PMID: 35863024 PMCID: PMC9430864 DOI: 10.1128/spectrum.02327-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cefoperazone-sulbactam (SCF)-resistant Pseudomonas aeruginosa poses a big challenge in the use of SCF to treat infection caused by the pathogen. We have recently shown exogenous nitrite-enabled killing of naturally and artificially evolved Pseudomonas aeruginosa strains (AP-RCLIN-EVO and AP-RLAB-EVO, respectively) by SCF. However, the underlying mechanism is unknown. Here, reprogramming metabolomics was adopted to investigate how nitrite enhanced the SCF-mediated killing efficacy. Nitrite-reprogrammed metabolome displayed an activated pyruvate cycle (P cycle), which was confirmed by elevated activity of pyruvate dehydrogenase (PDH), α-ketoglutarate dehydrogenase, succinate dehydrogenase, and malate dehydrogenase. The activated P cycle provided NADH for the electron transport chain and thereby increased reactive oxygen species (ROS), which potentiated SCF to kill AP-RCLIN-EVO and AP-RLAB-EVO. The nitrite-enabled killing of AP-RCLIN-EVO and AP-RLAB-EVO by SCF was inhibited by PDH inhibitor furfural and ROS scavenger N-Acetyl-L-cysteine but promoted by ROS promoter Fe3+. SCF alone could not induce ROS, but SCF-mediated killing efficacy was enhanced by ROS. In addition, the present study demonstrated that nitrite repressed antioxidants, which were partly responsible for the elevated ROS. These results reveal a nitrite-reprogrammed metabolome mechanism by which AP-RCLIN-EVO and AP-RLAB-EVO sensitivity to SCF is elevated. IMPORTANCE Antibiotic-resistant Pseudomonas aeruginosa has become a real concern in hospital-acquired infections, especially in critically ill and immunocompromised patients. Understanding antibiotic resistance mechanisms and developing novel control measures are highly appreciated. We have recently shown that a reduced nitrite-dependent NO biosynthesis contributes to cefoperazone-sulbactam (SCF) resistance, which is reverted by exogenous nitrite, in both naturally and artificially evolved P. aeruginosa strains (AP-RCLIN-EVO and AP-RLAB-EVO, respectively). However, the mechanism is unknown. The present study reports that the nitrite-enabled killing of AP-RCLIN-EVO and AP-RLAB-EVO by SCF is attributed to the promoted production of reactive oxygen species (ROS). Nitrite activates the pyruvate cycle to generate NADH for the electron transport chain, which in turn promotes ROS generation. Nitrite-potentiated SCF-mediated killing is decreased by pyruvate dehydrogenase inhibitor furfural and ROS scavenger N-Acetyl-L-cysteine but increased by ROS promoter Fe3+. Furthermore, SCF-mediated killing is promoted by H2O2 in a dose-dependent manner. In addition, the combination of nitrite and H2O2 greatly enhances SCF-mediated killing. These results not only disclose a nitrite-ROS-potentiated SCF-mediated killing, but also show SCF-mediated killing is dependent upon ROS.
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10
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Jiang X, Han M, Tran K, Patil NA, Ma W, Roberts KD, Xiao M, Sommer B, Schreiber F, Wang L, Velkov T, Li J. An Intelligent Strategy with All-Atom Molecular Dynamics Simulations for the Design of Lipopeptides against Multidrug-Resistant Pseudomonas aeruginosa. J Med Chem 2022; 65:10001-10013. [PMID: 35786900 DOI: 10.1021/acs.jmedchem.2c00657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Multidrug-resistant Gram-negative bacteria seriously threaten modern medicine due to the lack of efficacious therapeutic options. Their outer membrane (OM) is an essential protective fortress to exclude many antibiotics. Unfortunately, current structural biology methods are not able to resolve the membrane structure and it is difficult to examine the specific interaction between the OM and small molecules. These limitations hinder mechanistic understanding of antibiotic penetration through the OM and antibiotic discovery. Here, we developed biologically relevant OM models by quantitatively determining membrane lipidomics of Pseudomonas aeruginosa and elucidated how lipopolysaccharide modifications and OM vesicles mediated resistance to polymyxins. Supported by chemical biology and pharmacological assays, our multiscale molecular dynamics simulations provide an intelligent platform to quantify the membrane-penetrating thermodynamics of peptides and predict their antimicrobial activity. Through experimental validations with our in-house polymyxin analogue library, our computational strategy may have significant potential in accelerating the discovery of lipopeptides against bacterial "superbugs".
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Affiliation(s)
- Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Meiling Han
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Kevin Tran
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Wendong Ma
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Bjorn Sommer
- Department of Computer and Information Science, University of Konstanz, Konstanz 78457, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz 78457, Germany
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Tony Velkov
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne 3010, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
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11
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Chung WY, Zhu Y, Mahamad Maifiah MH, Hawala Shivashekaregowda NK, Wong EH, Abdul Rahim N. Exogenous metabolite feeding on altering antibiotic susceptibility in Gram-negative bacteria through metabolic modulation: a review. Metabolomics 2022; 18:47. [PMID: 35781167 DOI: 10.1007/s11306-022-01903-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/06/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND The rise of antimicrobial resistance at an alarming rate is outpacing the development of new antibiotics. The worrisome trends of multidrug-resistant Gram-negative bacteria have enormously diminished existing antibiotic activity. Antibiotic treatments may inhibit bacterial growth or lead to induce bacterial cell death through disruption of bacterial metabolism directly or indirectly. In light of this, it is imperative to have a thorough understanding of the relationship of bacterial metabolism with antimicrobial activity and leverage the underlying principle towards development of novel and effective antimicrobial therapies. OBJECTIVE Herein, we explore studies on metabolic analyses of Gram-negative pathogens upon antibiotic treatment. Metabolomic studies revealed that antibiotic therapy caused changes of metabolites abundance and perturbed the bacterial metabolism. Following this line of thought, addition of exogenous metabolite has been employed in in vitro, in vivo and in silico studies to activate the bacterial metabolism and thus potentiate the antibiotic activity. KEY SCIENTIFIC CONCEPTS OF REVIEW Exogenous metabolites were discovered to cause metabolic modulation through activation of central carbon metabolism and cellular respiration, stimulation of proton motive force, increase of membrane potential, improvement of host immune protection, alteration of gut microbiome, and eventually facilitating antibiotic killing. The use of metabolites as antimicrobial adjuvants may be a promising approach in the fight against multidrug-resistant pathogens.
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Affiliation(s)
- Wan Yean Chung
- School of Pharmacy, Taylor's University, 47500, Subang Jaya, Selangor, Malaysia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, 3800, Victoria, Australia
| | - Mohd Hafidz Mahamad Maifiah
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia (IIUM), 53100, Jalan Gombak, Selangor, Malaysia
| | - Naveen Kumar Hawala Shivashekaregowda
- Center for Drug Discovery and Molecular Pharmacology (CDDMP), Faculty of Health and Medical Sciences, Taylor's University, 47500, Subang Jaya, Selangor, Malaysia
| | - Eng Hwa Wong
- School of Medicine, Taylor's University, 47500, Subang Jaya, Selangor, Malaysia.
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12
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Hong J, Li X, Jiang M, Hong R. Co-expression Mechanism Analysis of Different Tachyplesin I-Resistant Strains in Pseudomonas aeruginosa Based on Transcriptome Sequencing. Front Microbiol 2022; 13:871290. [PMID: 35464984 PMCID: PMC9022664 DOI: 10.3389/fmicb.2022.871290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/10/2022] [Indexed: 11/23/2022] Open
Abstract
Tachyplesin I is a cationic antimicrobial peptide with 17 amino acids. The long-term continuous exposure to increased concentrations of tachyplesin I induced resistance in Pseudomonas aeruginosa. The global gene expression profiling of tachyplesin I–resistant P. aeruginosa strains PA-60 and PA-99 and the sensitive strain P. aeruginosa CGMCC1.2620 (PA1.2620) were conducted by transcriptome sequencing to analyze the common underlying mechanism of resistance to tachyplesin I in low- or high-resistance mutants. The co-expression patterns, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, sRNA target genes, and single-nucleotide polymorphism (SNP) change were analyzed for the co-expressed genes in this study. A total of 661 differentially co-expressed genes under treatments of PA1.2620 vs. PA-99 and PA1.2620 vs. PA-60 (HL) were divided into 12 kinds of expression patterns. GO and KEGG pathway enrichment analyses indicated that the enrichment of co-expressed genes was mainly associated with oxidoreductase activity, mismatched DNA binding, mismatch repair, RNA degradation of GO terms, aminoacyl-tRNA biosynthesis, and aminobenzoate degradation pathways, and so forth. The co-expressed resistance-related genes were mainly involved in antibiotic efflux and antibiotic inactivation. Seven co-expressed genes had SNP changes. Some co-expressed sRNAs were involved in P. aeruginosa resistance to tachyplesin I by regulating target genes and pathways related to resistance. The common resistance mechanism of P. aeruginosa among different mutants to tachyplesin I was mainly associated with the expression alteration of several genes and sRNA-regulated target genes related to resistance; few genes had base mutations. The findings of this study might provide guidance for understanding the resistance mechanism of P. aeruginosa to tachyplesin I.
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Affiliation(s)
- Jun Hong
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Xinyang Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Mengyao Jiang
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Ruofei Hong
- School of International Education, Henan University of Technology, Zhengzhou, China
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13
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Koçak E, Nigiz Ş, Özkan E, Erdoğan Kablan S, Hazirolan G, Nemutlu E, Kır S, Sağıroğlu M, Özkul C. Exometabolomic Analysis of Susceptible and Multi-Drug Resistant Pseudomonas aeruginosa. Lett Appl Microbiol 2022; 75:234-242. [PMID: 35419823 DOI: 10.1111/lam.13719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 11/30/2022]
Abstract
Multidrug resistant (MDR) Pseudomonas aeruginosa strains have recently become one of the major public health concerns worldwide leading to difficulties in selecting appropriate antibiotic treatment. Thus, it is important to elucidate the characteristics of MDR isolates. Herein, we aimed to determine the unique exometabolome profile of P. aeruginosa clinical isolates in monocultures that comprise high resistance to multiple antibiotics, and compare the differential metabolite profiles obtained from susceptible isolates by using GC/MS. Our results showed that partial least square-discriminant analysis (PLS-DA) score plot clearly discriminated the MDR and susceptible isolates indicating the altered exometabolite profiles, and highlighted the significantly enriched levels of trehalose and glutamic acid in MDR isolates. Expression of trehalose synthase (treS) was also 1.5 fold higher in MDR isolates, relatively to susceptible isolates. Overall, our study provides insights into the distinct footprints of MDR P. aeruginosa isolates in mono-culture.
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Affiliation(s)
- Engin Koçak
- Department of Analytical Chemistry, Faculty of Gulhane Pharmacy, Health Sciences University, Ankara, Turkey
| | - Şeyma Nigiz
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Ece Özkan
- Department of Analytical Chemistry, Faculty of Pharmacy, Başkent University, Ankara, Turkey
| | - Sevilay Erdoğan Kablan
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Gülşen Hazirolan
- Department of Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Emirhan Nemutlu
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Sedef Kır
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Meral Sağıroğlu
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Ceren Özkul
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
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Mohd Kamal K, Mahamad Maifiah MH, Abdul Rahim N, Hashim YZHY, Abdullah Sani MS, Azizan KA. Bacterial Metabolomics: Sample Preparation Methods. Biochem Res Int 2022; 2022:9186536. [PMID: 35465444 PMCID: PMC9019480 DOI: 10.1155/2022/9186536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/31/2022] [Indexed: 12/03/2022] Open
Abstract
Metabolomics is a comprehensive analysis of metabolites existing in biological systems. As one of the important "omics" tools, the approach has been widely employed in various fields in helping to better understand the complex cellular metabolic states and changes. Bacterial metabolomics has gained a significant interest as bacteria serve to provide a better subject or model at systems level. The approach in metabolomics is categorized into untargeted and targeted which serves different paradigms of interest. Nevertheless, the bottleneck in metabolomics has been the sample or metabolite preparation method. A custom-made method and design for a particular species or strain of bacteria might be necessary as most studies generally refer to other bacteria or even yeast and fungi that may lead to unreliable analysis. The paramount aspect of metabolomics design comprises sample harvesting, quenching, and metabolite extraction procedures. Depending on the type of samples and research objective, each step must be at optimal conditions which are significantly important in determining the final output. To date, there are no standardized nor single designated protocols that have been established for a specific bacteria strain for untargeted and targeted approaches. In this paper, the existing and current developments of sample preparation methods of bacterial metabolomics used in both approaches are reviewed. The review also highlights previous literature of optimized conditions used to propose the most ideal methods for metabolite preparation, particularly for bacterial cells. Advantages and limitations of methods are discussed for future improvement of bacterial metabolomics.
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Affiliation(s)
- Khairunnisa Mohd Kamal
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | - Mohd Hafidz Mahamad Maifiah
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | | | - Yumi Zuhanis Has-Yun Hashim
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | - Muhamad Shirwan Abdullah Sani
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | - Kamalrul Azlan Azizan
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM, Bangi, Selangor 43600, Malaysia
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15
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Abstract
AbstractThe complex composition of bacterial membranes has a significant impact on the understanding of pathogen function and their development towards antibiotic resistance. In addition to the inherent complexity and biosafety risks of studying biological pathogen membranes, the continual rise of antibiotic resistance and its significant economical and clinical consequences has motivated the development of numerous in vitro model membrane systems with tuneable compositions, geometries, and sizes. Approaches discussed in this review include liposomes, solid-supported bilayers, and computational simulations which have been used to explore various processes including drug-membrane interactions, lipid-protein interactions, host–pathogen interactions, and structure-induced bacterial pathogenesis. The advantages, limitations, and applicable analytical tools of all architectures are summarised with a perspective for future research efforts in architectural improvement and elucidation of resistance development strategies and membrane-targeting antibiotic mechanisms.
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16
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Chen YT, Yang KX, Dai ZY, Yi H, Peng XX, Li H, Chen ZG. Repressed Central Carbon Metabolism and Its Effect on Related Metabolic Pathways in Cefoperazone/Sulbactam-Resistant Pseudomonas aeruginosa. Front Microbiol 2022; 13:847634. [PMID: 35308347 PMCID: PMC8927769 DOI: 10.3389/fmicb.2022.847634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
Metabolic shift and antibiotic resistance have been reported in Pseudomonas aeruginosa. However, the global metabolic characteristics remain largely unknown. The present study characterizes the central carbon metabolism and its effect on other metabolic pathways in cefoperazone-sulbactam (SCF)-resistant P. aeruginosa (PA-RSCF). GC-MS-based metabolomics shows a repressed central carbon metabolism in PA-RSCF, which is confirmed by measuring expression of genes and activity of enzymes in the metabolism. Furthermore, expression of the genes that encode the enzymes for the first step of fatty acid biosynthesis, glutamate metabolism, and electron transport chain is reduced, confirmed by their enzymatic activity assay, and the key enzyme for riboflavin metabolism is also reduced, indicating the decreased metabolic flux to the four related metabolic pathways. Moreover, the role of the reduced riboflavin metabolism, being related to ROS generation, in SCF resistance is explored. Exogenous H2O2 potentiates SCF-mediated killing in a dose-dependent manner, suggesting that the decreased ROS resulted from the reduced riboflavin metabolism that contributed to the resistance. These results indicate that the repressed central carbon metabolism and related riboflavin metabolism contribute to SCF resistance, but increasing ROS can restore SCF sensitivity. These findings characterize the repressed central carbon metabolism and its effect on other metabolic pathways as the global metabolic features in PA-RSCF.
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Affiliation(s)
- Yue-tao Chen
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou, China
| | - Ke-xin Yang
- Department of Pediatrics, Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhen-yuan Dai
- Department of Pediatrics, Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huan Yi
- Department of Pediatrics, Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuan-xian Peng
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hui Li
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Hui Li,
| | - Zhuang-gui Chen
- Department of Pediatrics, Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Zhuang-gui Chen,
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17
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Tang XK, Su YB, Ye HQ, Dai ZY, Yi H, Yang KX, Zhang TT, Chen ZG. Glucose-Potentiated Amikacin Killing of Cefoperazone/Sulbactam Resistant Pseudomonas aeruginosa. Front Microbiol 2022; 12:800442. [PMID: 35310395 PMCID: PMC8928219 DOI: 10.3389/fmicb.2021.800442] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
Multidrug-resistant Pseudomonas aeruginosa has become one of global threat pathogens for human health due to insensitivity to antibiotics. Recently developed reprogramming metabolomics can identify biomarkers, and then, the biomarkers were used to revert the insensitivity and elevate antibiotic-mediated killing. Here, the methodology was used to study cefoperazone/sulbactam (SCF)-resistant P. aeruginosa (PA-RSCF) and identified reduced glycolysis and pyruvate cycle, a recent clarified cycle providing respiratory energy in bacteria, as the most key enriched pathways and the depressed glucose as one of the most crucial biomarkers. Further experiments showed that the depression of glucose was attributed to reduction of glucose transport. However, exogenous glucose reverted the reduction to elevate intracellular glucose via activating glucose transport. The elevated glucose fluxed to the glycolysis, pyruvate cycle, and electron transport chain to promote downstream proton motive force (PMF). Consistently, exogenous glucose did not promote SCF-mediated elimination but potentiated aminoglycosides-mediated killing since aminoglycosides uptake is PMF-dependent, where amikacin was the best one. The glucose-potentiated amikacin-mediated killing was effective to both lab-evolved PA-RSCF and clinical multidrug-resistant P. aeruginosa. These results reveal the depressed glucose uptake causes the reduced intracellular glucose and expand the application of metabolome-reprogramming on selecting conventional antibiotics to achieve the best killing efficacy.
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Affiliation(s)
- Xi-kang Tang
- Department of Pediatrics, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yu-bin Su
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Hui-qing Ye
- Department of Pediatrics, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhen-yuan Dai
- Department of Pediatrics, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huan Yi
- Department of Pediatrics, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ke-xin Yang
- Department of Pediatrics, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tian-tuo Zhang
- Department of Pulmonary & Critical Care Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhuang-gui Chen
- Department of Pediatrics, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Allergy, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Zhuang-gui Chen,
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18
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Guo H, Zhao T, Huang C, Chen J. The Role of the Two-Component System PhoP/PhoQ in Intrinsic Resistance of Yersinia enterocolitica to Polymyxin. Front Microbiol 2022; 13:758571. [PMID: 35222323 PMCID: PMC8867023 DOI: 10.3389/fmicb.2022.758571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 01/06/2022] [Indexed: 12/02/2022] Open
Abstract
Polymyxin is the “last resort” of antibiotics. The self-induced resistance to polymyxin in Gram-negative bacteria could be mediated by lipopolysaccharide (LPS) modification, which is regulated by the two-component system, PhoP/PhoQ. Yersinia enterocolitica is a common foodborne pathogen. However, PhoP/PhoQ has not been thoroughly studied in Y. enterocolitica. In this study, the functions of PhoP/PhoQ in Y. enterocolitica intrinsic resistance were investigated. The resistance of Y. enterocolitica was found to decrease with the deletion of PhoP/PhoQ. Further, PhoP/PhoQ was found to play an important role in maintaining membrane permeability, intercellular metabolism, and reducing membrane depolarization. Based on subsequent studies, the binding ability of polymyxin to Y. enterocolitica was decreased by the modification of LPS with structures, such as L-Ara4N and palmitate. Analysis of the gene transcription levels revealed that the LPS modification genes, pagP and arn operon, were downregulated with the deletion of PhoP/PhoQ in Y. enterocolitica during exposure to polymyxin. In addition, pmrA, pmrB, and eptA were downregulated in the mutants compared with the wild-type strain. Such findings demonstrate that PhoP/PhoQ contributes to the intrinsic resistance of Y. enterocolitica toward polymyxins. LPS modification with L-Ara4N or palmitate is mainly responsible for the resistance of Y. enterocolitica to polymyxins. The transcription of genes related to LPS modification and PmrA/PmrB can be both affected by PhoP/PhoQ in Y. enterocolitica. This study adds to current knowledge regarding the role of PhoP/PhoQ in intrinsic resistance of Y. enterocolitica to polymyxin.
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Nang SC, Li M, Harper M, Mandela E, Bergen PJ, Rolain JM, Zhu Y, Velkov T, Li J. Polymyxin causes cell envelope remodeling and stress responses in mcr-1-harboring Escherichia coli. Int J Antimicrob Agents 2021; 59:106505. [PMID: 34954369 DOI: 10.1016/j.ijantimicag.2021.106505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/11/2021] [Accepted: 12/17/2021] [Indexed: 11/28/2022]
Abstract
Polymyxins remain important last-line antibiotics against multidrug-resistant Gram-negative bacteria. Unfortunately, polymyxin resistance is emerging and the mobile polymyxin resistance gene, mcr is contributing to the wide dissemination of polymyxin resistance, especially among Escherichia coli, with mcr-1 being the most commonly found variant. The objective of this study was to provide mechanistic insights into concentration-dependent transcriptomic responses of mcr-harboring E. coli following polymyxin treatment. An mcr-1-carrying clinical isolate of E. coli (LH30) was treated with polymyxin B at 2 and 8 mg/L. Bacterial cultures were collected before and 1 h following treatment for viable counting and transcriptomic analysis. Growth of E. coli LH30 was unaffected by 2 mg/L polymyxin B, whereas killing of ∼2 log10 cfu/mL occurred with 8 mg/L at 1 h. All four phosphoethanolamine (pEtN) transferase genes (mcr-1, eptA, eptB and eptC) were upregulated (FC=2.4-4.0) by 8 mg/L polymyxin B, indicating that pEtN modifications were the preferred polymyxin resistance mechanism. The higher polymyxin B concentration also affected the expression of genes involved in fatty acid, lipopolysaccharide, lipid A, phospholipid biosynthesis, iron homeostasis and oxidative stress pathways. Our transcriptomic analysis revealed that cell envelope remodeling, pEtN modification, iron acquisition and oxidative stress protective mechanisms play a key role in the survival of mcr-carrying E. coli treated with polymyxin. These findings provide new mechanistic information at the gene expression level to counter polymyxin resistance.
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Affiliation(s)
- Sue C Nang
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Victoria, Australia
| | - Mengyao Li
- Department of Critical Care Medicine, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China; Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Marina Harper
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Victoria, Australia
| | - Eric Mandela
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Victoria, Australia
| | - Phillip J Bergen
- Centre for Medicine Use and Safety, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Yan Zhu
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Victoria, Australia
| | - Tony Velkov
- Department of Biochemistry and Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria, Australia
| | - Jian Li
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Victoria, Australia.
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20
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Jaisinghani N, Seeliger JC. Recent advances in the mass spectrometric profiling of bacterial lipids. Curr Opin Chem Biol 2021; 65:145-153. [PMID: 34600165 DOI: 10.1016/j.cbpa.2021.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 11/19/2022]
Abstract
Exploring the lipids of bacteria presents a predicament that may not be broadly recognized in a field dominated by the biology and biochemistry of eukaryotic - and especially, mammalian - lipids. Bacteria make multifarious metabolites that contain fatty acyl chains of unusual length and unsaturation attached to assorted headgroups, including sugars and fatty alcohols. Lipid profiling approaches developed for eukaryotic lipids often fail to detect, resolve, or identify bacterial lipids due to their wide range of polarities (including very hydrophobic species) and diverse positional and stereochemical variations. Global lipid profiling, or lipidomics, of bacteria has thus developed as a separate mission with methodological and scientific considerations tailored to the biology of these organisms. In this review, we summarize findings primarily from the last three years that exemplify recent advances and continuing challenges to learning about bacterial lipids.
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Affiliation(s)
- Neetika Jaisinghani
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jessica C Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA.
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21
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Inactivation of Nitrite-Dependent Nitric Oxide Biosynthesis Is Responsible for Overlapped Antibiotic Resistance between Naturally and Artificially Evolved Pseudomonas aeruginosa. mSystems 2021; 6:e0073221. [PMID: 34546070 PMCID: PMC8547483 DOI: 10.1128/msystems.00732-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Metabolic flexibility of Pseudomonas aeruginosa could lead to new strategies to combat bacterial infection. The present study used gas chromatography-mass spectrometry (GC-MS)-based metabolomics to investigate global metabolism in naturally and artificially evolved strains with cefoperazone-sulbactam (SCF) resistance (AP-RCLIN-EVO and AP-RLAB-EVO, respectively) from the same parent strain (AP-RCLIN). Inactivation of the pyruvate cycle and nitric oxide (NO) biosynthesis was identified as characteristic features of SCF resistance in both evolved strains. Nitrite-dependent NO biosynthesis instead of an arginine-dependent NO pathway is responsible for the reduced NO, which is attributed to lower nitrite and electrons from the oxidation of NADH to NAD+ provided by the pyruvate cycle. Exogenous fumarate, NADH, nitrate, and nitrite promoted the NO level and thereby potentiated SCF-mediated killing. Unexpectedly, fumarate caused the elevation of nitrite, while nitrite/nitrate resulted in the increase of Cyt bc1 complex (providing electrons). These interesting findings indicate that the nitrite-dependent NO biosynthesis and the pyruvate cycle are mutual to promote NO metabolism. In addition, the NO-potentiated sensitivity to SCF was validated by NO donor sodium nitroprusside. These results reveal an endogenous NO-mediated SCF resistance and develop its reversion by metabolites in P. aeruginosa. IMPORTANCE Infections with Pseudomonas aeruginosa have become a real concern among hospital-acquired infections, especially in cystic fibrosis patients and immunocompromised individuals. Control of the pathogen is challenging due to antibiotic resistance. Since bacterial metabolic state impacts sensitivity and resistance to antibiotics, exploring and disclosing bacterial metabolic mechanisms can be used to develop a metabolome-reprogramming approach to elevate bacterial sensitivity to antibiotics. Therefore, GC-MS-based metabolomics is used to explore the similarities and differences of metabolomes between naturally and artificially evolved cefoperazone-sulbactam (SCF)-resistant P. aeruginosa (AP-RCLIN-EVO and AP-RLAB-EVO, respectively) from the same parent strain (AP-RCLIN). It identifies the depressed nitrite-dependent nitric oxide (NO) biosynthesis as the most overlapping characteristic feature between AP-RCLIN-EVO and AP-RLAB-EVO. This is because the pyruvate cycle fluctuates, thereby generating fewer NADH and providing fewer electrons for nitrite-dependent NO biosynthesis than the control. Interestingly, exogenous fumarate, NADH, nitrate, and nitrite as well as NO donor sodium nitroprusside promote NO generation to elevate sensitivity to SCF. These results highlight the way to understand metabolic mechanisms of antibiotic resistance and explore metabolic modulation to combat the bacterial pathogen.
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22
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Metabolomics Comparison of Drug-Resistant and Drug-Susceptible Pseudomonas aeruginosa Strain (Intra- and Extracellular Analysis). Int J Mol Sci 2021; 22:ijms221910820. [PMID: 34639158 PMCID: PMC8509183 DOI: 10.3390/ijms221910820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas aeruginosa is a common human pathogen belonging to the ESKAPE group. The multidrug resistance of bacteria is a considerable problem in treating patients and may lead to increased morbidity and mortality rate. The natural resistance in these organisms is caused by the production of specific enzymes and biofilm formation, while acquired resistance is multifactorial. Precise recognition of potential antibiotic resistance on different molecular levels is essential. Metabolomics tools may aid in the observation of the flux of low molecular weight compounds in biochemical pathways yielding additional information about drug-resistant bacteria. In this study, the metabolisms of two P. aeruginosa strains were compared-antibiotic susceptible vs. resistant. Analysis was performed on both intra- and extracellular metabolites. The 1H NMR method was used together with multivariate and univariate data analysis, additionally analysis of the metabolic pathways with the FELLA package was performed. The results revealed the differences in P. aeruginosa metabolism of drug-resistant and drug-susceptible strains and provided direct molecular information about P. aeruginosa response for different types of antibiotics. The most significant differences were found in the turnover of amino acids. This study can be a valuable source of information to complement research on drug resistance in P. aeruginosa.
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23
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Goode A, Yeh V, Bonev BB. Interactions of polymyxin B with lipopolysaccharide-containing membranes. Faraday Discuss 2021; 232:317-329. [PMID: 34550139 PMCID: PMC8704168 DOI: 10.1039/d1fd00036e] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial resistance to antibiotics constantly remodels the battlefront between infections and antibiotic therapy. Polymyxin B, a cationic peptide with an anti-Gram-negative spectrum of activity is re-entering use as a last resort measure and as an adjuvant. We use fluorescence dequenching to investigate the role of the rough chemotype bacterial lipopolysaccharide from E. coli BL21 as a molecular facilitator of membrane disruption by LPS. The minimal polymyxin B/lipid ratio required for leakage onset increased from 5.9 × 10−4 to 1.9 × 10−7 in the presence of rLPS. We confirm polymyxin B activity against E. coli BL21 by the agar diffusion method and determined a MIC of 291 μg ml−1. Changes in lipid membrane stability and dynamics in response to polymyxin and the role of LPS are investigated by 31P NMR and high resolution 31P MAS NMR relaxation is used to monitor selective molecular interactions between polymyxin B and rLPS within bilayer lipid membranes. We observe a strong facilitating effect from rLPS on the membrane lytic properties of polymyxin B and a specific, pyrophosphate-mediated process of molecular recognition of LPS by polymyxin B. Polymyxin B uses bacterial LPS as docking receptor to cross the outer membrane.![]()
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Affiliation(s)
- Alice Goode
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
| | - Vivien Yeh
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
| | - Boyan B Bonev
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
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24
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Manzo G, Gianfanti F, Hind CK, Allison L, Clarke M, Hohenbichler J, Limantoro I, Martin B, Do Carmo Silva P, Ferguson PM, Hodgson-Casson AC, Fleck RA, Sutton JM, Phoenix DA, Mason AJ. Impacts of Metabolism and Organic Acids on Cell Wall Composition and Pseudomonas aeruginosa Susceptibility to Membrane Active Antimicrobials. ACS Infect Dis 2021; 7:2310-2323. [PMID: 34329558 DOI: 10.1021/acsinfecdis.1c00002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reliable antimicrobial susceptibility testing is essential in informing both clinical antibiotic therapy decisions and the development of new antibiotics. Mammalian cell culture media have been proposed as an alternative to bacteriological media, potentially representing some critical aspects of the infection environment more accurately. Here, we use a combination of NMR metabolomics and electron microscopy to investigate the response of Escherichia coli and Pseudomonas aeruginosa to growth in differing rich media to determine whether and how this determines metabolic strategies, the composition of the cell wall, and consequently susceptibility to membrane active antimicrobials including colistin and tobramycin. The NMR metabolomic approach is first validated by characterizing the expected E. coli acid stress response to fermentation and the accompanying changes in the cell wall composition, when cultured in glucose rich mammalian cell culture media. Glucose is not a major carbon source for P. aeruginosa but is associated with a response to osmotic stress and a modest increase in colistin tolerance. Growth of P. aeruginosa in a range of bacteriological media is supported by consumption of formate, an important electron donor in anaerobic respiration. In mammalian cell culture media, however, the overall metabolic strategy of P. aeruginosa is instead dependent on consumption of glutamine and lactate. Formate doping of mammalian cell culture media does not alter the overall metabolic strategy but is associated with polyamine catabolism, remodelling of both inner and outer membranes, and a modest sensitization of P. aeruginosa PAO1 to colistin. Further, in a panel of P. aeruginosa isolates an increase between 2- and 3-fold in sensitivity to tobramycin is achieved through doping with other organic acids, notably propionate which also similarly enhances the activity of colistin. Organic acids are therefore capable of nonspecifically influencing the potency of membrane active antimicrobials.
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Affiliation(s)
- Giorgia Manzo
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Federico Gianfanti
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Charlotte K. Hind
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG United Kingdom
| | - Leanne Allison
- Centre for Ultrastructural Imaging, Guy’s Campus, King’s College London, London SE1 1UL, United Kingdom
| | - Maria Clarke
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Julia Hohenbichler
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Ilene Limantoro
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Bethany Martin
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG United Kingdom
| | - Phoebe Do Carmo Silva
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG United Kingdom
| | - Philip M. Ferguson
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Alice C. Hodgson-Casson
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Roland A. Fleck
- Centre for Ultrastructural Imaging, Guy’s Campus, King’s College London, London SE1 1UL, United Kingdom
| | - J. Mark Sutton
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG United Kingdom
| | - David A. Phoenix
- School of Applied Science, London South Bank University, 103 Borough Road, London SE1 0AA, United Kingdom
| | - A. James Mason
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
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25
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Loss of RND-type multidrug efflux pumps triggers iron starvation and lipid A modifications in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2021; 65:e0059221. [PMID: 34252310 DOI: 10.1128/aac.00592-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Transporters belonging to the Resistance-Nodulation-Division (RND) superfamily of proteins are invariably present in the genomes of Gram-negative bacteria and are largely responsible for the intrinsic antibiotic resistance of these organisms. The number of genes encoding RND transporters per genome vary from one to sixteen and correlates with environmental versatilities of bacterial species. Pseudomonas aeruginosa PAO1 strain, a ubiquitous nosocomial pathogen, possesses twelve RND pumps, which are implicated in development of clinical multidrug resistance and known to contribute to virulence, quorum sensing and many other physiological functions. In this study, we analyzed how P. aeruginosa physiology adapts to the lack of RND-mediated efflux activities. A combination of transcriptomics, metabolomics, genetic and analytical approaches showed that the P. aeruginosa PΔ6 strain lacking six best characterized RND pumps activates a specific adaptation response that involves significant changes in abundance and activities of several transport systems, quorum sensing, iron acquisition and lipid A modifications. Our results demonstrate that these cells accumulate large quantities of pseudomonas quorum signal (PQS), which triggers iron starvation and activation of siderophore biosynthesis and acquisition pathways. The accumulation of iron in turn activates lipid A modification and membrane protection pathways. A transcriptionally regulated RND pump MuxABC-OpmB contributes to these transformations by controlling concentrations of coumarins. Our results suggest that these changes reduce the permeability barrier of the outer membrane and are needed to protect the cell envelope of efflux-deficient P. aeruginosa.
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26
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Gan BH, Gaynord J, Rowe SM, Deingruber T, Spring DR. The multifaceted nature of antimicrobial peptides: current synthetic chemistry approaches and future directions. Chem Soc Rev 2021; 50:7820-7880. [PMID: 34042120 PMCID: PMC8689412 DOI: 10.1039/d0cs00729c] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 12/13/2022]
Abstract
Bacterial infections caused by 'superbugs' are increasing globally, and conventional antibiotics are becoming less effective against these bacteria, such that we risk entering a post-antibiotic era. In recent years, antimicrobial peptides (AMPs) have gained significant attention for their clinical potential as a new class of antibiotics to combat antimicrobial resistance. In this review, we discuss several facets of AMPs including their diversity, physicochemical properties, mechanisms of action, and effects of environmental factors on these features. This review outlines various chemical synthetic strategies that have been applied to develop novel AMPs, including chemical modifications of existing peptides, semi-synthesis, and computer-aided design. We will also highlight novel AMP structures, including hybrids, antimicrobial dendrimers and polypeptides, peptidomimetics, and AMP-drug conjugates and consider recent developments in their chemical synthesis.
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Affiliation(s)
- Bee Ha Gan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Josephine Gaynord
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Sam M Rowe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Tomas Deingruber
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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27
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Aye SM, Galani I, Han ML, Karaiskos I, Creek DJ, Zhu Y, Lin YW, Velkov T, Giamarellou H, Li J. Lipid A profiling and metabolomics analysis of paired polymyxin-susceptible and -resistant MDR Klebsiella pneumoniae clinical isolates from the same patients before and after colistin treatment. J Antimicrob Chemother 2021; 75:2852-2863. [PMID: 32696049 DOI: 10.1093/jac/dkaa245] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The increased incidence of polymyxin-resistant MDR Klebsiella pneumoniae has become a major global health concern. OBJECTIVES To characterize the lipid A profiles and metabolome differences between paired polymyxin-susceptible and -resistant MDR K. pneumoniae clinical isolates. METHODS Three pairs of K. pneumoniae clinical isolates from the same patients were examined [ATH 7 (polymyxin B MIC 0.25 mg/L) versus ATH 8 (64 mg/L); ATH 15 (0.5 mg/L) versus ATH 16 (32 mg/L); and ATH 17 (0.5 mg/L) versus ATH 18 (64 mg/L)]. Lipid A and metabolomes were analysed using LC-MS and bioinformatic analysis was conducted. RESULTS The predominant species of lipid A in all three paired isolates were hexa-acylated and 4-amino-4-deoxy-l-arabinose-modified lipid A species were detected in the three polymyxin-resistant isolates. Significant metabolic differences were evident between the paired isolates. Compared with their corresponding polymyxin-susceptible isolates, the levels of metabolites in amino sugar metabolism (UDP-N-acetyl-α-d-glucosamine and UDP-N-α-acetyl-d-mannosaminuronate) and central carbon metabolism (e.g. pentose phosphate pathway and tricarboxylic acid cycle) were significantly reduced in all polymyxin-resistant isolates [fold change (FC) > 1.5, P < 0.05]. Similarly, nucleotides, amino acids and key metabolites in glycerophospholipid metabolism, namely sn-glycerol-3-phosphate and sn-glycero-3-phosphoethanolamine, were significantly reduced across all polymyxin-resistant isolates (FC > 1.5, P < 0.05) compared with polymyxin-susceptible isolates. However, higher glycerophospholipid levels were evident in polymyxin-resistant ATH 8 and ATH 16 (FC > 1.5, P < 0.05) compared with their corresponding susceptible isolates. CONCLUSIONS To our knowledge, this study is the first to reveal significant metabolic perturbations associated with polymyxin resistance in K. pneumoniae.
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Affiliation(s)
- Su Mon Aye
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Irene Galani
- Fourth Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Mei-Ling Han
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Ilias Karaiskos
- First Department of Internal Medicine-Infectious Diseases, Hygeia General Hospital, Athens, Greece
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052 Victoria, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Yu-Wei Lin
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Helen Giamarellou
- First Department of Internal Medicine-Infectious Diseases, Hygeia General Hospital, Athens, Greece
| | - Jian Li
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
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28
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Tao Y, Acket S, Beaumont E, Galez H, Duma L, Rossez Y. Colistin Treatment Affects Lipid Composition of Acinetobacter baumannii. Antibiotics (Basel) 2021; 10:antibiotics10050528. [PMID: 34063718 PMCID: PMC8147793 DOI: 10.3390/antibiotics10050528] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/01/2021] [Indexed: 12/15/2022] Open
Abstract
Multidrug-resistant Acinetobacter baumannii (A. baumannii) causes severe and often fatal healthcare-associated infections due partly to antibiotic resistance. There are no studies on A. baumannii lipidomics of susceptible and resistant strains grown at lethal and sublethal concentrations. Therefore, we analyzed the impact of colistin resistance on glycerolipids’ content by using untargeted lipidomics on clinical isolate. Nine lipid sub-classes were annotated, including phosphatidylcholine, rarely detected in the bacterial membrane among 130 different lipid species. The other lipid sub-classes detected are phosphatidylethanolamine (PE), phosphatidylglycerol (PG), lysophosphatidylethanolamine, hemibismonoacylglycerophosphate, cardiolipin, monolysocardiolipin, diacylglycerol, and triacylglycerol. Under lethal and sublethal concentrations of colistin, significant reduction of PE was observed on the resistant and susceptible strain, respectively. Palmitic acid percentage was higher at colistin at low concentration but only for the susceptible strain. When looking at individual lipid species, the most abundant PE and PG species (PE 34:1 and PG 34:1) are significantly upregulated when the susceptible and the resistant strains are cultivated with colistin. This is, to date, the most exhaustive lipidomics data compilation of A. baumannii cultivated in the presence of colistin. This work is highlighting the plasma membrane plasticity used by this gram-negative bacterium to survive colistin treatment.
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29
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Herndon JL, Peters RE, Hofer RN, Simmons TB, Symes SJ, Giles DK. Exogenous polyunsaturated fatty acids (PUFAs) promote changes in growth, phospholipid composition, membrane permeability and virulence phenotypes in Escherichia coli. BMC Microbiol 2020; 20:305. [PMID: 33046008 PMCID: PMC7552566 DOI: 10.1186/s12866-020-01988-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The utilization of exogenous fatty acids by Gram-negative bacteria has been linked to many cellular processes, including fatty acid oxidation for metabolic gain, assimilation into membrane phospholipids, and control of phenotypes associated with virulence. The expanded fatty acid handling capabilities have been demonstrated in several bacteria of medical importance; however, a survey of the polyunsaturated fatty acid responses in the model organism Escherichia coli has not been performed. The current study examined the impacts of exogenous fatty acids on E. coli. RESULTS All PUFAs elicited higher overall growth, with several fatty acids supporting growth as sole carbon sources. Most PUFAs were incorporated into membrane phospholipids as determined by Ultra performance liquid chromatography-mass spectrometry, whereas membrane permeability was variably affected as measured by two separate dye uptake assays. Biofilm formation, swimming motility and antimicrobial peptide resistance were altered in the presence of PUFAs, with arachidonic and docosahexaenoic acids eliciting strong alteration to these phenotypes. CONCLUSIONS The findings herein add E. coli to the growing list of Gram-negative bacteria with broader capabilities for utilizing and responding to exogenous fatty acids. Understanding bacterial responses to PUFAs may lead to microbial behavioral control regimens for disease prevention.
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Affiliation(s)
- Joshua L. Herndon
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN USA
| | - Rachel E. Peters
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN USA
| | - Rachel N. Hofer
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga, Chattanooga, TN USA
| | - Timothy B. Simmons
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN USA
| | - Steven J. Symes
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga, Chattanooga, TN USA
| | - David K. Giles
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN USA
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30
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Liu YY, Zhu Y, Wickremasinghe H, Bergen PJ, Lu J, Zhu XQ, Zhou QL, Azad M, Nang SC, Han ML, Lei T, Li J, Liu JH. Metabolic Perturbations Caused by the Over-Expression of mcr-1 in Escherichia coli. Front Microbiol 2020; 11:588658. [PMID: 33162965 PMCID: PMC7581681 DOI: 10.3389/fmicb.2020.588658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
Rapid dissemination of the plasmid-born polymyxin resistance gene mcr-1 poses a critical medical challenge. MCR-1 expression is tightly controlled and imposes a fitness cost on the bacteria. We used growth studies and metabolomics to examine growth and metabolic changes within E. coli TOP10 at 8 and 24 h in response to different levels of expression of mcr-1. Induction of mcr-1 greatly increased expression at 8 h and markedly reduced bacterial growth; membrane disruption and cell lysis were evident at this time. At 24 h, the expression of mcr-1 dramatically declined with restored growth and membrane integrity, indicating regulation of mcr-1 expression in bacteria to maintain membrane homeostasis. Intermediates of peptide and lipid biosynthesis were the most commonly affected metabolites when mcr-1 was overexpressed in E. coli. Cell wall biosynthesis was dramatically affected with the accumulation of lipids including fatty acids, glycerophospholipids and lysophosphatidylethanolamines, especially at 8 h. In contrast, levels of intermediate metabolites of peptides, amino sugars, carbohydrates and nucleotide metabolism and secondary metabolites significantly decreased. Moreover, the over-expression of mcr-1 resulted in a prolonged reduction in intermediates associated with pentose phosphate pathway and pantothenate and CoA biosynthesis. These findings indicate that over-expression of mcr-1 results in global metabolic perturbations that mainly involve disruption to the bacterial membrane, pentose phosphate pathway as well as pantothenate and CoA biosynthesis.
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Affiliation(s)
- Yi-Yun Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Biomedicine Discovery Institute and Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yan Zhu
- Biomedicine Discovery Institute and Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
| | - Hasini Wickremasinghe
- Biomedicine Discovery Institute and Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
| | - Phillip J Bergen
- Biomedicine Discovery Institute and Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
| | - Jing Lu
- Biomedicine Discovery Institute and Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
| | - Xiao-Qing Zhu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Qiao-Li Zhou
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Mohammad Azad
- Biomedicine Discovery Institute and Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
| | - Sue C Nang
- Biomedicine Discovery Institute and Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
| | - Mei-Ling Han
- Biomedicine Discovery Institute and Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
| | - Tao Lei
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jian Li
- Biomedicine Discovery Institute and Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
| | - Jian-Hua Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Nang SC, Han ML, Yu HH, Wang J, Torres VVL, Dai C, Velkov T, Harper M, Li J. Polymyxin resistance in Klebsiella pneumoniae: multifaceted mechanisms utilized in the presence and absence of the plasmid-encoded phosphoethanolamine transferase gene mcr-1. J Antimicrob Chemother 2020; 74:3190-3198. [PMID: 31365098 DOI: 10.1093/jac/dkz314] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/13/2019] [Accepted: 06/21/2019] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVES Until plasmid-mediated mcr-1 was discovered, it was believed that polymyxin resistance in Gram-negative bacteria was mainly mediated by the chromosomally-encoded EptA and ArnT, which modify lipid A with phosphoethanolamine (pEtN) and 4-amino-4-deoxy-l-arabinose (l-Ara4N), respectively. This study aimed to construct a markerless mcr-1 deletion mutant in Klebsiella pneumoniae, validate a reliable reference gene for reverse transcription quantitative PCR (RT-qPCR) and investigate the interactions among mcr-1, arnT and eptA, in response to polymyxin treatments using pharmacokinetics/pharmacodynamics (PK/PD). METHODS An isogenic markerless mcr-1 deletion mutant (II-503Δmcr-1) was generated from a clinical K. pneumoniae II-503 isolate. The efficacy of different polymyxin B dosage regimens was examined using an in vitro one-compartment PK/PD model and polymyxin resistance was assessed using population analysis profiles. The expression of mcr-1, eptA and arnT was examined using RT-qPCR with a reference gene pepQ, and lipid A was profiled using LC-MS. In vivo polymyxin B efficacy was investigated in a mouse thigh infection model. RESULTS In K. pneumoniae II-503, mcr-1 was constitutively expressed, irrespective of polymyxin exposure. Against II-503Δmcr-1, an initial bactericidal effect was observed within 4 h with polymyxin B at average steady-state concentrations of 1 and 3 mg/L, mimicking patient PK. However, substantial regrowth and concomitantly increased expression of eptA and arnT were detected. Predominant l-Ara4N-modified lipid A species were detected in II-503Δmcr-1 following polymyxin B treatment. CONCLUSIONS This is the first study demonstrating a unique markerless deletion of mcr-1 in a clinical polymyxin-resistant K. pneumoniae. The current polymyxin B dosage regimens are suboptimal against K. pneumoniae, regardless of mcr, and can lead to the emergence of resistance.
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Affiliation(s)
- Sue C Nang
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Mei-Ling Han
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Heidi H Yu
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jiping Wang
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Von Vergel L Torres
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Chongshan Dai
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Tony Velkov
- Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Marina Harper
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jian Li
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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Zhu Y, Lu J, Han M, Jiang X, Azad MAK, Patil NA, Lin Y, Zhao J, Hu Y, Yu HH, Chen K, Boyce JD, Dunstan RA, Lithgow T, Barlow CK, Li W, Schneider‐Futschik EK, Wang J, Gong B, Sommer B, Creek DJ, Fu J, Wang L, Schreiber F, Velkov T, Li J. Polymyxins Bind to the Cell Surface of Unculturable Acinetobacter baumannii and Cause Unique Dependent Resistance. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000704. [PMID: 32775156 PMCID: PMC7403960 DOI: 10.1002/advs.202000704] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/28/2020] [Indexed: 05/13/2023]
Abstract
Multidrug-resistant Acinetobacter baumannii is a top-priority pathogen globally and polymyxins are a last-line therapy. Polymyxin dependence in A. baumannii (i.e., nonculturable on agar without polymyxins) is a unique and highly-resistant phenotype with a significant potential to cause treatment failure in patients. The present study discovers that a polymyxin-dependent A. baumannii strain possesses mutations in both lpxC (lipopolysaccharide biosynthesis) and katG (reactive oxygen species scavenging) genes. Correlative multiomics analyses show a significantly remodeled cell envelope and remarkably abundant phosphatidylglycerol in the outer membrane (OM). Molecular dynamics simulations and quantitative membrane lipidomics reveal that polymyxin-dependent growth emerges only when the lipopolysaccharide-deficient OM distinctively remodels with ≥ 35% phosphatidylglycerol, and with "patch" binding on the OM by the rigid polymyxin molecules containing strong intramolecular hydrogen bonding. Rather than damaging the OM, polymyxins bind to the phosphatidylglycerol-rich OM and strengthen the membrane integrity, thereby protecting bacteria from external reactive oxygen species. Dependent growth is observed exclusively with polymyxin analogues, indicating a critical role of the specific amino acid sequence of polymyxins in forming unique structures for patch-binding to bacterial OM. Polymyxin dependence is a novel antibiotic resistance mechanism and the current findings highlight the risk of 'invisible' polymyxin-dependent isolates in the evolution of resistance.
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Affiliation(s)
- Yan Zhu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Jing Lu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Mei‐Ling Han
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Xukai Jiang
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Mohammad A. K. Azad
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Nitin A. Patil
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Yu‐Wei Lin
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Jinxin Zhao
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Yang Hu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Heidi H. Yu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Ke Chen
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - John D. Boyce
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Rhys A. Dunstan
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Trevor Lithgow
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | | | - Weifeng Li
- School of Physics and State Key Laboratory of Crystal MaterialsShandong UniversityJinan250100China
| | | | - Jiping Wang
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Bin Gong
- School of Computer Science and TechnologyShandong UniversityJinan250100China
| | - Bjorn Sommer
- Department of Computer and Information ScienceUniversity of KonstanzKonstanz78457Germany
| | - Darren J. Creek
- Drug Delivery, Disposition and DynamicsMonash Institute of Pharmaceutical SciencesMonash UniversityMelbourne3052Australia
| | - Jing Fu
- Department of Mechanical and Aerospace EngineeringMonash UniversityMelbourne3800Australia
| | - Lushan Wang
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao CampusQingdao266237China
| | - Falk Schreiber
- Department of Computer and Information ScienceUniversity of KonstanzKonstanz78457Germany
| | - Tony Velkov
- Department of Pharmacology and TherapeuticsUniversity of MelbourneMelbourne3010Australia
| | - Jian Li
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
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Adaptive and Mutational Responses to Peptide Dendrimer Antimicrobials in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2020; 64:AAC.02040-19. [PMID: 32015046 PMCID: PMC7179292 DOI: 10.1128/aac.02040-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/24/2020] [Indexed: 01/15/2023] Open
Abstract
Colistin (polymyxin E) is a last-resort antibiotic against multidrug-resistant isolates of Pseudomonas aeruginosa. However, the nephro-toxicity of colistin limits its use, spurring the interest in novel antimicrobial peptides (AMP). Here, we show that the synthetic AMP-dendrimer G3KL (MW 4,531.38 Da, 15 positive charges, MIC = 8 mg/liter) showed faster killing than polymyxin B (Pmx-B) with no detectable resistance selection in P. aeruginosa strain PA14. Colistin (polymyxin E) is a last-resort antibiotic against multidrug-resistant isolates of Pseudomonas aeruginosa. However, the nephro-toxicity of colistin limits its use, spurring the interest in novel antimicrobial peptides (AMP). Here, we show that the synthetic AMP-dendrimer G3KL (MW 4,531.38 Da, 15 positive charges, MIC = 8 mg/liter) showed faster killing than polymyxin B (Pmx-B) with no detectable resistance selection in P. aeruginosa strain PA14. Spontaneous mutants selected on Pmx-B, harboring loss of function mutations in the PhoQ sensor kinase gene, showed increased Pmx-B MICs and arnB operon expression (4-amino-l-arabinose addition to lipid A), but remained susceptible to dendrimers. Two mutants carrying a missense mutation in the periplasmic loop of the PmrB sensor kinase showed increased MICs for Pmx-B (8-fold) and G3KL (4-fold) but not for the dendrimer T7 (MW 4,885.64 Da, 16 positive charges, MIC = 8 mg/liter). The pmrB mutants showed increased expression of the arnB operon as well as of the speD2-speE2-PA4775 operon, located upstream of pmrAB, and involved in polyamine biosynthesis. Exogenous supplementation with the polyamines spermine and norspermine increased G3KL and T7 MICs in a phoQ mutant background but not in the PA14 wild type. This suggests that both addition of 4-amino-l-arabinose and secretion of polyamines are required to reduce susceptibility to dendrimers, probably neutralizing the negative charges present on the lipid A and the 2-keto-3-deoxyoctulosonic acid (KDO) sugars of the lipopolysaccharide (LPS), respectively. We further show by transcriptome analysis that the dendrimers G3KL and T7 induce adaptive responses through the CprRS two-component system in PA14.
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Hong J, Jiang H, Hu J, Wang L, Liu R. Transcriptome Analysis Reveals the Resistance Mechanism of Pseudomonas aeruginosa to Tachyplesin I. Infect Drug Resist 2020; 13:155-169. [PMID: 32021330 PMCID: PMC6970625 DOI: 10.2147/idr.s226687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/17/2019] [Indexed: 12/11/2022] Open
Abstract
Background Tachyplesin I is a cationic antimicrobial peptide with a typical cyclic antiparallel β-sheet structure. We previously demonstrated that long-term continuous exposure to increased concentration of tachyplesin I can induce resistant Gram-negative bacteria. However, no significant information is available about the resistance mechanism of Pseudomonas aeruginosa (P. aeruginosa) to tachyplesin I. Materials and Methods In this study, the global gene expression profiling of P. aeruginosa strain PA-99 and P. aeruginosa CGMCC1.2620 (PA1.2620) was conducted using transcriptome sequencing. For this purpose, outer membrane permeability and outer membrane proteins (OMPs) were further analyzed. Results Transcriptome sequencing detected 672 upregulated and 787 downregulated genes, covering Clusters of Orthologous Groups (COGs) of P. aeruginosa strain PA-99 compared with PA1.2620. Totally, 749 differentially expressed genes (DEGs) were assigned to 98 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and among them, a two-component regulatory system, a beta-lactam resistance system, etc. were involved in some known genes resistant to drugs. Additionally, we further attempted to indicate whether the resistance mechanism of P. aeruginosa to tachyplesin I was associated with the changes of outer membrane permeability and OMPs. Conclusion Our results indicated that P. aeruginosa resistant to tachyplesin I was mainly related to reduced entry of tachyplesin I into the bacterial cell due to overexpression of efflux pump, in addition to a decrease of outer membrane permeability. Our findings were also validated by pathway enrichment analysis and quantitative reverse transcription polymerase chain reaction (RT-qPCR). This study may provide a promising guidance for understanding the resistance mechanism of P. aeruginosa to tachyplesin I.
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Affiliation(s)
- Jun Hong
- College of Life Science and Engineering, Henan University of Urban Construction, Ping Dingshan 467036, People's Republic of China.,Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, Henan 467036, People's Republic of China
| | - Honghao Jiang
- College of Life Science and Engineering, Henan University of Urban Construction, Ping Dingshan 467036, People's Republic of China
| | - Jianye Hu
- College of Life Science and Engineering, Henan University of Urban Construction, Ping Dingshan 467036, People's Republic of China
| | - Lianzhe Wang
- College of Life Science and Engineering, Henan University of Urban Construction, Ping Dingshan 467036, People's Republic of China
| | - Ruifang Liu
- College of Life Science and Engineering, Henan University of Urban Construction, Ping Dingshan 467036, People's Republic of China
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Metabolomics Study of the Synergistic Killing of Polymyxin B in Combination with Amikacin against Polymyxin-Susceptible and -Resistant Pseudomonas aeruginosa. Antimicrob Agents Chemother 2019; 64:AAC.01587-19. [PMID: 31611351 DOI: 10.1128/aac.01587-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022] Open
Abstract
In the present study, we employed untargeted metabolomics to investigate the synergistic killing mechanism of polymyxin B in combination with an aminoglycoside, amikacin, against a polymyxin-susceptible isolate of Pseudomonas aeruginosa, FADDI-PA111 (MIC = 2 mg/liter for both polymyxin B and amikacin), and a polymyxin-resistant Liverpool epidemic strain (LES), LESB58 (the corresponding MIC for both polymyxin B and amikacin is 16 mg/liter). The metabolites were extracted 15 min, 1 h, and 4 h following treatment with polymyxin B alone (2 mg/liter for FADDI-PA111; 4 mg/liter for LESB58), amikacin alone (2 mg/liter), and both in combination and analyzed using liquid chromatography-mass spectrometry (LC-MS). At 15 min and 1 h, polymyxin B alone induced significant perturbations in glycerophospholipid and fatty acid metabolism pathways in FADDI-PA111 and, to a lesser extent, in LESB58. Amikacin alone at 1 and 4 h induced significant perturbations in peptide and amino acid metabolism, which is in line with the mode of action of aminoglycosides. Pathway analysis of FADDI-PA111 revealed that the synergistic effect of the combination was largely due to the inhibition of cell envelope biogenesis, which was driven initially by polymyxin B via suppression of key metabolites involved in lipopolysaccharide, peptidoglycan, and membrane lipids (15 min and 1 h) and later by amikacin (4 h). Overall, these novel findings demonstrate that the disruption of cell envelope biogenesis and central carbohydrate metabolism, decreased levels of amino sugars, and a downregulated nucleotide pool are the metabolic pathways associated with the synergistic killing of the polymyxin-amikacin combination against P. aeruginosa This mechanistic study might help optimize synergistic polymyxin B combinations in the clinical setting.
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36
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Mielko KA, Jabłoński SJ, Milczewska J, Sands D, Łukaszewicz M, Młynarz P. Metabolomic studies of Pseudomonas aeruginosa. World J Microbiol Biotechnol 2019; 35:178. [PMID: 31701321 PMCID: PMC6838043 DOI: 10.1007/s11274-019-2739-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/14/2019] [Indexed: 02/06/2023]
Abstract
Pseudomonas aeruginosa is a common, Gram-negative environmental organism. It can be a significant pathogenic factor of severe infections in humans, especially in cystic fibrosis patients. Due to its natural resistance to antibiotics and the ability to form biofilms, infection with this pathogen can cause severe therapeutic problems. In recent years, metabolomic studies of P. aeruginosa have been performed. Therefore, in this review, we discussed recent achievements in the use of metabolomics methods in bacterial identification, differentiation, the interconnection between genome and metabolome, the influence of external factors on the bacterial metabolome and identification of new metabolites produced by P. aeruginosa. All of these studies may provide valuable information about metabolic pathways leading to an understanding of the adaptations of bacterial strains to a host environment, which can lead to new drug development and/or elaboration of new treatment and diagnostics strategies for Pseudomonas.
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Affiliation(s)
- Karolina Anna Mielko
- Bioorganic Chemistry Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Norwida 4/6, 50-373, Wroclaw, Poland
| | - Sławomir Jan Jabłoński
- Biotransformation Department, University of Wroclaw, Plac Uniwersytecki 1, 50-137, Wroclaw, Poland
| | | | - Dorota Sands
- Mother and Child Institute, Kasprzaka 17a, 01-211, Warszawa, Poland
| | - Marcin Łukaszewicz
- Biotransformation Department, University of Wroclaw, Plac Uniwersytecki 1, 50-137, Wroclaw, Poland
| | - Piotr Młynarz
- Bioorganic Chemistry Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Norwida 4/6, 50-373, Wroclaw, Poland.
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Resistance and Heteroresistance to Colistin in Pseudomonas aeruginosa Isolates from Wenzhou, China. Antimicrob Agents Chemother 2019; 63:AAC.00556-19. [PMID: 31383654 DOI: 10.1128/aac.00556-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 06/28/2019] [Indexed: 01/26/2023] Open
Abstract
The goal was to investigate the mechanisms of colistin resistance and heteroresistance in Pseudomonas aeruginosa clinical isolates. Colistin resistance was determined by the broth microdilution method. Colistin heteroresistance was evaluated by population analysis profiling. Time-kill assays were also conducted. PCR sequencing was performed to detect the resistance genes among (hetero)resistant isolates, and quantitative real-time PCR assays were performed to determine their expression levels. Pulsed-field gel electrophoresis and multilocus sequence typing were performed. Lipid A characteristics were determined via matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS). Two resistant isolates and 9 heteroresistant isolates were selected in this study. Substitutions in PmrB were detected in 2 resistant isolates. Among heteroresistant isolates, 8 of 9 heteroresistant isolates had nonsynonymous PmrB substitutions, and 2 isolates, including 1 with a PmrB substitution, had PhoQ alterations. Correspondingly, the expression levels of pmrA or phoP were upregulated in PmrB- or PhoQ-substituted isolates. One isolate also found alterations in ParRS and CprRS. The transcript levels of the pmrH gene were observed to increase across all investigated isolates. MALDI-TOF MS showed additional 4-amino-4-deoxy-l-arabinose (l-Ara4N) moieties in lipid A profiles in (hetero)resistant isolates. In conclusion, both colistin resistance and heteroresistance in P. aeruginosa in this study mainly involved alterations of the PmrAB regulatory system. There were strong associations between mutations in specific genetic loci for lipid A synthesis and regulation of modifications to lipid A. The transition of colistin heteroresistance to resistance should be addressed in future clinical surveillance.
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Mutations in pmrB Confer Cross-Resistance between the LptD Inhibitor POL7080 and Colistin in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2019; 63:AAC.00511-19. [PMID: 31235628 PMCID: PMC6709506 DOI: 10.1128/aac.00511-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/18/2019] [Indexed: 01/23/2023] Open
Abstract
Pseudomonas aeruginosa is a major bacterial pathogen associated with a rising prevalence of antibiotic resistance. We evaluated the resistance mechanisms of P. aeruginosa against POL7080, a species-specific, first-in-class antibiotic in clinical trials that targets the lipopolysaccharide transport protein LptD. We isolated a series of POL7080-resistant strains with mutations in the two-component sensor gene pmrB. Pseudomonas aeruginosa is a major bacterial pathogen associated with a rising prevalence of antibiotic resistance. We evaluated the resistance mechanisms of P. aeruginosa against POL7080, a species-specific, first-in-class antibiotic in clinical trials that targets the lipopolysaccharide transport protein LptD. We isolated a series of POL7080-resistant strains with mutations in the two-component sensor gene pmrB. Transcriptomic and confocal microscopy studies support a resistance mechanism shared with colistin, involving lipopolysaccharide modifications that mitigate antibiotic cell surface binding.
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Han ML, Liu X, Velkov T, Lin YW, Zhu Y, Creek DJ, Barlow CK, Yu HH, Zhou Z, Zhang J, Li J. Comparative Metabolomics Reveals Key Pathways Associated With the Synergistic Killing of Colistin and Sulbactam Combination Against Multidrug-Resistant Acinetobacter baumannii. Front Pharmacol 2019; 10:754. [PMID: 31333468 PMCID: PMC6620532 DOI: 10.3389/fphar.2019.00754] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/11/2019] [Indexed: 11/20/2022] Open
Abstract
Background: Polymyxins are a last-line class of antibiotics against multidrug-resistant Acinetobacter baumannii. However, polymyxin resistance can emerge with monotherapy, highlighting the need for synergistic combination therapies. Polymyxins in combination with β-lactams have shown remarkable synergy against multidrug-resistant A. baumannii. Methods: Liquid chromatography–mass spectrometry-based metabolomics was conducted to investigate the metabolic perturbations in an A. baumannii clinical isolate, AB090342, in response to colistin (1 mg/L), sulbactam (128 mg/L), and their combination at 1, 4, and 24 h. Metabolomics data were analyzed using univariate and multivariate statistics, and metabolites showing ≥2-fold changes were subjected to pathway analysis. Results: The synergistic activity of colistin–sulbactam combination was initially driven by colistin through perturbation of fatty acid and phospholipid levels at 1 h. Cell wall biosynthesis was perturbed by sulbactam alone and the combination over 24 h; this was demonstrated by the decreased levels of two important precursors, uridine diphosphate-N-acetylglucosamine and uridine diphosphate-N-acetylmuramate, together with perturbed lysine and amino sugar metabolism. Moreover, sulbactam alone and the combination significantly depleted nucleotide metabolism and the associated arginine biosynthesis, glutamate metabolism, and pentose phosphate pathway. Notably, the colistin–sulbactam combination decreased amino acid and nucleotide levels more dramatically at 4 h compared with both monotherapies. Conclusions: This is the first metabolomics study revealing the time-dependent synergistic activity of colistin and sulbactam against A. baumannii, which was largely driven by sulbactam through the inhibition of cell wall biosynthesis. Our mechanistic findings may help optimizing synergistic colistin combinations in patients.
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Affiliation(s)
- Mei-Ling Han
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, VIC, Australia.,Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaofen Liu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Yu-Wei Lin
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Christopher K Barlow
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Heidi H Yu
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Zhihui Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Zhang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Jian Li
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, VIC, Australia.,Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
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Comparative Metabolomics and Transcriptomics Reveal Multiple Pathways Associated with Polymyxin Killing in Pseudomonas aeruginosa. mSystems 2019; 4:mSystems00149-18. [PMID: 30637340 PMCID: PMC6325167 DOI: 10.1128/msystems.00149-18] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/06/2018] [Indexed: 02/07/2023] Open
Abstract
Pseudomonas aeruginosa has been highlighted by the recent WHO Global Priority Pathogen List due to multidrug resistance. Without new antibiotics, polymyxins remain a last-line therapeutic option for this difficult-to-treat pathogen. The emergence of polymyxin resistance highlights the growing threat to our already very limited antibiotic armamentarium and the urgency to understand the exact mechanisms of polymyxin activity and resistance. Integration of the correlative metabolomics and transcriptomics results in the present study discovered that polymyxin treatment caused significant perturbations in the biosynthesis of lipids, lipopolysaccharide, and peptidoglycan, central carbon metabolism, and oxidative stress. Importantly, lipid A modifications were surprisingly rapid in response to polymyxin treatment at clinically relevant concentrations. This is the first study to reveal the dynamics of polymyxin-induced cellular responses at the systems level, which highlights that combination therapy should be considered to minimize resistance to the last-line polymyxins. The results also provide much-needed mechanistic information which potentially benefits the discovery of new-generation polymyxins. Polymyxins are a last-line therapy against multidrug-resistant Pseudomonas aeruginosa; however, resistance to polymyxins has been increasingly reported. Therefore, understanding the mechanisms of polymyxin activity and resistance is crucial for preserving their clinical usefulness. This study employed comparative metabolomics and transcriptomics to investigate the responses of polymyxin-susceptible P. aeruginosa PAK (polymyxin B MIC, 1 mg/liter) and its polymyxin-resistant pmrB mutant PAKpmrB6 (MIC, 16 mg/liter) to polymyxin B (4, 8, and 128 mg/liter) at 1, 4, and 24 h, respectively. Our results revealed that polymyxin B at 4 mg/liter induced different metabolic and transcriptomic responses between polymyxin-susceptible and -resistant P. aeruginosa. In strain PAK, polymyxin B significantly activated PmrAB and the mediated arn operon, leading to increased 4-amino-4-deoxy-L-arabinose (L-Ara4N) synthesis and the addition to lipid A. In contrast, polymyxin B did not increase lipid A modification in strain PAKpmrB6. Moreover, the syntheses of lipopolysaccharide and peptidoglycan were significantly decreased in strain PAK but increased in strain PAKpmrB6 due to polymyxin B treatment. In addition, 4 mg/liter polymyxin B significantly perturbed phospholipid and fatty acid levels and induced oxidative stress in strain PAK, but not in PAKpmrB6. Notably, the increased trehalose-6-phosphate levels indicate that polymyxin B potentially caused osmotic imbalance in both strains. Furthermore, 8 and 128 mg/liter polymyxin B significantly elevated lipoamino acid levels and decreased phospholipid levels but without dramatic changes in lipid A modification in wild-type and mutant strains, respectively. Overall, this systems study is the first to elucidate the complex and dynamic interactions of multiple cellular pathways associated with the polymyxin mode of action against P. aeruginosa. IMPORTANCEPseudomonas aeruginosa has been highlighted by the recent WHO Global Priority Pathogen List due to multidrug resistance. Without new antibiotics, polymyxins remain a last-line therapeutic option for this difficult-to-treat pathogen. The emergence of polymyxin resistance highlights the growing threat to our already very limited antibiotic armamentarium and the urgency to understand the exact mechanisms of polymyxin activity and resistance. Integration of the correlative metabolomics and transcriptomics results in the present study discovered that polymyxin treatment caused significant perturbations in the biosynthesis of lipids, lipopolysaccharide, and peptidoglycan, central carbon metabolism, and oxidative stress. Importantly, lipid A modifications were surprisingly rapid in response to polymyxin treatment at clinically relevant concentrations. This is the first study to reveal the dynamics of polymyxin-induced cellular responses at the systems level, which highlights that combination therapy should be considered to minimize resistance to the last-line polymyxins. The results also provide much-needed mechanistic information which potentially benefits the discovery of new-generation polymyxins.
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Han ML, Liu X, Velkov T, Lin YW, Zhu Y, Li M, Yu HH, Zhou Z, Creek DJ, Zhang J, Li J. Metabolic Analyses Revealed Time-Dependent Synergistic Killing by Colistin and Aztreonam Combination Against Multidrug-Resistant Acinetobacter baumannii. Front Microbiol 2018; 9:2776. [PMID: 30505298 PMCID: PMC6250834 DOI: 10.3389/fmicb.2018.02776] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022] Open
Abstract
Background: Polymyxins are a last-line class of antibiotics against multidrug-resistant Acinetobacter baumannii; however, polymyxin resistance can emerge with monotherapy. Therefore, synergistic combination therapy is a crucial strategy to reduce polymyxin resistance. Methods: This study conducted untargeted metabolomics to investigate metabolic responses of a multidrug-resistant (MDR) A. baumannii clinical isolate, AB090342, to colistin and aztreonam alone, and their combination at 1, 4, and 24 h. Metabolomics data were analyzed using univariate and multivariate statistics; metabolites showing ≥ 2-fold changes were subjected to bioinformatics analysis. Results: The synergistic action of colistin-aztreonam combination was initially driven by colistin via significant disruption of bacterial cell envelope, with decreased phospholipid and fatty acid levels at 1 h. Cell wall biosynthesis was inhibited at 4 and 24 h by aztreonam alone and the combination as shown by the decreased levels of two amino sugars, UDP-N-acetylglucosamine and UDP-N-acetylmuramate; these results suggested that aztreonam was primarily responsible for the synergistic killing at later time points. Moreover, aztreonam alone and the combination significantly depleted pentose phosphate pathway, amino acid, peptide and nucleotide metabolism, but elevated fatty acid and key phospholipid levels. Collectively, the combination synergy between colistin and aztreonam was mainly due to the inhibition of cell envelope biosynthesis via different metabolic perturbations. Conclusion: This metabolomics study is the first to elucidate multiple cellular pathways associated with the time-dependent synergistic action of colistin-aztreonam combination against MDR A. baumannii. Our results provide important mechanistic insights into optimizing synergistic colistin combinations in patients.
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Affiliation(s)
- Mei-Ling Han
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, VIC, Australia.,Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaofen Liu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Yu-Wei Lin
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Mengyao Li
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Heidi H Yu
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Zhihui Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Jing Zhang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Jian Li
- Biomedicine Discovery Institute, Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, VIC, Australia.,Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
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Hussein M, Han ML, Zhu Y, Schneider-Futschik EK, Hu X, Zhou QT, Lin YW, Anderson D, Creek DJ, Hoyer D, Li J, Velkov T. Mechanistic Insights From Global Metabolomics Studies into Synergistic Bactericidal Effect of a Polymyxin B Combination With Tamoxifen Against Cystic Fibrosis MDR Pseudomonas aeruginosa. Comput Struct Biotechnol J 2018; 16:587-599. [PMID: 30546859 PMCID: PMC6280556 DOI: 10.1016/j.csbj.2018.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 01/04/2023] Open
Abstract
Polymyxins are amongst the most important antibiotics in modern medicine, in recent times their clinical utility has been overshadowed by nosocomial outbreaks of polymyxin resistant MDR Gram-negative 'superbugs'. An effective strategy to surmount polymyxin resistance is combination therapy with FDA-approved non-antibiotic drugs. Herein we used untargeted metabolomics to investigate the mechanism(s) of synergy between polymyxin B and the selective estrogen receptor modulator (SERM) tamoxifen against a polymyxin-resistant MDR cystic fibrosis (CF) Pseudomonas aeruginosa FADDI-PA006 isolate (polymyxin B MIC=8 mg/L , it is an MDR polymyxin resistant P. aeruginosa isolated from the lungs of a CF patient). The metabolome of FADDI-PA006 was profiled at 15 min, 1 and 4 h following treatment with polymyxin B (2 mg/L), tamoxifen (8 mg/L) either as monotherapy or in combination. At 15 min, the combination treatment induced a marked decrease in lipids, primarily fatty acid and glycerophospholipid metabolites that are involved in the biosynthesis of bacterial membranes. In line with the polymyxin-resistant status of this strain, at 1 h, both polymyxin B and tamoxifen monotherapies produced little effect on bacterial metabolism. In contrast to the combination which induced extensive reduction (≥ 1.0-log2-fold, p ≤ 0.05; FDR ≤ 0.05) in the levels of essential intermediates involved in cell envelope biosynthesis. Overall, these novel findings demonstrate that the primary mechanisms underlying the synergistic bactericidal effect of the combination against the polymyxin-resistant P. aeruginosa CF isolate FADDI-PA006 involves a disruption of the cell envelope biogenesis and an inhibition of aminoarabinose LPS modifications that confer polymyxin resistance.
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Affiliation(s)
- Maytham Hussein
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville 3010, VIC, Australia
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Mei-Ling Han
- Monash Biomedicine Discovery Institute, Department of Microbiology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia
| | - Yan Zhu
- Monash Biomedicine Discovery Institute, Department of Microbiology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia
| | - Elena K. Schneider-Futschik
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville 3010, VIC, Australia
| | - Xiaohan Hu
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville 3010, VIC, Australia
| | - Qi Tony Zhou
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Yu-Wei Lin
- Monash Biomedicine Discovery Institute, Department of Microbiology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia
| | - Dovile Anderson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Daniel Hoyer
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville 3010, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville 3052, VIC, Australia
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla 92037, CA, USA
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville 3010, VIC, Australia
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