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Zhong Y, Guo J, Zheng Y, Lin H, Su Y. Metabolomics analysis of the lactobacillus plantarum ATCC 14917 response to antibiotic stress. BMC Microbiol 2024; 24:229. [PMID: 38943061 PMCID: PMC11212188 DOI: 10.1186/s12866-024-03385-3] [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: 12/18/2023] [Accepted: 06/18/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Lactobacillus plantarum has been found to play a significant role in maintaining the balance of intestinal flora in the human gut. However, it is sensitive to commonly used antibiotics and is often incidentally killed during treatment. We attempted to identify a means to protect L. plantarum ATCC14917 from the metabolic changes caused by two commonly used antibiotics, ampicillin, and doxycycline. We examined the metabolic changes under ampicillin and doxycycline treatment and assessed the protective effects of adding key exogenous metabolites. RESULTS Using metabolomics, we found that under the stress of ampicillin or doxycycline, L. plantarum ATCC14917 exhibited reduced metabolic activity, with purine metabolism a key metabolic pathway involved in this change. We then screened the key biomarkers in this metabolic pathway, guanine and adenosine diphosphate (ADP). The exogenous addition of each of these two metabolites significantly reduced the lethality of ampicillin and doxycycline on L. plantarum ATCC14917. Because purine metabolism is closely related to the production of reactive oxygen species (ROS), the results showed that the addition of guanine or ADP reduced intracellular ROS levels in L. plantarum ATCC14917. Moreover, the killing effects of ampicillin and doxycycline on L. plantarum ATCC14917 were restored by the addition of a ROS accelerator in the presence of guanine or ADP. CONCLUSIONS The metabolic changes of L. plantarum ATCC14917 under antibiotic treatments were determined. Moreover, the metabolome information that was elucidated can be used to help L. plantarum cope with adverse stress, which will help probiotics become less vulnerable to antibiotics during clinical treatment.
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Affiliation(s)
- Yilin Zhong
- Department of Cell Biology & Institute of Biomedicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, 510632, China
| | - Juan Guo
- Department of Cell Biology & Institute of Biomedicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, 510632, China
| | - Yu Zheng
- Department of Cell Biology & Institute of Biomedicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, 510632, China
| | - Huale Lin
- Department of Cell Biology & Institute of Biomedicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, 510632, China
| | - Yubin Su
- Department of Cell Biology & Institute of Biomedicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, 510632, China.
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2
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Squire S, Sebghati S, Hammond MC. Cytoplasmic Accumulation and Permeability of Antibiotics in Gram Positive and Gram Negative Bacteria Visualized in Real-Time via a Fluorogenic Tagging Strategy. ACS Chem Biol 2024; 19:3-8. [PMID: 38096425 PMCID: PMC10805102 DOI: 10.1021/acschembio.3c00510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 01/23/2024]
Abstract
In this study, we describe the first real-time live cell assay for compound accumulation and permeability in both Gram positive and Gram negative bacteria. The assay utilizes a novel fluorogenic tagging strategy that permits direct visualization of compound accumulation dynamics in the cytoplasm of live cells, unobscured by washing or other processing steps. Quantitative differences could be reproducibly measured by flow cytometry at compound concentrations below the limit of detection for MS-based approaches. We establish the fluorogenic assay in E. coli and B. subtilis and compare the intracellular accumulation of two antibiotics, ciprofloxacin and ampicillin, with related pharmacophores in these bacteria.
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Affiliation(s)
- Scott
O. Squire
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Sepehr Sebghati
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Ming C. Hammond
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
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3
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Loi VV, Busche T, Kuropka B, Müller S, Methling K, Lalk M, Kalinowski J, Antelmann H. Staphylococcus aureus adapts to the immunometabolite itaconic acid by inducing acid and oxidative stress responses including S-bacillithiolations and S-itaconations. Free Radic Biol Med 2023; 208:859-876. [PMID: 37793500 DOI: 10.1016/j.freeradbiomed.2023.09.031] [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: 08/14/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023]
Abstract
Staphylococcus aureus is a major pathogen, which has to defend against reactive oxygen and electrophilic species encountered during infections. Activated macrophages produce the immunometabolite itaconate as potent electrophile and antimicrobial upon pathogen infection. In this work, we used transcriptomics, metabolomics and shotgun redox proteomics to investigate the specific stress responses, metabolic changes and redox modifications caused by sublethal concentrations of itaconic acid in S. aureus. In the RNA-seq transcriptome, itaconic acid caused the induction of the GlnR, KdpDE, CidR, SigB, GraRS, PerR, CtsR and HrcA regulons and the urease-encoding operon, revealing an acid and oxidative stress response and impaired proteostasis. Neutralization using external urea as ammonium source improved the growth and decreased the expression of the glutamine synthetase-controlling GlnR regulon, indicating that S. aureus experienced ammonium starvation upon itaconic acid stress. In the extracellular metabolome, the amounts of acetate and formate were decreased, while secretion of pyruvate and the neutral product acetoin were strongly enhanced to avoid intracellular acidification. Exposure to itaconic acid affected the amino acid uptake and metabolism as revealed by the strong intracellular accumulation of lysine, threonine, histidine, aspartate, alanine, valine, leucine, isoleucine, cysteine and methionine. In the proteome, itaconic acid caused widespread S-bacillithiolation and S-itaconation of redox-sensitive antioxidant and metabolic enzymes, ribosomal proteins and translation factors in S. aureus, supporting its oxidative and electrophilic mode of action in S. aureus. In phenotype analyses, the catalase KatA, the low molecular weight thiol bacillithiol and the urease provided protection against itaconic acid-induced oxidative and acid stress in S. aureus. Altogether, our results revealed that under physiological infection conditions, such as in the acidic phagolysome, itaconic acid is a highly effective antimicrobial against multi-resistant S. aureus isolates, which acts as weak acid causing an acid, oxidative and electrophilic stress response, leading to S-bacillithiolation and itaconation.
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Affiliation(s)
- Vu Van Loi
- Freie Universität Berlin, Institute of Biology-Microbiology, D-14195, Berlin, Germany
| | - Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, D-33615, Bielefeld, Germany
| | - Benno Kuropka
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, D-14195, Berlin, Germany
| | - Susanne Müller
- Freie Universität Berlin, Institute of Biology-Microbiology, D-14195, Berlin, Germany
| | - Karen Methling
- Department of Cellular Biochemistry and Metabolomics, University of Greifswald, 17487, Greifswald, Germany
| | - Michael Lalk
- Department of Cellular Biochemistry and Metabolomics, University of Greifswald, 17487, Greifswald, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, D-33615, Bielefeld, Germany
| | - Haike Antelmann
- Freie Universität Berlin, Institute of Biology-Microbiology, D-14195, Berlin, Germany.
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4
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Zhang D, Yin F, Qin Q, Qiao L. Molecular responses during bacterial filamentation reveal inhibition methods of drug-resistant bacteria. Proc Natl Acad Sci U S A 2023; 120:e2301170120. [PMID: 37364094 PMCID: PMC10318954 DOI: 10.1073/pnas.2301170120] [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: 01/20/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Bacterial antimicrobial resistance (AMR) is among the most significant challenges to current human society. Exposing bacteria to antibiotics can activate their self-saving responses, e.g., filamentation, leading to the development of bacterial AMR. Understanding the molecular changes during the self-saving responses can reveal new inhibition methods of drug-resistant bacteria. Herein, we used an online microfluidics mass spectrometry system for real-time characterization of metabolic changes of bacteria during filamentation under the stimulus of antibiotics. Significant pathways, e.g., nucleotide metabolism and coenzyme A biosynthesis, correlated to the filamentation of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) were identified. A cyclic dinucleotide, c-di-GMP, which is derived from nucleotide metabolism and reported closely related to bacterial resistance and tolerance, was observed significantly up-regulated during the bacterial filamentation. By using a chemical inhibitor, ebselen, to inhibit diguanylate cyclases which catalyzes the synthesis of c-di-GMP, the minimum inhibitory concentration of ceftriaxone against ESBL-E. coli was significantly decreased. This inhibitory effect was also verified with other ESBL-E. coli strains and other beta-lactam antibiotics, i.e., ampicillin. A mutant strain of ESBL-E. coli by knocking out the dgcM gene was used to demonstrate that the inhibition of the antibiotic resistance to beta-lactams by ebselen was mediated through the inhibition of the diguanylate cyclase DgcM and the modulation of c-di-GMP levels. Our study uncovers the molecular changes during bacterial filamentation and proposes a method to inhibit antibiotic-resistant bacteria by combining traditional antibiotics and chemical inhibitors against the enzymes involved in bacterial self-saving responses.
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Affiliation(s)
- Dongxue Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai200000, China
| | - Fan Yin
- Department of Chemistry, Shanghai Stomatological Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai200000, China
| | - Qin Qin
- Changhai Hospital, The Naval Military Medical University, Shanghai200433, China
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai200000, China
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5
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Rao SPS, Gould MK, Noeske J, Saldivia M, Jumani RS, Ng PS, René O, Chen YL, Kaiser M, Ritchie R, Francisco AF, Johnson N, Patra D, Cheung H, Deniston C, Schenk AD, Cortopassi WA, Schmidt RS, Wiedemar N, Thomas B, Palkar R, Ghafar NA, Manoharan V, Luu C, Gable JE, Wan KF, Myburgh E, Mottram JC, Barnes W, Walker J, Wartchow C, Aziz N, Osborne C, Wagner J, Sarko C, Kelly JM, Manjunatha UH, Mäser P, Jiricek J, Lakshminarayana SB, Barrett MP, Diagana TT. Cyanotriazoles are selective topoisomerase II poisons that rapidly cure trypanosome infections. Science 2023; 380:1349-1356. [PMID: 37384702 DOI: 10.1126/science.adh0614] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023]
Abstract
Millions who live in Latin America and sub-Saharan Africa are at risk of trypanosomatid infections, which cause Chagas disease and human African trypanosomiasis (HAT). Improved HAT treatments are available, but Chagas disease therapies rely on two nitroheterocycles, which suffer from lengthy drug regimens and safety concerns that cause frequent treatment discontinuation. We performed phenotypic screening against trypanosomes and identified a class of cyanotriazoles (CTs) with potent trypanocidal activity both in vitro and in mouse models of Chagas disease and HAT. Cryo-electron microscopy approaches confirmed that CT compounds acted through selective, irreversible inhibition of trypanosomal topoisomerase II by stabilizing double-stranded DNA:enzyme cleavage complexes. These findings suggest a potential approach toward successful therapeutics for the treatment of Chagas disease.
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Affiliation(s)
- Srinivasa P S Rao
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Matthew K Gould
- College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jonas Noeske
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Manuel Saldivia
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Rajiv S Jumani
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Pearly S Ng
- Novartis Institute for Tropical Diseases, Singapore
| | - Olivier René
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Yen-Liang Chen
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Ryan Ritchie
- College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Nila Johnson
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
| | - Debjani Patra
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Harry Cheung
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Colin Deniston
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | | | | | - Remo S Schmidt
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Natalie Wiedemar
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Bryanna Thomas
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Rima Palkar
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
| | | | | | - Catherine Luu
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Jonathan E Gable
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Kah Fei Wan
- Novartis Institute for Tropical Diseases, Singapore
| | - Elmarie Myburgh
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Whitney Barnes
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - John Walker
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Charles Wartchow
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Natasha Aziz
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Colin Osborne
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Juergen Wagner
- Novartis Institute for Tropical Diseases, Singapore
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Christopher Sarko
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - John M Kelly
- London School of Hygiene and Tropical Medicine, London, UK
| | - Ujjini H Manjunatha
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Jan Jiricek
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Suresh B Lakshminarayana
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Michael P Barrett
- College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Thierry T Diagana
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
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6
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Liu J, Qi M, Yuan Z, Wong TY, Song X, Lam H. Nontargeted metabolomics reveals differences in the metabolite profiling among methicillin-resistant and methicillin-susceptible Staphylococcus aureus in response to antibiotics. Mol Omics 2022; 18:948-956. [PMID: 36218091 DOI: 10.1039/d2mo00229a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Staphylococcus aureus (S. aureus) causes infections and can be fatal. In the long-term struggle against antibiotics, S. aureus has acquired resistance toward antibiotics and become more difficult to kill. Metabolomics could directly reflect the responses of S. aureus toward antibiotics, which is effective for studying the resistance mechanism of S. aureus. In this study, based on a nontargeted metabolic figure printing technique, the metabolome of a pair of isogenic methicillin-susceptible and resistant S. aureus strains ATCC25923 (MSSA) and ATCC43300 (MRSA) treated with or without oxacillin was characterized. 7 and 29 significantly changed metabolites in MRSA and MSSA were identified by combined accurate mass and mass fragmentation analysis. Pathway enrichment analysis suggested that DNA repair and flavin biosynthesis are the universal pathways of both MSSA and MRSA under antibiotic stress. MRSA systematically and effectively fights against oxacillin through precise control of energy production, PBP2a substrate biosynthesis and antioxidant function. In contrast, MSSA lacks effective defense pathways against oxacillin. The different metabolome responses of MSSA and MRSA toward antibiotics provide us with new insights into how S. aureus develops antibiotic resistance.
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Affiliation(s)
- Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China. .,Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Mingyang Qi
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
| | - Zichen Yuan
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Tin Yan Wong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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7
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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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8
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Clostridioides difficile Modifies its Aromatic Compound Metabolism in Response to Amidochelocardin-Induced Membrane Stress. mSphere 2022; 7:e0030222. [PMID: 35993700 PMCID: PMC9599328 DOI: 10.1128/msphere.00302-22] [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: 11/20/2022] Open
Abstract
Amidochelocardin is a broad-spectrum antibiotic with activity against many Gram-positive and Gram-negative bacteria. According to recent data, the antibiotic effect of this atypical tetracycline is directed against the cytoplasmic membrane, which is associated with the dissipation of the membrane potential. Here, we investigated the effect of amidochelocardin on the proteome of Clostridioides difficile to gain insight into the membrane stress physiology of this important anaerobic pathogen. For the first time, the membrane-directed action of amidochelocardin was confirmed in an anaerobic pathogen. More importantly, our results revealed that aromatic compounds potentially play an important role in C. difficile upon dissipation of its membrane potential. More precisely, a simultaneously increased production of enzymes required for the synthesis of chorismate and two putative phenazine biosynthesis proteins point to the production of a hitherto unknown compound in response to membrane depolarization. Finally, increased levels of the ClnAB efflux system and its transcriptional regulator ClnR were found, which were previously found in response to cationic antimicrobial peptides like LL-37. Therefore, our data provide a starting point for a more detailed understanding of C. difficile's way to counteract membrane-active compounds. IMPORTANCE C. difficile is an important anaerobe pathogen causing mild to severe infections of the gastrointestinal tract. To avoid relapse of the infection following antibiotic therapy, antibiotics are needed that efficiently eradicate C. difficile from the intestinal tract. Since C. difficile was shown to be substantially sensitive to membrane-active antibiotics, it has been proposed that membrane-active antibiotics might be promising for the therapy of C. difficile infections. Therefore, we studied the response of C. difficile to amidochelocardin, a membrane-active antibiotic dissipating the membrane potential. Interestingly, C. difficile's response to amidochelocardin indicates a role of aromatic metabolites in mediating stress caused by dissipation of the membrane potential.
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9
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Rath A, Rautenschlein S, Rzeznitzeck J, Lalk M, Methling K, Rychlik I, Peh E, Kittler S, Waldmann KH, von Altrock A. Investigation on the colonisation of Campylobacter strains in the pig intestine depending on available metabolites. Comp Immunol Microbiol Infect Dis 2022; 88:101865. [PMID: 35914481 DOI: 10.1016/j.cimid.2022.101865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 10/16/2022]
Abstract
Campylobacter (C.) spp. represent one of the most important causes for food-borne bacterial pathogen in humans worldwide. The aim of this study was to investigate metabolic requirements of two Campylobacter strains of different species based on substrate utilisation (in vitro). Based on these results, a correlation between the colonisation and the available substrates in different intestinal sections was recorded using an animal model. Campylobacter coli (ST-5777) and C. jejuni (ST-122) were used to inoculate 16 pigs, respectively, and one group of 16 pigs was used as control. The strains differed significantly in substrate utilisation - C. coli was able to metabolise various substrates (acetate, asparagine, serine, fucose, and propionate), while C. jejuni only utilised serine. Metabolomic analysis of intestinal content from different gut sections showed the presence of all previously tested metabolites, except for fucose. A significantly larger amount of glucose was found in the jejunum of those pigs infected with C. coli, while neither strain utilised it in vitro. The analysis of the intestinal contents revealed a very low proportion of Campylobacterales in the total microbiome, suggesting that the small percentage of the inoculated Campylobacter strains in the gut microflora of the animals is too low to cause differences between the control and infected groups in the composition of the metabolome. Nevertheless, knowledge of specific nutritional requirements of the pathogens combined with proof of different metabolites in the intestinal segments may provide clues about the site of colonisation in the host and improve our understanding of this zoonotic germ.
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Affiliation(s)
- Alexandra Rath
- Clinic for Swine and Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany.
| | - Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover Foundation, 30559 Hannover, Germany
| | - Janina Rzeznitzeck
- Clinic for Poultry, University of Veterinary Medicine Hannover Foundation, 30559 Hannover, Germany
| | - Michael Lalk
- Institute for Pharmaceutical Biology, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Institute for Pharmaceutical Biology, University of Greifswald, Greifswald, Germany
| | - Ivan Rychlik
- Veterinary Research Institute, Brno, Czech Republic
| | - Elisa Peh
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Sophie Kittler
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Karl-Heinz Waldmann
- Clinic for Swine and Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany
| | - Alexandra von Altrock
- Clinic for Swine and Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany
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10
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Wu S, Yang K, Hong Y, Gong Y, Ni J, Yang N, Ding W. A New Perspective on the Antimicrobial Mechanism of Berberine Hydrochloride Against Staphylococcus aureus Revealed by Untargeted Metabolomic Studies. Front Microbiol 2022; 13:917414. [PMID: 35910599 PMCID: PMC9328669 DOI: 10.3389/fmicb.2022.917414] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
Berberine hydrochloride (BBR) is a natural product widely used in clinical medicine and animal production. It has a variety of antimicrobial effects, but its complex antimicrobial mechanism has not been clarified. This study aimed to discover the metabolic markers and gain a new perspective on the antibacterial mechanism of BBR. The effects of different inhibitory concentrations of BBR on the survival and growth of standard strain Staphylococcus aureus ATCC 25923 were analyzed by the bacteriostatic activity test. Differences in intracellular metabolites of S. aureus following 19 μg/ml BBR exposure for 1 h were investigated by combining non-targeted metabolomics techniques of gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). The results showed that the minimum inhibitory concentration of BBR against S. aureus was 51 μg/ml. A total of 368 and 3,454 putative metabolites were identified by GC-MS and LC-MS analyses, respectively. Principal component analysis showed the separation of intracellular metabolite profiles between BBR-exposed samples and non-exposed controls. Pathway activity profiling analysis indicated a global inhibition of metabolisms by BBR exposure, while enhancement was also found in nucleic acid metabolism, amino sugar, and nucleotide sugar metabolism. Several metabolic markers were screened out mainly based on their variable importance of projection values. Two pyridine dicarboxylic acids were significantly downregulated, suggesting the reduction of stress resistance. The oxidized phospholipid (PHOOA-PE) was accumulated, while lipid antioxidant gamma-tocopherol was decreased, and farnesyl PP, the synthetic precursor of another antioxidant (staphyloxanthin), was decreased below the detection threshold. This evidence indicates that BBR reduced the antioxidant capacity of S. aureus. Accumulation of the precursors (UDP-GlcNAc, CDP-ribitol, and CDP-glycerol) and downregulation of the key metabolite D-Ala-D-Ala suggest the inhibition of cell wall synthesis, especially the peptidoglycan synthesis. Metabolites involved in the shikimate pathway (such as 3-dehydroshikimate) and downstream aromatic amino acid synthesis were disturbed. This study provides the first metabolomics information on the antibacterial mechanism of BBR against S. aureus. The key metabolic markers screened in this study suggest that the shikimate pathway, staphyloxanthin synthesis, and peptidoglycan biosynthesis are new directions for further study of BBR antibacterial mechanism in the future.
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Affiliation(s)
- Shu Wu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Kun Yang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuhang Hong
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, China
| | - Yanju Gong
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jiajia Ni
- Research and Development Center, Guangdong Meilikang Bio-Sciences Ltd., Dongguan, China
- Dongguan Key Laboratory of Medical Bioactive Molecular Development and Translational Research, Guangdong Medical University, Dongguan, China
| | - Ni Yang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Weijun Ding
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Weijun Ding
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11
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Cui C, Zhu L, Wang Q, Liu R, Xie D, Guo Y, Yu D, Wang C, Chen D, Jiang P. A GC-MS-based untargeted metabolomics approach for comprehensive metabolic profiling of vancomycin-induced toxicity in mice. Heliyon 2022; 8:e09869. [PMID: 35855991 PMCID: PMC9287194 DOI: 10.1016/j.heliyon.2022.e09869] [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: 03/30/2022] [Revised: 05/16/2022] [Accepted: 06/30/2022] [Indexed: 12/31/2022] Open
Abstract
Background Vancomycin is a glycopeptide antibiotic that is commonly used for severe drug-resistant infections treatment. Application of vancomycin frequently leads to severe ototoxicity, hepatotoxicity, and nephrotoxicity; however, the comprehensive metabolic analysis of vancomycin-induced toxicity is lacking. Purpose This study attempted to investigate the metabolic changes after vancomycin administration in mice. Methods Experimental mice (n = 9) received continuous intraperitoneal injection of vancomycin (400 mg/kg) every day for 7 days, and mice in control group (n = 9) were treated with the same amount of normal saline. Pathological changes of the kidney were examined using haematoxylin and eosin (HE) staining. A gas chromatography-mass spectrometry (GC-MS) approach was used to identify discriminant metabolites in serum and various organs including the heart, liver, kidney, spleen, cerebral cortex, hippocampus, inner ear, lung, and intestine. The potential metabolites were identified using orthogonal partial least squares discrimination analysis (OPLS-DA). Subsequently, the MetaboAnalyst 5.0 (http://www.metaboanalyst.ca) and Kyoto Encyclopedia of Genes and Genomes database (KEGG, http://www.kegg.jp) were employed to depict the metabolic pathways. Results Compared with the control group, the vancomycin induced 13, 17, 27, 22, 16, 10, 17, 11, 10, and 7 differential metabolites in the serum, liver, kidney, heart, cerebral cortex, lung, spleen, intestine, hippocampus, and inner ear, respectively. Further pathway analyses identified that amino acids metabolism, fatty acids biosynthesis, energy metabolism, and lipid metabolism were disrupted after VCM exposure. Conclusion Vancomycin affects the metabolism in various organs in mice, which provides new insights for identification of vancomycin-induced toxicity, and facilitate to better understanding of the metabolic pathogenesis of vancomycin.
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Affiliation(s)
- Changmeng Cui
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining 272000, China
| | - Li Zhu
- Institute of Clinical Pharmacy and Pharmacology, Jining First People's Hospital, Jining Medical University, Jining 272000, China
| | - Qian Wang
- Department of Clinical Medicine, Jining Medical University, Jining 272000, China
| | - Ruijuan Liu
- Department of Pulmonary and Critical Care Medicine, Jining First People's Hospital, Jining 272000, China
| | - Dadi Xie
- Tengzhou Central People's Hospital, Tengzhou 277500, China
| | - Yujin Guo
- Institute of Clinical Pharmacy and Pharmacology, Jining First People's Hospital, Jining Medical University, Jining 272000, China
| | - Dingyi Yu
- Jining Life Science Center, Jining 272000, China
| | - Changshui Wang
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining 272000, China
| | - Dan Chen
- Institute of Clinical Pharmacy and Pharmacology, Jining First People's Hospital, Jining Medical University, Jining 272000, China
| | - Pei Jiang
- Institute of Clinical Pharmacy and Pharmacology, Jining First People's Hospital, Jining Medical University, Jining 272000, China
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12
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Metabolomic Profiles of Multidrug-Resistant Salmonella Typhimurium from Humans, Bovine, and Porcine Hosts. Animals (Basel) 2022; 12:ani12121518. [PMID: 35739855 PMCID: PMC9219436 DOI: 10.3390/ani12121518] [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: 04/01/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The global threat that is imposed by the resistance the pathogens develop to antimicrobial drugs is escalating. Tools to detect the resistance (with evidence on molecular and cellular outcomes) would reveal intricate mechanisms through which novel drugs could be developed. Approaches such as metabolomics, which involve metabolite detection, provide scientific evidence of metabolite expression of antimicrobial-resistant pathogens. The current study involved metabolomics of antimicrobial-resistant Salmonella Typhimurium collected from various hosts (human, porcine, bovine) and were exposed to antimicrobial drugs—ampicillin, chloramphenicol, streptomycin, sulfisoxazole, and tetracycline—as one set of the experiment. The same isolates were also cultured with no drug exposure as a comparison. There are certain pathways of metabolite expression that are impacted by drug exposure when compared to no drug exposure, meaning that the expressed metabolites could be potential targets for drug companies for the treatment of antimicrobial-resistant pathogens. Abstract Antimicrobial resistance (AMR) is a global public health threat, yet tools for detecting resistance patterns are limited and require advanced molecular methods. Metabolomic approaches produce metabolite profiles and help provide scientific evidence of differences in metabolite expressions between Salmonella Typhimurium from various hosts. This research aimed to evaluate the metabolomic profiles of S. Typhimurium associated with AMR and it compares profiles across various hosts. Three samples, each from bovine, porcine, and humans (total n = 9), were selectively chosen from an existing library to compare these nine isolates cultured under no drug exposure to the same isolates cultured in the presence of the antimicrobial drug panel ACSSuT (ampicillin, chloramphenicol, streptomycin, sulfisoxazole, tetracycline). This was followed by metabolomic profiling using UPLC and GC–mass spectrometry. The results indicated that the metabolite regulation was affected by antibiotic exposure, irrespective of the host species. When exposed to antibiotics, 59.69% and 40.31% of metabolites had increased and decreased expressions, respectively. The most significantly regulated metabolic pathway was aminoacyl-tRNA biosynthesis, which demonstrated increased expressions of serine, aspartate, alanine, and citric acid. Metabolites that showed decreased expressions included glutamate and pyruvate. This pathway and associated metabolites have known AMR associations and could be targeted for new drug discoveries and diagnostic methods.
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Weaver AJ, Borgogna TR, O’Shea-Stone G, Peters TR, Copié V, Voyich J, Teintze M. 18β-Glycyrrhetinic Acid Induces Metabolic Changes and Reduces Staphylococcus aureus Bacterial Cell-to-Cell Interactions. Antibiotics (Basel) 2022; 11:antibiotics11060781. [PMID: 35740189 PMCID: PMC9220049 DOI: 10.3390/antibiotics11060781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 12/04/2022] Open
Abstract
The rise in bacterial resistance to common antibiotics has raised an increased need for alternative treatment strategies. The natural antibacterial product, 18β-glycyrrhetinic acid (GRA) has shown efficacy against community-associated methicillin-resistant Staphylococcus aureus (MRSA), although its interactions against planktonic and biofilm modes of growth remain poorly understood. This investigation utilized biochemical and metabolic approaches to further elucidate the effects of GRA on MRSA. Prolonged exposure of planktonic MRSA cell cultures to GRA resulted in increased production of staphyloxanthin, a pigment known to exhibit antioxidant and membrane-stabilizing functions. Then, 1D 1H NMR analyses of intracellular metabolite extracts from MRSA treated with GRA revealed significant changes in intracellular polar metabolite profiles, including increased levels of succinate and citrate, and significant reductions in several amino acids, including branch chain amino acids. These changes reflect the MRSA response to GRA exposure, including potentially altering its membrane composition, which consumes branched chain amino acids and leads to significant energy expenditure. Although GRA itself had no significant effect of biofilm viability, it seems to be an effective biofilm disruptor. This may be related to interference with cell–cell aggregation, as treatment of planktonic MRSA cultures with GRA leads to a significant reduction in micro-aggregation. The dispersive nature of GRA on MRSA biofilms may prove valuable for treatment of such infections and could be used to increase susceptibility to complementary antibiotic therapeutics.
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Affiliation(s)
- Alan J. Weaver
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.J.W.J.); (G.O.-S.); (T.R.P.)
| | - Timothy R. Borgogna
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT 59717, USA;
| | - Galen O’Shea-Stone
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.J.W.J.); (G.O.-S.); (T.R.P.)
| | - Tami R. Peters
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.J.W.J.); (G.O.-S.); (T.R.P.)
| | - Valérie Copié
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.J.W.J.); (G.O.-S.); (T.R.P.)
- Correspondence: (V.C.); (J.V.); (M.T.); Tel.: +406-994-7244 (V.C.); +406-994-7184 (J.V.); +406-994-6515 (M.T.)
| | - Jovanka Voyich
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT 59717, USA;
- Correspondence: (V.C.); (J.V.); (M.T.); Tel.: +406-994-7244 (V.C.); +406-994-7184 (J.V.); +406-994-6515 (M.T.)
| | - Martin Teintze
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.J.W.J.); (G.O.-S.); (T.R.P.)
- Correspondence: (V.C.); (J.V.); (M.T.); Tel.: +406-994-7244 (V.C.); +406-994-7184 (J.V.); +406-994-6515 (M.T.)
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14
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Warrier T, Romano KP, Clatworthy AE, Hung DT. Integrated genomics and chemical biology herald an era of sophisticated antibacterial discovery, from defining essential genes to target elucidation. Cell Chem Biol 2022; 29:716-729. [PMID: 35523184 PMCID: PMC9893512 DOI: 10.1016/j.chembiol.2022.04.006] [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: 12/14/2021] [Revised: 03/08/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023]
Abstract
The golden age of antibiotic discovery in the 1940s-1960s saw the development and deployment of many different classes of antibiotics, revolutionizing the field of medicine. Since that time, our ability to discover antibiotics of novel structural classes or mechanisms has not kept pace with the ever-growing threat of antibiotic resistance. Recently, advances at the intersection of genomics and chemical biology have enabled efforts to better define the vulnerabilities of essential gene targets, to develop sophisticated whole-cell chemical screening methods that reveal target biology early, and to elucidate small molecule targets and modes of action more effectively. These new technologies have the potential to expand the chemical diversity of antibiotic candidates, as well as the breadth of targets. We illustrate how the latest tools of genomics and chemical biology are being integrated to better understand pathogen vulnerabilities and antibiotic mechanisms in order to inform a new era of antibiotic discovery.
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Affiliation(s)
- Thulasi Warrier
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Keith P Romano
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Anne E Clatworthy
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Deborah T Hung
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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15
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Wurster JI, Peterson RL, Belenky P. Streptozotocin-Induced Hyperglycemia Is Associated with Unique Microbiome Metabolomic Signatures in Response to Ciprofloxacin Treatment. Antibiotics (Basel) 2022; 11:585. [PMID: 35625229 PMCID: PMC9137574 DOI: 10.3390/antibiotics11050585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 02/01/2023] Open
Abstract
It is well recognized that the microbiome plays key roles in human health, and that damage to this system by, for example, antibiotic administration has detrimental effects. With this, there is collective recognition that off-target antibiotic susceptibility within the microbiome is a particularly troublesome side effect that has serious impacts on host well-being. Thus, a pressing area of research is the characterization of antibiotic susceptibility determinants within the microbiome, as understanding these mechanisms may inform the development of microbiome-protective therapeutic strategies. In particular, metabolic environment is known to play a key role in the different responses of this microbial community to antibiotics. Here, we explore the role of host dysglycemia on ciprofloxacin susceptibility in the murine cecum. We used a combination of 16S rRNA sequencing and untargeted metabolomics to characterize changes in both microbiome taxonomy and environment. We found that dysglycemia minimally impacted ciprofloxacin-associated changes in microbiome structure. However, from a metabolic perspective, host hyperglycemia was associated with significant changes in respiration, central carbon metabolism, and nucleotide synthesis-related metabolites. Together, these data suggest that host glycemia may influence microbiome function during antibiotic challenge.
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Affiliation(s)
| | | | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA; (J.I.W.); (R.L.P.)
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16
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Saleem M, Majeed MI, Nawaz H, Iqbal MA, Hassan A, Rashid N, Tahir M, Raza A, ul Hassan HM, Sabir A, Ashfaq R, Sharif S. Surface-Enhanced Raman Spectroscopy for the Characterization of the Antibacterial Properties of Imidazole Derivatives against Bacillus subtilis with Principal Component Analysis and Partial Least Squares–Discriminant Analysis. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2047997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Mudassar Saleem
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Adnan Iqbal
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ahmad Hassan
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad, Pakistan
| | - Muhammad Tahir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ali Raza
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Amina Sabir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Rayha Ashfaq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Sana Sharif
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
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17
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Surabhi S, Jachmann LH, Lalk M, Hammerschmidt S, Methling K, Siemens N. Bronchial Epithelial Cells Accumulate Citrate Intracellularly in Response to Pneumococcal Hydrogen Peroxide. ACS Infect Dis 2021; 7:2971-2978. [PMID: 34623132 DOI: 10.1021/acsinfecdis.1c00372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Community-acquired pneumonia is an infection of the lower respiratory tract caused by various viral and bacterial pathogens, including influenza A virus (IAV), Streptococcus pneumoniae, and Staphylococcus aureus. To understand the disease pathology, it is important to delineate host metabolic responses to an infection. In this study, metabolome profiling of mono- and coinfected human bronchial epithelial cells was performed. We show that IAV and S. aureus silently survive within the cells with almost negligible effects on the host metabolome. In contrast, S. pneumoniae significantly altered various host pathways such as glycolysis, tricarboxylic acid cycle, and amino acid metabolism. Intracellular citrate accumulation was the most prominent signature of pneumococcal infections and was directly attributed to the action of pneumococci-derived hydrogen peroxide. No coinfection specific metabolome signatures were observed.
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Affiliation(s)
- Surabhi Surabhi
- Department of Molecular Genetics and Infection Biology, University of Greifswald, D-17489 Greifswald, Germany
| | - Lana H. Jachmann
- Department of Molecular Genetics and Infection Biology, University of Greifswald, D-17489 Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, D-17489 Greifswald, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, University of Greifswald, D-17489 Greifswald, Germany
| | - Karen Methling
- Institute of Biochemistry, University of Greifswald, D-17489 Greifswald, Germany
| | - Nikolai Siemens
- Department of Molecular Genetics and Infection Biology, University of Greifswald, D-17489 Greifswald, Germany
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18
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Patel JS, Norambuena J, Al-Tameemi H, Ahn YM, Perryman AL, Wang X, Daher SS, Occi J, Russo R, Park S, Zimmerman M, Ho HP, Perlin DS, Dartois V, Ekins S, Kumar P, Connell N, Boyd JM, Freundlich JS. Bayesian Modeling and Intrabacterial Drug Metabolism Applied to Drug-Resistant Staphylococcus aureus. ACS Infect Dis 2021; 7:2508-2521. [PMID: 34342426 DOI: 10.1021/acsinfecdis.1c00265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the application of Bayesian modeling to identify chemical tools and/or drug discovery entities pertinent to drug-resistant Staphylococcus aureus infections. The quinoline JSF-3151 was predicted by modeling and then empirically demonstrated to be active against in vitro cultured clinical methicillin- and vancomycin-resistant strains while also exhibiting efficacy in a mouse peritonitis model of methicillin-resistant S. aureus infection. We highlight the utility of an intrabacterial drug metabolism (IBDM) approach to probe the mechanism by which JSF-3151 is transformed within the bacteria. We also identify and then validate two mechanisms of resistance in S. aureus: one mechanism involves increased expression of a lipocalin protein, and the other arises from the loss of function of an azoreductase. The computational and experimental approaches, discovery of an antibacterial agent, and elucidated resistance mechanisms collectively hold promise to advance our understanding of therapeutic regimens for drug-resistant S. aureus.
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Affiliation(s)
- Jimmy S. Patel
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Hassan Al-Tameemi
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Yong-Mo Ahn
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Alexander L. Perryman
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Xin Wang
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Samer S. Daher
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - James Occi
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Riccardo Russo
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Steven Park
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Matthew Zimmerman
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Hsin-Pin Ho
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - David S. Perlin
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Véronique Dartois
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Sean Ekins
- Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States
| | - Pradeep Kumar
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Nancy Connell
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Jeffrey M. Boyd
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Joel S. Freundlich
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
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19
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Kocak E, Nemutlu E, Kır S, Sagıroglu M, Özkul C. Integrative proteomics and metabolomics approach to elucidate the antimicrobial effect of simvastatin on Escherichia coli. Biomed Chromatogr 2021; 35:e5180. [PMID: 34043824 DOI: 10.1002/bmc.5180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 11/07/2022]
Abstract
Globally, simvastatin is one of the most commonly used statin drugs. Its antimicrobial properties have been investigated against various pathogens. However, its effect on biological processes in bacteria has been unclear. This study focused on altered biological and metabolic processes at protein and metabolite levels induced by simvastatin. MS-based proteomics and metabolomics were used to investigate the altered proteins and metabolites between experimental groups. Proteomics results showed that simvastatin induced various antimicrobial targets such as chaperon protein DnaK and cell division protein FtsZ. Metabolomics results revealed phenotypic changes in cells under simvastatin stress. Integrated proteomics and metabolomics result indicated that various metabolic processes were altered to adapt to stress conditions. Energy metabolism (glycolysis, tricarboxylic acid cycle, etc.), amino acid synthesis and ribosomal proteins, and purine and pyrimidine synthesis were induced by the effect of simvastatin. This study will contribute to the understanding of antimicrobial properties of statin drugs.
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Affiliation(s)
- Engin Kocak
- Department of Analytical Chemistry, Faculty of Gulhane Pharmacy, Health Sciences 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 Sagıroglu
- 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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20
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Sodhi KK, Kumar M, Balan B, Dhaulaniya AS, Shree P, Sharma N, Singh DK. Perspectives on the antibiotic contamination, resistance, metabolomics, and systemic remediation. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-020-04003-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AbstractAntibiotics have been regarded as the emerging contaminants because of their massive use in humans and veterinary medicines and their persistence in the environment. The global concern of antibiotic contamination to different environmental matrices and the emergence of antibiotic resistance has posed a severe impact on the environment. Different mass-spectrometry-based techniques confirm their presence in the environment. Antibiotics are released into the environment through the wastewater steams and runoff from land application of manure. The microorganisms get exposed to the antibiotics resulting in the development of antimicrobial resistance. Consistent release of the antibiotics, even in trace amount into the soil and water ecosystem, is the major concern because the antibiotics can lead to multi-resistance in bacteria which can cause hazardous effects on agriculture, aquaculture, human, and livestock. A better understanding of the correlation between the antibiotic use and occurrence of antibiotic resistance can help in the development of policies to promote the judicious use of antibiotics. The present review puts a light on the remediation, transportation, uptake, and antibiotic resistance in the environment along with a novel approach of creating a database for systemic remediation, and metabolomics for the cleaner and safer environment.
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21
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Gierse LC, Meene A, Schultz D, Schwaiger T, Karte C, Schröder C, Wang H, Wünsche C, Methling K, Kreikemeyer B, Fuchs S, Bernhardt J, Becher D, Lalk M, Study Group K, Urich T, Riedel K. A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function. Microorganisms 2020; 8:microorganisms8121887. [PMID: 33260576 PMCID: PMC7760263 DOI: 10.3390/microorganisms8121887] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/03/2020] [Accepted: 11/27/2020] [Indexed: 12/19/2022] Open
Abstract
Swine are regarded as promising biomedical models, but the dynamics of their gastrointestinal microbiome have been much less investigated than that of humans or mice. The aim of this study was to establish an integrated multi-omics protocol to investigate the fecal microbiome of healthy swine. To this end, a preparation and analysis protocol including integrated sample preparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integration linked microbiome composition with function, and metabolic activity with protein inventories, i.e., 16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites. 16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae and Clostridiaceae. Similar microbiome compositions in feces and colon, but not ileum samples, were observed, showing that feces can serve as minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition, e.g., temporal decreased abundance of Lactobacillaceae and Streptococcaceae during the experiment, were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed a rather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associated metaproteome functions, pointing towards functional redundancy among microbiome constituents. In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomy and functionality of the intestinal microbiome of swine.
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Affiliation(s)
- Laurin Christopher Gierse
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Alexander Meene
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Daniel Schultz
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany; (D.S.); (K.M.); (M.L.)
| | - Theresa Schwaiger
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Südufer 10, 17493 Greifswald, Germany; (T.S.); (C.K.); (C.S.)
| | - Claudia Karte
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Südufer 10, 17493 Greifswald, Germany; (T.S.); (C.K.); (C.S.)
| | - Charlotte Schröder
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Südufer 10, 17493 Greifswald, Germany; (T.S.); (C.K.); (C.S.)
| | - Haitao Wang
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Christine Wünsche
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Karen Methling
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany; (D.S.); (K.M.); (M.L.)
| | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Schillingallee 70, 18055 Rostock, Germany;
| | - Stephan Fuchs
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute Wernigerode, Burgstraße 37, 38855 Wernigerode, Germany;
| | - Jörg Bernhardt
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
| | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany; (D.S.); (K.M.); (M.L.)
| | | | - Tim Urich
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
- Correspondence: (T.U.); (K.R.); Tel.: +49-3834-420-5904 (T.U.); +49-3834-420-5900 (K.R.)
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany; (L.C.G.); (A.M.); (H.W.); (C.W.); (J.B.); (D.B.)
- Correspondence: (T.U.); (K.R.); Tel.: +49-3834-420-5904 (T.U.); +49-3834-420-5900 (K.R.)
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22
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Shen F, Ge C, Yuan P. Metabolomics Study Reveals Inhibition and Metabolic Dysregulation in Staphylococcus aureus Planktonic Cells and Biofilms Induced by Carnosol. Front Microbiol 2020; 11:538572. [PMID: 33072009 PMCID: PMC7530940 DOI: 10.3389/fmicb.2020.538572] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/27/2020] [Indexed: 02/05/2023] Open
Abstract
Staphylococcus aureus (S. aureus) is a global health threat accompanied by increasing in drug resistance. To combat this challenge, there is an urgent need to find alternative antimicrobial agents against S. aureus. This study investigated the antimicrobial efficacy of carnosol against S. aureus using an in vitro model. The effects of carnosol were determined based on the antimicrobial effects or formation and disruption of biofilms. Finally, metabolomics of S. aureus grown as planktonic cells and biofilms with carnosol treatment were analyzed using gas chromatography-mass spectrometry. The minimum inhibitory concentrations (MICs) of carnosol were 32 to 256 μg/mL against the sixteen tested S. aureus strains. Among the biofilms, we observed a reduction in bacterial motility of the S. aureus, biofilm development and preformed biofilm after carnosol treatment. Moreover, the significantly altered metabolic pathways upon carnosol treatment in S. aureus planktonic cells and biofilms were highly associated with the perturbation of glyoxylate and dicarboxylate metabolism, glycine, serine and threonine metabolism, arginine and proline metabolism, alanine, aspartate and glutamate metabolism, arginine biosynthesis, and aminoacyl-tRNA biosynthesis. In addition, glutathione metabolism, D-glutamine and D-glutamate metabolism were significantly changed in the biofilms. This study establishes the antibacterial and antibiofilm properties of carnosol, and will provide an alternative strategy for overcoming the drug resistance of S. aureus.
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Affiliation(s)
- Fengge Shen
- Xinxiang Key Laboratory of Molecular Neurology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Chunpo Ge
- Xinxiang Key Laboratory of Molecular Neurology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Peng Yuan
- School of Public Health, Xinxiang Medical University, Xinxiang, China
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23
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Han YY, Lin YC, Cheng WC, Lin YT, Teng LJ, Wang JK, Wang YL. Rapid antibiotic susceptibility testing of bacteria from patients' blood via assaying bacterial metabolic response with surface-enhanced Raman spectroscopy. Sci Rep 2020; 10:12538. [PMID: 32719444 PMCID: PMC7385103 DOI: 10.1038/s41598-020-68855-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022] Open
Abstract
Blood stream infection is one of the major public health issues characterized with high cost and high mortality. Timely effective antibiotics usage to control infection is crucial for patients’ survival. The standard microbiological diagnosis of infection however can last days. The delay in accurate antibiotic therapy would lead to not only poor clinical outcomes, but also to a rise in antibiotic resistance due to widespread use of empirical broad-spectrum antibiotics. An important measure to tackle this problem is fast determination of bacterial antibiotic susceptibility to optimize antibiotic treatment. We show that a protocol based on surface-enhanced Raman spectroscopy can obtain consistent antibiotic susceptibility test results from clinical blood-culture samples within four hours. The characteristic spectral signatures of the obtained spectra of Staphylococcus aureus and Escherichia coli—prototypic Gram-positive and Gram-negative bacteria—became prominent after an effective pretreatment procedure removed strong interferences from blood constituents. Using them as the biomarkers of bacterial metabolic responses to antibiotics, the protocol reported the susceptibility profiles of tested drugs against these two bacteria acquired from patients’ blood with high specificity, sensitivity and speed.
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Affiliation(s)
- Yin-Yi Han
- Department of Anesthesia, National Taiwan University Hospital, Taipei, Taiwan. .,Department of Traumatology, National Taiwan University Hospital, Taipei, Taiwan.
| | - Yi-Chun Lin
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei-Chih Cheng
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Yu-Tzu Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan.,Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Juen-Kai Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan. .,Center for Condensed Matter Sciences, National Taiwan University, Taipei, Taiwan. .,Center of Atomic Initiative for New Materials, National Taiwan University, Taipei, Taiwan.
| | - Yuh-Lin Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan. .,Department of Physics, National Taiwan University, Taipei, Taiwan.
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24
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Larson EC, Lim AL, Pond CD, Craft M, Čavužić M, Waldrop GL, Schmidt EW, Barrows LR. Pyrrolocin C and equisetin inhibit bacterial acetyl-CoA carboxylase. PLoS One 2020; 15:e0233485. [PMID: 32470050 PMCID: PMC7259786 DOI: 10.1371/journal.pone.0233485] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/06/2020] [Indexed: 11/25/2022] Open
Abstract
Antimicrobial resistance is a growing global health and economic concern. Current antimicrobial agents are becoming less effective against common bacterial infections. We previously identified pyrrolocins A and C, which showed activity against a variety of Gram-positive bacteria. Structurally similar compounds, known as pyrrolidinediones (e.g., TA-289, equisetin), also display antibacterial activity. However, the mechanism of action of these compounds against bacteria was undetermined. Here, we show that pyrrolocin C and equisetin inhibit bacterial acetyl-CoA carboxylase (ACC), the first step in fatty acid synthesis. We used transcriptomic data, metabolomic analysis, fatty acid rescue and acetate incorporation experiments to show that a major mechanism of action of the pyrrolidinediones is inhibition of fatty acid biosynthesis, identifying ACC as the probable molecular target. This hypothesis was further supported using purified proteins, demonstrating that biotin carboxylase is the inhibited component of ACC. There are few known antibiotics that target this pathway and, therefore, we believe that these compounds may provide the basis for alternatives to current antimicrobial therapy.
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Affiliation(s)
- Erica C. Larson
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, United States of America
| | - Albebson L. Lim
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, United States of America
| | - Christopher D. Pond
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, United States of America
| | - Matthew Craft
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Mirela Čavužić
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Grover L. Waldrop
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Louis R. Barrows
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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25
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Leonard A, Möhlis K, Schlüter R, Taylor E, Lalk M, Methling K. Exploring metabolic adaptation of Streptococcus pneumoniae to antibiotics. J Antibiot (Tokyo) 2020; 73:441-454. [PMID: 32210362 PMCID: PMC7292801 DOI: 10.1038/s41429-020-0296-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/31/2020] [Accepted: 02/09/2020] [Indexed: 02/07/2023]
Abstract
The Gram-positive bacterium Streptococcus pneumoniae is one of the common causes of community acquired pneumonia, meningitis, and otitis media. Analyzing the metabolic adaptation toward environmental stress conditions improves our understanding of its pathophysiology and its dependency on host-derived nutrients. In this study, extra- and intracellular metabolic profiles were evaluated to investigate the impact of antimicrobial compounds targeting different pathways of the metabolome of S. pneumoniae TIGR4Δcps. For the metabolomics approach, we analyzed the complex variety of metabolites by using 1H NMR, HPLC-MS, and GC–MS as different analytical techniques. Through this combination, we detected nearly 120 metabolites. For each antimicrobial compound, individual metabolic effects were detected that often comprised global biosynthetic pathways. Cefotaxime altered amino acids metabolism and carbon metabolism. The purine and pyrimidine metabolic pathways were mostly affected by moxifloxacin treatment. The combination of cefotaxime and azithromycin intensified the stress response compared with the use of the single antibiotic. However, we observed that three cell wall metabolites were altered only by treatment with the combination of the two antibiotics. Only moxifloxacin stress-induced alternation in CDP-ribitol concentration. Teixobactin-Arg10 resulted in global changes of pneumococcal metabolism. To meet the growing requirements for new antibiotics, our metabolomics approach has shown to be a promising complement to other OMICs investigations allowing insights into the mode of action of novel antimicrobial compounds.
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Affiliation(s)
- Anne Leonard
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Kevin Möhlis
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, F.-L-Jahn-Str. 15, 17489, Greifswald, Germany
| | - Edward Taylor
- University of Lincoln, School of Life Sciences, Green Lane, LN67DL, Lincoln, England, United Kingdom
| | - Michael Lalk
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Karen Methling
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
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26
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Jo SH, Song WS, Park HG, Lee JS, Jeon HJ, Lee YH, Kim W, Joo HS, Yang YH, Kim JS, Kim YG. Multi-omics based characterization of antibiotic response in clinical isogenic isolates of methicillin-susceptible/-resistant Staphylococcus aureus. RSC Adv 2020; 10:27864-27873. [PMID: 35516943 PMCID: PMC9055585 DOI: 10.1039/d0ra05407k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 07/17/2020] [Indexed: 12/30/2022] Open
Abstract
As demands for new antibiotics and strategies to control methicillin-resistant Staphylococcus aureus (MRSA) increase, there have been efforts to obtain more accurate and abundant information about the mechanism of the bacterial responses to antibiotics. However, most of the previous studies have investigated responses to antibiotics without considering the genetic differences between MRSA and methicillin-susceptible S. aureus (MSSA). Here, we initially applied a multi-omics approach into the clinical isolates (i.e., S. aureus WKZ-1 (MSSA) and S. aureus WKZ-2 (MRSA)) that are isogenic except for the mobile genetic element called staphylococcal cassette chromosome mec (SCCmec) type IV to explore the response to β-lactam antibiotics (oxacillin). First, the isogenic pair showed a similar metabolism without oxacillin treatment. The quantitative proteomics demonstrated that proteins involved in peptidoglycan biosynthesis (MurZ, PBP2, SgtB, PrsA), two-component systems (VrsSR, WalR, SaeSR, AgrA), oxidative stress (MsrA1, MsrB), and stringent response (RelQ) were differentially regulated after the oxacillin treatment of the isogenic isolates. In addition, targeted metabolic profiling showed that metabolites belonging to the building blocks (lysine, glutamine, acetyl-CoA, UTP) of peptidoglycan biosynthesis machinery were specifically decreased in the oxacillin-treated MRSA. These results indicate that the difference in metabolism of this isogenic pair with oxacillin treatment could be caused only by SCCmec type IV. Understanding and investigating the antibiotic response at the molecular level can, therefore, provide insight into drug resistance mechanisms and new opportunities for antibiotics development. We introduce clinical isogenic strain isolates and a multi-OMICS approach to observe a response to oxacillin of methicillin- susceptible/-resistant Staphylococcus aureus.![]()
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27
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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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28
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Lim AT, Vincent IM, Barrett MP, Gilbert IH. Small Polar Hits against S. aureus: Screening, Initial Hit Optimization, and Metabolomic Studies. ACS OMEGA 2019; 4:19199-19215. [PMID: 31763544 PMCID: PMC6869403 DOI: 10.1021/acsomega.9b02507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
The global prevalence of antibacterial resistance requires new antibacterial drugs with novel chemical scaffolds and modes of action. It is also vital to design compounds with optimal physicochemical properties to permeate the bacterial cell envelope. We described an approach of combining and integrating whole cell screening and metabolomics into early antibacterial drug discovery using a library of small polar compounds. Whole cell screening of a diverse library of small polar compounds against Staphylococcus aureus gave compound 2. Hit expansion was carried out to determine structure-activity relationships. A selection of compounds from this series, together with other screened active compounds, was subjected to an initial metabolomics study to provide a metabolic fingerprint of the mode of action. It was found that compound 2 and its analogues have a different mode of action from some of the known antibacterial compounds tested. This early study highlighted the potential of whole cell screening and metabolomics in early antibacterial drug discovery. Future works will require improving potency and performing orthogonal studies to confirm the modes of action.
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Affiliation(s)
- Andrew
S. T. Lim
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K.
| | - Isabel M. Vincent
- Glasgow
Polyomics, University of Glasgow, Wolfson
Wohl Cancer Research Centre, Garscube Campus, Bearsden G61 1QH, U.K.
| | - Michael P. Barrett
- Glasgow
Polyomics, University of Glasgow, Wolfson
Wohl Cancer Research Centre, Garscube Campus, Bearsden G61 1QH, U.K.
- Wellcome
Centre for Molecular Parasitology, Institute of Infection, Immunity
and Inflammation, University of Glasgow, Glasgow G12 8TA, U.K.
| | - Ian H. Gilbert
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K.
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29
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Marquès C, Collin V, Franceschi C, Charbonnel N, Chatellier S, Forestier C. Fosfomycin and Staphylococcus aureus: transcriptomic approach to assess effect on biofilm, and fate of unattached cells. J Antibiot (Tokyo) 2019; 73:91-100. [PMID: 31705133 DOI: 10.1038/s41429-019-0256-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/08/2019] [Accepted: 10/14/2019] [Indexed: 11/09/2022]
Abstract
Interest has been rekindled in the old antibiotic fosfomycin, partly because of its ability to penetrate biofilm. Using a transcriptomic approach, we investigated the modifications induced by fosfomycin in sessile cells of a clinical Staphylococcus aureus isolated from a device-associated infection. Cells still able to form biofilm after 4 h of incubation in the presence of subinhibitory concentrations of fosfomycin and cells from 24-h-old biofilm later submitted to fosfomycin had 6.77% and 9.41%, respectively, of differentially expressed genes compared with their antibiotic-free control. Fosfomycin induced mostly downregulation of genes assigned to nucleotide, amino acid and carbohydrate transport, and metabolism. Adhesins and capsular biosynthesis proteins encoding genes were downregulated in fosfomycin-grown biofilm, whereas the murein hydrolase regulator lgrA and a D-lactate dehydrogenase-encoding gene were upregulated. In fosfomycin-treated biofilm, the expression of genes encoding adhesins, the cell wall biosynthesis protein ScdA, and to a lesser extent the fosfomycin target MurA was also decreased. Unattached cells surrounding fosfomycin-grown biofilm showed greater ability to form aggregates than their counterparts obtained without fosfomycin. Reducing their global metabolism and lowering cell wall turnover would allow some S. aureus cells to grow in biofilm despite fosfomycin stress while promoting hyperadherent phenotype in the vicinity of the fosfomycin-treated biofilm.
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Affiliation(s)
- Claire Marquès
- bioMérieux SA, 38390, La Balme les Grottes, France.,Laboratoire des Microorganismes, Génome et Environnement, UMR CNRS 6023-Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | | | | | - Nicolas Charbonnel
- Laboratoire des Microorganismes, Génome et Environnement, UMR CNRS 6023-Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | | | - Christiane Forestier
- Laboratoire des Microorganismes, Génome et Environnement, UMR CNRS 6023-Université Clermont Auvergne, 63000, Clermont-Ferrand, France.
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30
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Sousa J, Westhoff P, Methling K, Lalk M. The Absence of Pyruvate Kinase Affects Glucose-Dependent Carbon Catabolite Repression in Bacillus subtilis. Metabolites 2019; 9:metabo9100216. [PMID: 31590319 PMCID: PMC6835821 DOI: 10.3390/metabo9100216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/30/2022] Open
Abstract
Pyruvate is a key intermediate of diverse metabolic pathways of central carbon metabolism. In addition to being the end product of glycolysis, pyruvate is an essential carbon distribution point to oxidative metabolism, amino acid and fatty acid syntheses, and overflow metabolite production. Hence, a tight regulation of pyruvate kinase (Pyk) activity is of great importance. This study aimed to analyze targeted metabolites from several pathways and possible changes in Bacillus subtilis lacking Pyk. Wild type and Δpyk cells were cultivated in chemically defined medium with glucose and pyruvate as carbon sources, and the extracted metabolites were analyzed by 1H-NMR, GC-MS, HPLC-MS, and LC-MS/MS. The results showed that the perturbation created in the pyruvate node drove an adaptation to new conditions by altering the nutritional compounds’ consumption. In Δpyk, pyruvate, which is subject to glucose-dependent carbon catabolite repression, did not comply with the hierarchy in carbon source utilization. Other metabolic alterations were observed such as the higher secretion of the overflow metabolites acetoin and 2,3-butanediol by Δpyk. Our results help to elucidate the regulatory transport of glucose and pyruvate in B. subtilis and possible metabolic reroute to alternative pathways in the absence of Pyk.
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Affiliation(s)
- Joana Sousa
- Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany.
- Innovayt S/A, Av. João Paulo II 30, 4715-213 Braga, Portugal.
| | - Philipp Westhoff
- Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany.
- Institute of Plant Biochemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, Düsseldorf, Germany.
| | - Karen Methling
- Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany.
| | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany.
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Lin YW, Han ML, Zhao J, Zhu Y, Rao G, Forrest A, Song J, Kaye KS, Hertzog P, Purcell A, Creek D, Zhou QT, Velkov T, Li J. Synergistic Combination of Polymyxin B and Enrofloxacin Induced Metabolic Perturbations in Extensive Drug-Resistant Pseudomonas aeruginosa. Front Pharmacol 2019; 10:1146. [PMID: 31632279 PMCID: PMC6785843 DOI: 10.3389/fphar.2019.01146] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/04/2019] [Indexed: 11/30/2022] Open
Abstract
Polymyxins are used as a last-resort class of antibiotics against multidrug-resistant (MDR) Gram-negative Pseudomonas aeruginosa. As polymyxin monotherapy is associated with potential development of resistance, combination therapy is highly recommended. This study investigated the mechanism underlying the synergistic killing of polymyxin B and enrofloxacin against extensive drug-resistant (XDR) P. aeruginosa. An XDR isolate P. aeruginosa 12196 was treated with clinically relevant concentrations of polymyxin B (2 mg/L) and enrofloxacin (1 mg/L) alone or in combination. Metabolome profiles were investigated from bacterial samples collected at 1-and 4-h posttreatment using liquid chromatography with tandem mass spectrometry (LC-MS/MS), and data were analyzed using univariate and multivariate statistics. Significantly perturbed metabolites (q < 0.05, fold change ≥ 2) were subjected to pathway analysis. The synergistic killing by polymyxin B–enrofloxacin combination was initially driven by polymyxin B as indicated by the perturbation of lipid metabolites at 1 h in particular. The killing was subsequently driven by enrofloxacin via the inhibition of DNA replication, resulting in the accumulation of nucleotides at 4 h. Furthermore, the combination uniquely altered levels of metabolites in energy metabolism and cell envelope biogenesis. Most importantly, the combination significantly minimized polymyxin resistance via the inhibition of lipid A modification pathway, which was most evident at 4 h. This is the first study to elucidate the synergistic mechanism of polymyxin B–enrofloxacin combination against XDR P. aeruginosa. The metabolomics approach taken in this study highlights its power to elucidate the mechanism of synergistic killing by antibiotic combinations at the systems level.
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Affiliation(s)
- Yu-Wei Lin
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Mei-Ling Han
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Jinxin Zhao
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Yan Zhu
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Gauri Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - Alan Forrest
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - Jiangning Song
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Keith S Kaye
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Paul Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Anthony Purcell
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Darren Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Qi Tony Zhou
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, IN, United States
| | - Tony Velkov
- Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, Australia
| | - Jian Li
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, VIC, Australia
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Danner MC, Robertson A, Behrends V, Reiss J. Antibiotic pollution in surface fresh waters: Occurrence and effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 664:793-804. [PMID: 30763859 DOI: 10.1016/j.scitotenv.2019.01.406] [Citation(s) in RCA: 416] [Impact Index Per Article: 83.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/25/2019] [Accepted: 01/30/2019] [Indexed: 05/25/2023]
Abstract
Worldwide, antibiotic usage exceeds 100,000 tons per year and there is increasing concern over the fate of these substances. Antibiotics are ubiquitous in the environment and significant concentrations have been detected in fresh waters. In this review, we highlight important aspects of antibiotic pollution in fresh waters: that concentrations of antibiotics in the environment are substantial, that micro-organisms are susceptible to this, that bacteria can evolve resistance in the environment, and that antibiotic pollution affects natural food webs while interacting with other stressors; which taken together poses a number of challenges for environmental scientists. In the literature, we found examples of considerable antibiotic pollution in fresh waters. In the Americas, antibiotic concentrations of up to 15 μg/L have been measured; with higher concentrations reported from European and African studies (over 10 μg/L and 50 μg/L respectively), and in Asian-pacific countries concentrations over 450 μg/L have been detected. While these concentrations might not be deemed harmful to humans, non-target freshwater organisms could be affected by them. Bioassays show that some of the antibiotics found in surface waters affect microbes at concentrations below 10 μg/L. Among the most potent antibiotics are those that prevail in streams and rivers in these concentrations, such as ciprofloxacin. Sub-lethal concentrations might not kill prokaryotes but contribute to increased bacterial resistance and change the composition of single-celled communities, as demonstrated in laboratory experiments. This has implications for the microbial food web (e.g. interactions among and between bacteria and their protozoan consumers) and by extension, larger organisms and ecosystem health. The fact that the effects of antibiotics are extremely context-dependent represents a challenge, particularly for in vitro research. We suggest future research avenues, taking into account food web experiments, antibiotics interacting with one another (and other stressors) and discuss how these can help to answer multi-layered research questions.
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Affiliation(s)
- Marie-Claire Danner
- Department of Life Sciences, Whitelands College, Roehampton University, London SW15 4JD, United Kingdom.
| | - Anne Robertson
- Department of Life Sciences, Whitelands College, Roehampton University, London SW15 4JD, United Kingdom
| | - Volker Behrends
- Department of Life Sciences, Whitelands College, Roehampton University, London SW15 4JD, United Kingdom
| | - Julia Reiss
- Department of Life Sciences, Whitelands College, Roehampton University, London SW15 4JD, United Kingdom
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Metabolomic Investigation of Staphylococcus aureus Antibiotic Susceptibility by Liquid Chromatography Coupled to High-Resolution Mass Spectrometry. Methods Mol Biol 2019; 1871:279-293. [PMID: 30276746 DOI: 10.1007/978-1-4939-8814-3_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Staphylococcus aureus is a major human pathogen that can readily acquire antibiotic resistance. For instance, methicillin-resistant S. aureus represents a major cause of hospital- and community-acquired bacterial infections. In this chapter, we first provide a detailed protocol for obtaining unbiased and reproducible S. aureus metabolic profiles. The resulting intracellular metabolome is then analyzed in an untargeted manner by using both hydrophilic interaction liquid chromatography and pentafluorophenyl-propyl columns coupled to high-resolution mass spectrometry. Such analyses are done in conjunction with our in-house spectral database to identify with high confidence as many meaningful S. aureus metabolites as possible. Under these conditions, we can routinely monitor more than 200 annotated S. aureus metabolites. We also indicate how this protocol can be used to investigate the metabolic differences between methicillin-resistant and susceptible strains.
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Qi J, Pang Y, An P, Jiang G, Kong Q, Ren X. Determination of metabolites of Geotrichum citri-aurantii treated with peppermint oil using liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. J Food Biochem 2018; 43:e12745. [PMID: 31353560 DOI: 10.1111/jfbc.12745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/12/2018] [Accepted: 11/16/2018] [Indexed: 02/06/2023]
Abstract
Sour rot is a leading disease of citrus fruit caused by the postharvest pathogen Geotrichum citri-aurantii. It has been reported that essential oils can be used as substitutes for synthetic fungicides to control the pathogen. In this study, changes in metabolites and antifungal effects of G. citri-aurantii treated with peppermint oil (PO) were investigated. The inhibition rate of the mycelial growth increased as the PO concentration increased, and 6 μl PO/disk resulted in a radial growth inhibition of 79.2%. The electrical conductivity of G. citri-aurantii treated with PO increased compared to the control. By comparing the metabolic profiles of treated and untreated G. citri-aurantii cells, a total of 53 distinct metabolites 9 were up-regulated and 44 were down-regulated were found, including 16 lipid metabolites, 6 carbohydrate metabolites, 2 amino acid metabolites, 5 alcohols, 2 glycoside metabolites, and 3 ketone metabolites, etc, and these metabolites are involved in 25 major metabolic pathways. PRACTICAL APPLICATIONS: Chemical fungicides can effectively control G. citri-aurantii during fruit postharvest period. However, synthetic chemical fungicides have gradually led to buildup of resistance of fungil, which seriously causes the frequent of food-borne diseases. PO extracted from natural plants can be used as natural additive in many foods due to their antioxidant, antibacterial, and antifungal properties. Therefore, PO can be considered as a promising bacteriostatic agent for the defense of G. citri-aurantii during fruit postharvest period.
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Affiliation(s)
- Jianrui Qi
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China
| | - Yaxing Pang
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China
| | - Peipei An
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China
| | - Guoshan Jiang
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China
| | - Qingjun Kong
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China.,College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Xueyan Ren
- Shaanxi Engineering Laboratory of Food Green Processing and Safety Control, Shaanxi Normal University, Xi'an, China.,College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
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A quantitative metabolomics study of bacterial metabolites in different domains. Anal Chim Acta 2018; 1037:237-244. [DOI: 10.1016/j.aca.2018.02.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 02/09/2018] [Accepted: 02/10/2018] [Indexed: 01/29/2023]
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Abstract
The aim of this study was to analyze the metabolome of several Klebsiella pneumoniae strains characterized by different resistance patterns. A total of 59 bacterial strains (27 carbapenemase-negative and 32 carbapenemase-positive) were included and their metabolic features were assessed in basal conditions. Moreover, 8 isolates (4 wild-type and 4 KPC-producers) were randomly selected to evaluate the impact of sub-lethal concentrations of meropenem on bacterial metabolism. The metabolomic analysis was performed by 1H-NMR spectroscopy both on filtered supernatants and cell lysates. A total of 40 and 20 molecules were quantified in the intracellular and the extracellular metabolome, respectively. While in basal conditions only five metabolites showed significant differences between carbapenemase-positive and negative strains, the use of meropenem had a profound impact on the whole bacterial metabolism. In the intracellular compartment, a reduction of different overflow metabolites and organic acids (e.g. formate, acetate, isobutyrate) was noticed, whereas, in the extracellular metabolome, the levels of several organic acids (e.g. succinate, acetate, formate, lactate) and amino acids (aspartate, threonine, lysine, alanine) were modified by meropenem stimulation. Interestingly, carbapenemase-positive and negative strains reacted differently to meropenem in terms of number and type of perturbed metabolites. In wild-type strains, meropenem had great impact on the metabolic pathways related to methane metabolism and alanine, aspartate and glutamate metabolism, whereas in KPC-producers the effect was predominant on pyruvate metabolism. The knowledge about the bacterial metabolic profiles could help to set up innovative diagnostic methods and new antimicrobial strategies to fight the global crisis against carbapenemase-positive K. pneumoniae.
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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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Shaulov Y, Shimokawa C, Trebicz-Geffen M, Nagaraja S, Methling K, Lalk M, Weiss-Cerem L, Lamm AT, Hisaeda H, Ankri S. Escherichia coli mediated resistance of Entamoeba histolytica to oxidative stress is triggered by oxaloacetate. PLoS Pathog 2018; 14:e1007295. [PMID: 30308066 PMCID: PMC6181410 DOI: 10.1371/journal.ppat.1007295] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/25/2018] [Indexed: 12/20/2022] Open
Abstract
Amebiasis, a global intestinal parasitic disease, is due to Entamoeba histolytica. This parasite, which feeds on bacteria in the large intestine of its human host, can trigger a strong inflammatory response upon invasion of the colonic mucosa. Whereas information about the mechanisms which are used by the parasite to cope with oxidative and nitrosative stresses during infection is available, knowledge about the contribution of bacteria to these mechanisms is lacking. In a recent study, we demonstrated that enteropathogenic Escherichia coli O55 protects E. histolytica against oxidative stress. Resin-assisted capture (RAC) of oxidized (OX) proteins coupled to mass spectrometry (OX-RAC) was used to investigate the oxidation status of cysteine residues in proteins present in E. histolytica trophozoites incubated with live or heat-killed E. coli O55 and then exposed to H2O2-mediated oxidative stress. We found that the redox proteome of E. histolytica exposed to heat-killed E. coli O55 is enriched with proteins involved in redox homeostasis, lipid metabolism, small molecule metabolism, carbohydrate derivative metabolism, and organonitrogen compound biosynthesis. In contrast, we found that proteins associated with redox homeostasis were the only OX-proteins that were enriched in E. histolytica trophozoites which were incubated with live E. coli O55. These data indicate that E. coli has a profound impact on the redox proteome of E. histolytica. Unexpectedly, some E. coli proteins were also co-identified with E. histolytica proteins by OX-RAC. We demonstrated that one of these proteins, E. coli malate dehydrogenase (EcMDH) and its product, oxaloacetate, are key elements of E. coli-mediated resistance of E. histolytica to oxidative stress and that oxaloacetate helps the parasite survive in the large intestine. We also provide evidence that the protective effect of oxaloacetate against oxidative stress extends to Caenorhabditis elegans.
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Affiliation(s)
- Yana Shaulov
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa Israel
| | - Chikako Shimokawa
- Department of Parasitology, Graduate School of Medicine, Gunma University, Showa-machi, Maebashi, Gunma, Japan
| | - Meirav Trebicz-Geffen
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa Israel
| | - Shruti Nagaraja
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa Israel
| | - Karen Methling
- University of Greifswald, Institute of Biochemistry, Greifswald, Germany
| | - Michael Lalk
- University of Greifswald, Institute of Biochemistry, Greifswald, Germany
| | - Lea Weiss-Cerem
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa, Israel
| | - Ayelet T. Lamm
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa, Israel
| | - Hajime Hisaeda
- Department of Parasitology, Graduate School of Medicine, Gunma University, Showa-machi, Maebashi, Gunma, Japan
- Department of Parasitology, National Institute of Infectious Diseases, Toyama, Shinjuku, Tokyo, Japan
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa Israel
- * E-mail:
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Adaptive Metabolism in Staphylococci: Survival and Persistence in Environmental and Clinical Settings. J Pathog 2018; 2018:1092632. [PMID: 30327733 PMCID: PMC6171259 DOI: 10.1155/2018/1092632] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/28/2018] [Accepted: 08/12/2018] [Indexed: 01/04/2023] Open
Abstract
Staphylococci are highly successful at colonizing a variety of dynamic environments, both nonpathogenic and those of clinical importance, and comprise the list of pathogens of global public health significance. Their remarkable survival and persistence can be attributed to a host of strategies, one of which is metabolic versatility—their ability to rapidly alter their metabolism in the presence of transient or long-term bacteriostatic and bactericidal conditions and facilitate cellular homeostasis. These attributes contribute to their widespread dissemination and challenging eradication particularly from clinical settings. The study of microbial behaviour at the metabolite level provides insight into mechanisms of survival and persistence under defined environmental and clinical conditions. This paper reviews the range of metabolic modulations that facilitate staphylococcal acclimatization and persistence in varying terrestrial and host conditions, and their public health ramifications in these settings.
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40
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The serine/threonine kinase Stk and the phosphatase Stp regulate cell wall synthesis in Staphylococcus aureus. Sci Rep 2018; 8:13693. [PMID: 30209409 PMCID: PMC6135852 DOI: 10.1038/s41598-018-32109-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/07/2018] [Indexed: 11/10/2022] Open
Abstract
The cell wall synthesis pathway producing peptidoglycan is a highly coordinated and tightly regulated process. Although the major components of bacterial cell walls have been known for decades, the complex regulatory network controlling peptidoglycan synthesis and many details of the cell division machinery are not well understood. The eukaryotic-like serine/threonine kinase Stk and the cognate phosphatase Stp play an important role in cell wall biosynthesis and drug resistance in S. aureus. We show that stp deletion has a pronounced impact on cell wall synthesis. Deletion of stp leads to a thicker cell wall and decreases susceptibility to lysostaphin. Stationary phase Δstp cells accumulate peptidoglycan precursors and incorporate higher amounts of incomplete muropeptides with non-glycine, monoglycine and monoalanine interpeptide bridges into the cell wall. In line with this cell wall phenotype, we demonstrate that the lipid II:glycine glycyltransferase FemX can be phosphorylated by the Ser/Thr kinase Stk in vitro. Mass spectrometric analyses identify Thr32, Thr36 and Ser415 as phosphoacceptors. The cognate phosphatase Stp dephosphorylates these phosphorylation sites. Moreover, Stk interacts with FemA and FemB, but is unable to phosphorylate them. Our data indicate that Stk and Stp modulate cell wall synthesis and cell division at several levels.
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Leonard A, Gierok P, Methling K, Gómez-Mejia A, Hammerschmidt S, Lalk M. Metabolic inventory of Streptococcus pneumoniae growing in a chemical defined environment. Int J Med Microbiol 2018; 308:705-712. [DOI: 10.1016/j.ijmm.2018.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 11/24/2022] Open
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Zhao X, Liu Z, Liu Z, Meng R, Shi C, Chen X, Bu X, Guo N. Phenotype and RNA-seq-Based transcriptome profiling of Staphylococcus aureus biofilms in response to tea tree oil. Microb Pathog 2018; 123:304-313. [PMID: 30041003 DOI: 10.1016/j.micpath.2018.07.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 03/06/2018] [Accepted: 07/20/2018] [Indexed: 01/31/2023]
Abstract
Staphylococcus aureus (S. aureus) is a Gram-positive bacterium that causes a wide range of diseases, including food poisoning. Tea tree oil (TTO), an essential oil distilled from Melaleuca alternifolia, is well-known for its antibacterial activities. TTO effectively inhibited all 19 tested strains of S. aureus biofilm and planktonic cells. Phenotype analyses of S. aureus biofilm cells exposed to TTO were performed by biofilm adhesion assays, eDNA detection and PIA release. RNA sequencing (RNA-seq) was used in our study to elucidate the mechanism of TTO as a potential antibacterial agent to evaluate differentially expressed genes (DEGs) and the functional network in S. aureus ATCC 29213 biofilms. TTO significantly changed (greater than a 2- or less than a 2-fold change) the expression of 304 genes in S. aureus contained in biofilms. The levels of genes related to the glycine, serine and threonine metabolism pathway, purine metabolism pathway, pyrimidine metabolism pathway and amino acid biosynthesis pathway were dramatically changed in the biofilm exposed to TTO. Furthermore, the expression changes identified by RNA-seq analysis were verified by real-time RT-PCR. To the best of our knowledge, this research is the first study to report the phenotype and expression profiles of S. aureus in biofilms exposed to TTO.
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Affiliation(s)
- Xingchen Zhao
- Department of Food Quality and Safety, School of Pharmaceutics and Food Science, Tonghua Normal University, 134000, China
| | - Zonghui Liu
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, 130062, China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | - Rizeng Meng
- Jilin Entry-Exit Inspection and Quarantine Bureau, Changchun, 130062, China
| | - Ce Shi
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, 130062, China
| | - Xiangrong Chen
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, 130062, China
| | - Xiujuan Bu
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, 130062, China
| | - Na Guo
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, 130062, China.
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Mack SG, Turner RL, Dwyer DJ. Achieving a Predictive Understanding of Antimicrobial Stress Physiology through Systems Biology. Trends Microbiol 2018. [PMID: 29530606 DOI: 10.1016/j.tim.2018.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The dramatic spread and diversity of antibiotic-resistant pathogens has significantly reduced the efficacy of essentially all antibiotic classes, bringing us ever closer to a postantibiotic era. Exacerbating this issue, our understanding of the multiscale physiological impact of antimicrobial challenge on bacterial pathogens remains incomplete. Concerns over resistance and the need for new antibiotics have motivated the collection of omics measurements to provide systems-level insights into antimicrobial stress responses for nearly 20 years. Although technological advances have markedly improved the types and resolution of such measurements, continued development of mathematical frameworks aimed at providing a predictive understanding of complex antimicrobial-associated phenotypes is critical to maximize the utility of multiscale data. Here we highlight recent efforts utilizing systems biology to enhance our knowledge of antimicrobial stress physiology. We provide a brief historical perspective of antibiotic-focused omics measurements, highlight new measurement discoveries and trends, discuss examples and opportunities for integrating measurements with mathematical models, and describe future challenges for the field.
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Affiliation(s)
- Sean G Mack
- Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Randi L Turner
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Daniel J Dwyer
- Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA; Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA; Institute for Physical Sciences & Technology, University of Maryland, College Park, MD 20742, USA; Department of Bioengineering, University of Maryland, College Park, MD 20742, USA; Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA.
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Gardner SG, Marshall DD, Daum RS, Powers R, Somerville GA. Metabolic Mitigation of Staphylococcus aureus Vancomycin Intermediate-Level Susceptibility. Antimicrob Agents Chemother 2018; 62:e01608-17. [PMID: 29109158 PMCID: PMC5740343 DOI: 10.1128/aac.01608-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/28/2017] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen whose infections are increasingly difficult to treat due to increased antibiotic resistance, including resistance to vancomycin. Vancomycin-intermediate S. aureus (VISA) strains develop resistance to vancomycin through adaptive changes that are incompletely understood. Central to this adaptation are metabolic changes that permit growth in the presence of vancomycin. To define the metabolic changes associated with adaptive resistance to vancomycin in S. aureus, the metabolomes of a vancomycin-sensitive and VISA strain pair isolated from the same patient shortly after vancomycin therapy began and following vancomycin treatment failure were analyzed. The metabolic adaptations included increases in acetogenesis, carbon flow through the pentose phosphate pathway, wall teichoic acid and peptidoglycan precursor biosynthesis, purine biosynthesis, and decreased tricarboxylic acid (TCA) cycle activity. The significance of these metabolic pathways for vancomycin-intermediate susceptibility was determined by assessing the synergistic potential of human-use-approved inhibitors of these pathways in combination with vancomycin against VISA strains. Importantly, inhibitors of amino sugar and purine biosynthesis acted synergistically with vancomycin to kill a diverse set of VISA strains, suggesting that combinatorial therapy could augment the efficacy of vancomycin even in patients infected with VISA strains.
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Affiliation(s)
- Stewart G Gardner
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Robert S Daum
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Greg A Somerville
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Schultz D, Schlüter R, Gerth U, Lalk M. Metabolic Perturbations in a Bacillus subtilis clpP Mutant during Glucose Starvation. Metabolites 2017; 7:metabo7040063. [PMID: 29186773 PMCID: PMC5746743 DOI: 10.3390/metabo7040063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 11/17/2022] Open
Abstract
Proteolysis is essential for all living organisms to maintain the protein homeostasis and to adapt to changing environmental conditions. ClpP is the main protease in Bacillus subtilis, and forms complexes with different Clp ATPases. These complexes play crucial roles during heat stress, but also in sporulation or cell morphology. Especially enzymes of cell wall-, amino acid-, and nucleic acid biosynthesis are known substrates of the protease ClpP during glucose starvation. The aim of this study was to analyze the influence of a clpP mutation on the metabolism in different growth phases and to search for putative new ClpP substrates. Therefore, B. subtilis 168 cells and an isogenic ∆clpP mutant were cultivated in a chemical defined medium, and the metabolome was analyzed by a combination of 1H-NMR, HPLC-MS, and GC-MS. Additionally, the cell morphology was investigated by electron microscopy. The clpP mutant showed higher levels of most glycolytic metabolites, the intermediates of the citric acid cycle, amino acids, and peptidoglycan precursors when compared to the wild-type. A strong secretion of overflow metabolites could be detected in the exo-metabolome of the clpP mutant. Furthermore, a massive increase was observed for the teichoic acid metabolite CDP-glycerol in combination with a swelling of the cell wall. Our results show a recognizable correlation between the metabolome and the corresponding proteome data of B. subtilisclpP mutant. Moreover, our results suggest an influence of ClpP on Tag proteins that are responsible for teichoic acids biosynthesis.
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Affiliation(s)
- Daniel Schultz
- Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany;
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, 17487 Greifswald, Germany;
| | - Ulf Gerth
- Institute of Microbiology, University of Greifswald, 17487 Greifswald, Germany;
| | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany;
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Schelli K, Zhong F, Zhu J. Comparative metabolomics revealing Staphylococcus aureus metabolic response to different antibiotics. Microb Biotechnol 2017; 10:1764-1774. [PMID: 28815967 PMCID: PMC5658637 DOI: 10.1111/1751-7915.12839] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/27/2017] [Accepted: 07/02/2017] [Indexed: 12/14/2022] Open
Abstract
It is known that changes in bacterial metabolism can contribute to the modulation of bacterial susceptibility to antibiotics. Understanding how bacterial metabolism is impacted by antibiotics may improve our understanding of the antibiotic mechanism of actions from a metabolic perspective. Here, we utilized a mass spectrometry‐based targeted metabolic profiling technique to characterize the metabolome of a pair of isogenic methicillin‐susceptible and resistant Staphylococcus aureus (MSSA and MRSA) strains RN450 and 450M treated with the sublethal dose of three antibiotics from different classes (β‐lactams, aminoglycosides and quinolones). These treatments induced a set of metabolic alterations after 6 h of co‐incubation with antibiotics. Similar and divergent metabolic perturbations were observed from different antibiotics to the tested strains. Different metabolic response from MSSA and MRSA to the same antibiotics was also detected in the study and indicated the potentially different stress response mechanism in MSSA and MRSA metabolism. This work has shown that a complex set of metabolic changes can be induced by a variety of antibiotics, and the comparative metabolomics strategy can provide a good understanding of this process from a metabolic perspective.
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Affiliation(s)
- Katie Schelli
- Department of Chemistry and Biochemistry, Miami University, 651 E High St., Oxford, OH, 45056, USA
| | - Fanyi Zhong
- Department of Chemistry and Biochemistry, Miami University, 651 E High St., Oxford, OH, 45056, USA
| | - Jiangjiang Zhu
- Department of Chemistry and Biochemistry, Miami University, 651 E High St., Oxford, OH, 45056, USA
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Antibiotic Effects on Methicillin-Resistant Staphylococcus aureus Cytoplasmic Peptidoglycan Intermediate Levels and Evidence for Potential Metabolite Level Regulatory Loops. Antimicrob Agents Chemother 2017; 61:AAC.02253-16. [PMID: 28320719 DOI: 10.1128/aac.02253-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/10/2017] [Indexed: 11/20/2022] Open
Abstract
Cytoplasmic peptidoglycan (PG) precursor levels were determined in methicillin-resistant Staphylococcus aureus (MRSA) after exposure to several cell wall-targeting antibiotics. Three experiments were performed: (i) exposure to 4× MIC levels (acute); (ii) exposure to sub-MIC levels (subacute); (iii) a time course experiment of the effect of vancomycin. In acute exposure experiments, fosfomycin increased UDP-GlcNAc, as expected, and resulted in substantially lower levels of total UDP-linked metabolite accumulation relative to other pathway inhibitors, indicating reduced entry into this pathway. Upstream inhibitors (fosfomycin, d-cycloserine, or d-boroalanine) reduced UDP-MurNAc-pentapeptide levels by more than fourfold. Alanine branch inhibitors (d-cycloserine and d-boroalanine) reduced d-Ala-d-Ala levels only modestly (up to 4-fold) but increased UDP-MurNAc-tripeptide levels up to 3,000-fold. Downstream pathway inhibitors (vancomycin, bacitracin, moenomycin, and oxacillin) increased UDP-MurNAc-pentapeptide levels up to 350-fold and UDP-MurNAc-l-Ala levels up to 80-fold, suggesting reduced MurD activity by downstream inhibitor action. Sub-MIC exposures demonstrated effects even at 1/8× MIC which strongly paralleled acute exposure changes. Time course data demonstrated that UDP-linked intermediate levels respond rapidly to vancomycin exposure, with several intermediates increasing three- to sixfold within minutes. UDP-linked intermediate level changes were also multiphasic, with some increasing, some decreasing, and some increasing and then decreasing. The total (summed) UDP-linked intermediate pool increased by 1,475 μM/min during the first 10 min after vancomycin exposure, providing a revised estimate of flux in this pathway during logarithmic growth. These observations outline the complexity of PG precursor response to antibiotic exposure in MRSA and indicate likely sites of regulation (entry and MurD).
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Loi VV, Harms M, Müller M, Huyen NTT, Hamilton CJ, Hochgräfe F, Pané-Farré J, Antelmann H. Real-Time Imaging of the Bacillithiol Redox Potential in the Human Pathogen Staphylococcus aureus Using a Genetically Encoded Bacilliredoxin-Fused Redox Biosensor. Antioxid Redox Signal 2017; 26:835-848. [PMID: 27462976 PMCID: PMC5444506 DOI: 10.1089/ars.2016.6733] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AIMS Bacillithiol (BSH) is utilized as a major thiol-redox buffer in the human pathogen Staphylococcus aureus. Under oxidative stress, BSH forms mixed disulfides with proteins, termed as S-bacillithiolation, which can be reversed by bacilliredoxins (Brx). In eukaryotes, glutaredoxin-fused roGFP2 biosensors have been applied for dynamic live imaging of the glutathione redox potential. Here, we have constructed a genetically encoded bacilliredoxin-fused redox biosensor (Brx-roGFP2) to monitor dynamic changes in the BSH redox potential in S. aureus. RESULTS The Brx-roGFP2 biosensor showed a specific and rapid response to low levels of bacillithiol disulfide (BSSB) in vitro that required the active-site Cys of Brx. Dynamic live imaging in two methicillin-resistant S. aureus (MRSA) USA300 and COL strains revealed fast and dynamic responses of the Brx-roGFP2 biosensor under hypochlorite and hydrogen peroxide (H2O2) stress and constitutive oxidation of the probe in different BSH-deficient mutants. Furthermore, we found that the Brx-roGFP2 expression level and the dynamic range are higher in S. aureus COL compared with the USA300 strain. In phagocytosis assays with THP-1 macrophages, the biosensor was 87% oxidized in S. aureus COL. However, no changes in the BSH redox potential were measured after treatment with different antibiotics classes, indicating that antibiotics do not cause oxidative stress in S. aureus. Conclusion and Innovation: This Brx-roGFP2 biosensor catalyzes specific equilibration between the BSH and roGFP2 redox couples and can be applied for dynamic live imaging of redox changes in S. aureus and other BSH-producing Firmicutes. Antioxid. Redox Signal. 26, 835-848.
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Affiliation(s)
- Vu Van Loi
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
| | - Manuela Harms
- 2 Junior Research Group Pathoproteomics, Ernst-Moritz-Arndt-University of Greifswald , Greifswald, Germany
| | - Marret Müller
- 3 Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald , Greifswald, Germany
| | - Nguyen Thi Thu Huyen
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
| | - Chris J Hamilton
- 4 School of Pharmacy, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
| | - Falko Hochgräfe
- 2 Junior Research Group Pathoproteomics, Ernst-Moritz-Arndt-University of Greifswald , Greifswald, Germany
| | - Jan Pané-Farré
- 3 Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald , Greifswald, Germany
| | - Haike Antelmann
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
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Dhali D, Coutte F, Arias AA, Auger S, Bidnenko V, Chataigné G, Lalk M, Niehren J, de Sousa J, Versari C, Jacques P. Genetic engineering of the branched fatty acid metabolic pathway ofBacillus subtilisfor the overproduction of surfactin C14isoform. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600574] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/13/2017] [Accepted: 03/31/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Debarun Dhali
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale; EA 7394 - ICV - Institut Charles Viollette; Lille France
| | - François Coutte
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale; EA 7394 - ICV - Institut Charles Viollette; Lille France
| | - Anthony Argüelles Arias
- MiPI, TERRA Research Centre, Gembloux Agro-Bio Tech; University of Liege; Passage des Déportés; Gembloux Belgium
| | - Sandrine Auger
- Micalis Institute, INRA, AgroParisTech; University Paris-Saclay; Jouy-en-Josas France
| | - Vladimir Bidnenko
- Micalis Institute, INRA, AgroParisTech; University Paris-Saclay; Jouy-en-Josas France
| | - Gabrielle Chataigné
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale; EA 7394 - ICV - Institut Charles Viollette; Lille France
| | - Michael Lalk
- Ernst-Moritz-Arndt-University Greifswald; Institute of Biochemistry; Greifswald Germany
| | - Joachim Niehren
- University Lille; BioComputing Team, CRIStAL Lab (CNRS UMR9189); Villeneuve d'Ascq France
- Inria Lille; Villeneuve d'Ascq France
| | - Joana de Sousa
- Ernst-Moritz-Arndt-University Greifswald; Institute of Biochemistry; Greifswald Germany
| | - Cristian Versari
- University Lille; BioComputing Team, CRIStAL Lab (CNRS UMR9189); Villeneuve d'Ascq France
| | - Philippe Jacques
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale; EA 7394 - ICV - Institut Charles Viollette; Lille France
- MiPI, TERRA Research Centre, Gembloux Agro-Bio Tech; University of Liege; Passage des Déportés; Gembloux Belgium
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Banerjee D, Parmar D, Bhattacharya N, Ghanate AD, Panchagnula V, Raghunathan A. A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD +/NADH + imbalance. BMC SYSTEMS BIOLOGY 2017; 11:51. [PMID: 28446174 PMCID: PMC5405553 DOI: 10.1186/s12918-017-0427-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/21/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens using benign metabolites. RESULTS Controlled laboratory evolutions established chloramphenicol and streptomycin resistant pathogens of Chromobacterium. These resistant pathogens showed higher growth rates and required higher lethal doses of antibiotic. Growth and viability testing identified malate, maleate, succinate, pyruvate and oxoadipate as resensitising agents for antibiotic therapy. Resistant genes were catalogued through whole genome sequencing. Intracellular metabolomic profiling identified violacein as a potential biomarker for resistance. The temporal variance of metabolites captured the linearized dynamics around the steady state and correlated to growth rate. A constraints-based flux balance model of the core metabolism was used to predict the metabolic basis of antibiotic susceptibility and resistance. CONCLUSIONS The model predicts electron imbalance and skewed NAD/NADH ratios as a result of antibiotics - chloramphenicol and streptomycin. The resistant pathogen rewired its metabolic networks to compensate for disruption of redox homeostasis. We foresee the utility of such scalable workflows in identifying metabolites for clinical isolates as inevitable solutions to mitigate antibiotic resistance.
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Affiliation(s)
- Deepanwita Banerjee
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, India
| | | | | | - Avinash D. Ghanate
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, India
| | | | - Anu Raghunathan
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, India
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