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Hussein M, Allobawi R, Zhao J, Yu H, Neville SL, Wilksch J, Wong LJM, Baker M, McDevitt CA, Rao GG, Li J, Velkov T. Integrated Transcriptomic and Metabolomic Mapping Reveals the Mechanism of Action of Ceftazidime/Avibactam against Pan-Drug-Resistant Klebsiella pneumoniae. ACS Infect Dis 2023; 9:2409-2422. [PMID: 37878861 PMCID: PMC10714405 DOI: 10.1021/acsinfecdis.3c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023]
Abstract
Here, we employed an integrated metabolomics and transcriptomics approach to investigate the molecular mechanism(s) of action of ceftazidime/avibactam against a pan-drug-resistant K. pneumoniae clinical isolate from a patient with urinary tract infection. Ceftazidime/avibactam induced time-dependent perturbations in the metabolome and transcriptome of the bacterium, mainly at 6 h, with minimal effects at 1 and 3 h. Metabolomics analysis revealed a notable reduction in essential lipids involved in outer membrane glycerolipid biogenesis. This disruption effect extended to peptidoglycan and lipopolysaccharide biosynthetic pathways, including lipid A and O-antigen assembly. Importantly, ceftazidime/avibactam not only affected the final steps of peptidoglycan biosynthesis in the periplasm, a common mechanism of ceftazidime action, but also influenced the synthesis of lipid-linked intermediates and early stages of cytoplasmic peptidoglycan synthesis. Furthermore, ceftazidime/avibactam substantially inhibited central carbon metabolism (e.g., the pentose phosphate pathway and tricarboxylic acid cycle). Consistently, the dysregulation of genes governing these metabolic pathways aligned with the metabolomics findings. Certain metabolomics and transcriptomics signatures associated with ceftazidime resistance were also perturbed. Consistent with the primary target of antibiotic activity, biochemical assays also confirmed the direct impact of ceftazidime/avibactam on peptidoglycan production. This study explored the intricate interactions of ceftazidime and avibactam within bacterial cells, including their impact on cell envelope biogenesis and central carbon metabolism. Our findings revealed the complexities of how ceftazidime/avibactam operates, such as hindering peptidoglycan formation in different cellular compartments. In summary, this study confirms the existing hypotheses about the antibacterial and resistance mechanisms of ceftazidime/avibactam while uncovering novel insights, including its impact on lipopolysaccharide formation.
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Affiliation(s)
- Maytham Hussein
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Rafah Allobawi
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Jinxin Zhao
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Heidi Yu
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Stephanie L. Neville
- Department
of Microbiology and Immunology, The Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jonathan Wilksch
- Department
of Microbiology and Immunology, The Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Labell J. M. Wong
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Mark Baker
- Discipline
of Biological Sciences, Priority Research Centre in Reproductive Biology,
Faculty of Science and IT, University of
Newcastle, University
Drive, Callaghan, NSW 2308, Australia
| | - Christopher A. McDevitt
- Department
of Microbiology and Immunology, The Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Gauri G. Rao
- Division
of Pharmacotherapy and Experimental Therapeutics, Eshelman School
of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7355, United
States
| | - Jian Li
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Tony Velkov
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
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Gonzalez-Jimenez I, Perlin DS, Shor E. Reactive oxidant species induced by antifungal drugs: identity, origins, functions, and connection to stress-induced cell death. Front Cell Infect Microbiol 2023; 13:1276406. [PMID: 37900311 PMCID: PMC10602735 DOI: 10.3389/fcimb.2023.1276406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/13/2023] [Indexed: 10/31/2023] Open
Abstract
Reactive oxidant species (ROS) are unstable, highly reactive molecules that are produced by cells either as byproducts of metabolism or synthesized by specialized enzymes. ROS can be detrimental, e.g., by damaging cellular macromolecules, or beneficial, e.g., by participating in signaling. An increasing body of evidence shows that various fungal species, including both yeasts and molds, increase ROS production upon exposure to the antifungal drugs currently used in the clinic: azoles, polyenes, and echinocandins. However, the implications of these findings are still largely unclear due to gaps in knowledge regarding the chemical nature, molecular origins, and functional consequences of these ROS. Because the detection of ROS in fungal cells has largely relied on fluorescent probes that lack specificity, the chemical nature of the ROS is not known, and it may vary depending on the specific fungus-drug combination. In several instances, the origin of antifungal drug-induced ROS has been identified as the mitochondria, but further experiments are necessary to strengthen this conclusion and to investigate other potential cellular ROS sources, such as the ER, peroxisomes, and ROS-producing enzymes. With respect to the function of the ROS, several studies have shown that they contribute to the drugs' fungicidal activities and may be part of drug-induced programmed cell death (PCD). However, whether these "pro-death" ROS are a primary consequence of the antifungal mechanism of action or a secondary consequence of drug-induced PCD remains unclear. Finally, several recent studies have raised the possibility that ROS induction can serve an adaptive role, promoting antifungal drug tolerance and the evolution of drug resistance. Filling these gaps in knowledge will reveal a new aspect of fungal biology and may identify new ways to potentiate antifungal drug activity or prevent the evolution of antifungal drug resistance.
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Affiliation(s)
- Irene Gonzalez-Jimenez
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
- Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, United States
- Lombardi Comprehensive Cancer Center and Department of Microbiology and Immunology, Georgetown University, Washington, DC, United States
| | - Erika Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
- Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, United States
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3
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Yan BB, Dong XS, Wang JP, Li XY, An L, Wang XR, Zhang LG, Meng QL, Wang C. Glutamate-pantothenate pathway promotes antibiotic resistance of Edwardsiella tarda. Front Microbiol 2023; 14:1264602. [PMID: 37779691 PMCID: PMC10533917 DOI: 10.3389/fmicb.2023.1264602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
Although cellular metabolic states have been shown to modulate bacterial susceptibility to antibiotics, the interaction between glutamate (Glu) and chloramphenicol (CAP) resistance remains unclear because of the specificity of antibiotics and bacteria. We found that the level of Glu was upregulated in the CAP-resistant strain of Edwardsiella tarda according to a comparative metabolomics approach based on LC-MS/MS. Furthermore, we verified that exogenous metabolites related to Glu, the tricarboxylic acid (TCA) cycle, and glutathione (GSH) metabolism could promote CAP resistance in survival assays. If GSH metabolism or the TCA cycle is inhibited by L-buthionine sulfoximine or propanedioic acid, the promotion of CAP resistance by Glu in the corresponding pathway disappears. According to metabolomic analysis, exogenous Glu could change pantothenate metabolism, affecting GSH biosynthesis and the TCA cycle. These results showed that the glutamate-pantothenate pathway could promote CAP resistance by being involved in the synthesis of GSH, entering the TCA cycle by direct deamination, or indirectly affecting the metabolism of the two pathways by pantothenate. These results extend our knowledge of the effect of Glu on antibiotic resistance and suggest that the potential effect, which may aggravate antibiotic resistance, should be considered before Glu and GSH administration in the clinic.
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Affiliation(s)
- Bei-bei Yan
- Department of Neonatology, Children’s Hospital Affiliated to Shandong University, Jinan, China
- Department of Neonatology, Jinan Children’s Hospital, Jinan, China
| | - Xue-sa Dong
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Jun-peng Wang
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Xiao-ying Li
- Department of Neonatology, Children’s Hospital Affiliated to Shandong University, Jinan, China
- Department of Neonatology, Jinan Children’s Hospital, Jinan, China
| | - Li An
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Xi-rong Wang
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Long-gang Zhang
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Qing-lei Meng
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Chao Wang
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
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4
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Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S, Belenky P. Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis. Microbiol Spectr 2023; 11:e0237623. [PMID: 37439681 PMCID: PMC10434222 DOI: 10.1128/spectrum.02376-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/14/2023] Open
Abstract
Antibiotic-induced gut microbiome dysbiosis (AID) is known to be influenced by host dietary composition. However, how and when diet modulates gut dysbiosis remains poorly characterized. Thus, here, we utilize a multi-omics approach to characterize how a diet supplemented with oats, a rich source of microbiota-accessible carbohydrates, or dextrose impacts amoxicillin-induced changes to gut microbiome structure and transcriptional activity. We demonstrate that oat administration during amoxicillin challenge provides greater protection from AID than the always oats or recovery oats diet groups. In particular, the group in which oats were provided at the time of antibiotic exposure induced the greatest protection against AID while the other oat diets saw greater effects after amoxicillin challenge. The oat diets likewise reduced amoxicillin-driven elimination of Firmicutes compared to the dextrose diet. Functionally, gut communities fed dextrose were carbohydrate starved and favored respiratory metabolism and consequent metabolic stress management while oat-fed communities shifted their transcriptomic profile and emphasized antibiotic stress management. The metabolic trends were exemplified when assessing transcriptional activity of the following two common gut commensal bacteria: Akkermansia muciniphila and Bacteroides thetaiotaomicron. These findings demonstrate that while host diet is important in shaping how antibiotics effect the gut microbiome composition and function, diet timing may play an even greater role in dietary intervention-based therapeutics. IMPORTANCE We utilize a multi-omics approach to demonstrate that diets supplemented with oats, a rich source of microbiota-accessible carbohydrates, are able to confer protection against antibiotic-induced dysbiosis (AID). Our findings affirm that not only is host diet important in shaping antibiotics effects on gut microbiome composition and function but also that the timing of these diets may play an even greater role in managing AID. This work provides a nuanced perspective on dietary intervention against AID and may be informative on preventing AID during routine antibiotic treatment.
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Affiliation(s)
- Stephen K. Costa
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Katherine Antosca
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Chapman N. Beekman
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Rachel L. Peterson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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5
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Dixneuf S, Chareire-Kleiberg AC, Mahé P, El Azami M, Kolytcheff C, Bellais S, Guyard C, Védrine C, Mallard F, Josso Q, Rol F. Single-cell scattering and auto-fluorescence-based fast antibiotic susceptibility testing for gram-negative and gram-positive bacteria. Front Microbiol 2023; 14:1232250. [PMID: 37601345 PMCID: PMC10436599 DOI: 10.3389/fmicb.2023.1232250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
In this study, we assess the scattering of light and auto-fluorescence from single bacterial cells to address the challenge of fast (<2 h), label-free phenotypic antimicrobial susceptibility testing (AST). Label-free flow cytometry is used for monitoring both the respiration-related auto-fluorescence in two different fluorescence channels corresponding to FAD and NADH, and the morphological and structural information contained in the light scattered by individual bacteria during incubation with or without antibiotic. Large multi-parameter data are analyzed using dimensionality reduction methods, based either on a combination of 2D binning and Principal Component Analysis, or with a one-class Support Vector Machine approach, with the objective to predict the Susceptible or Resistant phenotype of the strain. For the first time, both Escherichia coli (Gram-negative) and Staphylococcus epidermidis (Gram-positive) isolates were tested with a label-free approach, and, in the presence of two groups of bactericidal antibiotic molecules, aminoglycosides and beta-lactams. Our results support the feasibility of label-free AST in less than 2 h and suggest that single cell auto-fluorescence adds value to the Susceptible/Resistant phenotyping over single-cell scattering alone, in particular for the mecA+ Staphylococcus (i.e., resistant) strains treated with oxacillin.
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Affiliation(s)
| | | | | | | | | | | | - Cyril Guyard
- BIOASTER Technology Research Institute, Lyon, France
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Fan L, Pan Z, Liao X, Zhong Y, Guo J, Pang R, Chen X, Ye G, Su Y. Uracil restores susceptibility of methicillin-resistant Staphylococcus aureus to aminoglycosides through metabolic reprogramming. Front Pharmacol 2023; 14:1133685. [PMID: 36762116 PMCID: PMC9902350 DOI: 10.3389/fphar.2023.1133685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Background: Methicillin-resistant Staphylococcus aureus (MRSA) has now become a major nosocomial pathogen bacteria and resistant to many antibiotics. Therefore, Development of novel approaches to combat the disease is especially important. The present study aimed to provide a novel approach involving the use of nucleotide-mediated metabolic reprogramming to tackle intractable methicillin-resistant S. aureus (MRSA) infections. Objective: This study aims to explore the bacterial effects and mechanism of uracil and gentamicin in S. aureus. Methods: Antibiotic bactericidal assays was used to determine the synergistic bactericidal effect of uracil and gentamicin. How did uracil regulate bacterial metabolism including the tricarboxylic acid (TCA) cycle by GC-MS-based metabolomics. Next, genes and activity of key enzymes in the TCA cycle, PMF, and intracellular aminoglycosides were measured. Finally, bacterial respiration, reactive oxygen species (ROS), and ATP levels were also assayed in this study. Results: In the present study, we found that uracil could synergize with aminoglycosides to kill MRSA (USA300) by 400-fold. Reprogramming metabolomics displayed uracil reprogrammed bacterial metabolism, especially enhanced the TCA cycle to elevate NADH production and proton motive force, thereby promoting the uptake of antibiotics. Furthermore, uracil increased cellular respiration and ATP production, resulting the generation of ROS. Thus, the combined activity of uracil and antibiotics induced bacterial death. Inhibition of the TCA cycle or ROS production could attenuate bactericidal efficiency. Moreover, uracil exhibited bactericidal activity in cooperation with aminoglycosides against other pathogenic bacteria. In a mouse mode of MRSA infection, the combination of gentamicin and uracil increased the survival rate of infected mice. Conclusion: Our results suggest that uracil enhances the activity of bactericidal antibiotics to kill Gram-positive bacteria by modulating bacterial metabolism.
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Affiliation(s)
- Lvyuan Fan
- MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Zhiyu Pan
- MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xu Liao
- Center for Excellence in Regional Atmospheric Environment, and Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yilin Zhong
- MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Juan Guo
- MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xinhai Chen
- Institute of Infectious Diseases Shenzhen Bay Laboratory, Shenzhen, China
| | - Guozhu Ye
- Center for Excellence in Regional Atmospheric Environment, and Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China,*Correspondence: Yubin Su, ; Guozhu Ye,
| | - Yubin Su
- MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China,*Correspondence: Yubin Su, ; Guozhu Ye,
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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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Qian C, Jin L, Zhu L, Zhou Y, Chen J, Yang D, Xu X, Ding P, Li R, Zhao Z. Metabolomics-Driven Exploration of the Antibacterial Activity and Mechanism of 2-Methoxycinnamaldehyde. Front Microbiol 2022; 13:864246. [PMID: 35875567 PMCID: PMC9301309 DOI: 10.3389/fmicb.2022.864246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/07/2022] [Indexed: 11/25/2022] Open
Abstract
Methicillin-resistant Staphylococcus epidermidis (MRSE) is one of the most commonly found pathogens that may cause uncontrollable infections in immunocompromised and hospitalized patients. Compounds isolated from cinnamon such as cinnamaldehyde and cinnamic acid showed promising anti-oxidant, anti-tumor, and immunoregulatory effects; more importantly, these compounds also possess promising broad-spectrum antibacterial activity. In this study, the potential antibacterial activity of 2-methoxycinnamaldehyde (MCA), another compound in cinnamon, against MRSE was investigated. Combining the broth microdilution test, live/dead assay, and biofilm formation assay, we found MCA was able to inhibit the proliferation, as well as the biofilm formation of MRSE, indicating MCA could not only affect the growth of MRSE but also inhibit the pathogenic potential of this bacterium. Additionally, the results of scanning electron microscopy (SEM) and transmission electron microscopy (TEM) demonstrated that MCA caused morphological changes and the leakage of DNA, RNA, and cellular contents of MRSE. Due to the close relationship between cell wall synthesis, ROS formation, and cell metabolism, the ROS level and metabolic profile of MRSE were explored. Our study showed MCA significantly increased the ROS production in MRSE, and the following metabolomics analysis showed that the increased ROS production may partially be due to the increased metabolic flux through the TCA cycle. In addition, we noticed the metabolic flux through the pentose phosphate pathway (PPP) was upregulated accompanied by elevated ROS production. Therefore, the alterations in cell metabolism and increased ROS production could lead to the damage of the cell wall, which in turn decreased the proliferation of MRSE. In conclusion, MCA seemed to be a promising alternative antimicrobial agent to control MRSE infections.
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Affiliation(s)
- Chunguo Qian
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| | - Lu Jin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| | - Longping Zhu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| | - Yang Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| | - Jing Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Depo Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| | - Xinjun Xu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| | - Ping Ding
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Runnan Li
- Deqing County Dexin Agricultural Development Co., Ltd., Zhaoqing, China
| | - Zhimin Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
- *Correspondence: Zhimin Zhao,
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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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10
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Yuan Z, Wang J, Che R, God’spower BO, Zhou Y, Dong C, Li L, Chen M, Eliphaz N, Liu X, Li Y. Relationship between L-lactate dehydrogenase and multidrug resistance in Staphylococcus xylosus. Arch Microbiol 2021; 204:91. [DOI: 10.1007/s00203-021-02625-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 10/19/2022]
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11
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Matern WM, Parker H, Danchik C, Hoover L, Bader JS, Karakousis PC. Genetic Determinants of Intrinsic Antibiotic Tolerance in Mycobacterium avium. Microbiol Spectr 2021; 9:e0024621. [PMID: 34523947 PMCID: PMC8557931 DOI: 10.1128/spectrum.00246-21] [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: 05/11/2021] [Accepted: 08/06/2021] [Indexed: 11/20/2022] Open
Abstract
The Mycobacterium avium complex (MAC) is one of the most prevalent causes of nontuberculous mycobacteria pulmonary infection in the United States, and yet it remains understudied. Current MAC treatment requires more than a year of intermittent to daily combination antibiotic therapy, depending on disease severity. In order to shorten and simplify curative regimens, it is important to identify the innate bacterial factors contributing to reduced antibiotic susceptibility, namely, antibiotic tolerance genes. In this study, we performed a genome-wide transposon screen to elucidate M. avium genes that play a role in the bacterium's tolerance to first- and second-line antibiotics. We identified a total of 193 unique M. avium mutants with significantly altered susceptibility to at least one of the four clinically used antibiotics we tested, including two mutants (in DFS55_00905 and DFS55_12730) with panhypersusceptibility. The products of the antibiotic tolerance genes we have identified may represent novel targets for future drug development studies aimed at shortening the duration of therapy for MAC infections. IMPORTANCE The prolonged treatment required to eradicate Mycobacterium avium complex (MAC) infection is likely due to the presence of subpopulations of antibiotic-tolerant bacteria with reduced susceptibility to currently available drugs. However, little is known about the genes and pathways responsible for antibiotic tolerance in MAC. In this study, we performed a forward genetic screen to identify M. avium antibiotic tolerance genes, whose products may represent attractive targets for the development of novel adjunctive drugs capable of shortening the curative treatment for MAC infections.
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Affiliation(s)
- William M. Matern
- High-Throughput Biology Center, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Systems Approaches to Infectious Diseases (C-SAID), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Harley Parker
- Center for Systems Approaches to Infectious Diseases (C-SAID), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Carina Danchik
- Center for Systems Approaches to Infectious Diseases (C-SAID), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Leah Hoover
- Center for Systems Approaches to Infectious Diseases (C-SAID), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joel S. Bader
- High-Throughput Biology Center, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Systems Approaches to Infectious Diseases (C-SAID), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Petros C. Karakousis
- Center for Systems Approaches to Infectious Diseases (C-SAID), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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12
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Delftia acidovorans secretes substances that inhibit the growth of Staphylococcus epidermidis through TCA cycle-triggered ROS production. PLoS One 2021; 16:e0253618. [PMID: 34214099 PMCID: PMC8253425 DOI: 10.1371/journal.pone.0253618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/08/2021] [Indexed: 12/22/2022] Open
Abstract
The proportion of Staphylococcus aureus in the skin microbiome is associated with the severity of inflammation in the skin disease atopic dermatitis. Staphylococcus epidermidis, a commensal skin bacterium, inhibits the growth of S. aureus in the skin. Therefore, the balance between S. epidermidis and S. aureus in the skin microbiome is important for maintaining healthy skin. In the present study, we demonstrated that the heat-treated culture supernatant of Delftia acidovorans, a member of the skin microbiome, inhibits the growth of S. epidermidis, but not that of S. aureus. Comprehensive gene expression analysis by RNA sequencing revealed that culture supernatant of D. acidovorans increased the expression of genes related to glycolysis and the tricarboxylic acid cycle (TCA) cycle in S. epidermidis. Malonate, an inhibitor of succinate dehydrogenase in the TCA cycle, suppressed the inhibitory effect of the heat-treated culture supernatant of D. acidovorans on the growth of S. epidermidis. Reactive oxygen species production in S. epidermidis was induced by the heat-treated culture supernatant of D. acidovorans and suppressed by malonate. Further, the inhibitory effect of the heat-treated culture supernatant of D. acidovorans on the growth of S. epidermidis was suppressed by N-acetyl-L-cysteine, a free radical scavenger. These findings suggest that heat-resistant substances secreted by D. acidovorans inhibit the growth of S. epidermidis by inducing the production of reactive oxygen species via the TCA cycle.
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13
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Accumulation of Succinyl Coenzyme A Perturbs the Methicillin-Resistant Staphylococcus aureus (MRSA) Succinylome and Is Associated with Increased Susceptibility to Beta-Lactam Antibiotics. mBio 2021; 12:e0053021. [PMID: 34182779 PMCID: PMC8437408 DOI: 10.1128/mbio.00530-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Penicillin binding protein 2a (PBP2a)-dependent resistance to β-lactam antibiotics in methicillin-resistant Staphylococcus aureus (MRSA) is regulated by the activity of the tricarboxylic acid (TCA) cycle via a poorly understood mechanism. We report that mutations in sucC and sucD, but not other TCA cycle enzymes, negatively impact β-lactam resistance without changing PBP2a expression. Increased intracellular levels of succinyl coenzyme A (succinyl-CoA) in the sucC mutant significantly perturbed lysine succinylation in the MRSA proteome. Suppressor mutations in sucA or sucB, responsible for succinyl-CoA biosynthesis, reversed sucC mutant phenotypes. The major autolysin (Atl) was the most succinylated protein in the proteome, and increased Atl succinylation in the sucC mutant was associated with loss of autolytic activity. Although PBP2a and PBP2 were also among the most succinylated proteins in the MRSA proteome, peptidoglycan architecture and cross-linking were unchanged in the sucC mutant. These data reveal that perturbation of the MRSA succinylome impacts two interconnected cell wall phenotypes, leading to repression of autolytic activity and increased susceptibility to β-lactam antibiotics.
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14
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Bischofberger AM, Pfrunder Cardozo KR, Baumgartner M, Hall AR. Evolution of honey resistance in experimental populations of bacteria depends on the type of honey and has no major side effects for antibiotic susceptibility. Evol Appl 2021; 14:1314-1327. [PMID: 34025770 PMCID: PMC8127710 DOI: 10.1111/eva.13200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/24/2020] [Accepted: 01/25/2021] [Indexed: 01/01/2023] Open
Abstract
With rising antibiotic resistance, alternative treatments for communicable diseases are increasingly relevant. One possible alternative for some types of infections is honey, used in wound care since before 2000 BCE and more recently in licensed, medical-grade products. However, it is unclear whether medical application of honey results in the evolution of bacterial honey resistance and whether this has collateral effects on other bacterial traits such as antibiotic resistance. Here, we used single-step screening assays and serial transfer at increasing concentrations to isolate honey-resistant mutants of Escherichia coli. We only detected bacteria with consistently increased resistance to the honey they evolved in for two of the four tested honey products, and the observed increases were small (maximum twofold increase in IC90). Genomic sequencing and experiments with single-gene knockouts showed a key mechanism by which bacteria increased their honey resistance was by mutating genes involved in detoxifying methylglyoxal, which contributes to the antibacterial activity of Leptospermum honeys. Crucially, we found no evidence that honey adaptation conferred cross-resistance or collateral sensitivity against nine antibiotics from six different classes. These results reveal constraints on bacterial adaptation to different types of honey, improving our ability to predict downstream consequences of wider honey application in medicine.
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Affiliation(s)
| | | | | | - Alex R. Hall
- Institute of Integrative BiologyETH ZurichZurichSwitzerland
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15
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Ye J, Su Y, Peng X, Li H. Reactive Oxygen Species-Related Ceftazidime Resistance Is Caused by the Pyruvate Cycle Perturbation and Reverted by Fe 3 + in Edwardsiella tarda. Front Microbiol 2021; 12:654783. [PMID: 33995314 PMCID: PMC8113649 DOI: 10.3389/fmicb.2021.654783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/23/2021] [Indexed: 12/24/2022] Open
Abstract
Reactive oxygen species (ROS) are related to antibiotic resistance and have been reported in bacteria. However, whether ROS contribute to ceftazidime resistance and plays a role in ceftazidime-mediated killing is unknown. The present study showed lower ROS production in ceftazidime-resistant Edwardsiella tarda (LTB4-RCAZ) than that in LTB4-sensitive E. tarda (LTB4-S), two isogenic E. tarda LTB4 strains, which was related to bacterial viability in the presence of ceftazidime. Consistently, ROS promoter Fe3+ and inhibitor thiourea elevated and reduced the ceftazidime-mediated killing, respectively. Further investigation indicated that the reduction of ROS is related to inactivation of the pyruvate cycle, which provides sources for ROS biosynthesis, but not superoxide dismutase (SOD) and catalase (CAT), which degrade ROS. Interestingly, Fe3+ promoted the P cycle, increased ROS biosynthesis, and thereby promoted ceftazidime-mediated killing. The Fe3+-induced potentiation is generalizable to cephalosporins and clinically isolated multidrug-resistant pathogens. These results show that ROS play a role in bacterial resistance and sensitivity to ceftazidime. More importantly, the present study reveals a previously unknown mechanism that Fe3+ elevates ROS production via promoting the P cycle.
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Affiliation(s)
- Jingzhou Ye
- Center for Proteomics and Metabolomics, State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yubin Su
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xuanxian Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hui Li
- Center for Proteomics and Metabolomics, State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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16
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Targeting bioenergetics is key to counteracting the drug-tolerant state of biofilm-grown bacteria. PLoS Pathog 2020; 16:e1009126. [PMID: 33351859 PMCID: PMC7787680 DOI: 10.1371/journal.ppat.1009126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 01/06/2021] [Accepted: 11/05/2020] [Indexed: 12/30/2022] Open
Abstract
Embedded in an extracellular matrix, biofilm-residing bacteria are protected from diverse physicochemical insults. In accordance, in the human host the general recalcitrance of biofilm-grown bacteria hinders successful eradication of chronic, biofilm-associated infections. In this study, we demonstrate that upon addition of promethazine, an FDA approved drug, antibiotic tolerance of in vitro biofilm-grown bacteria can be abolished. We show that following the addition of promethazine, diverse antibiotics are capable of efficiently killing biofilm-residing cells at minimal inhibitory concentrations. Synergistic effects could also be observed in a murine in vivo model system. PMZ was shown to increase membrane potential and interfere with bacterial respiration. Of note, antibiotic killing activity was elevated when PMZ was added to cells grown under environmental conditions that induce low intracellular proton levels. Our results imply that biofilm-grown bacteria avoid antibiotic killing and become tolerant by counteracting intracellular alkalization through the adaptation of metabolic and transport functions. Abrogation of antibiotic tolerance by interfering with the cell’s bioenergetics promises to pave the way for successful eradication of biofilm-associated infections. Repurposing promethazine as a biofilm-sensitizing drug has the potential to accelerate the introduction of new treatments for recalcitrant, biofilm-associated infections into the clinic. At sub-minimal inhibitory concentrations, phenothiazines have been shown to inhibit virulence as well as the formation of biofilms in a wide range of different bacterial pathogens. In this study, we analyzed the anti-bacterial effect of the FDA-approved drug, promethazine, on biofilm-grown Pseudomonas aeruginosa. We demonstrate that PMZ interferes with bacterial bioenergetics and sensitizes biofilm-grown P. aeruginosa cells to bactericidal activity of several different classes of antibiotics by several orders of magnitude. This effect was most pronounced when cells were grown under environmental conditions that induce low intracellular proton levels. Thus, it seems that a reduced proton efflux in cells that exhibit decreased respiratory activity due to their biofilm mode of growth might explain their general antimicrobial tolerance. The use of PMZ as an antibiotic sensitizer holds promise that targeting tolerance mechanisms of biofilm-grown bacteria could become a practicable way to change the way physicians treat biofilm-associated infections.
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17
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Cabral DJ, Wurster JI, Korry BJ, Penumutchu S, Belenky P. Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin. mSystems 2020; 5:e00317-20. [PMID: 32723789 PMCID: PMC7394352 DOI: 10.1128/msystems.00317-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/08/2020] [Indexed: 02/07/2023] Open
Abstract
Dietary composition and antibiotic use have major impacts on the structure and function of the gut microbiome, often resulting in dysbiosis. Despite this, little research has been done to explore the role of host diet as a determinant of antibiotic-induced microbiome disruption. Here, we utilize a multi-omic approach to characterize the impact of Western-style diet consumption on ciprofloxacin-induced changes to gut microbiome structure and transcriptional activity. We found that Western diet consumption dramatically increased Bacteroides abundances and shifted the community toward the metabolism of simple sugars and mucus glycoproteins. Mice consuming a Western-style diet experienced a greater expansion of Firmicutes following ciprofloxacin treatment than those eating a control diet. Transcriptionally, we found that ciprofloxacin reduced the abundance of tricarboxylic acid (TCA) cycle transcripts on both diets, suggesting that carbon metabolism plays a key role in the response of the gut microbiome to this antibiotic. Despite this, we observed extensive diet-dependent differences in the impact of ciprofloxacin on microbiota function. In particular, at the whole-community level we detected an increase in starch degradation, glycolysis, and pyruvate fermentation following antibiotic treatment in mice on the Western diet, which we did not observe in mice on the control diet. Similarly, we observed diet-specific changes in the transcriptional activity of two important commensal bacteria, Akkermansia muciniphila and Bacteroides thetaiotaomicron, involving diverse cellular processes such as nutrient acquisition, stress responses, and capsular polysaccharide (CPS) biosynthesis. These findings demonstrate that host diet plays a role in determining the impacts of ciprofloxacin on microbiome composition and microbiome function.IMPORTANCE Due to the growing incidence of disorders related to antibiotic-induced dysbiosis, it is essential to determine how our "Western"-style diet impacts the response of the microbiome to antibiotics. While diet and antibiotics have profound impacts on gut microbiome composition, little work has been done to examine their combined effects. Previous work has shown that nutrient availability, influenced by diet, plays an important role in determining the extent of antibiotic-induced disruption to the gut microbiome. Thus, we hypothesize that the Western diet will shift microbiota metabolism toward simple sugar and mucus degradation and away from polysaccharide utilization. Because of bacterial metabolism's critical role in antibiotic susceptibility, this change in baseline metabolism will impact how the structure and function of the microbiome are impacted by ciprofloxacin exposure. Understanding how diet modulates antibiotic-induced microbiome disruption will allow for the development of dietary interventions that can alleviate many of the microbiome-dependent complications of antibiotic treatment.
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Affiliation(s)
- Damien J Cabral
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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18
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Huang C, Liu LZ, Kong HK, Law COK, Hoa PQ, Ho PL, Lau TCK. A novel incompatibility group X3 plasmid carrying bla NDM-1 encodes a small RNA that regulates host fucose metabolism and biofilm formation. RNA Biol 2020; 17:1767-1776. [PMID: 32594845 DOI: 10.1080/15476286.2020.1780040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The emergence of New Delhi metallo-beta-lactamase (NDM-1) has become a major health threat to clinical managements of gram-negative bacteria infections. A novel incompatibility group X3 plasmid (IncX3) pNDM-HN380 carrying bla NDM-1 has recently been found to epidemiologically link with multiple geographical areas in China. In this paper, we studied the metabolic responses of host bacteria E. coli J53 upon introduction of pNDM-HN380. A reduction of bacterial motility was observed in J53/pNDM-HN380. We profiled the RNA repertoires of the transconjugants and found a downregulation of genes involved in flagella and chemotaxis metabolic pathways at logarithmic (log) phase. We also identified a novel intragenic region (IGR) small RNA plas2. The plasmid-transcribed sRNA IGR plas2 was further characterized as a regulator of fucRwhich controls the fucose metabolism. By knockdown of IGR plas2 using an antisense decoy, we managed to inhibit the formation of bacterial biofilm of the host. Our study demonstrated a potential way of utilizing plasmid-transcribed sRNA against infectious bacteria.
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Affiliation(s)
- Chuan Huang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong , Hong Kong, Hong Kong Special Administrative Region
| | - Liang-Zhe Liu
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong , Hong Kong, Hong Kong Special Administrative Region
| | - Hoi-Kuan Kong
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong , Hong Kong, Hong Kong Special Administrative Region
| | - Carmen O K Law
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong , Hong Kong, Hong Kong Special Administrative Region
| | - Pham Quynh Hoa
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong , Hong Kong, Hong Kong Special Administrative Region
| | - Pak-Leung Ho
- Department of Microbiology, The University of Hong Kong , Hong Kong, Hong Kong Special Administrative Region
| | - Terrence C K Lau
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong , Hong Kong, Hong Kong Special Administrative Region
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19
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Cabral DJ, Penumutchu S, Reinhart EM, Zhang C, Korry BJ, Wurster JI, Nilson R, Guang A, Sano WH, Rowan-Nash AD, Li H, Belenky P. Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome. Cell Metab 2019; 30:800-823.e7. [PMID: 31523007 PMCID: PMC6948150 DOI: 10.1016/j.cmet.2019.08.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/24/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Although antibiotics disturb the structure of the gut microbiota, factors that modulate these perturbations are poorly understood. Bacterial metabolism is an important regulator of susceptibility in vitro and likely plays a large role within the host. We applied a metagenomic and metatranscriptomic approach to link antibiotic-induced taxonomic and transcriptional responses within the murine microbiome. We found that antibiotics significantly alter the expression of key metabolic pathways at the whole-community and single-species levels. Notably, Bacteroides thetaiotaomicron, which blooms in response to amoxicillin, upregulated polysaccharide utilization. In vitro, we found that the sensitivity of this bacterium to amoxicillin was elevated by glucose and reduced by polysaccharides. Accordingly, we observed that dietary composition affected the abundance and expansion of B. thetaiotaomicron, as well as the extent of microbiome disruption with amoxicillin. Our work indicates that the metabolic environment of the microbiome plays a role in the response of this community to antibiotics.
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Affiliation(s)
- Damien J Cabral
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Elizabeth M Reinhart
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Rachael Nilson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - August Guang
- Center for Computation & Visualization, Brown University, Brown University, Providence, RI 02906, USA; Center for Computational Biology of Human Disease, Brown University, Providence, RI 02906, USA
| | - William H Sano
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA.
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20
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Liu X, Wang J, Chen M, Che R, Ding W, Yu F, Zhou Y, Cui W, Xiaoxu X, God'spower BO, Li Y. Comparative proteomic analysis reveals drug resistance of Staphylococcus xylosus ATCC700404 under tylosin stress. BMC Vet Res 2019; 15:224. [PMID: 31266490 PMCID: PMC6604186 DOI: 10.1186/s12917-019-1959-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/13/2019] [Indexed: 12/13/2022] Open
Abstract
Background As a kind of opportunist pathogen, Staphylococcus xylosus (S. xylosus) can cause mastitis. Antibiotics are widely used for treating infected animals and tylosin is a member of such group. Thus, the continuous use of antibiotics in dairy livestock enterprise will go a long way in increasing tylosin resistance. However, the mechanism of tylosin-resistant S. xylosus is not clear. Here, isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics methods was used to find resistance-related proteins. Results We compared the differential expression of S. xylosus in response to tylosin stress by iTRAQ. A total of 155 proteins (59 up-regulated, 96 down-regulated) with the fold-change of >1.2 or <0.8 (p value ≤0.05) were observed between the S. xylosus treated with 1/2 MIC (0.25 μg/mL) tylosin and the untreated S. xylosus. Bioinformatic analysis revealed that these proteins play important roles in stress-response and transcription. Then, in order to verify the relationship between the above changed proteins and mechanism of tylosin-resistant S. xylosus, we induced the tylosin-resistant S. xylosus, and performed quantitative PCR analysis to verify the changes in the transcription proteins and the stress-response proteins in tylosin-resistant S. xylosus at the mRNA level. The data displayed that ribosomal protein L23 (rplw), thioredoxin(trxA) and Aldehyde dehydrogenase A(aldA-1) are up-regulated in the tylosin-resistant S. xylosus, compared with the tylosin-sensitive strains. Conclusion Our findings demonstrate the important of stress-response and transcription in the tylosin resistance of S. xylosus and provide an insight into the prevention of this resistance, which would aid in finding new medicines . Electronic supplementary material The online version of this article (10.1186/s12917-019-1959-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Liu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Jinpeng Wang
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Mo Chen
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Ruixiang Che
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Wenya Ding
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Fei Yu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Yonghui Zhou
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Wenqiang Cui
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Xing Xiaoxu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Bello-Onaghise God'spower
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Yanhua Li
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China.
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21
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Influence of Reactive Oxygen Species on De Novo Acquisition of Resistance to Bactericidal Antibiotics. Antimicrob Agents Chemother 2018; 62:AAC.02354-17. [PMID: 29581120 DOI: 10.1128/aac.02354-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/22/2018] [Indexed: 12/16/2022] Open
Abstract
The radical-based theory proposes that three major classes of bactericidal antibiotics, i.e., β-lactams, quinolones, and aminoglycosides, have in common the downstream formation of lethal levels of reactive oxygen species (ROS) as part of the killing mechanism. If bactericidal antibiotics exhibit a common mechanism, then it is to be expected that the acquisition of resistance against these drugs would have some shared traits as well. Indeed, cells made resistant to one bactericidal antibiotic more rapidly became resistant to another. This effect was absent after induced resistance to a bacteriostatic drug. De novo acquisition of resistance to one bactericidal antibiotic provided partial protection to killing by bactericidal antibiotics from a different class. This protective effect was observed in short-term experiments. No protective effect was detected during 24-h exposures, suggesting that cross-resistance did not occur. In the wild-type strain, exposure to bactericidal antibiotics increased intracellular ROS levels. This increase in ROS levels was not observed when strains resistant to these drugs were exposed to the same concentrations. These results indicate that de novo acquisition of resistance to the bactericidal drugs tested involves a common cellular response that provides protection against ROS accumulation upon exposure to this type of antibiotics. A central mechanism or at least a few common elements within the separate mechanisms possibly play a role during the acquisition of antibiotic resistance.
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22
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Antibiotic Persistence as a Metabolic Adaptation: Stress, Metabolism, the Host, and New Directions. Pharmaceuticals (Basel) 2018; 11:ph11010014. [PMID: 29389876 PMCID: PMC5874710 DOI: 10.3390/ph11010014] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/25/2018] [Accepted: 01/27/2018] [Indexed: 12/16/2022] Open
Abstract
Persistence is a phenomenon during which a small fraction of a total bacterial population survives treatment with high concentrations of antibiotics for an extended period of time. In conjunction with biofilms, antibiotic persisters represent a major cause of recalcitrant and recurring infections, resulting in significant morbidity and mortality. In this review, we discuss the clinical significance of persister cells and the central role of bacterial metabolism in their formation, specifically with respect to carbon catabolite repression, sugar metabolism, and growth regulation. Additionally, we will examine persister formation as an evolutionary strategy used to tolerate extended periods of stress and discuss some of the response mechanisms implicated in their formation. To date, the vast majority of the mechanistic research examining persistence has been conducted in artificial in vitro environments that are unlikely to be representative of host conditions. Throughout this review, we contextualize the existing body of literature by discussing how in vivo conditions may create ecological niches that facilitate the development of persistence. Lastly, we identify how the development of next-generation sequencing and other “big data” tools may enable researchers to examine persistence mechanisms within the host to expand our understanding of their clinical importance.
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Slachmuylders L, Van Acker H, Brackman G, Sass A, Van Nieuwerburgh F, Coenye T. Elucidation of the mechanism behind the potentiating activity of baicalin against Burkholderia cenocepacia biofilms. PLoS One 2018; 13:e0190533. [PMID: 29293658 PMCID: PMC5749847 DOI: 10.1371/journal.pone.0190533] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/16/2017] [Indexed: 11/19/2022] Open
Abstract
Reduced antimicrobial susceptibility due to resistance and tolerance has become a serious threat to human health. An approach to overcome this reduced susceptibility is the use of antibiotic adjuvants, also known as potentiators. These are compounds that have little or no antibacterial effect on their own but increase the susceptibility of bacterial cells towards antimicrobial agents. Baicalin hydrate, previously described as a quorum sensing inhibitor, is such a potentiator that increases the susceptibility of Burkholderia cenocepacia J2315 biofilms towards tobramycin. The goal of the present study is to elucidate the molecular mechanisms behind the potentiating activity of baicalin hydrate and related flavonoids. We first determined the effect of multiple flavonoids on susceptibility of B. cenocepacia J2315 towards tobramycin. Increased antibiotic susceptibility was most pronounced in combination with apigenin 7-O-glucoside and baicalin hydrate. For baicalin hydrate, also other B. cepacia complex strains and other antibiotics were tested. The potentiating effect was only observed for aminoglycosides and was both strain- and aminoglycoside-dependent. Subsequently, gene expression was compared between baicalin hydrate treated and untreated cells, in the presence and absence of tobramycin. This revealed that baicalin hydrate affected cellular respiration, resulting in increased reactive oxygen species production in the presence of tobramycin. We subsequently showed that baicalin hydrate has an impact on oxidative stress via several pathways including oxidative phosphorylation, glucarate metabolism and by modulating biosynthesis of putrescine. Furthermore, our data strongly suggest that the influence of baicalin hydrate on oxidative stress is unrelated to quorum sensing. Our data indicate that the potentiating effect of baicalin hydrate is due to modulating the oxidative stress response, which in turn leads to increased tobramycin-mediated killing.
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Affiliation(s)
- Lisa Slachmuylders
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Heleen Van Acker
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Gilles Brackman
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | | | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
- * E-mail:
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Chan H, Ho J, Liu X, Zhang L, Wong SH, Chan MT, Wu WK. Potential and use of bacterial small RNAs to combat drug resistance: a systematic review. Infect Drug Resist 2017; 10:521-532. [PMID: 29290689 PMCID: PMC5736357 DOI: 10.2147/idr.s148444] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Over the decades, new antibacterial agents have been developed in an attempt to combat drug resistance, but they remain unsuccessful. Recently, a novel class of bacterial gene expression regulators, bacterial small RNAs (sRNAs), has received increasing attention toward their involvement in antibiotic resistance. This systematic review aimed to discuss the potential of these small molecules as antibacterial drug targets. Methods Two investigators performed a comprehensive search of MEDLINE, EmBase, and ISI Web of Knowledge from inception to October 2016, without restriction on language. We included all in vitro and in vivo studies investigating the role of bacterial sRNA in antibiotic resistance. Risk of bias of the included studies was assessed by a modified guideline of Systematic Review Center for Laboratory Animal Experimentation (SYRCLE). Results Initial search yielded 432 articles. After exclusion of non-original articles, 20 were included in this review. Of these, all studies examined bacterial-type strains only. There were neither relevant in vivo nor clinical studies. The SYRCLE scores ranged from to 5 to 7, with an average of 5.9. This implies a moderate risk of bias. sRNAs influenced the antibiotics susceptibility through modulation of gene expression relevant to efflux pumps, cell wall synthesis, and membrane proteins. Conclusion Preclinical studies on bacterial-type strains suggest that modulation of sRNAs could enhance bacterial susceptibility to antibiotics. Further studies on clinical isolates and in vivo models are needed to elucidate the therapeutic value of sRNA modulation on treatment of multidrug-resistant bacterial infection.
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Affiliation(s)
- Hung Chan
- Department of Anesthesia and Intensive Care
| | - Jeffery Ho
- Department of Anesthesia and Intensive Care
| | | | - Lin Zhang
- Department of Anesthesia and Intensive Care.,State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences.,School of Biomedical Sciences, Faculty of Medicine
| | - Sunny Hei Wong
- State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences.,Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Shatin, Hong Kong
| | | | - William Kk Wu
- Department of Anesthesia and Intensive Care.,State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences
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25
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Yang JH, Bening SC, Collins JJ. Antibiotic efficacy-context matters. Curr Opin Microbiol 2017; 39:73-80. [PMID: 29049930 DOI: 10.1016/j.mib.2017.09.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/09/2017] [Accepted: 09/06/2017] [Indexed: 02/01/2023]
Abstract
Antibiotic lethality is a complex physiological process, sensitive to external cues. Recent advances using systems approaches have revealed how events downstream of primary target inhibition actively participate in antibiotic death processes. In particular, altered metabolism, translational stress and DNA damage each contribute to antibiotic-induced cell death. Moreover, environmental factors such as oxygen availability, extracellular metabolites, population heterogeneity and multidrug contexts alter antibiotic efficacy by impacting bacterial metabolism and stress responses. Here we review recent studies on antibiotic efficacy and highlight insights gained on the involvement of cellular respiration, redox stress and altered metabolism in antibiotic lethality. We discuss the complexity found in natural environments and highlight knowledge gaps in antibiotic lethality that may be addressed using systems approaches.
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Affiliation(s)
- Jason H Yang
- Institute for Medical Engineering & Science, Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA
| | - Sarah C Bening
- Institute for Medical Engineering & Science, Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA
| | - James J Collins
- Institute for Medical Engineering & Science, Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan Cir, Boston, MA 02115, USA.
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Machuca J, Recacha E, Briales A, Díaz-de-Alba P, Blazquez J, Pascual Á, Rodríguez-Martínez JM. Cellular Response to Ciprofloxacin in Low-Level Quinolone-Resistant Escherichia coli. Front Microbiol 2017; 8:1370. [PMID: 28769919 PMCID: PMC5516121 DOI: 10.3389/fmicb.2017.01370] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/05/2017] [Indexed: 11/13/2022] Open
Abstract
Bactericidal activity of quinolones has been related to a combination of DNA fragmentation, reactive oxygen species (ROS) production and programmed cell death (PCD) systems. The underlying molecular systems responsible for reducing bactericidal effect during antimicrobial therapy in low-level quinolone resistance (LLQR) phenotypes need to be clarified. To do this and also define possible new antimicrobial targets, the transcriptome profile of isogenic Escherichia coli harboring quinolone resistance mechanisms in the presence of a clinical relevant concentration of ciprofloxacin was evaluated. A marked differential response to ciprofloxacin of either up- or downregulation was observed in LLQR strains. Multiple genes implicated in ROS modulation (related to the TCA cycle, aerobic respiration and detoxification systems) were upregulated (sdhC up to 63.5-fold) in mutants with LLQR. SOS system components were downregulated (recA up to 30.7-fold). yihE, a protective kinase coding for PCD, was also upregulated (up to 5.2-fold). SdhC inhibition sensitized LLQR phenotypes (up to ΔLog = 2.3 after 24 h). At clinically relevant concentrations of ciprofloxacin, gene expression patterns in critical systems to bacterial survival and mutant development were significantly modified in LLQR phenotypes. Chemical inhibition of SdhC (succinate dehydrogenase) validated modulation of ROS as an interesting target for bacterial sensitization.
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Affiliation(s)
- Jesús Machuca
- Unidad Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena y Virgen del RocíoSeville, Spain
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de SevillaSevilla, Spain
| | - Esther Recacha
- Unidad Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena y Virgen del RocíoSeville, Spain
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de SevillaSevilla, Spain
| | - Alejandra Briales
- Red Española de Investigación en Patología Infecciosa, Instituto de Salud Carlos IIIMadrid, Spain
- Departamento de Microbiología, Universidad de SevillaSevilla, Spain
| | - Paula Díaz-de-Alba
- Unidad Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena y Virgen del RocíoSeville, Spain
| | - Jesús Blazquez
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de SevillaSevilla, Spain
- Red Española de Investigación en Patología Infecciosa, Instituto de Salud Carlos IIIMadrid, Spain
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Álvaro Pascual
- Unidad Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena y Virgen del RocíoSeville, Spain
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de SevillaSevilla, Spain
- Red Española de Investigación en Patología Infecciosa, Instituto de Salud Carlos IIIMadrid, Spain
| | - José-Manuel Rodríguez-Martínez
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de SevillaSevilla, Spain
- Red Española de Investigación en Patología Infecciosa, Instituto de Salud Carlos IIIMadrid, Spain
- Departamento de Microbiología, Universidad de SevillaSevilla, Spain
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Dotto C, Lombarte Serrat A, Cattelan N, Barbagelata MS, Yantorno OM, Sordelli DO, Ehling-Schulz M, Grunert T, Buzzola FR. The Active Component of Aspirin, Salicylic Acid, Promotes Staphylococcus aureus Biofilm Formation in a PIA-dependent Manner. Front Microbiol 2017; 8:4. [PMID: 28167931 PMCID: PMC5253544 DOI: 10.3389/fmicb.2017.00004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 01/03/2017] [Indexed: 01/10/2023] Open
Abstract
Aspirin has provided clear benefits to human health. But salicylic acid (SAL) -the main aspirin biometabolite- exerts several effects on eukaryote and prokaryote cells. SAL can affect, for instance, the expression of Staphylococcus aureus virulence factors. SAL can also form complexes with iron cations and it has been shown that different iron chelating molecules diminished the formation of S. aureus biofilm. The aim of this study was to elucidate whether the iron content limitation caused by SAL can modify the S. aureus metabolism and/or metabolic regulators thus changing the expression of the main polysaccharides involved in biofilm formation. The exposure of biofilm to 2 mM SAL induced a 27% reduction in the intracellular free Fe2+ concentration compared with the controls. In addition, SAL depleted 23% of the available free Fe2+ cation in culture media. These moderate iron-limited conditions promoted an intensification of biofilms formed by strain Newman and by S. aureus clinical isolates related to the USA300 and USA100 clones. The slight decrease in iron bioavailability generated by SAL was enough to induce the increase of PIA expression in biofilms formed by methicillin-resistant as well as methicillin-sensitive S. aureus strains. S. aureus did not produce capsular polysaccharide (CP) when it was forming biofilms under any of the experimental conditions tested. Furthermore, SAL diminished aconitase activity and stimulated the lactic fermentation pathway in bacteria forming biofilms. The polysaccharide composition of S. aureus biofilms was examined and FTIR spectroscopic analysis revealed a clear impact of SAL in a codY-dependent manner. Moreover, SAL negatively affected codY transcription in mature biofilms thus relieving the CodY repression of the ica operon. Treatment of mice with SAL induced a significant increase of S aureus colonization. It is suggested that the elevated PIA expression induced by SAL might be responsible for the high nasal colonization observed in mice. SAL-induced biofilms may contribute to S. aureus infection persistence in vegetarian individuals as well as in patients that frequently consume aspirin.
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Affiliation(s)
- Cristian Dotto
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires Buenos Aires, Argentina
| | - Andrea Lombarte Serrat
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires Buenos Aires, Argentina
| | - Natalia Cattelan
- Facultad de Ciencias Exactas, Centro de Investigación y Desarrollo de Fermentaciones Industriales (CINDEFI), Centro Científico Technológico Consejo Nacional de Investigaciones Científicas y Tócnicas (CTT CONICET La Plata), Universidad Nacional de La Plata La Plata, Argentina
| | - María S Barbagelata
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires Buenos Aires, Argentina
| | - Osvaldo M Yantorno
- Facultad de Ciencias Exactas, Centro de Investigación y Desarrollo de Fermentaciones Industriales (CINDEFI), Centro Científico Technológico Consejo Nacional de Investigaciones Científicas y Tócnicas (CTT CONICET La Plata), Universidad Nacional de La Plata La Plata, Argentina
| | - Daniel O Sordelli
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires Buenos Aires, Argentina
| | - Monika Ehling-Schulz
- Functional Microbiology, Institute for Microbiology, University of Veterinary Medicine Vienna, Austria
| | - Tom Grunert
- Functional Microbiology, Institute for Microbiology, University of Veterinary Medicine Vienna, Austria
| | - Fernanda R Buzzola
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires Buenos Aires, Argentina
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28
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Van Acker H, Gielis J, Acke M, Cools F, Cos P, Coenye T. The Role of Reactive Oxygen Species in Antibiotic-Induced Cell Death in Burkholderia cepacia Complex Bacteria. PLoS One 2016; 11:e0159837. [PMID: 27438061 PMCID: PMC4954720 DOI: 10.1371/journal.pone.0159837] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 07/08/2016] [Indexed: 11/19/2022] Open
Abstract
It was recently proposed that bactericidal antibiotics, besides through specific drug-target interactions, kill bacteria by a common mechanism involving the production of reactive oxygen species (ROS). However, this mechanism involving the production of hydroxyl radicals has become the subject of a lot of debate. Since the contribution of ROS to antibiotic mediated killing most likely depends on the conditions, differences in experimental procedures are expected to be at the basis of the conflicting results. In the present study different methods (ROS specific stainings, gene-expression analyses, electron paramagnetic resonance, genetic and phenotypic experiments, detection of protein carbonylation and DNA oxidation) to measure the production of ROS upon antibiotic treatment in Burkholderia cepacia complex (Bcc) bacteria were compared. Different classes of antibiotics (tobramycin, ciprofloxacin, meropenem) were included, and both planktonic and biofilm cultures were studied. Our results indicate that some of the methods investigated were not sensitive enough to measure antibiotic induced production of ROS, including the spectrophotometric detection of protein carbonylation. Secondly, other methods were found to be useful only in specific conditions. For example, an increase in the expression of OxyR was measured in Burkholderia cenocepacia K56-2 after treatment with ciprofloxacin or meropenem (both in biofilms and planktonic cultures) but not after treatment with tobramycin. In addition results vary with the experimental conditions and the species tested. Nevertheless our data strongly suggest that ROS contribute to antibiotic mediated killing in Bcc species and that enhancing ROS production or interfering with the protection against ROS may form a novel strategy to improve antibiotic treatment.
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Affiliation(s)
- Heleen Van Acker
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Jan Gielis
- Department of Thoracic Surgery, Antwerp Surgical Training and Anatomy Research Centre (ASTARC), Antwerp University, Antwerp, Belgium
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Marloes Acke
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Freya Cools
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
- * E-mail:
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29
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Chaudhari SS, Thomas VC, Sadykov MR, Bose JL, Ahn DJ, Zimmerman MC, Bayles KW. The LysR-type transcriptional regulator, CidR, regulates stationary phase cell death in Staphylococcus aureus. Mol Microbiol 2016; 101:942-53. [PMID: 27253847 DOI: 10.1111/mmi.13433] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 11/29/2022]
Abstract
The Staphylococcus aureus LysR-type transcriptional regulator, CidR, activates the expression of two operons including cidABC and alsSD that display pro- and anti-death functions, respectively. Although several investigations have focused on the functions of different genes associated with these operons, the collective role of the CidR regulon in staphylococcal physiology is not clearly understood. Here we reveal that the primary role of this regulon is to limit acetate-dependent potentiation of cell death in staphylococcal populations. Although both CidB and CidC promote acetate generation and cell death, the CidR-dependent co-activation of CidA and AlsSD counters the effects of CidBC by redirecting intracellular carbon flux towards acetoin formation. From a mechanistic standpoint, we demonstrate that CidB is necessary for full activation of CidC, whereas CidA limits the abundance of CidC in the cell.
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Affiliation(s)
- Sujata S Chaudhari
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5900, USA
| | - Vinai C Thomas
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5900, USA
| | - Marat R Sadykov
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5900, USA
| | - Jeffrey L Bose
- Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, MSN 3029, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Daniel J Ahn
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5900, USA
| | - Matthew C Zimmerman
- Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kenneth W Bayles
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5900, USA.
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30
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Qi F, Zhao X, Kitahara Y, Li T, Ou X, Du W, Liu D, Huang J. Integrative transcriptomic and proteomic analysis of the mutant lignocellulosic hydrolyzate-tolerant Rhodosporidium toruloides. Eng Life Sci 2016; 17:249-261. [PMID: 32624772 DOI: 10.1002/elsc.201500143] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/15/2015] [Accepted: 01/14/2016] [Indexed: 12/15/2022] Open
Abstract
The oleaginous yeast Rhodosporidium toruloides has been considered as an economical lipid producer because it transforms carbohydrates from lignocellulosic hydrolyzate into triglycerides; however, R. toruloides cannot survive in hydrolyzate due to the inhibitors co-produced by hydrolysis. We have previously reported a plasma mutagenesis-generated mutant strain M18 that had strong tolerance for the stress environments of hydrolyzate. Here, we applied transcriptomic and proteomic approaches to analyze the global metabolic responses to the stress in hydrolyzate of R. toruloides and elucidate the tolerant mechanism of the mutant strain. The results showed that 57% genes matched and correlated well with their corresponding proteins. Five hundred and seven genes and 366 proteins had their transcription and expression levels changed, respectively, and 39 key genes with significantly changed transcription and expression levels (≥5-fold changes) were identified. The results demonstrated that four cellular processes and their key genes are likely related to the mechanism of tolerance of M18 strain. Enhanced expression of the key genes in R. toruloides could improve the cellular stress tolerance to lignocellulosic hydrolyzate, while the altered expression of most key genes is probably not caused by mutagenesis, but induced by stressful environments of the hydrolyzate.
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Affiliation(s)
- Feng Qi
- College of Life Sciences Fujian Normal University Fuzhou, Fujian China.,Institute of Applied Chemistry Department of Chemical Engineering Tsinghua University Beijing China
| | - Xuebing Zhao
- Institute of Applied Chemistry Department of Chemical Engineering Tsinghua University Beijing China
| | - Yuki Kitahara
- Department of Bioengineering Tokyo Institute of Technology Yokohama, Kanagawa Japan
| | - Tian Li
- Institute of Applied Chemistry Department of Chemical Engineering Tsinghua University Beijing China
| | - Xianjin Ou
- Institute of Applied Chemistry Department of Chemical Engineering Tsinghua University Beijing China
| | - Wei Du
- Institute of Applied Chemistry Department of Chemical Engineering Tsinghua University Beijing China
| | - Dehua Liu
- Institute of Applied Chemistry Department of Chemical Engineering Tsinghua University Beijing China
| | - Jianzhong Huang
- College of Life Sciences Fujian Normal University Fuzhou, Fujian China
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31
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Belenky P, Ye JD, Porter CBM, Cohen NR, Lobritz MA, Ferrante T, Jain S, Korry BJ, Schwarz EG, Walker GC, Collins JJ. Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage. Cell Rep 2015; 13:968-80. [PMID: 26565910 DOI: 10.1016/j.celrep.2015.09.059] [Citation(s) in RCA: 320] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/04/2015] [Accepted: 09/17/2015] [Indexed: 01/16/2023] Open
Abstract
Understanding how antibiotics impact bacterial metabolism may provide insight into their mechanisms of action and could lead to enhanced therapeutic methodologies. Here, we profiled the metabolome of Escherichia coli after treatment with three different classes of bactericidal antibiotics (?-lactams, aminoglycosides, quinolones). These treatments induced a similar set of metabolic changes after 30 min that then diverged into more distinct profiles at later time points. The most striking changes corresponded to elevated concentrations of central carbon metabolites, active breakdown of the nucleotide pool, reduced lipid levels, and evidence of an elevated redox state. We examined potential end-target consequences of these metabolic perturbations and found that antibiotic-treated cells exhibited cytotoxic changes indicative of oxidative stress, including higher levels of protein carbonylation, malondialdehyde adducts, nucleotide oxidation, and double-strand DNA breaks. This work shows that bactericidal antibiotics induce a complex set of metabolic changes that are correlated with the buildup of toxic metabolic by-products.
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Affiliation(s)
- Peter Belenky
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA; Department of Molecular Microbiology and Immunology, Brown University, 171 Meeting Street, Providence, RI 02912, USA.
| | - Jonathan D Ye
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA
| | - Caroline B M Porter
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Nadia R Cohen
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Michael A Lobritz
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Thomas Ferrante
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Saloni Jain
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, 171 Meeting Street, Providence, RI 02912, USA
| | - Eric G Schwarz
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - James J Collins
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA.
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Chambers L, Yang Y, Littier H, Ray P, Zhang T, Pruden A, Strickland M, Knowlton K. Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces following Therapeutic Administration of Third Generation Cephalosporin. PLoS One 2015; 10:e0133764. [PMID: 26258869 PMCID: PMC4530880 DOI: 10.1371/journal.pone.0133764] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/01/2015] [Indexed: 11/19/2022] Open
Abstract
Although dairy manure is widely applied to land, it is relatively understudied compared to other livestock as a potential source of antibiotic resistance genes (ARGs) to the environment and ultimately to human pathogens. Ceftiofur, the most widely used antibiotic used in U.S. dairy cows, is a 3rd generation cephalosporin, a critically important class of antibiotics to human health. The objective of this study was to evaluate the effect of typical ceftiofur antibiotic treatment on the prevalence of ARGs in the fecal microbiome of dairy cows using a metagenomics approach. β-lactam ARGs were found to be elevated in feces from Holstein cows administered ceftiofur (n = 3) relative to control cows (n = 3). However, total numbers of ARGs across all classes were not measurably affected by ceftiofur treatment, likely because of dominance of unaffected tetracycline ARGs in the metagenomics libraries. Functional analysis via MG-RAST further revealed that ceftiofur treatment resulted in increases in gene sequences associated with "phages, prophages, transposable elements, and plasmids", suggesting that this treatment also enriched the ability to horizontally transfer ARGs. Additional functional shifts were noted with ceftiofur treatment (e.g., increase in genes associated with stress, chemotaxis, and resistance to toxic compounds; decrease in genes associated with metabolism of aromatic compounds and cell division and cell cycle), along with measureable taxonomic shifts (increase in Bacterioidia and decrease in Actinobacteria). This study demonstrates that ceftiofur has a broad, measureable and immediate effect on the cow fecal metagenome. Given the importance of 3rd generation cephalospirins to human medicine, their continued use in dairy cattle should be carefully considered and waste treatment strategies to slow ARG dissemination from dairy cattle manure should be explored.
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Affiliation(s)
- Lindsey Chambers
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Ying Yang
- University of Hong Kong, Hong Kong, China
| | - Heather Littier
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Partha Ray
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Tong Zhang
- University of Hong Kong, Hong Kong, China
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Michael Strickland
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Katharine Knowlton
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail:
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Antibiotic efficacy is linked to bacterial cellular respiration. Proc Natl Acad Sci U S A 2015; 112:8173-80. [PMID: 26100898 DOI: 10.1073/pnas.1509743112] [Citation(s) in RCA: 457] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacteriostatic and bactericidal antibiotic treatments result in two fundamentally different phenotypic outcomes--the inhibition of bacterial growth or, alternatively, cell death. Most antibiotics inhibit processes that are major consumers of cellular energy output, suggesting that antibiotic treatment may have important downstream consequences on bacterial metabolism. We hypothesized that the specific metabolic effects of bacteriostatic and bactericidal antibiotics contribute to their overall efficacy. We leveraged the opposing phenotypes of bacteriostatic and bactericidal drugs in combination to investigate their activity. Growth inhibition from bacteriostatic antibiotics was associated with suppressed cellular respiration whereas cell death from most bactericidal antibiotics was associated with accelerated respiration. In combination, suppression of cellular respiration by the bacteriostatic antibiotic was the dominant effect, blocking bactericidal killing. Global metabolic profiling of bacteriostatic antibiotic treatment revealed that accumulation of metabolites involved in specific drug target activity was linked to the buildup of energy metabolites that feed the electron transport chain. Inhibition of cellular respiration by knockout of the cytochrome oxidases was sufficient to attenuate bactericidal lethality whereas acceleration of basal respiration by genetically uncoupling ATP synthesis from electron transport resulted in potentiation of the killing effect of bactericidal antibiotics. This work identifies a link between antibiotic-induced cellular respiration and bactericidal lethality and demonstrates that bactericidal activity can be arrested by attenuated respiration and potentiated by accelerated respiration. Our data collectively show that antibiotics perturb the metabolic state of bacteria and that the metabolic state of bacteria impacts antibiotic efficacy.
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Staphylococcus aureus adapts to oxidative stress by producing H2O2-resistant small-colony variants via the SOS response. Infect Immun 2015; 83:1830-44. [PMID: 25690100 PMCID: PMC4399076 DOI: 10.1128/iai.03016-14] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/10/2015] [Indexed: 12/30/2022] Open
Abstract
The development of chronic and recurrent Staphylococcus aureus infections is associated with the emergence of slow-growing mutants known as small-colony variants (SCVs), which are highly tolerant of antibiotics and can survive inside host cells. However, the host and bacterial factors which underpin SCV emergence during infection are poorly understood. Here, we demonstrate that exposure of S. aureus to sublethal concentrations of H2O2 leads to a specific, dose-dependent increase in the population frequency of gentamicin-resistant SCVs. Time course analyses revealed that H2O2 exposure caused bacteriostasis in wild-type cells during which time SCVs appeared spontaneously within the S. aureus population. This occurred via a mutagenic DNA repair pathway that included DNA double-strand break repair proteins RexAB, recombinase A, and polymerase V. In addition to triggering SCV emergence by increasing the mutation rate, H2O2 also selected for the SCV phenotype, leading to increased phenotypic stability and further enhancing the size of the SCV subpopulation by reducing the rate of SCV reversion to the wild type. Subsequent analyses revealed that SCVs were significantly more resistant to the toxic effects of H2O2 than wild-type bacteria. With the exception of heme auxotrophs, gentamicin-resistant SCVs displayed greater catalase activity than wild-type bacteria, which contributed to their resistance to H2O2. Taken together, these data reveal a mechanism by which S. aureus adapts to oxidative stress via the production of a subpopulation of H2O2-resistant SCVs with enhanced catalase production.
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Thomas VC, Chaudhari SS, Jones J, Zimmerman MC, Bayles KW. Electron Paramagnetic Resonance (EPR) Spectroscopy to Detect Reactive Oxygen Species in Staphylococcus aureus. Bio Protoc 2015; 5:e1586. [PMID: 27182534 DOI: 10.21769/bioprotoc.1586] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Under aerobic conditions, Staphylococcus aureus (S. aureus) primarily metabolizes glucose to acetic acid. Although normally S. aureus is able to re-utilize acetate as a carbon source following glucose exhaustion, significantly high levels of acetate in the culture media may not only be growth inhibitory but also potentiates cell death in stationary phase cultures by a mechanism dependent on cytoplasmic acidification. One consequence of acetic acid toxicity is the production of reactive oxygen species (ROS). The present protocol describes the detection of ROS in S. aureus undergoing cell death by electron paramagnetic resonance (EPR) spectroscopy. Using 1-hydroxy-3-methoxycarbonyl-2,2,5,5-tetramethylpyrrolidine (CMH) as a cell permeable spin probe, we demonstrate the detection of various oxygen radicals generated by bacteria. Although standardized for S. aureus, the methods described here should be easily adapted for other bacterial species. This protocol is adapted from Thomas et al. (2014) and Thomas et al. (2010).
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Affiliation(s)
- Vinai Chittezham Thomas
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, USA
| | - Sujata S Chaudhari
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, USA
| | - Jocelyn Jones
- Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, USA
| | - Matthew C Zimmerman
- Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, USA
| | - Kenneth W Bayles
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, USA
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Prax M, Bertram R. Metabolic aspects of bacterial persisters. Front Cell Infect Microbiol 2014; 4:148. [PMID: 25374846 PMCID: PMC4205924 DOI: 10.3389/fcimb.2014.00148] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 10/05/2014] [Indexed: 12/23/2022] Open
Abstract
Persister cells form a multi-drug tolerant subpopulation within an isogenic culture of bacteria that are genetically susceptible to antibiotics. Studies with different Gram negative and Gram positive bacteria have identified a large number of genes associated with the persister state. In contrast, the revelation of persister metabolism has only been addressed recently. We here summarize metabolic aspects of persisters, which includes an overview about the bifunctional role of selected carbohydrates as both triggers for the exit from the drug tolerant state and metabolites which persisters feed on. Also alarmones as indicators for starvation have been shown to influence persister levels via different signaling cascades involving the activation of toxin-antitoxin systems and other regulatory factors. Finally, recent data obtained by (13)C-isotopolog profiling demonstrated an active amino acid anabolism in Staphylococcus aureus cultures challenged with high drug concentrations. Understanding the metabolism of persister cells poses challenges but also paves the way for the development of anti-persister compounds.
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Affiliation(s)
- Marcel Prax
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen Tübingen, Germany
| | - Ralph Bertram
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen Tübingen, Germany
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Dwyer DJ, Collins JJ, Walker GC. Unraveling the physiological complexities of antibiotic lethality. Annu Rev Pharmacol Toxicol 2014; 55:313-32. [PMID: 25251995 DOI: 10.1146/annurev-pharmtox-010814-124712] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We face an impending crisis in our ability to treat infectious disease brought about by the emergence of antibiotic-resistant pathogens and a decline in the development of new antibiotics. Urgent action is needed. This review focuses on a less well-understood aspect of antibiotic action: the complex metabolic events that occur subsequent to the interaction of antibiotics with their molecular targets and play roles in antibiotic lethality. Independent lines of evidence from studies of the action of bactericidal antibiotics on diverse bacteria collectively suggest that the initial interactions of drugs with their targets cannot fully account for the antibiotic lethality and that these interactions elicit the production of reactive oxidants including reactive oxygen species that contribute to bacterial cell death. Recent challenges to this concept are considered in the context of the broader literature of this emerging area of research. Possible ways that this new knowledge might be exploited to improve antibiotic therapy are also considered.
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Affiliation(s)
- Daniel J Dwyer
- Department of Cell Biology and Molecular Genetics, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742;
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TCA cycle-mediated generation of ROS is a key mediator for HeR-MRSA survival under β-lactam antibiotic exposure. PLoS One 2014; 9:e99605. [PMID: 24932751 PMCID: PMC4059655 DOI: 10.1371/journal.pone.0099605] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/15/2014] [Indexed: 11/24/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a major multidrug resistant pathogen responsible for several difficult-to-treat infections in humans. Clinical Hetero-resistant (HeR) MRSA strains, mostly associated with persistent infections, are composed of mixed cell populations that contain organisms with low levels of resistance (hetero-resistant HeR) and those that display high levels of drug resistance (homo-resistant HoR). However, the full understanding of β-lactam-mediated HeR/HoR selection remains to be completed. In previous studies we demonstrated that acquisition of the HoR phenotype during exposure to β-lactam antibiotics depended on two key elements: (1) activation of the SOS response, a conserved regulatory network in bacteria that is induced in response to DNA damage, resulting in increased mutation rates, and (2) adaptive metabolic changes redirecting HeR-MRSA metabolism to the tricarboxylic acid (TCA) cycle in order to increase the energy supply for cell-wall synthesis. In the present work, we identified that both main mechanistic components are associated through TCA cycle-mediated reactive oxygen species (ROS) production, which temporally affects DNA integrity and triggers activation of the SOS response resulting in enhanced mutagenesis. The present work brings new insights into a role of ROS generation on the development of resistance to β-lactam antibiotics in a model of natural occurrence, emphasizing the cytoprotective role in HeR-MRSA survival mechanism.
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Antibiotics induce redox-related physiological alterations as part of their lethality. Proc Natl Acad Sci U S A 2014; 111:E2100-9. [PMID: 24803433 DOI: 10.1073/pnas.1401876111] [Citation(s) in RCA: 578] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Deeper understanding of antibiotic-induced physiological responses is critical to identifying means for enhancing our current antibiotic arsenal. Bactericidal antibiotics with diverse targets have been hypothesized to kill bacteria, in part by inducing production of damaging reactive species. This notion has been supported by many groups but has been challenged recently. Here we robustly test the hypothesis using biochemical, enzymatic, and biophysical assays along with genetic and phenotypic experiments. We first used a novel intracellular H2O2 sensor, together with a chemically diverse panel of fluorescent dyes sensitive to an array of reactive species to demonstrate that antibiotics broadly induce redox stress. Subsequent gene-expression analyses reveal that complex antibiotic-induced oxidative stress responses are distinct from canonical responses generated by supraphysiological levels of H2O2. We next developed a method to quantify cellular respiration dynamically and found that bactericidal antibiotics elevate oxygen consumption, indicating significant alterations to bacterial redox physiology. We further show that overexpression of catalase or DNA mismatch repair enzyme, MutS, and antioxidant pretreatment limit antibiotic lethality, indicating that reactive oxygen species causatively contribute to antibiotic killing. Critically, the killing efficacy of antibiotics was diminished under strict anaerobic conditions but could be enhanced by exposure to molecular oxygen or by the addition of alternative electron acceptors, indicating that environmental factors play a role in killing cells physiologically primed for death. This work provides direct evidence that, downstream of their target-specific interactions, bactericidal antibiotics induce complex redox alterations that contribute to cellular damage and death, thus supporting an evolving, expanded model of antibiotic lethality.
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Paulander W, Wang Y, Folkesson A, Charbon G, Løbner-Olesen A, Ingmer H. Bactericidal antibiotics increase hydroxyphenyl fluorescein signal by altering cell morphology. PLoS One 2014; 9:e92231. [PMID: 24647480 PMCID: PMC3960231 DOI: 10.1371/journal.pone.0092231] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/06/2014] [Indexed: 11/19/2022] Open
Abstract
It was recently proposed that for bactericidal antibiotics a common killing mechanism contributes to lethality involving indirect stimulation of hydroxyl radical (OH•) formation. Flow cytometric detection of OH• by hydroxyphenyl fluorescein (HPF) probe oxidation was used to support this hypothesis. Here we show that increased HPF signals in antibiotics-exposed bacterial cells are explained by fluorescence associated with increased cell size, and do not reflect reactive oxygen species (ROS) concentration. Independently of antibiotics, increased fluorescence was seen for elongated cells expressing the oxidative insensitive green fluorescent protein (GFP). Although our data question the role of ROS in lethality of antibiotics other research approaches point to important interplays between basic bacterial metabolism and antibiotic susceptibility. To underpin such relationships, methods for detecting bacterial metabolites at a cellular level are needed.
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Affiliation(s)
- Wilhelm Paulander
- Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg C, Denmark
- * E-mail:
| | - Ying Wang
- Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg C, Denmark
| | - Anders Folkesson
- Department of Microbial Ecology and Animal health, Technical University of Denmark, Frederiksberg C, Denmark
| | - Godefroid Charbon
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Hanne Ingmer
- Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg C, Denmark
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