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Zhong Y, Guo J, Zhang Z, Zheng Y, Yang M, Su Y. Exogenous NADH promotes the bactericidal effect of aminoglycoside antibiotics against Edwardsiella tarda. Virulence 2024; 15:2367647. [PMID: 38884466 PMCID: PMC11185186 DOI: 10.1080/21505594.2024.2367647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/09/2024] [Indexed: 06/18/2024] Open
Abstract
The global surge in multidrug-resistant bacteria owing to antibiotic misuse and overuse poses considerable risks to human and animal health. With existing antibiotics losing their effectiveness and the protracted process of developing new antibiotics, urgent alternatives are imperative to curb disease spread. Notably, improving the bactericidal effect of antibiotics by using non-antibiotic substances has emerged as a viable strategy. Although reduced nicotinamide adenine dinucleotide (NADH) may play a crucial role in regulating bacterial resistance, studies examining how the change of metabolic profile and bacterial resistance following by exogenous administration are scarce. Therefore, this study aimed to elucidate the metabolic changes that occur in Edwardsiella tarda (E. tarda), which exhibits resistance to various antibiotics, following the exogenous addition of NADH using metabolomics. The effects of these alterations on the bactericidal activity of neomycin were investigated. NADH enhanced the effectiveness of aminoglycoside antibiotics against E. tarda ATCC15947, achieving bacterial eradication at low doses. Metabolomic analysis revealed that NADH reprogrammed the ATCC15947 metabolic profile by promoting purine metabolism and energy metabolism, yielding increased adenosine triphosphate (ATP) levels. Increased ATP levels played a crucial role in enhancing the bactericidal effects of neomycin. Moreover, exogenous NADH promoted the bactericidal efficacy of tetracyclines and chloramphenicols. NADH in combination with neomycin was effective against other clinically resistant bacteria, including Aeromonas hydrophila, Vibrio parahaemolyticus, methicillin-resistant Staphylococcus aureus, and Listeria monocytogenes. These results may facilitate the development of effective approaches for preventing and managing E. tarda-induced infections and multidrug resistance in aquaculture and clinical settings.
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Affiliation(s)
- Yilin Zhong
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, People’s Republic of China
| | - Juan Guo
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, People’s Republic of China
| | - Ziyi Zhang
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, People’s Republic of China
| | - Yu Zheng
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, People’s Republic of China
| | - Manjun Yang
- Xizang Key Laboratory of Veterinary Drug, Xizang Vocational Technical College, Lasa, Xizang, People’s Republic of China
| | - Yubin Su
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, People’s Republic of China
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2
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Avci FG. Unraveling bacterial stress responses: implications for next-generation antimicrobial solutions. World J Microbiol Biotechnol 2024; 40:285. [PMID: 39073503 PMCID: PMC11286680 DOI: 10.1007/s11274-024-04090-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
The accelerated spread of antimicrobial-resistant bacteria has caused a serious health problem and rendered antimicrobial treatments ineffective. Innovative approaches are crucial to overcome the health threat posed by resistant pathogens and prevent the emergence of untreatable infections. Triggering stress responses in bacteria can diminish susceptibility to various antimicrobials by inducing resistance mechanisms. Therefore, a thorough understanding of stress response control, especially in relation to antimicrobial resistance, offers valuable perspectives for innovative and efficient therapeutic approaches to combat antimicrobial resistance. The aim of this study was to evaluate the stress responses of 8 different bacteria by analyzing reporter metabolites, around which significant alterations were observed, using a pathway-driven computational approach. For this purpose, the transcriptomic data that the bacterial pathogens were grown under 11 different stress conditions mimicking the human host environments were integrated with the genome-scale metabolic models of 8 pathogenic species (Enterococcus faecalis OG1R, Escherichia coli EPEC O127:H6 E2348/69, Escherichia coli ETEC H10407, Escherichia coli UPEC 536, Klebsiella pneumoniae MGH 78578, Pseudomonas aeruginosa PAO1, Staphylococcus aureus MRSA252, and Staphylococcus aureus MSSA476). The resulting reporter metabolites were enriched in multiple metabolic pathways, with cofactor biosynthesis being the most important. The results of this study will serve as a guide for the development of antimicrobial agents as they provide a first insight into potential drug targets.
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Affiliation(s)
- Fatma Gizem Avci
- Department of Bioengineering, Faculty of Engineering and Natural Sciences, Üsküdar University, Istanbul, Türkiye.
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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3
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Lv X, Gao Z, Li B, Zhou W, Zhang S, Wang X. Mass spectrometry-based metabolomics for the investigation of antibiotic-bacterial interactions. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39004897 DOI: 10.1002/mas.21899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/14/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024]
Abstract
With the development of analytical technologies especially mass spectrometry, metabolomics is becoming increasingly hot in the field of studying antibiotic-bacterial interactions. On the one hand, metabolomics can reveal metabolic perturbations in bacteria in the presence of antibiotics and expose metabolic mechanisms. On the other hand, through in-depth analysis of bacterial metabolic profiles, biomarkers and bioactive secondary metabolites with great potential as drug precursors can be discovered. This review focuses on the experimental workflow of bacterial metabolomics and its application to study the interaction between bacteria and antibiotics. Metabolomics improves the understanding of antibiotic lethality, reveals metabolic perturbations in antibiotic-resistant bacteria, guides the diagnosis and antibiotic treatment of infectious diseases, and aids in the exploration of antibacterial metabolites in nature. Furthermore, current limitations and directions for future developments in this area are discussed.
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Affiliation(s)
- Xiaoyuan Lv
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, Engineering Research Center of Cell & Therapeutic Antibody, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenye Gao
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, Engineering Research Center of Cell & Therapeutic Antibody, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Bingjie Li
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, Engineering Research Center of Cell & Therapeutic Antibody, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiu Zhou
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, Engineering Research Center of Cell & Therapeutic Antibody, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Shengman Zhang
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, Engineering Research Center of Cell & Therapeutic Antibody, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Wang
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, Engineering Research Center of Cell & Therapeutic Antibody, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai, China
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4
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Laborda P, Gil‐Gil T, Martínez JL, Hernando‐Amado S. Preserving the efficacy of antibiotics to tackle antibiotic resistance. Microb Biotechnol 2024; 17:e14528. [PMID: 39016996 PMCID: PMC11253305 DOI: 10.1111/1751-7915.14528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024] Open
Abstract
Different international agencies recognize that antibiotic resistance is one of the most severe human health problems that humankind is facing. Traditionally, the introduction of new antibiotics solved this problem but various scientific and economic reasons have led to a shortage of novel antibiotics at the pipeline. This situation makes mandatory the implementation of approaches to preserve the efficacy of current antibiotics. The concept is not novel, but the only action taken for such preservation had been the 'prudent' use of antibiotics, trying to reduce the selection pressure by reducing the amount of antibiotics. However, even if antibiotics are used only when needed, this will be insufficient because resistance is the inescapable outcome of antibiotics' use. A deeper understanding of the alterations in the bacterial physiology upon acquisition of resistance and during infection will help to design improved strategies to treat bacterial infections. In this article, we discuss the interconnection between antibiotic resistance (and antibiotic activity) and bacterial metabolism, particularly in vivo, when bacteria are causing infection. We discuss as well how understanding evolutionary trade-offs, as collateral sensitivity, associated with the acquisition of resistance may help to define evolution-based therapeutic strategies to fight antibiotic resistance and to preserve currently used antibiotics.
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Affiliation(s)
- Pablo Laborda
- Department of Clinical MicrobiologyRigshospitaletCopenhagenDenmark
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Peng LT, Tian SQ, Guo WX, Chen XW, Wu JH, Liu YL, Peng B. α-Ketoglutarate downregulates thiosulphate metabolism to enhance antibiotic killing. Int J Antimicrob Agents 2024; 64:107214. [PMID: 38795933 DOI: 10.1016/j.ijantimicag.2024.107214] [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: 01/02/2024] [Revised: 05/12/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
Potentiation of the effects of currently available antibiotics is urgently required to tackle the rising antibiotics resistance. The pyruvate (P) cycle has been shown to play a critical role in mediating aminoglycoside antibiotic killing, but the mechanism remains unexplored. In this study, we investigated the effects of intermediate metabolites of the P cycle regarding the potentiation of gentamicin. We found that α-ketoglutarate (α-KG) has the best synergy with gentamicin compared to the other metabolites. This synergistic killing effect was more effective with aminoglycosides than other types of antibiotics, and it was effective against various types of bacterial pathogens. Using fish and mouse infection models, we confirmed that the synergistic killing effect occurred in vivo. Furthermore, functional proteomics showed that α-KG downregulated thiosulphate metabolism. Upregulation of thiosulphate metabolism by exogenous thiosulphate counteracted the killing effect of gentamicin. The role of thiosulphate metabolism in antibiotic resistance was further confirmed using thiosulphate reductase knockout mutants. These mutants were more sensitive to gentamicin killing, and less tolerant to antibiotics compared to their parental strain. Thus, our study highlights a strategy for potentiating antibiotic killing by using a metabolite that reduces antibiotic resistance.
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Affiliation(s)
- Liao-Tian Peng
- State Key Laboratory of Bio-Control, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Si-Qi Tian
- State Key Laboratory of Bio-Control, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Wei-Xu Guo
- State Key Laboratory of Bio-Control, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China; Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xuan-Wei Chen
- State Key Laboratory of Bio-Control, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Jia-Han Wu
- State Key Laboratory of Bio-Control, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ying-Li Liu
- State Key Laboratory of Bio-Control, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Bo Peng
- State Key Laboratory of Bio-Control, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
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Wu P, Lee PC, Chang TE, Hsieh YC, Chiou JJ, Lin CH, Huang YL, Lin YT, Huo TI, Schnabl B, Lee KC, Hou MC. Fecal Carriage of Multidrug-Resistant Organisms Increases the Risk of Hepatic Encephalopathy in Cirrhotic Patients: Insights from Gut Microbiota and Metabolite Features. RESEARCH SQUARE 2024:rs.3.rs-4328129. [PMID: 38766152 PMCID: PMC11100873 DOI: 10.21203/rs.3.rs-4328129/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background Impact of fecal colonization by multidrug-resistant organisms (MDROs) on changes in gut microbiota and associated metabolites, as well as its role in cirrhosis-associated outcomes, has not been thoroughly investigated. Methods Eighty-eight cirrhotic patients and 22 healthy volunteers were prospectively enrolled with analysis conducted on plasma metabolites, fecal MDROs, and microbiota. Patients were followed for a minimum of one year. Predictive factors for cirrhosis-associated outcomes were identified using Cox proportional hazards regression models, and risk factors for fecal MDRO carriage were assessed using logistic regression model. Correlations between microbiota and metabolic profiles were evaluated through Spearman's rank test. Results Twenty-nine (33%) cirrhotic patients exhibited MDRO carriage, with a notably higher rate of hepatic encephalopathy (HE) in MDRO carriers (20.7% vs. 3.2%, p = 0.008). Cox regression analysis identified higher serum lipopolysaccharide levels and fecal MDRO carriage as predictors for HE development. Logistic regression analysis showed that MDRO carriage is an independent risk factor for developing HE. Microbiota analysis showed a significant dissimilarity of fecal microbiota between cirrhotic patients with and without MDRO carriage (p = 0.033). Thirty-two metabolites exhibiting significantly different expression levels among healthy controls, cirrhotic patients with and without MDRO carriage were identified. Six of the metabolites showed correlation with specific bacterial taxa expression in MDRO carriers, with isoaustin showing significantly higher levels in MDRO carriers experiencing HE compared to those who did not. Conclusion Fecal MDRO carriage is associated with altered gut microbiota, metabolite modulation, and an elevated risk of HE occurrence within a year.
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Affiliation(s)
| | | | | | | | | | | | - Yi-Long Huang
- National Yang Ming Chiao Tung University - Yangming Campus
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7
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Rosli NA, Al-Maleki AR, Loke MF, Tay ST, Rofiee MS, Teh LK, Salleh MZ, Vadivelu J. Exposure of Helicobacter pylori to clarithromycin in vitro resulting in the development of resistance and triggers metabolic reprogramming associated with virulence and pathogenicity. PLoS One 2024; 19:e0298434. [PMID: 38446753 PMCID: PMC10917248 DOI: 10.1371/journal.pone.0298434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/23/2024] [Indexed: 03/08/2024] Open
Abstract
In H. pylori infection, antibiotic-resistance is one of the most common causes of treatment failure. Bacterial metabolic activities, such as energy production, bacterial growth, cell wall construction, and cell-cell communication, all play important roles in antimicrobial resistance mechanisms. Identification of microbial metabolites may result in the discovery of novel antimicrobial therapeutic targets and treatments. The purpose of this work is to assess H. pylori metabolomic reprogramming in order to reveal the underlying mechanisms associated with the development of clarithromycin resistance. Previously, four H. pylori isolates were induced to become resistant to clarithromycin in vitro by incrementally increasing the concentrations of clarithromycin. Bacterial metabolites were extracted using the Bligh and Dyer technique and analyzed using metabolomic fingerprinting based on Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry (LC-Q-ToF-MS). The data was processed and analyzed using the MassHunter Qualitative Analysis and Mass Profiler Professional software. In parental sensitivity (S), breakpoint isolates (B), and induced resistance isolates (R) H. pylori isolates, 982 metabolites were found. Furthermore, based on accurate mass, isotope ratios, abundances, and spacing, 292 metabolites matched the metabolites in the Agilent METLIN precise Mass-Personal Metabolite Database and Library (AM-PCDL). Several metabolites associated with bacterial virulence, pathogenicity, survival, and proliferation (L-leucine, Pyridoxone [Vitamine B6], D-Mannitol, Sphingolipids, Indoleacrylic acid, Dulcitol, and D-Proline) were found to be elevated in generated resistant H. pylori isolates when compared to parental sensitive isolates. The elevated metabolites could be part of antibiotics resistance mechanisms. Understanding the fundamental metabolome changes in the course of progressing from clarithromycin-sensitive to breakpoint to resistant in H. pylori clinical isolates may be a promising strategy for discovering novel alternatives therapeutic targets.
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Affiliation(s)
- Naim Asyraf Rosli
- Faculty of Medicine, Department of Medical Microbiology, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Anis Rageh Al-Maleki
- Faculty of Medicine, Department of Medical Microbiology, Universiti Malaya, Kuala Lumpur, Malaysia
- Faculty of Medicine and Health Sciences, Department of Medical Microbiology, Sana’a University, Sana’a, Yemen
| | - Mun Fai Loke
- Camtech Biomedical Pte Ltd, Singapore, Singapore
| | - Sun Tee Tay
- Faculty of Medicine, Department of Medical Microbiology, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Mohd Salleh Rofiee
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor, Malaysia
| | - Jamuna Vadivelu
- Faculty of Medicine, Medical Education Research and Development Unit (MERDU), Universiti Malaya, Kuala Lumpur, Malaysia
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Yi J, Liu C, Yang P, Wu ZC, Du CJ, Shen N. Exogenous glutathione reverses meropenem resistance in carbapenem-resistant Klebsiella pneumoniae. Front Pharmacol 2023; 14:1327230. [PMID: 38174220 PMCID: PMC10762803 DOI: 10.3389/fphar.2023.1327230] [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: 10/24/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Background: The rate of carbapenem-resistant Klebsiella pneumoniae (CRKP) infection has been increasing rapidly worldwide and, poses a significant risk to human health. Effective methods are urgently needed to address treatment failures related to antibiotic resistance. Recent research has reported that some drugs in combination with antibiotics have displayed synergistic killing of resistant bacteria. Here, we investigated whether glutathione (GSH) can synergize with meropenem, and enhance its effectiveness against CRKP. Methods: Synergistic activity was assessed by checkerboard and time-killing assays. The mechanism of these combinations was assessed by total ROS and membrane permeability assays. The bacterial metabolites were assessed by LC‒MS/MS. Results: The FICIs of GSH and meropenem were approximately 0.5 and the combined treatment with GSH and meropenem resulted in a more than 2log10 CFU/mL reduction in bacteria compared to the individual treatments. These findings indicated the synergistic effect of the two drugs. Moreover, the meropenem MIC of CRKP was reduced to less than 4 mg/L when combined with 6 mg/mL GSH, indicating that GSH could significantly reverse resistance to meropenem in bacteria. The production of ROS in bacteria was determined by flow cytometry. After adding GSH, the ROS in the GSH group and the combined group was significantly higher than that in the control and meropenem groups, but there was no significant difference between the combined and GSH groups. The metabolic disturbance caused by GSH alone and in combination with meropenem was significant intracellularly and extracellularly, especially in terms of glycerophospholipid metabolism, indicating that the synergistic effect of the combined use of GSH and meropenem was relevant to glycerophospholipid metabolism. In addition, we measured the cell membrane permeability. The cell membrane permeability of the combination group was significantly higher than that of the blank control or monotreatment groups. This confirmed that the GSH can serve as a meropenem enhancers by disturbing glycerophospholipid metabolism and increasing cell membrane permeability. Conclusion: GSH and meropenem display a synergistic effect, wherein GSH increases the sensitivity of CRKP to meropenem. The synergy and susceptibility effects are thought to related to the increased membrane permeability resulting from the perturbations in glycerophospholipid metabolism, presenting a novel avenue for CRKP treatment.
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Affiliation(s)
- Juan Yi
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Chao Liu
- Department of Infectious Disease, Peking University Third Hospital, Beijing, China
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Ping Yang
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Zhen-chao Wu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Chun-jing Du
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Ning Shen
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
- Department of Infectious Disease, Peking University Third Hospital, Beijing, China
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
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Ferreira MADM, da Silveira WB, Nikoloski Z. PARROT: Prediction of enzyme abundances using protein-constrained metabolic models. PLoS Comput Biol 2023; 19:e1011549. [PMID: 37856550 PMCID: PMC10617714 DOI: 10.1371/journal.pcbi.1011549] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/31/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Protein allocation determines the activity of cellular pathways and affects growth across all organisms. Therefore, different experimental and machine learning approaches have been developed to quantify and predict protein abundance and how they are allocated to different cellular functions, respectively. Yet, despite advances in protein quantification, it remains challenging to predict condition-specific allocation of enzymes in metabolic networks. Here, using protein-constrained metabolic models, we propose a family of constrained-based approaches, termed PARROT, to predict how much of each enzyme is used based on the principle of minimizing the difference between a reference and an alternative growth condition. To this end, PARROT variants model the minimization of enzyme reallocation using four different (combinations of) distance functions. We demonstrate that the PARROT variant that minimizes the Manhattan distance between the enzyme allocation of a reference and an alternative condition outperforms existing approaches based on the parsimonious distribution of fluxes or enzymes for both Escherichia coli and Saccharomyces cerevisiae. Further, we show that the combined minimization of flux and enzyme allocation adjustment leads to inconsistent predictions. Together, our findings indicate that minimization of protein allocation rather than flux redistribution is a governing principle determining steady-state pathway activity for microorganism grown in alternative growth conditions.
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Affiliation(s)
| | | | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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Resci I, Cilia G. The use of honey bee (Apis mellifera L.) as biological monitors for pathogenic bacteria and antimicrobial resistance: A systematic review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:122120. [PMID: 37385360 DOI: 10.1016/j.envpol.2023.122120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/06/2023] [Accepted: 06/26/2023] [Indexed: 07/01/2023]
Abstract
The phenomenon of antimicrobial resistance (AMR) is an increasingly real and relevant health problem. It is essential to verify the spread of this phenomenon in the environment. The European honey bee, Apis mellifera L., is a globally managed pollinator continuously used for biomonitoring thanks to its morphological and behavioural characteristics. During their foraging activities, a large number of honey bees move in the area surrounding the hive within a 1.5 km of radius. Besides, their body covered with hair and bristles are able to intercept pollen and minute particles, such as atmospheric particles, contaminants and microorganisms. For these reasons, A. mellifera L. is widely used as an environmental sentinel, especially for detecting pollutants, pesticides, microorganisms, and AMR. This systematic review aimed to collect and summarize the role of honey bee colonies as a biological monitor of AMR pathogenic bacteria and the environmental spread of antimicrobial resistance genes (ARGs). From honey bees were isolated a wide range of pathogenic and environmental bacteria strains, harbouring AMR and ARGs. However, AMR and ARGs were detected not only in environmental bacteria but also in symbiotic bacteria colonizing the bee gut. This systematic review highlights the employment of potential use of honey bees as AMR sentinel helpful for ecosystem health to implement possible control measures for humans, animals and plants, in the context of the "One-Health" approach.
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Affiliation(s)
- Ilaria Resci
- Research Centre for Agriculture and Environment (CREA-AA), Council for Agricultural Research and Agricultural Economics Analysis, Via di Corticella 133, 40128, Bologna, Italy
| | - Giovanni Cilia
- Research Centre for Agriculture and Environment (CREA-AA), Council for Agricultural Research and Agricultural Economics Analysis, Via di Corticella 133, 40128, Bologna, Italy.
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11
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Guo J, Pan Z, Fan L, Zhong Y, Pang R, Su Y. Effect of Three Different Amino Acids Plus Gentamicin Against Methicillin-Resistant Staphylococcus aureus. Infect Drug Resist 2023; 16:4741-4754. [PMID: 37496695 PMCID: PMC10366528 DOI: 10.2147/idr.s411658] [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: 03/29/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023] Open
Abstract
Background The issue of methicillin-resistant Staphylococcus aureus (MRSA) resistant to many antibiotics and causing serious infectious diseases is a growing healthcare concern. Purpose In recent years, exogenous administration of metabolites in combination with antibiotics can re-sensitize resistant bacteria to antibiotics; however, their effects vary, and their underlying mechanism of action remains elusive. Methods We assessed the bactericidal effects of the three amino acids in combination with gentamicin in vitro and in vivo. Subsequently, we explored the role of these amino acids on the metabolomics of MRSA using Liquid chromatography-tandem mass spectrometry (LC-MS/MS). Furthermore, we performed the downstream analyses using MetaboAnalyst and Interactive Pathways Explorer. Results Exogenous threonine showed the best bactericidal efficacy with gentamicin, followed by glycine, wherein serine had no effect. Amino acid treatments mainly up-regulated the metabolites, increased the amino acid abundance, and significantly activated metabolisms; these effects were consistent with the bactericidal efficacy of the three amino acids. Most amino acids participated in the tricarboxylic acid cycle, and threonine supplementation increased the activities of citrate synthase, isocitrate dehydrogenase and α-ketoglutarate dehydrogenase, whereas glycine increased activities of citrate synthase and α-ketoglutarate dehydrogenase, and serine did not affect the activities of any of the three key enzymes. We identified 24 biomarkers in the three groups, among which glutamic acid and cysteine showed a gradient decrease and increase, respectively. Subsequent analyses revealed that glutamic acid but not cysteine promoted the bactericidal effect of gentamicin synergistically. Conclusion Threonine has the best synergistic effect in reversing bacterial resistance compared to glycine and serine. We show that different amino acids combined with an antibiotic mainly affect amino acid metabolism and act via different metabolic regulatory mechanisms, which could help develop effective strategies for tackling MRSA infections.
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Affiliation(s)
- Juan Guo
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Zhiyu Pan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Lvyuan Fan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People’s Republic of China
| | - Yilin Zhong
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People’s Republic of 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, People’s Republic of China
| | - Yubin Su
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People’s Republic of China
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12
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den Hartog I, Karu N, Zwep LB, Voorn GP, van de Garde EM, Hankemeier T, van Hasselt JC. Differential metabolic host response to pathogens associated with community-acquired pneumonia. Metabol Open 2023; 18:100239. [PMID: 37025095 PMCID: PMC10070890 DOI: 10.1016/j.metop.2023.100239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Background Metabolic changes induced by the host immune response to pathogens found in patients with community-acquired pneumonia (CAP) may provide insight into its pathogenesis. In this study, we characterized differences in the host metabolic response to common CAP-associated pathogens. Method Targeted metabolomic profiling was performed on serum samples obtained from hospitalized CAP patients (n = 119) at admission. We quantified 347 unique metabolites across multiple biochemical classes, including amines, acylcarnitines, and signaling lipids. We evaluated if unique associations between metabolite levels and specific CAP-associated pathogens could be identified. Results Several acylcarnitines were found to be elevated in C. burnetii and herpes simplex virus and lowered in M. pneumoniae as compared to other pathogens. Phenylalanine and kynurenine were found elevated in L. pneumophila as compared to other pathogens. S-methylcysteine was elevated in patients with M. pneumoniae, and these patients also showed lowered cortisol levels in comparison to almost all other pathogens. For the herpes simplex virus, we observed a unique elevation of eicosanoids and several amines. Many lysophosphatidylcholines showed an altered profile in C. burnetii versus S. pneumoniae, L. pneumophila, and respiratory syncytial virus. Finally, phosphatidylcholines were negatively affected by the influenza virus in comparison to S. pneumoniae. Conclusions In this exploratory analysis, metabolites from different biochemical classes were found to be altered in serum samples from patients with different CAP-associated pathogens, which may be used for hypothesis generation in studies on differences in pathogen host response and pathogenesis of CAP.
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Affiliation(s)
- Ilona den Hartog
- Division of Systems Pharmacology & Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Naama Karu
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Laura B. Zwep
- Division of Systems Pharmacology & Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - G. Paul Voorn
- Department of Medical Microbiology and Immunology, St. Antonius Hospital, Nieuwegein, the Netherlands
| | - Ewoudt M.W. van de Garde
- Division of Pharmacoepidemiology and Clinical Pharmacology, Department of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
- Department of Clinical Pharmacy, St. Antonius Hospital, Nieuwegein, the Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - J.G. Coen van Hasselt
- Division of Systems Pharmacology & Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
- Corresponding author.
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13
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Cui X, Xu X, Hu Y, Li R, Liu Q. Mechanism of Qiguiyin Decoction Treats Pulmonary Infection Caused by Pseudomonas aeruginosa Based on Gut Microbiota and Metabolomics. Infect Drug Resist 2023; 16:3073-3084. [PMID: 37222987 PMCID: PMC10202261 DOI: 10.2147/idr.s405033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Background Qiguiyin decoction (QGYD) was a traditional Chinese medicine (TCM) used to treat Pseudomonas aeruginosa infection in China. This study investigated the therapeutic effect and the potential mechanism of QGYD on carbapenem-resistant Pseudomonas aeruginosa (CRPA) infection. Materials and Methods Pulmonary infections were induced in mice by CRPA. The therapeutic effect of QGYD was evaluated by lung index and pulmonary pathology. The potential effects of QGYD on intestinal flora were detected by gut microbiome. The overall metabolism regulation of QGYD in blood was investigated by metabonomics. Next, the correlation between intestinal flora and metabolites was analyzed to illustrate the relationship between the regulatory effects of QGYD on metabolites and the beneficial effects of intestinal flora. Results QGYD has significant therapeutic effect on CRPA infection. QGYD profoundly inhibited the excessive accumulation of Deferribacteres and Mucispirillum at phylum and genus levels, respectively. Eleven potential metabolites that were abnormally expressed by CRPA infection and significantly reversed by QGYD were identified. Ten of the eleven metabolites significantly regulated by QGYD were related to Deferribacteres. Deferribacteres showed significant positive correlation with DL-lactic acid, phenylalanine and other metabolites and significant negative correlation with vitamin k1. At the genus level, Mucispirillum was closely related to metabolites significantly regulated by QGYD. Mucispirillum was positively correlated with metabolites such as Dl-lactate and negatively correlated with vitamin k1. Conclusion QGYD can improve CRPA infection and has the effect of regulating intestinal flora and metabolism. It was a promising drug against infection.
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Affiliation(s)
- Xuran Cui
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, People’s Republic of China
- Beijing Institute of Chinese Medicine, Beijing, 100010, People’s Republic of China
- Beijing Key Laboratory of Basic Research with Traditional Chinese Medicine on Infectious Diseases, Beijing, 100010, People’s Republic of China
| | - Xiaolong Xu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, People’s Republic of China
- Beijing Institute of Chinese Medicine, Beijing, 100010, People’s Republic of China
- Beijing Key Laboratory of Basic Research with Traditional Chinese Medicine on Infectious Diseases, Beijing, 100010, People’s Republic of China
| | - Yahui Hu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, People’s Republic of China
- Beijing Key Laboratory of Basic Research with Traditional Chinese Medicine on Infectious Diseases, Beijing, 100010, People’s Republic of China
| | - Rui Li
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, People’s Republic of China
- Beijing Key Laboratory of Basic Research with Traditional Chinese Medicine on Infectious Diseases, Beijing, 100010, People’s Republic of China
| | - Qingquan Liu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, People’s Republic of China
- Beijing Institute of Chinese Medicine, Beijing, 100010, People’s Republic of China
- Beijing Key Laboratory of Basic Research with Traditional Chinese Medicine on Infectious Diseases, Beijing, 100010, People’s Republic of China
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14
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Cho THS, Pick K, Raivio TL. Bacterial envelope stress responses: Essential adaptors and attractive targets. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119387. [PMID: 36336206 DOI: 10.1016/j.bbamcr.2022.119387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/05/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Millions of deaths a year across the globe are linked to antimicrobial resistant infections. The need to develop new treatments and repurpose of existing antibiotics grows more pressing as the growing antimicrobial resistance pandemic advances. In this review article, we propose that envelope stress responses, the signaling pathways bacteria use to recognize and adapt to damage to the most vulnerable outer compartments of the microbial cell, are attractive targets. Envelope stress responses (ESRs) support colonization and infection by responding to a plethora of toxic envelope stresses encountered throughout the body; they have been co-opted into virulence networks where they work like global positioning systems to coordinate adhesion, invasion, microbial warfare, and biofilm formation. We highlight progress in the development of therapeutic strategies that target ESR signaling proteins and adaptive networks and posit that further characterization of the molecular mechanisms governing these essential niche adaptation machineries will be important for sparking new therapeutic approaches aimed at short-circuiting bacterial adaptation.
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Affiliation(s)
- Timothy H S Cho
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Kat Pick
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Tracy L Raivio
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
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15
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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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16
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Almutairi L, Yu B, Dyne E, Ojaym A, Kim MH. Mild magnetic hyperthermia is synergistic with an antibiotic treatment against dual species biofilms consisting of S. aureus and P. aeruginosa by enhancing metabolic activity. Int J Hyperthermia 2023; 40:2226845. [PMID: 37369371 PMCID: PMC10406516 DOI: 10.1080/02656736.2023.2226845] [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: 04/20/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
OBJECTIVE The wound biofilm infections that develop tolerance to standard-of-care antimicrobial treatment has been increasing. The objective of this study was to demonstrate a proof-of-concept of mild magnetic nanoparticle (MNP)/alternating magnetic field (AMF) hyperthermia as an anti-biofilm therapy against multispecies biofilm infections. METHODS Using both an in vitro cell culture and in vivo murine model of wound infection, we investigated whether MNP/AMF hyperthermia applied at a mild thermal dosage would be synergistically effective against dual species biofilm infection consisting of S. aureus and P. aeruginosa when combined with a broad-spectrum antibiotic, ciprofloxacin (CIP). RESULTS The combined treatment of MNP/AMF hyperthermia and CIP to the wounds of diabetic mice (db/db mice) significantly reduced the CFU number of S. aureus and P. aeruginosa by 2-log and 3-log, respectively, compared to the untreated control group, whereas either mild MNP/AMF hyperthermia or CIP treatment alone had little effect on the eradication of both bacteria. Our gene microarray data obtained from the culture of S. aureus biofilm suggest that mild MNP/AMF could shift the expression of genes for cellular respiration from anaerobic fermentation to an aerobic glycolytic/tricarboxylic acid cycle (TCA) pathway, implicating that the beneficial effect of mild MNP/AMF hyperthermia on the increased susceptibility of biofilm bacteria to an antibiotic treatment is associated with an increased metabolic activity. CONCLUSION Our results support the translational potential of mild MNP/AMF as an adjunctive therapy that can be combined with a broad-spectrum antibiotic treatment for the management of wound biofilm infections associated with multispecies bacteria.
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Affiliation(s)
- Layla Almutairi
- School of Biomedical Sciences, Kent State University, Kent, OH 44242 USA
- Department of Biology, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Bing Yu
- Department of Biological Sciences, Kent State University, Kent, OH 44242 USA
| | - Eric Dyne
- School of Biomedical Sciences, Kent State University, Kent, OH 44242 USA
| | - Alhussain Ojaym
- School of Biomedical Sciences, Kent State University, Kent, OH 44242 USA
| | - Min-Ho Kim
- School of Biomedical Sciences, Kent State University, Kent, OH 44242 USA
- Department of Biological Sciences, Kent State University, Kent, OH 44242 USA
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17
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Systems Biology: New Insight into Antibiotic Resistance. Microorganisms 2022; 10:microorganisms10122362. [PMID: 36557614 PMCID: PMC9781975 DOI: 10.3390/microorganisms10122362] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Over the past few decades, antimicrobial resistance (AMR) has emerged as an important threat to public health, resulting from the global propagation of multidrug-resistant strains of various bacterial species. Knowledge of the intrinsic factors leading to this resistance is necessary to overcome these new strains. This has contributed to the increased use of omics technologies and their extrapolation to the system level. Understanding the mechanisms involved in antimicrobial resistance acquired by microorganisms at the system level is essential to obtain answers and explore options to combat this resistance. Therefore, the use of robust whole-genome sequencing approaches and other omics techniques such as transcriptomics, proteomics, and metabolomics provide fundamental insights into the physiology of antimicrobial resistance. To improve the efficiency of data obtained through omics approaches, and thus gain a predictive understanding of bacterial responses to antibiotics, the integration of mathematical models with genome-scale metabolic models (GEMs) is essential. In this context, here we outline recent efforts that have demonstrated that the use of omics technology and systems biology, as quantitative and robust hypothesis-generating frameworks, can improve the understanding of antibiotic resistance, and it is hoped that this emerging field can provide support for these new efforts.
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18
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Banerji A, Benesh K. Incorporating Microbial Species Interaction in Management of Freshwater Toxic Cyanobacteria: A Systems Science Challenge. AQUATIC ECOLOGY 2022; 3:570-587. [PMID: 36643215 PMCID: PMC9836389 DOI: 10.3390/ecologies3040042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water resources are critically important, but also pose risks of exposure to toxic and pathogenic microbes. Increasingly, a concern is toxic cyanobacteria, which have been linked to the death and disease of humans, domesticated animals, and wildlife in freshwater systems worldwide. Management approaches successful at reducing cyanobacterial abundance and toxin production have tended to be short-term solutions applied on small scales (e.g., algaecide application) or solutions that entail difficult multifaceted investments (e.g., modification of landscape and land use to reduce nutrient inputs). However, implementation of these approaches can be undermined by microbial species interactions that (a) provide toxic cyanobacteria with protection against the method of control or (b) permit toxic cyanobacteria to be replaced by other significant microbial threats. Understanding these interactions is necessary to avoid such scenarios and can provide a framework for novel strategies to enhance freshwater resource management via systems science (e.g., pairing existing physical and chemical approaches against cyanobacteria with ecological strategies such as manipulation of natural enemies, targeting of facilitators, and reduction of benthic occupancy and recruitment). Here, we review pertinent examples of the interactions and highlight potential applications of what is known.
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Affiliation(s)
- Aabir Banerji
- US Environmental Protection Agency, Office of Research & Development, Duluth, MN 55804, USA
| | - Kasey Benesh
- Oak Ridge Institute for Science & Education, Oak Ridge, TN 37830, USA
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19
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Zhou Y, Yong Y, Zhu C, Yang H, Fang B. Exogenous D-ribose promotes gentamicin treatment of several drug-resistant Salmonella. Front Microbiol 2022; 13:1053330. [PMID: 36419438 PMCID: PMC9676500 DOI: 10.3389/fmicb.2022.1053330] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 10/21/2022] [Indexed: 07/28/2023] Open
Abstract
The metabolic microenvironment of bacteria impacts drug efficacy. However, the metabolic mechanisms of drug-resistant Salmonella spp. remain largely unknown. This study characterized the metabolic mechanism of gentamicin-resistant Salmonella Choleraesuis and found that D-ribose increased the gentamicin-mediated killing of this bacteria. Non-targeted metabolomics of homologous gentamicin-susceptible Salmonella Choleraesuis (SCH-S) and gentamicin-resistant S. Choleraesuis (SCH-R) was performed using UHPLC-Q-TOF MS. The metabolic signature of SCH-R included disrupted central carbon metabolism and energy metabolism, along with dysregulated amino acid and nucleotide metabolism, vitamin and cofactor metabolism, and fatty acid synthesis. D-ribose, the most suppressed metabolite in SCH-R, was shown to strengthen gentamicin efficacy against SCH-R and a clinically isolated multidrug-resistant strain. This metabolite had a similar impact on Salmonella. Derby and Salmonella. Typhimurium. D-ribose activates central carbon metabolism including glycolysis, the pentose phosphate pathway (PPP), and the tricarboxylic acid cycle (TCA cycle), increases the abundance of NADH, polarizes the electron transport chain (ETC), and elevates the proton motive force (PMF) of cells, and induces drug uptake and cell death. These findings suggest that central carbon metabolism plays a critical role in the acquisition of gentamicin resistance by Salmonella, and that D-ribose may serve as an antibiotic adjuvant for gentamicin treatment of resistant bacterial infections.
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Affiliation(s)
- Yanhong Zhou
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Yan Yong
- Guangdong Wens Dahuanong Biotechnology Limited Company, Yun Fu, China
| | - Chunyang Zhu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Heng Yang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Binghu Fang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
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20
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Shen X, Shao W, Wang C, Liang L, Chen S, Zhang S, Rusu M, Snyder MP. Deep learning-based pseudo-mass spectrometry imaging analysis for precision medicine. Brief Bioinform 2022; 23:6659741. [PMID: 35947990 DOI: 10.1093/bib/bbac331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/02/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics provides systematic profiling of metabolic. Yet, its applications in precision medicine (disease diagnosis) have been limited by several challenges, including metabolite identification, information loss and low reproducibility. Here, we present the deep-learning-based Pseudo-Mass Spectrometry Imaging (deepPseudoMSI) project (https://www.deeppseudomsi.org/), which converts LC-MS raw data to pseudo-MS images and then processes them by deep learning for precision medicine, such as disease diagnosis. Extensive tests based on real data demonstrated the superiority of deepPseudoMSI over traditional approaches and the capacity of our method to achieve an accurate individualized diagnosis. Our framework lays the foundation for future metabolic-based precision medicine.
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Affiliation(s)
- Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Center for Genomics and Personalized Medicine, Stanford, CA, USA
| | - Wei Shao
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chuchu Wang
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Liang Liang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Center for Genomics and Personalized Medicine, Stanford, CA, USA
| | - Songjie Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Center for Genomics and Personalized Medicine, Stanford, CA, USA
| | - Sai Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Center for Genomics and Personalized Medicine, Stanford, CA, USA
| | - Mirabela Rusu
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Center for Genomics and Personalized Medicine, Stanford, CA, USA
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21
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Weaver AJ, Borgogna TR, O’Shea-Stone G, Peters TR, Copié V, Voyich J, Teintze M. 18β-Glycyrrhetinic Acid Induces Metabolic Changes and Reduces Staphylococcus aureus Bacterial Cell-to-Cell Interactions. Antibiotics (Basel) 2022; 11:antibiotics11060781. [PMID: 35740189 PMCID: PMC9220049 DOI: 10.3390/antibiotics11060781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 12/04/2022] Open
Abstract
The rise in bacterial resistance to common antibiotics has raised an increased need for alternative treatment strategies. The natural antibacterial product, 18β-glycyrrhetinic acid (GRA) has shown efficacy against community-associated methicillin-resistant Staphylococcus aureus (MRSA), although its interactions against planktonic and biofilm modes of growth remain poorly understood. This investigation utilized biochemical and metabolic approaches to further elucidate the effects of GRA on MRSA. Prolonged exposure of planktonic MRSA cell cultures to GRA resulted in increased production of staphyloxanthin, a pigment known to exhibit antioxidant and membrane-stabilizing functions. Then, 1D 1H NMR analyses of intracellular metabolite extracts from MRSA treated with GRA revealed significant changes in intracellular polar metabolite profiles, including increased levels of succinate and citrate, and significant reductions in several amino acids, including branch chain amino acids. These changes reflect the MRSA response to GRA exposure, including potentially altering its membrane composition, which consumes branched chain amino acids and leads to significant energy expenditure. Although GRA itself had no significant effect of biofilm viability, it seems to be an effective biofilm disruptor. This may be related to interference with cell–cell aggregation, as treatment of planktonic MRSA cultures with GRA leads to a significant reduction in micro-aggregation. The dispersive nature of GRA on MRSA biofilms may prove valuable for treatment of such infections and could be used to increase susceptibility to complementary antibiotic therapeutics.
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Affiliation(s)
- Alan J. Weaver
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.J.W.J.); (G.O.-S.); (T.R.P.)
| | - Timothy R. Borgogna
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT 59717, USA;
| | - Galen O’Shea-Stone
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.J.W.J.); (G.O.-S.); (T.R.P.)
| | - Tami R. Peters
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.J.W.J.); (G.O.-S.); (T.R.P.)
| | - Valérie Copié
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.J.W.J.); (G.O.-S.); (T.R.P.)
- Correspondence: (V.C.); (J.V.); (M.T.); Tel.: +406-994-7244 (V.C.); +406-994-7184 (J.V.); +406-994-6515 (M.T.)
| | - Jovanka Voyich
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT 59717, USA;
- Correspondence: (V.C.); (J.V.); (M.T.); Tel.: +406-994-7244 (V.C.); +406-994-7184 (J.V.); +406-994-6515 (M.T.)
| | - Martin Teintze
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.J.W.J.); (G.O.-S.); (T.R.P.)
- Correspondence: (V.C.); (J.V.); (M.T.); Tel.: +406-994-7244 (V.C.); +406-994-7184 (J.V.); +406-994-6515 (M.T.)
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