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Ansari MS, Zohib M, Kumari M, Yadav V, Pal RK, Tripathi S, Jain A, Biswal BK, Arora A. Structural and biophysical characterization of PadR family protein Rv0047c of Mycobacterium tuberculosis H37Rv. J Struct Biol 2025:108211. [PMID: 40403899 DOI: 10.1016/j.jsb.2025.108211] [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: 02/19/2025] [Revised: 04/22/2025] [Accepted: 05/19/2025] [Indexed: 05/24/2025]
Abstract
The members of the PadR family of transcriptional regulators are important for cell survival in toxic environments and play an important role in detoxification, pathogenicity, and multi-drug resistance. Rv0047c of Mycobacterium tuberculosis H37Rv is annotated as a PadR family protein. We have characterized the stability and structure of Rv0047c. Rv0047c forms a stable dimer in solution. Its stability is characterized by a thermal melting transition temperature (Tm) of 55.3 °C. The crystal structure of Rv0047c was determined at a resolution of 3.15 Å. The structure indicates the biological unit to be dimer with each monomer having a characteristic N-terminal winged-helix-turn-helix DNA binding domain and a C-terminal dimerization domain. The N-terminal domain is composed of four helices, α1, α2, α3, and α4 and two beta strands β1 and β2. The C-terminal dimerization domain (CTD) consists two long helices α6 and α7. The two domains are connected by helix α5. A short helical turn (helix αa, residue 89-92), leads to compaction of the α4-α5 loop. Rv0047c exhibits specificity in binding to an upstream region having an inverted repeat sequence. This binding is dependent upon Y18 and Y40 residue of Rv0047c, which are highly conserved among the PadR family. Overall, our results suggest a transcription regulatory role for Rv0047c, similar to other PadR family proteins.
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Affiliation(s)
- Md Samsuddin Ansari
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Zohib
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Meera Kumari
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Vikash Yadav
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ravi Kant Pal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India
| | - Sarita Tripathi
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Anupam Jain
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Bichitra Kumar Biswal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India
| | - Ashish Arora
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Tao Z, Tian C, Zhong C, Ji B, Li W, Zhao Y. The role of NhaA protein in modulating antibiotic tolerance in Escherichia coli. Int J Biol Macromol 2025; 311:143721. [PMID: 40316115 DOI: 10.1016/j.ijbiomac.2025.143721] [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: 12/21/2024] [Revised: 04/08/2025] [Accepted: 04/29/2025] [Indexed: 05/04/2025]
Abstract
As microbial resistance and recurrent bacterial infections escalate, the growing understanding of the interplay between antibiotic resistance and tolerance has sparked significant interest in the latter. Previous studies have demonstrated that the deletion of cation/proton antiporters (CPAs) induces bacterial phenotypes, such as slow growth and prolonged lag phases, which contribute to the development of tolerance. This study investigates the role of the NhaA protein in antibiotic tolerance in Escherichia coli using CRISPR/Cas9 gene editing to delete the NhaA protein. Our results suggest that the NhaA protein plays a key role in modulating antibiotic tolerance. In response to NhaA deletion, E. coli adapts through multiple mechanisms, including changes in membrane permeability, enhanced efflux activity, increased membrane fluidity, disruption of the proton motive force (PMF), and a reduction in intracellular ATP levels. These adaptive changes collectively promote the development of antibiotic tolerance. Understanding these tolerance mechanisms could uncover new therapeutic targets, help prevent the emergence of tolerance, or sustain bacteria cells in a tolerant state, providing crucial strategies to combat the rise of antibiotic-resistant bacteria.
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Affiliation(s)
- Zhen Tao
- School of Life Science and Bio-Pharmaceutics, Shenyang Pharmaceutical University, Shenyang, Liaoning Province 110016, PR China
| | - Chuanjun Tian
- School of Life Science and Bio-Pharmaceutics, Shenyang Pharmaceutical University, Shenyang, Liaoning Province 110016, PR China
| | - Chunyan Zhong
- School of Life Science and Bio-Pharmaceutics, Shenyang Pharmaceutical University, Shenyang, Liaoning Province 110016, PR China
| | - Bingjie Ji
- School of Life Science and Bio-Pharmaceutics, Shenyang Pharmaceutical University, Shenyang, Liaoning Province 110016, PR China
| | - Wenwen Li
- School of Life Science and Bio-Pharmaceutics, Shenyang Pharmaceutical University, Shenyang, Liaoning Province 110016, PR China
| | - Yongshan Zhao
- School of Life Science and Bio-Pharmaceutics, Shenyang Pharmaceutical University, Shenyang, Liaoning Province 110016, PR China.
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3
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Lembke HK, Nauta KM, Hunter RC, Carlson EE. Evaluating the Link between Efflux Pump Expression and Motility Phenotypes in Pseudomonas aeruginosa Treated with Virulence Inhibitors. ACS Infect Dis 2025. [PMID: 40287835 DOI: 10.1021/acsinfecdis.5c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2025]
Abstract
Antibiotic resistance continues to rise as a global health threat. Novel antivirulence strategies diminish the drive for evolutionary pressure but still hinder a pathogen's ability to infect a host. Treatment of the highly virulent Pseudomonas aeruginosa strain PA14 with virulence inhibitors (R-2 and R-6) elicited widely varying transcriptional profiles. Of interest, the expression of a family of resistance-nodulation-division (RND) efflux pumps implicated in the intrinsic drug resistance of P. aeruginosa was significantly altered by R-2 and R-6 treatment. While structurally similar, these inhibitors caused differential expression of various RND efflux pumps within the Mex family─the R-2 treatment stimulated the expression of mexEF-oprN, while the R-6 treatment led to increased mexAB-oprM expression. Further expansion into a small library of virulence inhibitors revealed chemical motifs that trigger increases in the level of RND efflux pump expression. Additionally, activation of these efflux pumps suggests a low accumulation of virulence inhibitors in WT PA14. Treatment of an efflux pump-deficient strain with R-2 or R-6 resulted in inhibition of several virulence factors; for example, R-2 was found to abolish swimming motility. Collectively, treatment with either R-2 or R-6 gives rise to a convoluted transcriptomic response confounded by the impact of efflux pump expression on the system. However, understanding the moieties that lead to high expression of the efflux pumps enables the further rational design of novel virulence inhibitors that do not cause RND efflux pump activation.
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Affiliation(s)
- Hannah K Lembke
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States of America
| | - Kelsie M Nauta
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States of America
| | - Ryan C Hunter
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, SUNY at Buffalo, 955 Main Street, Buffalo, New York 14051, United States of America
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States of America
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St SE, Minneapolis, Minnesota 55455, United States of America
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States of America
- Department of Pharmacology, University of Minnesota, 321 Church St SE, Minneapolis, Minnesota 55455, United States of America
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4
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Duda-Madej A, Viscardi S, Niezgódka P, Szewczyk W, Wińska K. The Impact of Plant-Derived Polyphenols on Combating Efflux-Mediated Antibiotic Resistance. Int J Mol Sci 2025; 26:4030. [PMID: 40362268 PMCID: PMC12071758 DOI: 10.3390/ijms26094030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2025] [Revised: 04/16/2025] [Accepted: 04/22/2025] [Indexed: 05/15/2025] Open
Abstract
The global healthcare system is increasingly challenged by the rising prevalence of multidrug-resistant bacteria and the limited therapeutic options for related infections. Efflux-mediated antibiotic resistance represents a significant obstacle, primarily due to the absence of drugs specifically designed to target bacterial efflux pumps. Recent research has identified polyphenols, a broad class of plant-derived organic compounds, as potential inhibitors of efflux pump activity. This review consolidates data on the inhibitory properties of eight widely distributed polyphenols: curcumin, quercetin, luteolin, tannic acid, naringenin, epigallocatechin-3-gallate, ellagic acid, and resveratrol. These compounds have demonstrated the capacity to inhibit efflux pumps, either through direct interference with bacterial protein function or by downregulating the expression of genes encoding pump subunits. Importantly, several polyphenols exhibit synergistic interactions with antibiotics, including colistin, ciprofloxacin, and tetracycline. For instance, quercetin has shown inhibitory potency comparable to that of established efflux pump inhibitors such as verapamil and reserpine. These findings suggest that polyphenols represent promising candidates for the development of novel efflux pump inhibitors. However, further research is required to validate their efficacy and safety and facilitate their translation into clinical applications for combating antibiotic resistance.
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Affiliation(s)
- Anna Duda-Madej
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, Chałubińskiego 4, 50-368 Wrocław, Poland
| | - Szymon Viscardi
- Faculty of Medicine, Wroclaw Medical University, Ludwika Pasteura 1, 50-367 Wrocław, Poland; (S.V.); (P.N.); (W.S.)
| | - Piotr Niezgódka
- Faculty of Medicine, Wroclaw Medical University, Ludwika Pasteura 1, 50-367 Wrocław, Poland; (S.V.); (P.N.); (W.S.)
| | - Wiktoria Szewczyk
- Faculty of Medicine, Wroclaw Medical University, Ludwika Pasteura 1, 50-367 Wrocław, Poland; (S.V.); (P.N.); (W.S.)
| | - Katarzyna Wińska
- Department of Food Chemistry and Biocatalysis, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, C. K. Norwida 25, 50-375 Wrocław, Poland;
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5
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Mukherjee S, Chakravarty S, Haldar J. Revitalizing Antibiotics with Macromolecular Engineering: Tackling Gram-Negative Superbugs and Mixed Species Bacterial Biofilm Infections In Vivo. Biomacromolecules 2025; 26:2211-2226. [PMID: 40040432 DOI: 10.1021/acs.biomac.4c01520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2025]
Abstract
The escalating prevalence of multidrug-resistant Gram-negative pathogens, coupled with dwindling antibiotic development, has created a critical void in the clinical pipeline. This alarming issue is exacerbated by the formation of biofilms by these superbugs and their frequent coexistence in mixed-species biofilms, conferring extreme antibiotic tolerance. Herein, we present an amphiphilic cationic macromolecule, ACM-AHex, as an innovative antibiotic adjuvant to rejuvenate and repurpose resistant antibiotics, for instance, rifampicin, fusidic acid, erythromycin, and chloramphenicol. ACM-AHex mildly perturbs the bacterial membrane, enhancing antibiotic permeability, hampers efflux machinery, and produces reactive oxygen species, resulting in a remarkable 64-1024-fold potentiation in antibacterial activity. The macromolecule reduces bacterial virulence and macromolecule-drug cocktail significantly eradicate both mono- and multispecies bacterial biofilms, achieving >99.9% bacterial reduction in the murine biofilm infection model. Demonstrating potent biocompatibility across multiple administration routes, ACM-AHex offers a promising strategy to restore obsolete antibiotics and combat recalcitrant Gram-negative biofilm-associated infections, advocating for further clinical evaluation as a next-generation macromolecular antibiotic adjuvant.
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Affiliation(s)
- Sudip Mukherjee
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
| | - Sayan Chakravarty
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
| | - Jayanta Haldar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
- School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
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Kumar P, Singampalli A, Bandela R, Srimounika B, Rajyalakshmi SI, Devi A, Nanduri S, Venkata Madhavi Y. Spirocyclic compounds: potential drug leads in the fight against Mycobacterium tuberculosis. Future Med Chem 2025; 17:819-837. [PMID: 40103373 PMCID: PMC12026180 DOI: 10.1080/17568919.2025.2479413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Accepted: 03/05/2025] [Indexed: 03/20/2025] Open
Abstract
TB drug discovery needs scientists' attention since drug resistance in TB, including extensively drug-resistant TB (XDR-TB) and multidrug-resistant TB (MDR-TB), is a major healthcare concern. Since millions of fatalities from tuberculosis are recorded each year, there is an urgent need to discover new anti-tubercular medications that will either eradicate or control the disease. Spiro compounds have garnered a lot of attention in medicinal chemistry these days because of various biological activities mainly because of their adaptability and structural resemblance to significant pharmacophores. This article overviews the synthesis and activity of spirocyclic compounds as anti-tubercular agents. Both synthesized and naturally occurring spiro chemicals exhibit antitubercular properties. The promising antitubercular potential shown by some of the spirocyclic compounds has attracted scientists to explore them further to develop molecules with improved pharmacodynamic and pharmacokinetic properties and new mechanisms of action with enhanced safety and efficacy in tuberculosis. The current review covers the exploration of spiro compounds from the year 2004 to 2024 for the combat of Tuberculosis. This review gives the comprehensive advancements in this scaffold which would help the logical design of powerful, less toxic, and more effective spirocyclic anti-TB medicinal molecules.
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Affiliation(s)
- Pardeep Kumar
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Anuradha Singampalli
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Rani Bandela
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Bellapukonda Srimounika
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Sugali Indravath Rajyalakshmi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Ankita Devi
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Srinivas Nanduri
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Yaddanapudi Venkata Madhavi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
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7
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Yang Y, Hyeon H, Joo M, Lee K, Shin E. Small regulatory RNAs as key modulators of antibiotic resistance in pathogenic bacteria. J Microbiol 2025; 63:e2501027. [PMID: 40313153 DOI: 10.71150/jm.2501027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Accepted: 02/18/2025] [Indexed: 05/03/2025]
Abstract
The escalating antibiotic resistance crisis poses a significant challenge to global public health, threatening the efficacy of current treatments and driving the emergence of multidrug-resistant pathogens. Among the various factors associated with bacterial antibiotic resistance, small regulatory RNAs (sRNAs) have emerged as pivotal post-transcriptional regulators which orchestrate bacterial adaptation to antibiotic pressure via diverse mechanisms. This review consolidates the current knowledge on sRNA-mediated mechanisms, focusing on drug uptake, drug efflux systems, lipopolysaccharides, cell wall modification, biofilm formation, and mutagenesis. Recent advances in transcriptomics and functional analyses have revealed novel sRNAs and their regulatory networks, expanding our understanding of resistance mechanisms. These findings highlight the potential of targeting sRNA-mediated pathways as an innovative therapeutic strategy to combat antibiotic resistance, and offer promising avenues for managing challenging bacterial infections.
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Affiliation(s)
- Yubin Yang
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hana Hyeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Minju Joo
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Eunkyoung Shin
- Department of Microbiology, Catholic University of Daegu School of Medicine, Daegu 42472, Republic of Korea
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Roque Paulo CL, Alexandre PRF, Araujo ACF, Almeida RS, Albuquerque ES, Oliveira-Tintino CDDM, Nascimento IJS, Araújo-Júnior JX, da Silva-Junior EF, de Aquino TM, Mendonça-Junior FJB, de Araújo-Neto JB, Silva Leandro MKDN, de Menezes IRA, Coutinho HDM, Rocha JE. Evaluation of the Efflux Pump Inhibition Activity of Thiadiazine-Derived Compounds Against the Staphylococcus aureus 1199B Strain. Pharmaceuticals (Basel) 2025; 18:323. [PMID: 40143101 PMCID: PMC11945367 DOI: 10.3390/ph18030323] [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: 01/23/2025] [Revised: 02/18/2025] [Accepted: 02/20/2025] [Indexed: 03/28/2025] Open
Abstract
Background: Substances with antibacterial properties have become crucial in light of the continuous increase in infections caused by multidrug-resistant bacteria. In this context, thiadiazines have emerged as heterocyclic compounds already known for their pharmacological activities. However, their potential as antibacterial agents and inhibitors of the efflux system found in resistant bacteria remains poorly understood. From this perspective, the present study highlights the synthesis of thiadiazine-derived compounds and evaluates their antibacterial activity and efflux pump inhibition against the Staphylococcus aureus 1199B strain. Methods: To this end, Minimum Inhibitory Concentration (MIC) tests were conducted, along with the analysis of antibacterial activity through the inhibition of the NorA efflux system using 96-well microdilution assays. Additionally, to assess efflux system inhibition, ethidium bromide (EtBr) fluorescence emission tests were performed, alongside in silico molecular docking studies. Results: Based on the results obtained, it was observed that compound IJ28 exhibited direct activity against the tested SA 1199B strains, with an MIC of 512 µg/mL. It also demonstrated antibacterial activity through efflux pump inhibition, resulting in increased fluorescence rates emitted by EtBr. Compound IJ28 showed a more significant reduction in the Minimum Inhibitory Concentration (MIC) of ethidium bromide, decreasing from 26.6 µg/mL to 0.5 µg/mL, compared to the other compounds. Conclusions: Therefore, it is essential to conduct further studies to investigate the mechanism of action and clarify the feasibility and effects of compound IJ28 as a potential antibacterial agent.
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Affiliation(s)
- Cicera Laura Roque Paulo
- Laboratory of Microbiology and Molecular Biology—LMBM, Regional University of Cariri—URCA, Crato 63105-000, CE, Brazil; (C.L.R.P.); (P.R.F.A.); (A.C.F.A.); (R.S.A.); (E.S.A.); (C.D.d.M.O.-T.); (M.K.d.N.S.L.); (J.E.R.)
| | - Priscilla Ramos Freitas Alexandre
- Laboratory of Microbiology and Molecular Biology—LMBM, Regional University of Cariri—URCA, Crato 63105-000, CE, Brazil; (C.L.R.P.); (P.R.F.A.); (A.C.F.A.); (R.S.A.); (E.S.A.); (C.D.d.M.O.-T.); (M.K.d.N.S.L.); (J.E.R.)
| | - Ana Carolina Ferreira Araujo
- Laboratory of Microbiology and Molecular Biology—LMBM, Regional University of Cariri—URCA, Crato 63105-000, CE, Brazil; (C.L.R.P.); (P.R.F.A.); (A.C.F.A.); (R.S.A.); (E.S.A.); (C.D.d.M.O.-T.); (M.K.d.N.S.L.); (J.E.R.)
| | - Ray Silva Almeida
- Laboratory of Microbiology and Molecular Biology—LMBM, Regional University of Cariri—URCA, Crato 63105-000, CE, Brazil; (C.L.R.P.); (P.R.F.A.); (A.C.F.A.); (R.S.A.); (E.S.A.); (C.D.d.M.O.-T.); (M.K.d.N.S.L.); (J.E.R.)
| | - Emílio Sousa Albuquerque
- Laboratory of Microbiology and Molecular Biology—LMBM, Regional University of Cariri—URCA, Crato 63105-000, CE, Brazil; (C.L.R.P.); (P.R.F.A.); (A.C.F.A.); (R.S.A.); (E.S.A.); (C.D.d.M.O.-T.); (M.K.d.N.S.L.); (J.E.R.)
| | - Cícera Datiane de Morais Oliveira-Tintino
- Laboratory of Microbiology and Molecular Biology—LMBM, Regional University of Cariri—URCA, Crato 63105-000, CE, Brazil; (C.L.R.P.); (P.R.F.A.); (A.C.F.A.); (R.S.A.); (E.S.A.); (C.D.d.M.O.-T.); (M.K.d.N.S.L.); (J.E.R.)
| | - Igor J. S. Nascimento
- Laboratory of Medicinal Chemistry, Institute of Pharmaceutical Sciences, Federal University of Alagoas, Maceió 57072-900, AL, Brazil; (I.J.S.N.); (J.X.A.-J.)
| | - João Xavier Araújo-Júnior
- Laboratory of Medicinal Chemistry, Institute of Pharmaceutical Sciences, Federal University of Alagoas, Maceió 57072-900, AL, Brazil; (I.J.S.N.); (J.X.A.-J.)
| | - Edeildo Ferreira da Silva-Junior
- Biological and Molecular Chemistry Research Group, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió 57072-900, AL, Brazil;
| | - Thiago Mendonça de Aquino
- Laboratory of Synthesis and Research in Medicinal Chemistry, Research Group on Therapeutic Strategies—GPET, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió 57072-900, AL, Brazil;
| | | | - José Bezerra de Araújo-Neto
- Postgraduate Program in Biological Sciences, Biosciences Center, Federal University of Pernambuco, Recife 50740-570, PE, Brazil;
| | - Maria Karollyna do Nascimento Silva Leandro
- Laboratory of Microbiology and Molecular Biology—LMBM, Regional University of Cariri—URCA, Crato 63105-000, CE, Brazil; (C.L.R.P.); (P.R.F.A.); (A.C.F.A.); (R.S.A.); (E.S.A.); (C.D.d.M.O.-T.); (M.K.d.N.S.L.); (J.E.R.)
| | - Irwin Rose Alencar de Menezes
- Laboratory of Pharmacology and Molecular Chemistry—LFQM, Regional University of Cariri—URCA, Crato 63105-000, CE, Brazil
| | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology—LMBM, Regional University of Cariri—URCA, Crato 63105-000, CE, Brazil; (C.L.R.P.); (P.R.F.A.); (A.C.F.A.); (R.S.A.); (E.S.A.); (C.D.d.M.O.-T.); (M.K.d.N.S.L.); (J.E.R.)
| | - Janaina Esmeraldo Rocha
- Laboratory of Microbiology and Molecular Biology—LMBM, Regional University of Cariri—URCA, Crato 63105-000, CE, Brazil; (C.L.R.P.); (P.R.F.A.); (A.C.F.A.); (R.S.A.); (E.S.A.); (C.D.d.M.O.-T.); (M.K.d.N.S.L.); (J.E.R.)
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9
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Ahmad M, Aduru SV, Smith RP, Zhao Z, Lopatkin AJ. The role of bacterial metabolism in antimicrobial resistance. Nat Rev Microbiol 2025:10.1038/s41579-025-01155-0. [PMID: 39979446 DOI: 10.1038/s41579-025-01155-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2025] [Indexed: 02/22/2025]
Abstract
The relationship between bacterial metabolism and antibiotic treatment is complex. On the one hand, antibiotics leverage cell metabolism to function. On the other hand, increasing research has highlighted that the metabolic state of the cell also impacts all aspects of antibiotic biology, from drug efficacy to the evolution of antimicrobial resistance (AMR). Given that AMR is a growing threat to the current global antibiotic arsenal and ability to treat infectious diseases, understanding these relationships is key to improving both public and human health. However, quantifying the contribution of metabolism to antibiotic activity and subsequent bacterial evolution has often proven challenging. In this Review, we discuss the complex and often bidirectional relationships between metabolism and the various facets of antibiotic treatment and response. We first summarize how antibiotics leverage metabolism for their function. We then focus on the converse of this relationship by specifically delineating the unique contribution of metabolism to three distinct but related arms of antibiotic biology: antibiotic efficacy, AMR evolution and AMR mechanisms. Finally, we note the relevance of metabolism in clinical contexts and explore the future of metabolic-based strategies for personalized antimicrobial therapies. A deeper understanding of these connections is crucial for the broader scientific community to address the growing crisis of AMR and develop future effective therapeutics.
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Affiliation(s)
- Mehrose Ahmad
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Sai Varun Aduru
- Department of Chemical Engineering, University of Rochester, Rochester, NY, USA
| | - Robert P Smith
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Zirui Zhao
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Allison J Lopatkin
- Department of Chemical Engineering, University of Rochester, Rochester, NY, USA.
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA.
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, USA.
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10
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Moubayed NMS, Alsabbagh R, Smiline GAS, Gunasekaran S, Alshihri S, Sabour A. Evaluation of phyto-gallic acid as a potential inhibitor of Staphylococcus aureus efflux pump mediated tetracycline resistance: an in-vitro and in-silico study. Nat Prod Res 2025; 39:625-632. [PMID: 38733626 DOI: 10.1080/14786419.2024.2349810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024]
Abstract
Plants contain many bioactive compounds with potent antibacterial and efflux pump inhibitory activity (EPI). In this study, gallic acid extracted from pomegranate molasses by analytical HPLC holds promise as an EPI drug for Staphylococcus aureus mediated tetracycline resistance, it lowered the bacterial resistance and reversed the mechanism via tet family efflux pump, using molecular technique and in-silico molecular docking analysis. Extracted gallic acid combined with tetracycline demonstrated a significant decrease in the minimal inhibitory concentration MIC compared to its single activity. Similarly, little growth and lower fluorescence of S. aureus were observed on ethidium bromide (2.5 mg/mL) agar plates, indicating a reversible efflux pump mechanism and a potent EPI activity. Molecular docking demonstrated a promising affinity binding energy between gallic acid and tet efflux genes, opening a new baseline in bacterial infection treatment. PCR for tetK and Qac A/B genes failed to show any relation between tet genes and gallic acid.
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Affiliation(s)
- Nadine M S Moubayed
- Department of Botany and Microbiology, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Ruba Alsabbagh
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Girija A S Smiline
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, Chennai, Tamilnadu, India
| | - Shoba Gunasekaran
- Department of Biotechnology, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous), University of Madras, Chennai, Tamil Nadu, India
| | - Sameeha Alshihri
- Department of Botany and Microbiology, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Amal Sabour
- Department of Botany and Microbiology, Science College, King Saud University, Riyadh, Saudi Arabia
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11
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Magossi G, Gzyl KE, Holman DB, Nagaraja TG, Amachawadi R, Amat S. Genomic and metabolic characterization of Trueperella pyogenes isolated from domestic and wild animals. Appl Environ Microbiol 2025; 91:e0172524. [PMID: 39745423 PMCID: PMC11784230 DOI: 10.1128/aem.01725-24] [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: 09/05/2024] [Accepted: 11/25/2024] [Indexed: 02/01/2025] Open
Abstract
Trueperella pyogenes is an important bacterial pathogen implicated in infections such as mastitis, metritis, pneumonia, and liver abscesses in both domestic and wild animals, as well as endocarditis and prosthetic joint infections in humans. Understanding the genomic and metabolic features that enable T. pyogenes to colonize different anatomical sites within a host and its inter-kingdom transmission and survival is important for the effective control of this pathogen. We employed whole-genome sequencing, phenotype microarrays, and antimicrobial susceptibility testing to identify genomic, metabolic and phenotypic features, and antimicrobial resistance (AMR) genes in T. pyogenes recovered from different livestock, companion, and wildlife animals. For comparative genomic analysis, 83 T. pyogenes genomes, including 60 isolated in the current study and 23 publicly available genomes were evaluated. These genomes represented T. pyogenes strains originating from 16 different body sites of 11 different animal hosts (e.g., cattle, swine, ovine, deer, bison, horse, chamois, and cat). Additionally, 49 T. pyogenes isolates (cattle, sheep, deer, swine, and cats) were evaluated for phenotypic AMR using disk diffusion, and for metabolic profiling using the Biology GENIII MicroPlates. The T. pyogenes strains were found not to be host- or body site-specific. The presence of conserved virulence genes (plo and fimA), as well as genotypic and phenotypic AMR may contribute to the ability of T. pyogenes to cause infections in livestock, wildlife, and pets. Most of the tested isolates metabolized diverse carbon sources and chemical compounds, suggesting that this metabolic versatility may enhance the survival, competitiveness, and pathogenic potential of T. pyogenes.IMPORTANCETrueperella pyogenes is an important animal pathogen with zoonotic potential, posing a significant health concern to both animals and humans due to its ability to cause infections across different animal host species and tissues. Current understanding of this pathogen's adaptability and survival mechanisms is limited. Here, we evaluated the genomic, virulence, metabolic, and antimicrobial resistance (AMR) characteristics of T. pyogenes recovered from 16 different body sites of 11 different animal hosts (livestock, companion, and wild animals). We identified multiple AMR and virulence genes that may enable T. pyogenes for sustained infection and transmission. Additionally, T. pyogenes strains displayed metabolic versatility which could also contribute to its ability to thrive in diverse environments. Understanding the genomic and metabolic, and AMR characteristics that enable T. pyogenes to colonize different anatomical sites within a host and its transmission between different animal species is important for the effective control of this pathogen.
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Affiliation(s)
- Gabriela Magossi
- Microbiological Sciences Department, North Dakota State University, Fargo, North Dakota, USA
| | - Katherine E. Gzyl
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - T. G. Nagaraja
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | | | - Samat Amat
- Microbiological Sciences Department, North Dakota State University, Fargo, North Dakota, USA
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12
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Zeng FF, Chen ZH, Luo FH, Liu CJ, Yang X, Zhang FX, Shi W. Sophorae tonkinensis radix et rhizoma: A comprehensive review of the ethnopharmacology, phytochemistry, pharmacology, pharmacokinetics, toxicology and detoxification strategy. JOURNAL OF ETHNOPHARMACOLOGY 2025; 337:118784. [PMID: 39244176 DOI: 10.1016/j.jep.2024.118784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/08/2024] [Accepted: 09/02/2024] [Indexed: 09/09/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Sophorae tonkinensis Radix et Rhizoma (STR), the dried root and rhizome of Sophora tonkinensis Gagnep., is commonly used in the treatment of tonsillitis and pharyngitis, throat soreness and throat obstruction, swelling and aching of gum, etc. in China or other Asian countries. STR is usually used as the core herb in traditional Chinese medicine preparations, such as "Biyanling Tablets", "Fufang Muji Granules" and "Ganyanling Injections", etc. AIM OF THE REVIEW: This review aimed to provide a comprehensive analysis of STR in terms of botany, traditional use, phytochemistry, ethnopharmacology, pharmacology, pharmacokinetics, toxicology and detoxification strategy, to provide a rational application in future research. MATERIALS AND METHODS The information involved in the study was gathered from a variety of electronic resources, including China National Knowledge Infrastructure (CNKI), SciFinder, Google Scholar, PubMed, Web of Science, and Chinese Masters and Doctoral Dissertations. RESULTS Till now, a total of 333 chemical components have been identified in STR, including 85 alkaloids, 124 flavonoids, 24 triterpenes, 27 triterpene saponins, 34 organic acids, 8 polysaccharides, etc. STR and its main active constituents have cardiovascular protection, anti-tumor activity, anti-inflammatory activity, antipyretic activity, analgesic activity, antibacterial activity, antifungal activity, antiviral activity, and hepatoprotective activity, etc. However, toxic effects of STR on the liver, nerves, heart, and gastrointestinal tract have also been observed. To mitigate these risks, STR needs attenuation before use, with the most common detoxification methods being processing and combined use with other drugs. The pharmacokinetics of STR in vivo and traditional and clinical prescriptions containing STR have been sorted out. Despite the potential therapeutic benefits of STR, further research is warranted to elucidate its hepatotoxicity, particularly in vivo, exploring aspects such as in vivo metabolism, distribution, and mechanisms. CONCLUSION This review serves to emphasize the therapeutic potential of STR and highlights the crucial need to address its toxicity concerns before considering clinical application. Further research is required to comprehensively investigate the toxicological properties of STR, with particular emphasis on its hepatotoxicity and neurotoxicity. Such research endeavors have the potential to standardize the rational application of STR for optimal therapeutic outcomes.
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Affiliation(s)
- Fen-Fen Zeng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Zi-Hao Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Fu-Hui Luo
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Cheng-Jun Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Xia Yang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Feng-Xiang Zhang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China.
| | - Wei Shi
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China.
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Nasralddin NA, Haeili M, Karimzadeh S, Alsahlani F. Tetracycline and chloramphenicol exposure induce decreased susceptibility to tigecycline and genetic alterations in AcrAB-TolC efflux pump regulators in Escherichia coli and Klebsiella pneumoniae. PLoS One 2025; 20:e0315847. [PMID: 39841693 PMCID: PMC11753663 DOI: 10.1371/journal.pone.0315847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 12/02/2024] [Indexed: 01/30/2025] Open
Abstract
Tigecycline (Tgc), a third-generation tetracycline is found as the last line of defense against multi-drug resistant bacteria. Recent increased rate of resistance to tgc, a human-restricted agent among animal bacteria poses a significant global health challenge. Overuse of first generation tetracyclines (Tet) and phenicols in animals have been suggested to be associated with Tgc resistance development. In the current study we aimed to determine the effect of tetracycline (Tet) and chloramphenicol (Chl) overexposure on Tgc susceptibility. A Tet and Chl-susceptible isolate of K. pneumoniae and E. coli were exposed to successively increasing concentrations of tetracycline and chloramphenicol separately until a ≥4 times increase in Tet and Chl MICs was observed. Susceptibility changes to several antimicrobial agents were tested using disk diffusion and broth dilution methods. The genetic alterations of genes coding for major AcrAB regulators including acrR (repressor of acrAB), ramR (repressor of ramA), soxR (repressor of soxS) in K. pneumoniae and lon (proteolytic degradation of MarA), marR (repressor of marA), acrR and soxR in E. coli were investigated. The expression level of acrB was measured using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method. The excessive exposure (15 to 40 selection cycles) of studied bacteria to both antibiotics significantly decreased susceptibility of Tet-resistant (R) and Chl-R variants of E. coli (n = 6) and K. pneumoniae (n = 6) to several groups of antibiotics including tigecycline (4-16 and 8-64 times respectively) and quinolones. About 58% of variants (n = 7) carried genetic alterations in AcrAB regulators including ramR (frameshift mutations/locus deletion), MarR (L33R, A70T, G15S amino acid substitutions) and Lon (L630F change, frameshift mutation) which were associated with acrB upregulation. Our study demonstrated the capacity of chloramphenicol and tetracycline exposure for selection of mutants which revealed tigecycline resistance/decreased susceptibility mostly mediated by active efflux mechanism. Unaltered acrB expression level in some strains indicates possible contribution of other efflux pumps or non-efflux-based mechanisms in the development of multiple- antibiotic resistance phenotype.
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Affiliation(s)
- Nian Anwar Nasralddin
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mehri Haeili
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Sasan Karimzadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Fatemeh Alsahlani
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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Habib MB, Shah NA, Amir A, Alghamdi HA, Tariq MH, Nisa K, Ammoun M. Decoding MexB efflux pump genes: structural, molecular, and phylogenetic analysis of multidrug-resistant and extensively drug-resistant Pseudomonas aeruginosa. Front Cell Infect Microbiol 2025; 14:1519737. [PMID: 39906216 PMCID: PMC11791646 DOI: 10.3389/fcimb.2024.1519737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Accepted: 12/19/2024] [Indexed: 02/06/2025] Open
Abstract
Objective Emerging drug resistance in Pseudomonas aeruginosa is of great concern in clinical settings. P. aeruginosa activates its efflux-pump system in order to evade the effect of antibiotics. The current investigation aims to detect MexB genes in P. aeruginosa, their structural and molecular analysis and their impact on antimicrobial susceptibility profiling. Methods A total of 42 clinical specimens were aseptically collected from hospitalized patients who had underlying infections related to medical implants. Matrix-assisted laser desorption ionization-time of flight (MALDI-ToF) were used for the identification of isolates. The methods used in this study were antibiotic susceptibility profiling, minimum inhibitory concentration (MIC), polymerase chain reaction (PCR), sanger sequencing, phylogenetic analysis, MolProbity score, Ramachandran plot analysis and multiple sequence alignment. Results The highest resistance was shown by P. aeruginosa against cefoperazone (67%), gentamycin and amikacin (66%) each, followed by cefotaxime (64%). The prevalence of multi-drug resistant (MDR) and extensively drug resistant (XDR) was 57% and 12%, respectively. The presence of an active efflux-pump system was indicated by the MexB genes found in most of the resistant isolates (p<0.05). Following addition of efflux pump inhibitor carbonyl cyanide m-chlorophenyl hydrazone (CCCP), a significant decrease (p<0.05) in MIC was observed in resistance, that revealed the presence of active efflux pump system. Phylogenetic analysis revealed evolutionary relationships with the P. aeruginosa strains isolated in Switzerland, Denmark and Germany. Protein domain architecture revealed that MexB gene proteins were involved in particular efflux pump function. Protein sequences aligned by multiple sequence alignment revealed conserved regions and sequence variants, which suggested antibiotic translocation and evolutionary divergence. These highly conserved regions could be used for diagnostic purposes of efflux pump MexB genes. Conclusion To avoid their spread in hospital settings, responsible authorities ought to begin rigorous initiatives in order to reduce the prevalence of multi-drug resistant, extensively drug resistant, and efflux pump carrying isolates in clinical settings.
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Affiliation(s)
| | - Naseer Ali Shah
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Afreenish Amir
- Department of Microbiology, National Institute of Health, Islamabad, Pakistan
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha, Saudi Arabia
| | | | - Kiran Nisa
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Mariam Ammoun
- Department of Pathology, Viva Health Laboratories, Windsor, United Kingdom
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15
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Corbella M, Moreira C, Bello‐Madruga R, Torrent Burgas M, Kamerlin SCL, Blair JMA, Sancho‐Vaello E. Targeting MarA N-terminal domain dynamics to prevent DNA binding. Protein Sci 2025; 34:e5258. [PMID: 39660948 PMCID: PMC11633057 DOI: 10.1002/pro.5258] [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: 06/20/2024] [Revised: 10/14/2024] [Accepted: 11/30/2024] [Indexed: 12/12/2024]
Abstract
Efflux is one of the mechanisms employed by Gram-negative bacteria to become resistant to routinely used antibiotics. The inhibition of efflux by targeting their regulators is a promising strategy to re-sensitize bacterial pathogens to antibiotics. AcrAB-TolC is the main resistance-nodulation-division efflux pump in Enterobacteriaceae. MarA is an AraC/XylS family global regulator that regulates more than 40 genes related to the antimicrobial resistance phenotype, including acrAB. The aim of this work was to understand the role of the N-terminal helix of MarA in the mechanism of DNA binding. An N-terminal deletion of MarA showed that the N-terminal helix is critical for recognition of the functional marboxes. By engineering two double cysteine variants of MarA that form a disulfide bond between the N-terminal helix and the hydrophobic core of one of the helices in direct DNA contact, and combining in vitro electrophoretic mobility assays, in vivo measurements of acrAB transcription using a GFP reporter system, and molecular dynamic simulations, it was shown that the immobilization of the N-terminal helix of MarA prevents binding to DNA. This inhibited conformation seems to be universal for the monomeric members of the AraC/XylS family, as suggested by additional molecular dynamics simulations of the two-domain protein Rob. These results point to the N-terminal helix of the AraC/XylS family monomeric regulators as a promising target for the development of inhibitors.
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Affiliation(s)
- Marina Corbella
- Science for Life Laboratory, Department of Chemistry‐BMCUppsala UniversityUppsalaSweden
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB)Universitat de BarcelonaBarcelonaSpain
| | - Cátia Moreira
- Science for Life Laboratory, Department of Chemistry‐BMCUppsala UniversityUppsalaSweden
| | - Roberto Bello‐Madruga
- Department of Biochemistry and Molecular BiologyUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | - Marc Torrent Burgas
- Department of Biochemistry and Molecular BiologyUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | - Shina C. L. Kamerlin
- Science for Life Laboratory, Department of Chemistry‐BMCUppsala UniversityUppsalaSweden
- School of Chemistry and BiochemistryGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Jessica M. A. Blair
- College of Medicine and Health, Department of Microbes, Infection and MicrobiomesInstitute of Microbiology and Infection, University of BirminghamBirminghamUK
| | - Enea Sancho‐Vaello
- Department of Biochemistry and Molecular BiologyUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
- College of Medicine and Health, Department of Microbes, Infection and MicrobiomesInstitute of Microbiology and Infection, University of BirminghamBirminghamUK
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16
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Pudhuvai B, Beneš K, Čurn V, Bohata A, Lencova J, Vrzalova R, Barta J, Matha V. The Daunomycin: Biosynthesis, Actions, and the Search for New Solutions to Enhance Production. Microorganisms 2024; 12:2639. [PMID: 39770841 PMCID: PMC11676270 DOI: 10.3390/microorganisms12122639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 12/04/2024] [Accepted: 12/17/2024] [Indexed: 01/05/2025] Open
Abstract
Daunorubicin (DNR) is an anthracycline antibiotic originating from soil-dwelling actinobacteria extensively used to treat malignant tumors. Over the decades, extensive attempts were made to enhance the production of anthracyclines by introducing genetic modifications and mutations in combination with media optimization, but the target production levels remain comparatively low. Developing an appropriate culture medium to maximize the yield of DNR and preventing autotoxicity for the producing organism remains a challenge. Our prospective review sheds light on a method involving perturbation that enhances the precursors to regulate the type II PKS pathway, enhancing cells' capacity to increase secondary metabolite production. The suggested method also entails the preparation of culture media for the cultivation of Streptomyces sp. and enhanced yield of DNR, as well as making it inactive with iron or its reduced forms following efflux from the producer. The iron or iron-DNR complex is encapsulated by oleic acid or lipid micelle layers in the culture media, finally resulting in the generated inactive DNR and the DNR-iron-oil complex. This idea has the potential to protect the producer organism from autotoxicity and prevent the inhibition of metabolite production. The approach of substituting sugar with oil in culture media has a dual role wherein it promotes Streptomyces growth by utilizing lipids as an energy source and encapsulating the generated DNR-iron complex in the medium. In this review, we discussed aspects like anthracycline producers, biosynthesis pathways, and gene regulation; side effects of DNR; mechanisms for autotoxicity evasion; and culture media components for the enhancement of DNR production in Streptomyces sp. We anticipate that our work will help researchers working with secondary metabolites production and decipher a methodology that would enhance DNR yield and facilitate the extraction of the resulting DNR by lowering costs in large-scale fermentation.
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Affiliation(s)
- Baveesh Pudhuvai
- Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic;
| | - Karel Beneš
- VUAB Pharma A.S, Nemanicka 2722, 370 01 České Budějovice, Czech Republic; (K.B.); (V.M.)
| | - Vladislav Čurn
- Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic;
| | - Andrea Bohata
- Department of Plant Production, Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (J.L.); (R.V.); (J.B.)
| | - Jana Lencova
- Department of Plant Production, Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (J.L.); (R.V.); (J.B.)
| | - Radka Vrzalova
- Department of Plant Production, Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (J.L.); (R.V.); (J.B.)
| | - Jan Barta
- Department of Plant Production, Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (J.L.); (R.V.); (J.B.)
| | - Vladimir Matha
- VUAB Pharma A.S, Nemanicka 2722, 370 01 České Budějovice, Czech Republic; (K.B.); (V.M.)
- Department of Plant Production, Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (J.L.); (R.V.); (J.B.)
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17
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Rajput P, Nahar KS, Rahman KM. Evaluation of Antibiotic Resistance Mechanisms in Gram-Positive Bacteria. Antibiotics (Basel) 2024; 13:1197. [PMID: 39766587 PMCID: PMC11672434 DOI: 10.3390/antibiotics13121197] [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: 10/24/2024] [Revised: 11/30/2024] [Accepted: 12/05/2024] [Indexed: 01/11/2025] Open
Abstract
The prevalence of resistance in Gram-positive bacterial infections is rapidly rising, presenting a pressing global challenge for both healthcare systems and economies. The WHO categorizes these bacteria into critical, high, and medium priority groups based on the urgency for developing new antibiotics. While the first priority pathogen list was issued in 2017, the 2024 list remains largely unchanged. Despite six years having passed, the progress that has been made in developing novel treatment approaches remains insufficient, allowing antimicrobial resistance to persist and worsen on a global scale. Various strategies have been implemented to address this growing threat by targeting specific resistance mechanisms. This review evaluates antimicrobial resistance (AMR) in Gram-positive bacteria, highlighting its critical impact on global health due to the rise of multidrug-resistant pathogens. It focuses on the unique cell wall structure of Gram-positive bacteria, which influences their identification and susceptibility to antibiotics. The review explores the mechanisms of AMR, including enzymatic inactivation, modification of drug targets, limiting drug uptake, and increased drug efflux. It also examines the resistance strategies employed by high-priority Gram-positive pathogens such as Staphylococcus aureus, Streptococcus pneumoniae, and Enterococcus faecium, as identified in the WHO's 2024 priority list.
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Affiliation(s)
- Pratiksing Rajput
- Institute of Pharmaceutical Science, King’s College London, 150 Stamford Street, London SE1 9NH, UK;
| | - Kazi S. Nahar
- Department of Natural Sciences, Faculty of Science & Technology, Middlesex University, The Burroughs, Hendon, London NW4 4BT, UK;
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, King’s College London, 150 Stamford Street, London SE1 9NH, UK;
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18
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Chanket W, Pipatthana M, Sangphukieo A, Harnvoravongchai P, Chankhamhaengdecha S, Janvilisri T, Phanchana M. The complete catalog of antimicrobial resistance secondary active transporters in Clostridioides difficile: evolution and drug resistance perspective. Comput Struct Biotechnol J 2024; 23:2358-2374. [PMID: 38873647 PMCID: PMC11170357 DOI: 10.1016/j.csbj.2024.05.027] [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: 02/08/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024] Open
Abstract
Secondary active transporters shuttle substrates across eukaryotic and prokaryotic membranes, utilizing different electrochemical gradients. They are recognized as one of the antimicrobial efflux pumps among pathogens. While primary active transporters within the genome of C. difficile 630 have been completely cataloged, the systematical study of secondary active transporters remains incomplete. Here, we not only identify secondary active transporters but also disclose their evolution and role in drug resistance in C. difficile 630. Our analysis reveals that C. difficile 630 carries 147 secondary active transporters belonging to 27 (super)families. Notably, 50 (34%) of them potentially contribute to antimicrobial resistance (AMR). AMR-secondary active transporters are structurally classified into five (super)families: the p-aminobenzoyl-glutamate transporter (AbgT), drug/metabolite transporter (DMT) superfamily, major facilitator (MFS) superfamily, multidrug and toxic compound extrusion (MATE) family, and resistance-nodulation-division (RND) family. Surprisingly, complete RND genes found in C. difficile 630 are likely an evolutionary leftover from the common ancestor with the diderm. Through protein structure comparisons, we have potentially identified six novel AMR-secondary active transporters from DMT, MATE, and MFS (super)families. Pangenome analysis revealed that half of the AMR-secondary transporters are accessory genes, which indicates an important role in adaptive AMR function rather than innate physiological homeostasis. Gene expression profile firmly supports their ability to respond to a wide spectrum of antibiotics. Our findings highlight the evolution of AMR-secondary active transporters and their integral role in antibiotic responses. This marks AMR-secondary active transporters as interesting therapeutic targets to synergize with other antibiotic activity.
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Affiliation(s)
- Wannarat Chanket
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Methinee Pipatthana
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Apiwat Sangphukieo
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Shen S, Tang C, Yang W, Ding L, Han R, Shi Q, Guo Y, Yin D, Hu F. In vitro mimicry of in vivo KPC mutations by ceftazidime-avibactam: phenotypes, mechanisms, genetic structure and kinetics of enzymatic hydrolysis. Emerg Microbes Infect 2024; 13:2356146. [PMID: 38743401 PMCID: PMC11151810 DOI: 10.1080/22221751.2024.2356146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
Ceftazidime-avibactam (CZA) is employed for the treatment of infections caused by Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP). Resistance to CZA is frequently linked to point mutations in the blaKPC. We conducted in vitro simulations of in vivo blaKPC mutations using CZA. Four pre-therapy KPC-KP isolates (K1, K2, K3, and K4) were evaluated, all initially exhibited susceptibility to CZA and produced KPC-2. The crucial distinction was that following CZA treatment, the blaKPC-2 mutated in K1, K2, and K3, rendering them resistant to CZA, while K4 achieved microbiological clearance, and blaKPC-2 remained unaltered. The induction assay identified various blaKPC-2 variants, including blaKPC-25, blaKPC-127, blaKPC-100, blaKPC-128, blaKPC-137, blaKPC-138, blaKPC-144 and blaKPC-180. Our findings suggest that the resistance of KPC-KP to CZA primarily results from the emergence of KPC variants, complemented by increased blaKPC expression. A close correlation exists between avibactam concentration and the rate of increased CZA minimum Inhibitory concentration, as well as blaKPC mutation. Inadequate avibactam concentration is more likely to induce resistance in strains against CZA, there is also a higher likelihood of mutation in the blaKPC-2 and the optimal avibactam ratio remains to be determined. Simultaneously, we selected a blaKPC-33-producing K. pneumoniae strain (mutated from blaKPC-2) and induced it with imipenem and meropenem, respectively. The blaKPC-2 was detected during the process, indicating that the mutation is reversible. Clinical use of carbapenems to treat KPC variant strains increases the risk of infection, as the gene can mutate back to blaKPC-2, rendering the strain even more cross-resistant to carbapenems and CZA.
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Affiliation(s)
- Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People’s Republic of China
| | - Chengkang Tang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People’s Republic of China
| | - Weiwei Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People’s Republic of China
| | - Li Ding
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People’s Republic of China
| | - Renru Han
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People’s Republic of China
| | - Qingyu Shi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People’s Republic of China
| | - Yan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People’s Republic of China
| | - Dandan Yin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People’s Republic of China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People’s Republic of China
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20
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Zhao Y, Xu H, Wang H, Wang P, Chen S. Multidrug resistance in Pseudomonas aeruginosa: genetic control mechanisms and therapeutic advances. MOLECULAR BIOMEDICINE 2024; 5:62. [PMID: 39592545 PMCID: PMC11599538 DOI: 10.1186/s43556-024-00221-y] [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: 07/25/2024] [Revised: 10/23/2024] [Accepted: 10/23/2024] [Indexed: 11/28/2024] Open
Abstract
Pseudomonas aeruginosa is a significant opportunistic pathogen, and its complex mechanisms of antibiotic resistance pose a challenge to modern medicine. This literature review explores the advancements made from 1979 to 2024 in understanding the regulatory networks of antibiotic resistance genes in Pseudomonas aeruginosa, with a particular focus on the molecular underpinnings of these resistance mechanisms. The review highlights four main pathways involved in drug resistance: reducing outer membrane permeability, enhancing active efflux systems, producing antibiotic-inactivating enzymes, and forming biofilms. These pathways are intricately regulated by a combination of genetic regulation, transcriptional regulators, two-component signal transduction, DNA methylation, and small RNA molecules. Through an in-depth analysis and synthesis of existing literature, we identify key regulatory elements mexT, ampR, and argR as potential targets for novel antimicrobial strategies. A profound understanding of the core control nodes of drug resistance offers a new perspective for therapeutic intervention, suggesting that modulating these elements could potentially reverse resistance and restore bacterial susceptibility to antibiotics. The review looks forward to future research directions, proposing the use of gene editing and systems biology to further understand resistance mechanisms and to develop effective antimicrobial strategies against Pseudomonas aeruginosa. This review is expected to provide innovative solutions to the problem of drug resistance in infectious diseases.
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Affiliation(s)
- Yuanjing Zhao
- State Key Laboratory of South Western Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China
| | - Haoran Xu
- State Key Laboratory of South Western Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China
| | - Hui Wang
- State Key Laboratory of South Western Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China
| | - Ping Wang
- State Key Laboratory of South Western Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China.
| | - Simin Chen
- State Key Laboratory of South Western Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China.
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21
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Chen Y, Liu F, Sha A, Xu M, Rao Z, Zhang X. The mechanisms of environmental stress tolerance in Gluconobacter oxydans: progress and perspectives. Crit Rev Biotechnol 2024:1-14. [PMID: 39566930 DOI: 10.1080/07388551.2024.2426011] [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: 02/01/2024] [Revised: 09/07/2024] [Accepted: 09/24/2024] [Indexed: 11/22/2024]
Abstract
Gluconobacter oxydans have been widely used in industrial compound production for their incomplete oxidation ability. However, they are often subjected to a wide variety of severe environmental stresses, such as extreme pH, high temperature, osmotic pressure, and organic solvents, which greatly repress microbial growth viability and productivity. As typical biocatalysis chassis cells with a high tolerance to external environmental stresses, it is extremely important to construct highly tolerant chassis cells and understand the tolerance mechanisms of G. oxydans and how different stresses interact with the cell: membranes, phospholipid bilayers, transporters, and chaperone proteins. In this review, we discuss and summarize the mechanisms of environmental stress tolerance in G. oxydans, and the promising strategies that can be used to further construct tolerant strains are prospected.
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Affiliation(s)
- Yan Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Fei Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Aobo Sha
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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22
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Zorman M, Kokot M, Zdovc I, Senerovic L, Mandic M, Zidar N, Cotman AE, Durcik M, Peterlin Mašič L, Minovski N, Anderluh M, Hrast Rambaher M. Enhancing Antibacterial Efficacy: Combining Novel Bacterial Topoisomerase Inhibitors with Efflux Pump Inhibitors and Other Agents Against Gram-Negative Bacteria. Antibiotics (Basel) 2024; 13:1081. [PMID: 39596774 PMCID: PMC11591509 DOI: 10.3390/antibiotics13111081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 11/10/2024] [Accepted: 11/12/2024] [Indexed: 11/29/2024] Open
Abstract
BACKGROUND The novel bacterial topoisomerase inhibitors (NBTIs) developed in our laboratory show potent on-target enzyme inhibition but suffer from low activity against Gram-negative bacteria. METHODS With the aim of improving the antibacterial activity of our compounds against Gram-negative bacteria, we tested them in combination with different efflux pump inhibitors (EPIs), a strategy that showed promise in several other classes of antimicrobials. We also investigated the combined effect of NBTIs with ATP-competitive inhibitors of bacterial type II topoisomerases (ACIs), as well as the antibiofilm properties of our compounds and the combination with EPIs against early and mature Acietobacter baumannii biofilm. RESULTS Our results demonstrate that combinations of NBTIs with EPI Phenylalanine-arginyl-β-naphthylamide significantly reduce the corresponding NBTIs' minimal inhibitory concentration values and show potentiation of A. baumannii biofilm inhibition as compared to NBTIs alone. Although combinations of NBITs and ACIs did not show synergistic effects, the FIC index value calculations revealed additive effects for all the combinations of a selected NBTI in combination with three ACIs in all the assayed Gram-negative bacteria from the ESKAPE group. CONCLUSIONS These results show for the first time that combinations of NBTIs with either EPIs or a different class of the topoisomerase inhibitors may be a beneficial strategy to combat difficult-to-treat bacterial infections.
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Affiliation(s)
- Maša Zorman
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; (M.Z.); (M.K.); (N.M.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia; (N.Z.); (A.E.C.); (M.D.); (L.P.M.); (M.A.)
| | - Maja Kokot
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; (M.Z.); (M.K.); (N.M.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia; (N.Z.); (A.E.C.); (M.D.); (L.P.M.); (M.A.)
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia;
| | - Lidija Senerovic
- Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (L.S.); (M.M.)
| | - Mina Mandic
- Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (L.S.); (M.M.)
| | - Nace Zidar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia; (N.Z.); (A.E.C.); (M.D.); (L.P.M.); (M.A.)
| | - Andrej Emanuel Cotman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia; (N.Z.); (A.E.C.); (M.D.); (L.P.M.); (M.A.)
| | - Martina Durcik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia; (N.Z.); (A.E.C.); (M.D.); (L.P.M.); (M.A.)
| | - Lucija Peterlin Mašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia; (N.Z.); (A.E.C.); (M.D.); (L.P.M.); (M.A.)
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; (M.Z.); (M.K.); (N.M.)
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia; (N.Z.); (A.E.C.); (M.D.); (L.P.M.); (M.A.)
| | - Martina Hrast Rambaher
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia; (N.Z.); (A.E.C.); (M.D.); (L.P.M.); (M.A.)
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Sinha S, Aggarwal S, Singh DV. Efflux pumps: gatekeepers of antibiotic resistance in Staphylococcus aureus biofilms. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:368-377. [PMID: 39568862 PMCID: PMC11576857 DOI: 10.15698/mic2024.11.839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 10/01/2024] [Accepted: 10/08/2024] [Indexed: 11/22/2024]
Abstract
Staphylococcus aureus, a versatile human pathogen, poses a significant challenge in healthcare settings due to its ability to develop antibiotic resistance and form robust biofilms. Understanding the intricate mechanisms underlying the antibiotic resistance is crucial for effective infection treatment and control. This comprehensive review delves into the multifaceted roles of efflux pumps in S. aureus, with a focus on their contribution to antibiotic resistance and biofilm formation. Efflux pumps, integral components of the bacterial cell membrane, are responsible for expelling a wide range of toxic substances, including antibiotics, from bacterial cells. By actively extruding antibiotics, these pumps reduce intracellular drug concentrations, rendering antibiotics less effective. Moreover, efflux pumps have emerged as significant contributors to both antibiotic resistance and biofilm formation in S. aureus. Biofilms, structured communities of bacterial cells embedded in a protective matrix, enable S. aureus to adhere to surfaces, evade host immune responses, and resist antibiotic therapy. Efflux pumps play a pivotal role in the development and maintenance of S. aureus biofilms. However, the interplay between efflux pumps, antibiotic resistance and biofilm formation remains unexplored in S. aureus. This review aims to elucidate the complex relationship between efflux pumps, antibiotic resistance and biofilm formation in S. aureus with the aim to aid in the development of potential therapeutic targets for combating S. aureus infections, especially those associated with biofilms. The insights provided herein may contribute to the advancement of novel strategies to overcome antibiotic resistance and disrupt biofilm formation in this clinically significant pathogen.
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Affiliation(s)
- Shweta Sinha
- Department of Biotechnology, School of Earth, Biological and Environmental Sciences, Central University of South Bihar Gaya, 824236 India
| | - Shifu Aggarwal
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023 India
- Current Address: Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts USA
| | - Durg Vijai Singh
- Department of Biotechnology, School of Earth, Biological and Environmental Sciences, Central University of South Bihar Gaya, 824236 India
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24
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Nguyen MH, Nguyen TYN, Le THN, Le TNT, Chau NTN, Le TMH, Huy Nguyen BQ. Medicinal plants as a potential resource for the discovery of novel structures towards cancer drug resistance treatment. Heliyon 2024; 10:e39229. [PMID: 39492898 PMCID: PMC11530815 DOI: 10.1016/j.heliyon.2024.e39229] [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: 04/01/2024] [Revised: 08/23/2024] [Accepted: 10/09/2024] [Indexed: 11/05/2024] Open
Abstract
Despite extensive research in chemotherapy, global cancer concerns persist, exacerbated by the challenge of drug resistance, which imposes economic and medical burdens. Natural compounds, particularly secondary metabolites from medicinal plants, present promising avenues for overcoming cancer drug resistance due to their diverse structures and essential pharmacological effects. This review provides a comprehensive exploration of cancer cell resistance mechanisms and target actions for reversing resistance and highlights the in vitro and in vivo efficacy of noteworthy alkaloids, flavonoids, and other compounds, emphasizing their potential as therapeutic agents. The molecular properties supporting ligand interactions are thoroughly examined, providing a robust theoretical foundation. The review concludes by discussing methods including quantitative structure-activity relationships and molecular docking, offering insights into screening potential candidates. Current trends in clinical treatment, contributing to a holistic understanding of the multifaceted approaches to address cancer drug resistance are also outlined.
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Affiliation(s)
- Minh Hien Nguyen
- University of Health Sciences, Vietnam National University Ho Chi Minh City, YA1 Administrative Building, Hai Thuong Lan Ong Street, Dong Hoa Ward, Di An City, Binh Duong Province, Viet Nam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc City, Ho Chi Minh city, Viet Nam
| | - Thi Yen Nhi Nguyen
- University of Health Sciences, Vietnam National University Ho Chi Minh City, YA1 Administrative Building, Hai Thuong Lan Ong Street, Dong Hoa Ward, Di An City, Binh Duong Province, Viet Nam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc City, Ho Chi Minh city, Viet Nam
- Faculty of Applied Science, Ho Chi Minh City University of Technology, Vietnam National University Ho Chi Minh City, 268 Ly Thuong Kiet Street Ward 14, District 10, Ho Chi Minh City, Viet Nam
| | - Thien Han Nguyen Le
- University of Health Sciences, Vietnam National University Ho Chi Minh City, YA1 Administrative Building, Hai Thuong Lan Ong Street, Dong Hoa Ward, Di An City, Binh Duong Province, Viet Nam
| | - Thi Ngoc Tam Le
- University of Health Sciences, Vietnam National University Ho Chi Minh City, YA1 Administrative Building, Hai Thuong Lan Ong Street, Dong Hoa Ward, Di An City, Binh Duong Province, Viet Nam
| | - Ngoc Trong Nghia Chau
- University of Health Sciences, Vietnam National University Ho Chi Minh City, YA1 Administrative Building, Hai Thuong Lan Ong Street, Dong Hoa Ward, Di An City, Binh Duong Province, Viet Nam
| | - Tu Manh Huy Le
- University of Health Sciences, Vietnam National University Ho Chi Minh City, YA1 Administrative Building, Hai Thuong Lan Ong Street, Dong Hoa Ward, Di An City, Binh Duong Province, Viet Nam
| | - Bui Quoc Huy Nguyen
- The University of Danang - VN-UK Institute for Research and Executive Education, 41 Le Duan Street, Hai Chau 1 Ward, Hai Chau District, Danang City, Viet Nam
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25
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Sakagianni A, Koufopoulou C, Koufopoulos P, Feretzakis G, Kalles D, Paxinou E, Myrianthefs P, Verykios VS. The Synergy of Machine Learning and Epidemiology in Addressing Carbapenem Resistance: A Comprehensive Review. Antibiotics (Basel) 2024; 13:996. [PMID: 39452262 PMCID: PMC11505168 DOI: 10.3390/antibiotics13100996] [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: 09/19/2024] [Revised: 10/16/2024] [Accepted: 10/19/2024] [Indexed: 10/26/2024] Open
Abstract
BACKGROUND/OBJECTIVES Carbapenem resistance poses a significant threat to public health by undermining the efficacy of one of the last lines of antibiotic defense. Addressing this challenge requires innovative approaches that can enhance our understanding and ability to combat resistant pathogens. This review aims to explore the integration of machine learning (ML) and epidemiological approaches to understand, predict, and combat carbapenem-resistant pathogens. It examines how leveraging large datasets and advanced computational techniques can identify patterns, predict outbreaks, and inform targeted intervention strategies. METHODS The review synthesizes current knowledge on the mechanisms of carbapenem resistance, highlights the strengths and limitations of traditional epidemiological methods, and evaluates the transformative potential of ML. Real-world applications and case studies are used to demonstrate the practical benefits of combining ML and epidemiology. Technical and ethical challenges, such as data quality, model interpretability, and biases, are also addressed, with recommendations provided for overcoming these obstacles. RESULTS By integrating ML with epidemiological analysis, significant improvements can be made in predictive accuracy, identifying novel patterns in disease transmission, and designing effective public health interventions. Case studies illustrate the benefits of interdisciplinary collaboration in tackling carbapenem resistance, though challenges such as model interpretability and data biases must be managed. CONCLUSIONS The combination of ML and epidemiology holds great promise for enhancing our capacity to predict and prevent carbapenem-resistant infections. Future research should focus on overcoming technical and ethical challenges to fully realize the potential of these approaches. Interdisciplinary collaboration is key to developing sustainable strategies to combat antimicrobial resistance (AMR), ultimately improving patient outcomes and safeguarding public health.
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Affiliation(s)
| | - Christina Koufopoulou
- Anesthesiology Department, Aretaieio Hospital, National and Kapodistrian University of Athens, 11528 Athens, Greece;
| | - Petros Koufopoulos
- Internal Medicine Department, Sismanogleio General Hospital, 15126 Marousi, Greece;
| | - Georgios Feretzakis
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece; (G.F.); (D.K.); (E.P.)
| | - Dimitris Kalles
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece; (G.F.); (D.K.); (E.P.)
| | - Evgenia Paxinou
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece; (G.F.); (D.K.); (E.P.)
| | - Pavlos Myrianthefs
- Faculty of Nursing, School of Health Sciences, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Vassilios S. Verykios
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece; (G.F.); (D.K.); (E.P.)
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26
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Salama GG, El-Mahdy TS, Moustafa WH, Emara M. Downregulation of Klebsiella pneumoniae RND efflux pump genes following indole signal produced by Escherichia coli. BMC Microbiol 2024; 24:312. [PMID: 39182027 PMCID: PMC11344464 DOI: 10.1186/s12866-024-03443-w] [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: 04/06/2024] [Accepted: 07/26/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND More than a century has passed since it was discovered that many bacteria produce indole, but research into the actual biological roles of this molecule is just now beginning. The influence of indole on bacterial virulence was extensively investigated in indole-producing bacteria like Escherichia coli. To gain a deeper comprehension of its functional role, this study investigated how indole at concentrations of 0.5-1.0 mM found in the supernatant of Escherichia coli stationary phase culture was able to alter the virulence of non-indole-producing bacteria, such as Pseudomonas aeruginosa, Proteus mirabilis, and Klebsiella pneumoniae, which are naturally exposed to indole in mixed infections with Escherichia coli. RESULTS Biofilm formation, antimicrobial susceptibility, and efflux pump activity were the three phenotypic tests that were assessed. Indole was found to influence antibiotic susceptibly of Pseudomonas aeruginosa, Proteus mirabilis and Klebsiella pneumoniae to ciprofloxacin, imipenem, ceftriaxone, ceftazidime, and amikacin through significant reduction in MIC with fold change ranged from 4 to 16. Biofilm production was partially abrogated in both 32/45 Pseudomonas aeruginosa and all eight Proteus mirabilis, while induced biofilm production was observed in 30/40 Klebsiella pneumoniae. Moreover, acrAB and oqxAB, which encode four genes responsible for resistance-nodulation-division multidrug efflux pumps in five isolates of Klebsiella pneumoniae were investigated genotypically using quantitative real-time (qRT)-PCR. This revealed that all four genes exhibited reduced expression indicated by 2^-ΔΔCT < 1 in indole-treated isolates compared to control group. CONCLUSION The outcomes of qRT-PCR investigation of efflux pump expression have established a novel clear correlation of the molecular mechanism that lies beneath the influence of indole on bacterial antibiotic tolerance. This research provides novel perspectives on the various mechanisms and diverse biological functions of indole signaling and how it impacts the pathogenicity of non-indole-producing bacteria.
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Affiliation(s)
- Galila G Salama
- Faculty of Pharmacy, Department of Microbiology and Immunology, Helwan University, P.O. Box 11795, Ain-Helwan, Cairo, Egypt
| | - Taghrid S El-Mahdy
- Faculty of Pharmacy, Department of Microbiology and Immunology, Helwan University, P.O. Box 11795, Ain-Helwan, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology, and Information (MTI), Cairo, Egypt
| | - Walaa H Moustafa
- Faculty of Pharmacy, Department of Microbiology and Immunology, Helwan University, P.O. Box 11795, Ain-Helwan, Cairo, Egypt
| | - Mohamed Emara
- Faculty of Pharmacy, Department of Microbiology and Immunology, Helwan University, P.O. Box 11795, Ain-Helwan, Cairo, Egypt.
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27
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Ikpe F, Williams T, Orok E, Ikpe A. Antimicrobial resistance: use of phage therapy in the management of resistant infections. Mol Biol Rep 2024; 51:925. [PMID: 39167154 DOI: 10.1007/s11033-024-09870-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
The emergence and increase in antimicrobial resistance (AMR) is now widely recognized as a major public health challenge. Traditional antimicrobial drugs are becoming increasingly ineffective, while the development of new antibiotics is waning. As a result, alternative treatments for infections are garnering increased interest. Among these alternatives, bacteriophages, also known as phages, are gaining renewed attention and are reported to offer a promising solution to alleviate the burden of bacterial infections. This review discusses the current successes of phage therapy (PT) against multidrug-resistant organisms (MDROs), such as Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter spp. The review also compares the efficacy of PT with that of chemical antibiotics, reporting on its benefits and limitations, while highlighting its impact on the human gut microbiome and immune system. Despite its potential, phage therapy is reported to face challenges such as the narrow antibacterial range, the complexity of developing phage cocktails, and the need for precise dosing and duration protocols. Nevertheless, continued research, improved regulatory frameworks, and increased public awareness are essential to realize its full potential and integration into standard medical practice, paving the way for innovative treatments that can effectively manage infections in an era of rising antimicrobial resistance.
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Affiliation(s)
- Favour Ikpe
- Department of Pharmaceutical Microbiology and Biotechnology, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Tonfamoworio Williams
- Department of Pharmaceutical Microbiology and Biotechnology, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Edidiong Orok
- Department of Clinical Pharmacy and Public Health, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria.
| | - Augustine Ikpe
- Department of Sciences, Champion Group of Schools, Okene, Kogi State, Nigeria
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28
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Alves LDF, Moore JB, Kell DB. The Biology and Biochemistry of Kynurenic Acid, a Potential Nutraceutical with Multiple Biological Effects. Int J Mol Sci 2024; 25:9082. [PMID: 39201768 PMCID: PMC11354673 DOI: 10.3390/ijms25169082] [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: 07/19/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 09/03/2024] Open
Abstract
Kynurenic acid (KYNA) is an antioxidant degradation product of tryptophan that has been shown to have a variety of cytoprotective, neuroprotective and neuronal signalling properties. However, mammalian transporters and receptors display micromolar binding constants; these are consistent with its typically micromolar tissue concentrations but far above its serum/plasma concentration (normally tens of nanomolar), suggesting large gaps in our knowledge of its transport and mechanisms of action, in that the main influx transporters characterized to date are equilibrative, not concentrative. In addition, it is a substrate of a known anion efflux pump (ABCC4), whose in vivo activity is largely unknown. Exogeneous addition of L-tryptophan or L-kynurenine leads to the production of KYNA but also to that of many other co-metabolites (including some such as 3-hydroxy-L-kynurenine and quinolinic acid that may be toxic). With the exception of chestnut honey, KYNA exists at relatively low levels in natural foodstuffs. However, its bioavailability is reasonable, and as the terminal element of an irreversible reaction of most tryptophan degradation pathways, it might be added exogenously without disturbing upstream metabolism significantly. Many examples, which we review, show that it has valuable bioactivity. Given the above, we review its potential utility as a nutraceutical, finding it significantly worthy of further study and development.
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Affiliation(s)
- Luana de Fátima Alves
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - J. Bernadette Moore
- School of Food Science & Nutrition, University of Leeds, Leeds LS2 9JT, UK;
- Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Søltofts Plads, 2800 Kongens Lyngby, Denmark
- Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
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Belay WY, Getachew M, Tegegne BA, Teffera ZH, Dagne A, Zeleke TK, Abebe RB, Gedif AA, Fenta A, Yirdaw G, Tilahun A, Aschale Y. Mechanism of antibacterial resistance, strategies and next-generation antimicrobials to contain antimicrobial resistance: a review. Front Pharmacol 2024; 15:1444781. [PMID: 39221153 PMCID: PMC11362070 DOI: 10.3389/fphar.2024.1444781] [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: 06/06/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Antibacterial drug resistance poses a significant challenge to modern healthcare systems, threatening our ability to effectively treat bacterial infections. This review aims to provide a comprehensive overview of the types and mechanisms of antibacterial drug resistance. To achieve this aim, a thorough literature search was conducted to identify key studies and reviews on antibacterial resistance mechanisms, strategies and next-generation antimicrobials to contain antimicrobial resistance. In this review, types of resistance and major mechanisms of antibacterial resistance with examples including target site modifications, decreased influx, increased efflux pumps, and enzymatic inactivation of antibacterials has been discussed. Moreover, biofilm formation, and horizontal gene transfer methods has also been included. Furthermore, measures (interventions) taken to control antimicrobial resistance and next-generation antimicrobials have been discussed in detail. Overall, this review provides valuable insights into the diverse mechanisms employed by bacteria to resist the effects of antibacterial drugs, with the aim of informing future research and guiding antimicrobial stewardship efforts.
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Affiliation(s)
- Wubetu Yihunie Belay
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Melese Getachew
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Bantayehu Addis Tegegne
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Zigale Hibstu Teffera
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Abebe Dagne
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Tirsit Ketsela Zeleke
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Rahel Belete Abebe
- Department of clinical pharmacy, College of medicine and health sciences, University of Gondar, Gondar, Ethiopia
| | - Abebaw Abie Gedif
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Abebe Fenta
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Getasew Yirdaw
- Department of environmental health science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Adane Tilahun
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Yibeltal Aschale
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
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Dubey AK, Sardana D, Verma T, Alam P, Chattopadhyay A, Nandini SS, Khamari B, Bulagonda EP, Sen S, Nandi D. Quantifying Membrane Alterations with Tailored Fluorescent Dyes: A Rapid Antibiotic Resistance Profiling Methodology. ACS Infect Dis 2024; 10:2836-2859. [PMID: 39024306 DOI: 10.1021/acsinfecdis.4c00249] [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] [Indexed: 07/20/2024]
Abstract
Accurate detection of bacterial antibiotic sensitivity is crucial for theranostics and the containment of antibiotic-resistant infections. However, the intricate task of detecting and quantifying the antibiotic-induced changes in the bacterial cytoplasmic membrane, and their correlation with other metabolic pathways leading to antibiotic resistance, poses significant challenges. Using a novel class of 4-aminophthalimide (4AP)-based fluorescent dyes with precisely tailored alkyl chains, namely 4AP-C9 and 4AP-C13, we quantify stress-mediated alterations in E. coli membranes. Leveraging the unique depth-dependent positioning and environment-sensitive fluorescence properties of these dyes, we detect antibiotic-induced membrane damage through single-cell imaging and monitoring the fluorescence peak maxima difference ratio (PMDR) of the dyes within the bacterial membrane, complemented by other methods. The correlation between the ROS-induced cytoplasmic membrane damage and the PMDR of dyes quantifies sensitivity against bactericidal antibiotics, which correlates to antibiotic-induced lipid peroxidation. Significantly, our findings largely extend to clinical isolates of E. coli and other ESKAPE pathogens like K. pneumoniae and Enterobacter subspecies. Our data reveal that 4AP-Cn probes can potentially act as precise scales to detect antibiotic-induced membrane damage ("thinning") occurring at a subnanometer scale through the quantification of dyes' PMDR, making them promising membrane dyes for rapid detection of bacterial antibiotic resistance, distinguishing sensitive and resistant infections with high specificity in a clinical setup.
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Affiliation(s)
- Ashim Kumar Dubey
- Undergraduate Programme, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Deepika Sardana
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Taru Verma
- Centre for BioSystems, Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Parvez Alam
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Avik Chattopadhyay
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Santhi Sanil Nandini
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Balaram Khamari
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Eswarappa Pradeep Bulagonda
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Sobhan Sen
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
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de Oliveira JR, de Morais Oliveira-Tintino CD, Carneiro JNP, Dos Santos AG, de Lima AM, Soares AM, Morais-Braga MFB, Coutinho HDM, Nicolete R. Crotamine derived from Crotalus durissus terrificus venom combined with drugs increases in vitro antibacterial and antifungal activities. Arch Microbiol 2024; 206:368. [PMID: 39107625 DOI: 10.1007/s00203-024-04096-z] [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: 05/23/2024] [Revised: 07/25/2024] [Accepted: 07/28/2024] [Indexed: 08/15/2024]
Abstract
This study investigated crotamine (CTA), a peptide derived from the venom of the South American rattlesnake Crotalus durissus terrificus, known for its exceptional cell penetration potential. The objective was to explore the antibacterial and antifungal activity of CTA, its ability to inhibit efflux pumps and evaluate the effectiveness of its pharmacological combination with antibiotics and antifungals. In microbiological assays, CTA in combination with antibiotics was tested against strains of S. aureus and the inhibition of NorA, Tet(K) and MepA efflux pumps was also evaluated. CTA alone did not present clinically relevant direct antibacterial action, presenting MIC > 209.7 µM against strains S. aureus 1199B, IS-58, K2068. The standard efflux pump inhibitor CCCP showed significant effects in all negative relationships to assay reproducibility. Against the S. aureus 1199B strain, CTA (20.5 µM) associated with norfloxacin diluted 10 × (320.67 µM) showed a potentiating effect, in relation to the control. Against the S. aureus IS-58 strain, the CTA associated with tetracycline did not show a significant combinatorial effect, either with 2304 or 230.4 µM tetracycline. CTA at a concentration of 2.05 µM associated with ciprofloxacin at a concentration of 309.4 µM showed a significant potentiating effect. In association with EtBr, CTA at concentrations of 2.05 and 20.5 µM potentiated the effect in all strains tested, reducing the prevention of NorA, Tet(K) and MepA efflux pumps. In the C. albicans strain, a potentiating effect of fluconazole (334.3 µM) was observed when combined with CTA (2.05 µM). Against the C. tropicalis strain, a significant effect was also observed in the association of fluconazole 334.3 µM, where CTA 2.05 µM considerably reduced fungal growth and decreased the potentiation of fluconazole. Against the C. krusei strain, no significant potentiating effect of fluconazole was obtained by CTA. Our results indicate that CTA in pharmacological combination potentiates the effects of antibiotics and antifungal. This represents a new and promising antimicrobial strategy for treating a wide variety of infections.
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Affiliation(s)
- Juliana Ramos de Oliveira
- Rede Nordeste de Biotecnologia (Renorbio), Fortaleza, CE, Brazil
- Fundação Oswaldo Cruz, Fiocruz, Fiocruz Ceará, Eusébio, CE, Brazil
| | | | | | | | - Anderson Maciel de Lima
- Laboratório de Biotecnologia e Educação Aplicadas à Saúde Única (LABIOPROT), Fiocruz Rondônia, Porto Velho, RO, Brazil
| | - Andreimar Martins Soares
- Laboratório de Biotecnologia e Educação Aplicadas à Saúde Única (LABIOPROT), Fiocruz Rondônia, Porto Velho, RO, Brazil
- Centro Universitário São Lucas (São Lucas PVH), Porto Velho, RO, Brazil
- Instituto Nacional de Ciência e Tecnologia de Epidemiologia da Amazônia Ocidental (INCT EPiAmO), Porto Velho, RO, Brazil
- Rede de Pesquisa e CONhecimento de EXcelência na Amazônia Ocidental/Oriental (RED-Conexao), Manaus, AM, Brazil
| | | | | | - Roberto Nicolete
- Rede Nordeste de Biotecnologia (Renorbio), Fortaleza, CE, Brazil.
- Fundação Oswaldo Cruz, Fiocruz, Fiocruz Ceará, Eusébio, CE, Brazil.
- Rede de Pesquisa e CONhecimento de EXcelência na Amazônia Ocidental/Oriental (RED-Conexao), Manaus, AM, Brazil.
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Klenotic PA, Yu EW. Structural analysis of resistance-nodulation cell division transporters. Microbiol Mol Biol Rev 2024; 88:e0019823. [PMID: 38551344 PMCID: PMC11332337 DOI: 10.1128/mmbr.00198-23] [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] [Indexed: 06/28/2024] Open
Abstract
SUMMARYInfectious bacteria have both intrinsic and acquired mechanisms to combat harmful biocides that enter the cell. Through adaptive pressures, many of these pathogens have become resistant to many, if not all, of the current antibiotics used today to treat these often deadly infections. One prominent mechanism is the upregulation of efflux systems, especially the resistance-nodulation-cell division class of exporters. These tripartite systems consist of an inner membrane transporter coupled with a periplasmic adaptor protein and an outer membrane channel to efficiently transport a diverse array of substrates from inside the cell to the extracellular space. Detailed mechanistic insight into how these inner membrane transporters recognize and shuttle their substrates can ultimately inform both new antibiotic and efflux pump inhibitor design. This review examines the structural basis of substrate recognition of these pumps and the molecular mechanisms underlying multidrug extrusion, which in turn mediate antimicrobial resistance in bacterial pathogens.
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Affiliation(s)
- Philip A. Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Zhou W, Ding W, Wu X, Sun J, Bai W. Microbial synthesis of anthocyanins and pyranoanthocyanins: current bottlenecks and potential solutions. Crit Rev Food Sci Nutr 2024:1-18. [PMID: 38935054 DOI: 10.1080/10408398.2024.2369703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Anthocyanins (ACNs) are secondary metabolites found in plants. Due to their impressive biological activities, ACNs have gained significant popularity and extensive application within the food, pharmaceutical, and nutraceutical industries. A derivative of ACNs: pyranoanthocyanins (PACNs) possesses more stable properties and interesting biological activities. However, conventional methods for the production of ACNs, including chemical synthesis and plant extraction, involve organic solvents. Microbial synthesis of ACNs from renewable biomass, such as amino acids or flavonoids, is considered a sustainable and environmentally friendly method for large-scale production of ACNs. Recently, the construction of microbial cell factories (MCFs) for the efficient biosynthesis of ACNs and PACNs has attracted much attention. In this review, we summarize the cases of microbial synthesis of ACNs, and analyze the bottlenecks in reconstructing the metabolic pathways for synthesizing PACNs in microorganisms. Consequently, there is an urgent need to investigate the mechanisms behind the development of MCFs for PACNs synthesis. Such research also holds significant promise for advancing the production of food pigments. Meanwhile, we propose potential solutions to the bottleneck problem based on metabolic engineering and enzyme engineering. Finally, the development prospects of natural food and biotechnology are discussed.
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Affiliation(s)
- Weijie Zhou
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangdong, China
| | - Weiqiu Ding
- Institute of Microbial Biotechnology, Jinan University, Guangzhou, Guangdong, China
| | - Xingyuan Wu
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangdong, China
| | - Jianxia Sun
- Department of Food Science and Engineering, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangdong, China
| | - Weibin Bai
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangdong, China
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Vignolini T, Capitanio M, Caldini C, Gardini L, Pavone FS. Highly inclined light sheet allows volumetric super-resolution imaging of efflux pumps distribution in bacterial biofilms. Sci Rep 2024; 14:12902. [PMID: 38839922 PMCID: PMC11153600 DOI: 10.1038/s41598-024-63729-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/31/2024] [Indexed: 06/07/2024] Open
Abstract
Bacterial biofilms are highly complex communities in which isogenic bacteria display different gene expression patterns and organize in a three-dimensional mesh gaining enhanced resistance to biocides. The molecular mechanisms behind such increased resistance remain mostly unknown, also because of the technical difficulties in biofilm investigation at the sub-cellular and molecular level. In this work we focus on the AcrAB-TolC protein complex, a multidrug efflux pump found in Enterobacteriaceae, whose overexpression is associated with most multiple drug resistance (MDR) phenotypes occurring in Gram-negative bacteria. We propose an optical method to quantify the expression level of the AcrAB-TolC pump within the biofilm volume at the sub-cellular level, with single-molecule sensitivity. Through a combination of super-resolution PALM with single objective light sheet and precision genome editing, we can directly quantify the spatial distribution of endogenous AcrAB-TolC pumps expressed in both planktonic bacteria and, importantly, within the bacterial biofilm volume. We observe a gradient of pump density within the biofilm volume and over the course of biofilm maturation. Notably, we propose an optical method that could be broadly employed to achieve volumetric super-resolution imaging of thick samples.
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Affiliation(s)
- T Vignolini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy.
- Parasite RNA Biology Group, Institut Pasteur, Université Paris Cité, 75015, Paris, France.
| | - M Capitanio
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
| | - C Caldini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
| | - L Gardini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
- National Institute of Optics, National Research Council, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
| | - F S Pavone
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
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Suzuki S, Morita Y, Ishige S, Kai K, Kawasaki K, Matsushita K, Ogura K, Miyoshi-Akiyama† T, Shimizu T. Effects of quorum sensing-interfering agents, including macrolides and furanone C-30, and an efflux pump inhibitor on nitrosative stress sensitivity in Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001464. [PMID: 38900549 PMCID: PMC11263931 DOI: 10.1099/mic.0.001464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Long-term administration of certain macrolides is efficacious in patients with persistent pulmonary Pseudomonas aeruginosa infection, despite how limited the clinically achievable concentrations are, being far below their MICs. An increase in the sub-MIC of macrolide exposure-dependent sensitivity to nitrosative stress is a typical characteristic of P. aeruginosa. However, a few P. aeruginosa clinical isolates do not respond to sub-MIC of macrolide treatment. Therefore, we examined the effects of sub-MIC of erythromycin (EM) on the sensitivity to nitrosative stress together with an efflux pump inhibitor (EPI) phenylalanine arginyl β-naphthylamide (PAβN). The sensitivity to nitrosative stress increased, suggesting that the efflux pump was involved in inhibiting the sub-MIC of macrolide effect. Analysis using efflux pump-mutant P. aeruginosa revealed that MexAB-OprM, MexXY-OprM, and MexCD-OprJ are factors in reducing the sub-MIC of macrolide effect. Since macrolides interfere with quorum sensing (QS), we demonstrated that the QS-interfering agent furanone C-30 (C-30) producing greater sensitivity to nitric oxide (NO) stress than EM. The effect of C-30 was decreased by overproduction of MexAB-OprM. To investigate whether the increase in the QS-interfering agent exposure-dependent sensitivity to nitrosative stress is characteristic of P. aeruginosa clinical isolates, we examined the viability of P. aeruginosa treated with NO. Although treatment with EM could reduce cell viability, a high variability in EM effects was observed. Conversely, C-30 was highly effective at reducing cell viability. Treatment with both C-30 and PAβN was sufficiently effective against the remaining isolates. Therefore, the combination of a QS-interfering agent and an EPI could be effective in treating P. aeruginosa infections.
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Affiliation(s)
- Shin Suzuki
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba, 260-8670, Japan
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chiba, 260-8677, Japan
| | - Yuji Morita
- Department of Infection Control Science, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo, 204-8588, Japan
| | - Shota Ishige
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba, 260-8670, Japan
| | - Kiyohiro Kai
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba, 260-8670, Japan
| | - Kenji Kawasaki
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chiba, 260-8677, Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chiba, 260-8677, Japan
| | - Kohei Ogura
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto, 6110011, Japan
| | - Tohru Miyoshi-Akiyama†
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Takeshi Shimizu
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba, 260-8670, Japan
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Singh G, Rana A, Smriti. Decoding antimicrobial resistance: unraveling molecular mechanisms and targeted strategies. Arch Microbiol 2024; 206:280. [PMID: 38805035 DOI: 10.1007/s00203-024-03998-2] [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: 03/31/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Antimicrobial resistance poses a significant global health threat, necessitating innovative approaches for combatting it. This review explores various mechanisms of antimicrobial resistance observed in various strains of bacteria. We examine various strategies, including antimicrobial peptides (AMPs), novel antimicrobial materials, drug delivery systems, vaccines, antibody therapies, and non-traditional antibiotic treatments. Through a comprehensive literature review, the efficacy and challenges of these strategies are evaluated. Findings reveal the potential of AMPs in combating resistance due to their unique mechanisms and lower propensity for resistance development. Additionally, novel drug delivery systems, such as nanoparticles, show promise in enhancing antibiotic efficacy and overcoming resistance mechanisms. Vaccines and antibody therapies offer preventive measures, although challenges exist in their development. Non-traditional antibiotic treatments, including CRISPR-Cas systems, present alternative approaches to combat resistance. Overall, this review underscores the importance of multifaceted strategies and coordinated global efforts to address antimicrobial resistance effectively.
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Affiliation(s)
- Gagandeep Singh
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India
| | - Anita Rana
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India.
| | - Smriti
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India
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37
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Zhang G, Wang H, Zhang Z, Zhang L, Guo G, Yang J, Yuan F, Ju F. Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework. Brief Bioinform 2024; 25:bbae319. [PMID: 39007592 PMCID: PMC11247404 DOI: 10.1093/bib/bbae319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/18/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
High-throughput DNA sequencing technologies decode tremendous amounts of microbial protein-coding gene sequences. However, accurately assigning protein functions to novel gene sequences remain a challenge. To this end, we developed FunGeneTyper, an extensible framework with two new deep learning models (i.e., FunTrans and FunRep), structured databases, and supporting resources for achieving highly accurate (Accuracy > 0.99, F1-score > 0.97) and fine-grained classification of antibiotic resistance genes (ARGs) and virulence factor genes. Using an experimentally confirmed dataset of ARGs comprising remote homologous sequences as the test set, our framework achieves by-far-the-best performance in the discovery of new ARGs from human gut (F1-score: 0.6948), wastewater (0.6072), and soil (0.5445) microbiomes, beating the state-of-the-art bioinformatics tools and sequence alignment-based (F1-score: 0.0556-0.5065) and domain-based (F1-score: 0.2630-0.5224) annotation approaches. Furthermore, our framework is implemented as a lightweight, privacy-preserving, and plug-and-play neural network module, facilitating its versatility and accessibility to developers and users worldwide. We anticipate widespread utilization of FunGeneTyper (https://github.com/emblab-westlake/FunGeneTyper) for precise classification of protein-coding gene functions and the discovery of numerous valuable enzymes. This advancement will have a significant impact on various fields, including microbiome research, biotechnology, metagenomics, and bioinformatics.
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Affiliation(s)
- Guoqing Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
- Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Hui Wang
- Representation Learning Laboratory, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Zhiguo Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Lu Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Guibing Guo
- Software College, Northeastern University, Shenyang, Liaoning 110169, China
| | - Jian Yang
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Fajie Yuan
- Representation Learning Laboratory, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
- Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang 310030, China
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
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Lee T, Lee S, Kim MK, Ahn JH, Park JS, Seo HW, Park KH, Chong Y. 3- O-Substituted Quercetin: an Antibiotic-Potentiating Agent against Multidrug-Resistant Gram-Negative Enterobacteriaceae through Simultaneous Inhibition of Efflux Pump and Broad-Spectrum Carbapenemases. ACS Infect Dis 2024; 10:1624-1643. [PMID: 38652574 DOI: 10.1021/acsinfecdis.3c00715] [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] [Indexed: 04/25/2024]
Abstract
The discovery of safe and efficient inhibitors against efflux pumps as well as metallo-β-lactamases (MBL) is one of the main challenges in the development of multidrug-resistant (MDR) reversal agents which can be utilized in the treatment of carbapenem-resistant Gram-negative bacteria. In this study, we have identified that introduction of an ethylene-linked sterically demanding group at the 3-OH position of the previously reported MDR reversal agent di-F-Q endows the resulting compounds with hereto unknown multitarget inhibitory activity against both efflux pumps and broad-spectrum β-lactamases including difficult-to-inhibit MBLs. A molecular docking study of the multitarget inhibitors against efflux pump, as well as various classes of β-lactamases, revealed that the 3-O-alkyl substituents occupy the novel binding sites in efflux pumps as well as carbapenemases. Not surprisingly, the multitarget inhibitors rescued the antibiotic activity of a carbapenem antibiotic, meropenem (MEM), in NDM-1 (New Delhi Metallo-β-lactamase-1)-producing carbapenem-resistant Enterobacteriaceae (CRE), and they reduced MICs of MEM more than four-fold (synergistic effect) in 8-9 out of 14 clinical strains. The antibiotic-potentiating activity of the multitarget inhibitors was also demonstrated in CRE-infected mouse model. Taken together, these results suggest that combining inhibitory activity against two critical targets in MDR Gram-negative bacteria, efflux pumps, and β-lactamases, in one molecule is possible, and the multitarget inhibitors may provide new avenues for the discovery of safe and efficient MDR reversal agents.
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Affiliation(s)
- Taegum Lee
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea
| | - Seongyeon Lee
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea
| | - Mi Kyoung Kim
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea
| | - Joong Hoon Ahn
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea
| | - Ji Sun Park
- Infectious Disease Research Center, Korea Research Institute of Bioscience & Biotechnology, Yuseong-gu, Daejeon 34141, Korea
| | - Hwi Won Seo
- Infectious Disease Research Center, Korea Research Institute of Bioscience & Biotechnology, Yuseong-gu, Daejeon 34141, Korea
| | - Ki-Ho Park
- Department of Infectious Disease, Kyung Hee University School of Medicine, Seoul 02447, Korea
| | - Youhoon Chong
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea
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Saini M, Gaurav A, Hussain A, Pathania R. Small Molecule IITR08367 Potentiates Antibacterial Efficacy of Fosfomycin against Acinetobacter baumannii by Efflux Pump Inhibition. ACS Infect Dis 2024; 10:1711-1724. [PMID: 38562022 DOI: 10.1021/acsinfecdis.4c00077] [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] [Indexed: 04/04/2024]
Abstract
Fosfomycin is a broad-spectrum single-dose therapy approved for treating lower urinary tract infections. Acinetobacter baumannii, one of the five major UTI-causing pathogens, is intrinsically resistant to fosfomycin. Reduced uptake and active efflux are major reasons for this intrinsic resistance. AbaF, a major facilitator superfamily class of transporter in A. baumannii, is responsible for fosfomycin efflux and biofilm formation. This study describes the identification and validation of a novel small-molecule efflux pump inhibitor that potentiates fosfomycin efficacy against A. baumannii. An AbaF inhibitor screening was performed against Escherichia coli KAM32/pUC18_abaF, using the noninhibitory concentration of 24 putative efflux pump inhibitors. The inhibitory activity of IITR08367 [bis(4-methylbenzyl) disufide] against fosfomycin/H+ antiport was validated using ethidium bromide efflux, quinacrine-based proton-sensitive fluorescence, and membrane depolarization assays. IITR08367 inhibits fosfomycin/H+ antiport activity by perturbing the transmembrane proton gradient. IITR08367 is a nontoxic molecule that potentiates fosfomycin activity against clinical strains of A. baumannii and prevents biofilm formation by inhibiting efflux pump (AbaF). The IITR08367-fosfomycin combination reduced bacterial burden by > 3 log10 in kidney and bladder tissue in the murine UTI model. Overall, fosfomycin, in combination with IITR08367, holds the potential to treat urinary tract infections caused by A. baumannii.
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Affiliation(s)
- Mahak Saini
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247 667, India
| | - Amit Gaurav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247 667, India
| | - Arsalan Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247 667, India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247 667, India
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Martin ALAR, Pereira RLS, Rocha JE, Farias PAM, Freitas TS, Caldas FRDL, Figueredo FG, Sampaio NFL, Oliveira-Tintino CDDM, Tintino SR, da Hora GCA, Lima MCP, de Menezes IRA, Carvalho DT, Coutinho HDM, Fonteles MMF. Unlocking bacterial defense: Exploring the potent inhibition of NorA efflux pump by coumarin derivatives in Staphylococcus aureus. Microb Pathog 2024; 190:106608. [PMID: 38503396 DOI: 10.1016/j.micpath.2024.106608] [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: 11/24/2023] [Revised: 02/27/2024] [Accepted: 03/03/2024] [Indexed: 03/21/2024]
Abstract
The occurrence of bacterial resistance has been increasing, compromising the treatment of various infections. The high virulence of Staphylococcus aureus allows for the maintenance of the infectious process, causing many deaths and hospitalizations. The MepA and NorA efflux pumps are transporter proteins responsible for expelling antimicrobial agents such as fluoroquinolones from the bacterial cell. Coumarins are phenolic compounds that have been studied for their diverse biological actions, including against bacteria. A pharmacokinetic in silico characterization of compounds C10, C11, C13, and C14 was carried out according to the principles of Lipinski's Rule of Five, in addition to searching for similarity in ChemBL and subsequent search for publications in CAS SciFinder. All compounds were evaluated for their in vitro antibacterial and modulatory activity against standard and multidrug-resistant Gram-positive and Gram-negative strains. The effect of coumarins C9, C10, C11, C13, and C14 as efflux pump inhibitors in Staphylococcus aureus strains was evaluated using the microdilution method (MepA or NorA) and fluorimetry (NorA). The behavior of coumarins regarding the efflux pump was determined from their interaction properties with the membrane and coumarin-protein using molecular docking and molecular dynamics simulations. Only the isolated coumarin compound C13 showed antibacterial activity against standard strains of Staphylococcus aureus and Escherichia coli. However, the other tested coumarins showed modulatory capacity for fluoroquinolone and aminoglycoside antibacterials. Compounds C10, C13, and C14 were effective in reducing the MIC of both antibiotics for both multidrug-resistant strains, while C11 potentiated the effect of norfloxacin and gentamicin for Gram-positive and Gram-negative bacteria and only norfloxacin for Gram-negative. Only coumarin C14 produced synergistic effects when associated with ciprofloxacin in MepA-carrying strains. All tested coumarins have the ability to inhibit the NorA efflux pump present in Staphylococcus aureus, both in reducing the MIC and inducing increased ethidium bromide fluorescence emission in fluorimetry. The findings of this study offer an atomistic perspective on the potential of coumarins as active inhibitors of the NorA pump, highlighting their specific mode of action mainly targeting protein inhibition. In molecular docking, it was observed that coumarins are capable of interacting with various amino acid residues of the NorA pump. The simulation showed that coumarin C10 can cross the bilayer; however, the other coumarins interacted with the membrane but were unable to cross it. Coumarins demonstrated their potentiating role in the effect of norfloxacin through a dual mechanism: efflux pump inhibition through direct interaction with the protein (C9, C10, C11, and C13) and increased interaction with the membrane (C10 and C13). In the context of pharmacokinetic prediction studies, the studied structures have a suitable chemical profile for possible oral use. We suggest that coumarin derivatives may be an interesting alternative in the future for the treatment of resistant bacterial infections, with the possibility of a synergistic effect with other antibacterials, although further studies are needed to characterize their therapeutic effects and toxicity.
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Affiliation(s)
- Ana Luíza A R Martin
- Department of Physiology and Pharmacology, Federal University of Ceará - UFC, 60430-160, Fortaleza, Brazil; Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil; School of Medicine, Medical Education Institute - IDOMED, 63048-080, Juazeiro do Norte, Brazil
| | | | - Janaína Esmeraldo Rocha
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil
| | - Pablo A M Farias
- School of Medicine, Medical Education Institute - IDOMED, 63048-080, Juazeiro do Norte, Brazil; CECAPE College, 63024-015, Juazeiro do Norte, Brazil
| | - Thiago S Freitas
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil
| | | | - Fernando G Figueredo
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil; School of Medicine, Medical Education Institute - IDOMED, 63048-080, Juazeiro do Norte, Brazil
| | - Nadghia Figueiredo Leite Sampaio
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil; School of Medicine, Medical Education Institute - IDOMED, 63048-080, Juazeiro do Norte, Brazil
| | | | - Saulo Relison Tintino
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil
| | | | | | - Irwin Rose A de Menezes
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil
| | - Diogo T Carvalho
- School of Pharmacy, Federal University of Alfenas - UNIFAL, 37130-001, Alfenas, Brazil
| | - Henrique D M Coutinho
- Department of Biological Chemistry, Regional University of Cariri - URCA. 63105-000, Crato, Brazil.
| | - Marta M F Fonteles
- Department of Physiology and Pharmacology, Federal University of Ceará - UFC, 60430-160, Fortaleza, Brazil
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Santana JEG, Oliveira-Tintino CDDM, Alencar GG, Siqueira GM, Almeida-Bezerra JW, Viana Rodrigues JP, Pinheiro Gonçalves VB, Nicolete R, Tintino SR, Coutinho HDM, Silva TGD. Liposomal nanoformulations with trans-caryophyllene and caryophyllene oxide: do they have an inhibitory action on the efflux pumps NorA, Tet(K), MsrA, and MepA? Chem Biol Interact 2024; 393:110945. [PMID: 38460934 DOI: 10.1016/j.cbi.2024.110945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/09/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
This study aimed to evaluate the antibacterial and inhibitory action of NorA, Tet(K), MsrA and MepA efflux pumps in S. aureus strains using the sesquiterpenes named trans-caryophyllene and caryophyllene oxide, both isolated and encapsulated in liposomes. The antibacterial and inhibitory action of these efflux pumps was evaluated through the serial microdilution test in 96-well microplates. Each sesquiterpene and liposome/sesquiterpene was combined with antibiotics and ethidium bromide (EtBr). The antibiotics named norfloxacin, tetracycline and erythromycin were used. The 1199 B, IS-58, RN4220 and K2068 S. aureus strains carrying NorA, Tet(K), MsrA and MepA, respectively, were tested. In the fluorescence measurement test, K2068 S. aureus was incubated with the sesquiterpenes and EtBr, and the fluorescence emission by EtBr was measured. The tested substances did not show direct antibacterial activity, with MIC >1024 μg/mL. Nonetheless, the isolated trans-caryophyllene and caryophyllene oxide reduced the MIC of antibiotics and EtBr, indicating inhibition of NorA, Tet(K) and MsrA. In the fluorescence test, these same sesquiterpenes increased fluorescence emission, indicating inhibition of MepA. Therefore, the sesquiterpenes named trans-caryophyllene and caryophyllene oxide did not show direct antibacterial action; however, in their isolated form, they showed possible inhibitory action on NorA, Tet(K), MsrA and MepA efflux pumps. They may also act in antibiotic potentiation. Further studies are needed to identify the mechanisms involved in antibiotic potentiation and efflux pump inhibitory action.
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Affiliation(s)
| | | | - Gabriel Gonçalves Alencar
- Departament of Biological Chemistry, Universidade Regional Do Cariri (URCA), Crato, 63105-010, Ceará, Brazil
| | - Gustavo Miguel Siqueira
- Departament of Biological Chemistry, Universidade Regional Do Cariri (URCA), Crato, 63105-010, Ceará, Brazil
| | | | | | | | - Roberto Nicolete
- Oswaldo Cruz Foundation (Fiocruz Ceará), Eusebio, 61773-270, Ceará, Brazil
| | - Saulo Relison Tintino
- Departament of Biological Chemistry, Universidade Regional Do Cariri (URCA), Crato, 63105-010, Ceará, Brazil
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Daw Elbait G, Daou M, Abuoudah M, Elmekawy A, Hasan SW, Everett DB, Alsafar H, Henschel A, Yousef AF. Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater. PLoS One 2024; 19:e0298325. [PMID: 38578803 PMCID: PMC10997137 DOI: 10.1371/journal.pone.0298325] [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: 05/29/2023] [Accepted: 01/18/2024] [Indexed: 04/07/2024] Open
Abstract
Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas. ARGs that confer resistance to 11 antibiotic classes have been identified in these wastewater samples using both methods, with the most abundant observed classes of ARGs conferring resistance to aminoglycoside, multidrug-resistance (MDR), macrolide-lincosamide-streptogramin B (MLSB), tetracycline and beta-lactams. In comparing the methods, we observed a strong correlation of relative abundance of ARGs obtained by the two tested methods for the majority of antibiotic classes. Finally, we investigated the source of discrepancies in the results obtained by the two methods. This analysis revealed that false negatives were more likely to occur in qPCR due to mutated primer target sites, whereas ARGs with incomplete or low coverage were not detected by the sequencing method due to the parameters set in the bioinformatics pipeline. Indeed, despite the good correlation between the methods, each has its advantages and disadvantages which are also discussed here. By using both methods together, a more robust ARG surveillance program can be established. Overall, the work described here can aid wastewater treatment plants that plan on implementing an ARG surveillance program.
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Affiliation(s)
- Gihan Daw Elbait
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mariane Daou
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Miral Abuoudah
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed Elmekawy
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Shadi W. Hasan
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Chemical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Dean B. Everett
- Department of Pathology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Infection Research Unit, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Emirates Bio-research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Andreas Henschel
- Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed F. Yousef
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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Koti K, Rodas-Gonzalez A, Nadon C, McAllister T, Yang X, Narváez-Bravo C. Evaluating disinfectant efficacy on mixed biofilms comprising Shiga toxigenic Escherichia coli, lactic acid bacteria, and spoilage microorganisms. Front Microbiol 2024; 15:1360645. [PMID: 38633705 PMCID: PMC11021663 DOI: 10.3389/fmicb.2024.1360645] [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: 12/23/2023] [Accepted: 03/07/2024] [Indexed: 04/19/2024] Open
Abstract
This study aimed to investigate the impact of temperature and the presence of other microorganisms on the susceptibility of STEC to biocides. Mature biofilms were formed at both 10°C and 25°C. An inoculum of planktonic bacteria comprising 106 CFU/mL of spoilage bacteria and 103 CFU/mL of a single E. coli strain (O157, O111, O103, and O12) was used to form mixed biofilms. The following bacterial combinations were tested: T1: Carnobacterium piscicola + Lactobacillus bulgaricus + STEC, T2: Comamonas koreensis + Raoultella terrigena + STEC, and T3: Pseudomonas aeruginosa + C. koreensis + STEC. Tested biocides included quaternary ammonium compounds (Quats), sodium hypochlorite (Shypo), sodium hydroxide (SHyd), hydrogen peroxide (HyP), and BioDestroy®-organic peroxyacetic acid (PAA). Biocides were applied to 6-day-old biofilms. Minimum Bactericidal Concentrations (MBC) and Biofilm Eradication Concentrations (BEC) were determined. Planktonic cells and single-species biofilms exhibited greater susceptibility to sanitizers (p < 0.0001). Lactobacillus and Carnobacterium were more susceptible than the rest of the tested bacteria (p < 0.0001). Single species biofilms formed by E. coli O111, O121, O157, and O45 showed resistance (100%) to Shypo sanitizer (200 ppm) at 25°C. From the most effective to the least effective, sanitizer performance on single-species biofilms was PAA > Quats > HyP > SHyd > Shypo. In multi-species biofilms, spoilage bacteria within T1, T2, and T3 biofilms showed elevated resistance to SHyd (30%), followed by quats (23.25%), HyP (15.41%), SHypo (9.70%), and BioDestroy® (3.42%; p < 0.0001). Within T1, T2, and T3, the combined STEC strains exhibited superior survival to Quats (23.91%), followed by HyP (19.57%), SHypo (18.12%), SHyd (16.67%), and BioDestroy® (4.35%; p < 0.0001). O157:H7-R508 strains were less tolerant to Quats and Shypo when combined with T2 and T3 (p < 0.0001). O157:H7 and O103:H2 strains in mixed biofilms T1, T2, and T3 exhibited higher biocide resistance than the weak biofilm former, O145:H2 (p < 0.0001). The study shows that STEC within multi-species biofilms' are more tolerant to disinfectants.
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Affiliation(s)
- Kavitha Koti
- Department of Food and Human Nutritional Science, University of Manitoba, Winnipeg, MB, Canada
| | | | - Celine Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Tim McAllister
- Department of Food and Human Nutritional Science, University of Manitoba, Winnipeg, MB, Canada
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Xianqin Yang
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
| | - Claudia Narváez-Bravo
- Department of Food and Human Nutritional Science, University of Manitoba, Winnipeg, MB, Canada
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Yadav V, Zohib M, Singh S, Pal RK, Tripathi S, Jain A, Biswal BK, Dasgupta A, Arora A. Structural and biophysical characterization of PadR family protein Rv1176c of Mycobacterium tuberculosis H37Rv. Int J Biol Macromol 2024; 263:130455. [PMID: 38417748 DOI: 10.1016/j.ijbiomac.2024.130455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/01/2024]
Abstract
Rv1176c of Mycobacterium tuberculosis H37Rv belongs to the PadR-s1 subfamily of the PadR family of protein. Rv1176c forms a stable dimer in solution. Its stability is characterized by a thermal melting transition temperature (Tm) of 39.4 °C. The crystal structure of Rv1176c was determined at a resolution of 2.94 Å, with two monomers in the asymmetric unit. Each monomer has a characteristic N-terminal winged-helix-turn-helix DNA-binding domain. Rv1176c C-terminal is a coiled-coil dimerization domain formed of α-helices α5 to α7. In the Rv1176c dimer, there is domain-swapping of the C-terminal domain in comparison to other PadR homologs. In the dimer, there is a long inter-subunit tunnel in which different ligands can bind. Rv1176c was found to bind to the promoter region of its own gene with high specificity. M. smegmatis MC2 155 genome lacks homolog of Rv1176c. Therefore, it was used as a surrogate to characterize the functional role of Rv1176c. Expression of Rv1176c in M. smegmatis MC2 155 cells imparted enhanced tolerance towards oxidative stress. Rv1176c expressing M. smegmatis MC2 155 cells exhibited enhanced intracellular survival in J774A.1 murine macrophage cells. Overall, our studies demonstrate Rv1176c to be a PadR-s1 subfamily transcription factor that can moderate the effect of oxidative stress.
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Affiliation(s)
- Vikash Yadav
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Zohib
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shriya Singh
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Ravi Kant Pal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India
| | - Sarita Tripathi
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Anupam Jain
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Bichitra Kumar Biswal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India
| | - Arunava Dasgupta
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashish Arora
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Radha S, Ahamed AS, Gutmann JL, Bhavani S, Rajaraman G, Chittrarasu M. Comparative Evaluation of Antibacterial Efficacy, Molecular Docking of Ethanolic Extract of Blackseed, Seaweed and Calcium Hydroxide Intracanal Medicament with Enterococcus Faecalis Antigens. JOURNAL OF PHARMACY AND BIOALLIED SCIENCES 2024; 16:S1731-S1735. [PMID: 38882822 PMCID: PMC11174239 DOI: 10.4103/jpbs.jpbs_1152_23] [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: 11/09/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 06/18/2024] Open
Abstract
Aim To evaluate the inhibitory effect of ethanolic extract blackseed, seaweed, and calcium hydroxide intracanal medicament with Enterococcus faecalis biofilm. To study the binding interaction between the active components of blackseed and seaweed against the enterococcal surface protein of (E. faecalis) by molecular docking. Materials and Methods The ethanolic extracts of blackseed and seaweed were prepared using the Soxhlet apparatus. They were divided into three groups, namely, |Group I: Calcium hydroxide, Group II: Blackseed, and Group III: Seaweed. The antibacterial activity of the three groups was detected employing various concentrations ranging from 250, 125, and 62.5 μg/ml and based on the zone of inhibition. The inhibitory potential of medicaments to inhibit E. faecalis growth at various stages and kinetics plate were assessed following biofilm architecture evaluation by crystal violet biofilm assay. With the Swissdock suite, the molecular docking procedure was carried out. PyMOL version 4.1.5 was the program used for visualization. Since enterococcal surface protein (Esp) is primarily involved in the formation of biofilms, it was chosen as the target protein of E. faecalis. Based on their chromatographic investigations, Group II Thymoquinone (TQ) and Group III Ledenoxide were chosen as ligands. Results The percentage of inhibition of E. faecalis biofilm was analyzed as statistically significant observed within groups. On post-hoc analysis, significant differences were present between the groups (P < 0.05). Molecular docking reveals binding energies of thymoquinone (Group II) and ledenoxide (Group III) against the enterococcal surface protein of E. faecalis were -6.90 Kcal/mol and -6.44 Kcal/mol, respectively. Conclusion Compared to seaweed, black seed extract exhibited higher antibacterial activity against the E. faecalis biofilm in microbial inhibition and molecular interaction.
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Affiliation(s)
- S Radha
- Department of Conservative Dentistry and Endodontics, Government Dental College and Hospital, Cuddalor Dt, Tamil Nadu, India
| | - A Shafie Ahamed
- Department of Conservative Dentistry and Endodontics, Government Dental College and Hospital, Cuddalor Dt, Tamil Nadu, India
| | - James L Gutmann
- Texas A & M University, College of Dentistry, Dallas Texas, USA
| | - S Bhavani
- Department of Conservative Dentistry and Endodontics, Government Dental College and Hospital, Cuddalor Dt, Tamil Nadu, India
| | - G Rajaraman
- Department of Conservative Dentistry and Endodontics, Government Dental College and Hospital, Cuddalor Dt, Tamil Nadu, India
| | - M Chittrarasu
- Department of Conservative Dentistry and Endodontics, Vivekanantha Dental College for Women, Elayampalayam, Namakkal, Tamil Nadu, India
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Ren J, Wang M, Zhou W, Liu Z. Efflux pumps as potential targets for biofilm inhibition. Front Microbiol 2024; 15:1315238. [PMID: 38596384 PMCID: PMC11002903 DOI: 10.3389/fmicb.2024.1315238] [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: 10/10/2023] [Accepted: 01/26/2024] [Indexed: 04/11/2024] Open
Abstract
Biofilms account for a great deal of infectious diseases and contribute significantly to antimicrobial resistance. Efflux pumps confer antimicrobial resistance to microorganisms and involve multiple processes of biofilm formation. Efflux pump inhibitors (EPIs) are attracting considerable attention as a biofilm inhibition strategy. The regulatory functions of efflux pumps in biofilm formation such as mediating adherence, quorum sensing (QS) systems, and the expression of biofilm-associated genes have been increasingly identified. The versatile properties confer efflux pumps both positive and negative effects on biofilm formation. Furthermore, the expression and function of efflux pumps in biofilm formation are species-specific. Therefore, this review aims to detail the double-edged sword role of efflux pumps in biofilm formation to provide potential inhibition targets and give an overview of the effects of EPIs on biofilm formation.
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Affiliation(s)
| | | | - Wenjuan Zhou
- Department of Implantology, Yantai Stomatological Hospital Affiliated to Binzhou Medical University, Yantai, China
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47
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Zack KM, Sorenson T, Joshi SG. Types and Mechanisms of Efflux Pump Systems and the Potential of Efflux Pump Inhibitors in the Restoration of Antimicrobial Susceptibility, with a Special Reference to Acinetobacter baumannii. Pathogens 2024; 13:197. [PMID: 38535540 PMCID: PMC10974122 DOI: 10.3390/pathogens13030197] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/11/2025] Open
Abstract
Bacteria express a plethora of efflux pumps that can transport structurally varied molecules, including antimicrobial agents and antibiotics, out of cells. Thus, efflux pump systems participate in lowering intracellular concentrations of antibiotics, which allows phenotypic multidrug-resistant (MDR) bacteria to survive effectively amid higher concentrations of antibiotics. Acinetobacter baumannii is one of the classic examples of pathogens that can carry multiple efflux pump systems, which allows these bacteria to be MDR-to-pan-drug resistant and is now considered a public health threat. Therefore, efflux pumps in A. baumannii have gained major attention worldwide, and there has been increased interest in studying their mechanism of action, substrates, and potential efflux pump inhibitors (EPIs). Efflux pump inhibitors are molecules that can inhibit efflux pumps, rendering pathogens susceptible to antimicrobial agents, and are thus considered potential therapeutic agents for use in conjunction with antibiotics. This review focuses on the types of various efflux pumps detected in A. baumannii, their molecular mechanisms of action, the substrates they transport, and the challenges in developing EPIs that can be clinically useful in reference to A. baumannii.
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Affiliation(s)
- Kira M. Zack
- Center for Surgical Infections and Biofilms, Department of Surgery, College of Medicine, Drexel University, Philadelphia, PA 19104, USA;
| | - Trent Sorenson
- Center for Surgical Infections and Biofilms, Drexel School of Biomedical Engineering, Science & Health Systems, Drexel University, Philadelphia, PA 19104, USA;
| | - Suresh G. Joshi
- Center for Surgical Infections and Biofilms, Department of Surgery, College of Medicine, Drexel University, Philadelphia, PA 19104, USA;
- Center for Surgical Infections and Biofilms, Drexel School of Biomedical Engineering, Science & Health Systems, Drexel University, Philadelphia, PA 19104, USA;
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48
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Saleh NM, Ezzat H, El-Sayyad GS, Zedan H. Regulation of overexpressed efflux pump encoding genes by cinnamon oil and trimethoprim to abolish carbapenem-resistant Acinetobacter baumannii clinical strains. BMC Microbiol 2024; 24:52. [PMID: 38331716 PMCID: PMC10851603 DOI: 10.1186/s12866-024-03194-8] [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: 09/12/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024] Open
Abstract
Resistance mechanisms are a shelter for Acinetobacter baumannii to adapt to our environment which causes difficulty for the infections to be treated and WHO declares this organism on the top of pathogens priority for new drug development. The most common mechanism that develops drug resistance is the overexpression of the efflux pump, especially Resistance-nodulation-cell division (RND) family, to almost most antibiotics. The study is designed to detect RND efflux pump genes in A. baumannii, and its correlation to multidrug resistance, in particular, the carbapenems resistance Acinetobacter baumannii (CRAB), and using different inhibitors that restore the antibiotic susceptibility of imipenem. Clinical A. baumannii isolates were recovered from different Egyptian hospitals in Intensive care unit (ICU). The expression of genes in two strains was analyzed using RT-PCR before and after inhibitor treatment. About 100 clinical A. baumannii isolates were recovered and identified and recorded as MDR strains with 75% strains resistant to imipenem. adeB, adeC, adeK, and adeJ were detected in thirty- seven the carbapenems resistance Acinetobacter baumannii (CRAB) strains. Cinnamomum verum oil, Trimethoprim, and Omeprazole was promising inhibitor against 90% of the carbapenems resistance Acinetobacter baumannii (CRAB) strains with a 2-6-fold decrease in imipenem MIC. Downregulation of four genes was associated with the addition of those inhibitors to imipenem for two the carbapenems resistance Acinetobacter baumannii (CRAB) (ACN15 and ACN99) strains, and the effect was confirmed in 24 h killing kinetics. Our investigation points to the carbapenems resistance Acinetobacter baumannii (CRAB) strain's prevalence in Egyptian hospitals with the idea to revive the imipenem activity using natural and chemical drugs as inhibitors that possessed high synergistic activity.
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Affiliation(s)
- Neveen M Saleh
- Department of Microbiology, Egyptian Drug Authority (former National Organization for Drug Control and Research (NODCAR), Giza, Egypt.
| | - Hadeer Ezzat
- Department of Microbiology, Egyptian Drug Authority (former National Organization for Drug Control and Research (NODCAR), Giza, Egypt
| | - Gharieb S El-Sayyad
- Microbiology and Immunology Department, Faculty of Pharmacy, Ahram Canadian University (ACU), 6th October City, Giza, Egypt.
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, New Galala City, Suez, Egypt.
- Drug Microbiology Lab., Drug Radiation Research Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt.
| | - Hamdallah Zedan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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49
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Hooks GM, Ayala JC, Holley CL, Dhulipala V, Beggs GA, Perfect JR, Schumacher MA, Shafer WM, Brennan RG. Hormonal steroids induce multidrug resistance and stress response genes in Neisseria gonorrhoeae by binding to MtrR. Nat Commun 2024; 15:1153. [PMID: 38326294 PMCID: PMC10850145 DOI: 10.1038/s41467-024-45195-1] [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: 08/30/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Transcriptional regulator MtrR inhibits the expression of the multidrug efflux pump operon mtrCDE in the pathogenic bacterium Neisseria gonorrhoeae. Here, we show that MtrR binds the hormonal steroids progesterone, β-estradiol, and testosterone, which are present at urogenital infection sites, as well as ethinyl estrogen, a component of some hormonal contraceptives. Steroid binding leads to the decreased affinity of MtrR for cognate DNA, increased mtrCDE expression, and enhanced antimicrobial resistance. Furthermore, we solve crystal structures of MtrR bound to each steroid, thus revealing their binding mechanisms and the conformational changes that induce MtrR.
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Affiliation(s)
- Grace M Hooks
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Julio C Ayala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- STD Laboratory Reference and Research Branch, Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Concerta L Holley
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Vijaya Dhulipala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Grace A Beggs
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - John R Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - William M Shafer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Laboratories of Microbial Pathogenesis, VA Medical Research Service, Veterans Affairs Medical Center, Decatur, GA, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard G Brennan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
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50
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Wilhelm J, Pos KM. Molecular insights into the determinants of substrate specificity and efflux inhibition of the RND efflux pumps AcrB and AdeB. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001438. [PMID: 38358391 PMCID: PMC10924465 DOI: 10.1099/mic.0.001438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
Gram-negative bacterial members of the Resistance Nodulation and cell Division (RND) superfamily form tripartite efflux pump systems that span the cell envelope. One of the intriguing features of the multiple drug efflux members of this superfamily is their ability to recognize different classes of antibiotics, dyes, solvents, bile salts, and detergents. This review provides an overview of the molecular mechanisms of multiple drug efflux catalysed by the tripartite RND efflux system AcrAB-TolC from Eschericha coli. The determinants for sequential or simultaneous multiple substrate binding and efflux pump inhibitor binding are discussed. A comparison is made with the determinants for substrate binding of AdeB from Acinetobacter baumannii, which acts within the AdeABC multidrug efflux system. There is an apparent general similarity between the structures of AcrB and AdeB and their substrate specificity. However, the presence of distinct conformational states and different drug efflux capacities as revealed by single-particle cryo-EM and mutational analysis suggest that the drug binding and transport features exhibited by AcrB may not be directly extrapolated to the homolog AdeB efflux pump.
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Affiliation(s)
- Julia Wilhelm
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Klaas Martinus Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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