1
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Murtha AN, Kazi MI, Kim EY, Torres FV, Rosch KM, Dörr T. Multiple resistance factors collectively promote inoculum-dependent dynamic survival during antimicrobial peptide exposure in Enterobacter cloacae. PLoS Pathog 2024; 20:e1012488. [PMID: 39186812 DOI: 10.1371/journal.ppat.1012488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 08/08/2024] [Indexed: 08/28/2024] Open
Abstract
Antimicrobial peptides (AMPs) are a promising tool with which to fight rising antibiotic resistance. However, pathogenic bacteria are equipped with several AMP defense mechanisms, whose contributions to AMP resistance are often poorly defined. Here, we evaluate the genetic determinants of resistance to an insect AMP, cecropin B, in the opportunistic pathogen Enterobacter cloacae. Single-cell analysis of E. cloacae's response to cecropin revealed marked heterogeneity in cell survival, phenotypically reminiscent of heteroresistance (the ability of a subpopulation to grow in the presence of supra-MIC concentration of antimicrobial). The magnitude of this response was highly dependent on initial E. cloacae inoculum. We identified 3 genetic factors which collectively contribute to E. cloacae resistance in response to the AMP cecropin: The PhoPQ-two-component system, OmpT-mediated proteolytic cleavage of cecropin, and Rcs-mediated membrane stress response. Altogether, our data suggest that multiple, independent mechanisms contribute to AMP resistance in E. cloacae.
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Affiliation(s)
- Andrew N Murtha
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Misha I Kazi
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
| | - Eileen Y Kim
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
| | - Facundo V Torres
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Kelly M Rosch
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, United States of America
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2
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Baghdasaryan O, Contreras-Llano LE, Khan S, Wang A, Hu CMJ, Tan C. Fabrication of cyborg bacterial cells as living cell-material hybrids using intracellular hydrogelation. Nat Protoc 2024:10.1038/s41596-024-01035-6. [PMID: 39174659 DOI: 10.1038/s41596-024-01035-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 06/11/2024] [Indexed: 08/24/2024]
Abstract
The production of living therapeutics, cell-based delivery of drugs and gene-editing tools and the manufacturing of bio-commodities all share a common concept: they use either a synthetic or a living cell chassis to achieve their primary engineering or therapeutic goal. Live-cell chassis face limitations inherent to their auto-replicative nature and the complexity of the cellular context. This limitation highlights the need for a new chassis combining the engineering simplicity of synthetic materials and the functionalities of natural cells. Here, we describe a protocol to assemble a synthetic polymeric network inside bacterial cells, rendering them incapable of cell division and allowing them to resist environmental stressors such as high pH, hydrogen peroxide and cell-wall-targeting antibiotics that would otherwise kill unmodified bacteria. This cellular bioengineering protocol details how bacteria can be transformed into single-lifespan devices that are resistant to environmental stressors and possess programable functionality. We designate the modified bacteria as cyborg bacterial cells. This protocol expands the synthetic biology toolset, conferring precise control over living cells and creating a versatile cell chassis for biotechnology, biomedical engineering and living therapeutics. The protocol, including the preparation of gelation reagents and chassis strain, can be completed in 4 d. The implementation of the protocol requires expertise in microbiology techniques, hydrogel chemistry, fluorescence microscopy and flow cytometry. Further functionalization of the cyborg bacterial cells and adaptation of the protocol requires skills ranging from synthetic genetic circuit engineering to hydrogel polymerization chemistries.
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Affiliation(s)
| | - Luis E Contreras-Llano
- Biomedical Engineering, University of California Davis, Davis, CA, USA
- Department of Surgery, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Shahid Khan
- Biomedical Engineering, University of California Davis, Davis, CA, USA
| | - Aijun Wang
- Biomedical Engineering, University of California Davis, Davis, CA, USA
- Department of Surgery, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Che-Ming Jack Hu
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan.
| | - Cheemeng Tan
- Biomedical Engineering, University of California Davis, Davis, CA, USA.
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3
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Nasu T, Maeda S. Escherichia coli persisters in biofilm can perform horizontal gene transfer by transformation. Biochem Biophys Res Commun 2024; 738:150549. [PMID: 39167960 DOI: 10.1016/j.bbrc.2024.150549] [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: 08/06/2024] [Accepted: 08/13/2024] [Indexed: 08/23/2024]
Abstract
Persisters represent a subset of cells that exhibit transient tolerance to antimicrobials. These persisters can withstand sudden exposure to antimicrobials, even as the majority of normal cells perish. In this study, we have demonstrated the capacity of ampicillin-tolerant and alkali-tolerant persisters to execute horizontal gene transfer via in situ transformation within biofilms. Air-solid biofilms, comprising two Escherichia coli populations each with a distinct plasmid, were formed on agar media. They were treated with lethal doses of ampicillin or NaOH for 24 h, followed by a 1-min glass-ball roll. This process led to a high frequency of horizontal plasmid transfer (10-7-10-6 per cell) from dead cells to surviving persisters within the biofilms. Plasmid transfer was DNase-sensitive and also occurred by adding purified plasmid DNA to plasmid-free biofilms, demonstrating a transformation mechanism. This marks the first evidence of persisters' novel ability for horizontal gene transfer, via transformation.
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Affiliation(s)
- Tsubasa Nasu
- Graduate School of Humanities and Sciences, Nara Women's University, 630-8506, Kitauoya-nishimachi, Nara, Japan
| | - Sumio Maeda
- Graduate School of Humanities and Sciences, Nara Women's University, 630-8506, Kitauoya-nishimachi, Nara, Japan.
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4
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Saoudi B, Bariz K, Saci S, Belounis Y, Ait Issad H, Abbaci M, Mustapha MA, Nabti EH, Alenazy R, Alhussaini MS, Alyahya AAI, Alqasmi M, Alhumaidi MS, Almufarriji FM, Houali K. Enhancing Antibiotic Efficacy and Combating Biofilm Formation: Evaluating the Synergistic Potential of Origanum vulgare Essential Oil against Multidrug-Resistant Gram-Negative Bacteria. Microorganisms 2024; 12:1651. [PMID: 39203493 PMCID: PMC11356740 DOI: 10.3390/microorganisms12081651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
Multidrug-resistant (MDR) Gram-negative bacteria remain a global public health issue due to the barrier imposed by their outer membrane and their propensity to form biofilms. It is becoming imperative to develop new antibacterial strategies. In this context, this study aims to evaluate the antibacterial efficacy of Origanum vulgare essential oil (OEO), alone and in combination with antibiotics, as well as its antibiofilm action against multidrug-resistant Gram-negative strains. OEO components were identified by gas chromatography-mass spectrometry (GC-MS), and antibacterial activity was assessed using the agar diffusion test and the microdilution method. Interactions between OEO and antibiotics were examined using the checkerboard method, while antibiofilm activity was analyzed using the crystal violet assay. Chemical analysis revealed that carvacrol was the major compound in OEO (61.51%). This essential oil demonstrated activity against all the tested strains, with inhibition zone diameters (IZDs) reaching 32.3 ± 1.5 mm. The combination of OEO with different antibiotics produced synergistic and additive effects, leading to a reduction of up to 98.44% in minimum inhibitory concentrations (MICs). In addition, this essential oil demonstrated an ability to inhibit and even eradicate biofilm formation. These results suggest that OEO could be exploited in the development of new molecules, combining its metabolites with antibiotics.
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Affiliation(s)
- Bilal Saoudi
- Laboratory of Analytical Biochemistry and Biotechnology, Faculty of Biological and Agronomic Sciences, Mouloud Mammeri University of Tizi-Ouzou, Tizi Ouzou 15000, Algeria; (B.S.); (K.B.); (S.S.); (Y.B.)
| | - Karim Bariz
- Laboratory of Analytical Biochemistry and Biotechnology, Faculty of Biological and Agronomic Sciences, Mouloud Mammeri University of Tizi-Ouzou, Tizi Ouzou 15000, Algeria; (B.S.); (K.B.); (S.S.); (Y.B.)
| | - Sarah Saci
- Laboratory of Analytical Biochemistry and Biotechnology, Faculty of Biological and Agronomic Sciences, Mouloud Mammeri University of Tizi-Ouzou, Tizi Ouzou 15000, Algeria; (B.S.); (K.B.); (S.S.); (Y.B.)
| | - Yousra Belounis
- Laboratory of Analytical Biochemistry and Biotechnology, Faculty of Biological and Agronomic Sciences, Mouloud Mammeri University of Tizi-Ouzou, Tizi Ouzou 15000, Algeria; (B.S.); (K.B.); (S.S.); (Y.B.)
| | - Hakima Ait Issad
- Laboratoire Ressources Naturelles, Mouloud Mammeri University of Tizi-Ouzou, Tizi Ouzou 15000, Algeria;
| | - Mohamed Abbaci
- Centre de Recherche Scientifique et Technique en Analyses Physico—Chimiques CRAPC, Bou Ismail 42004, Algeria; (M.A.); (M.A.M.)
| | - Mohamed Abou Mustapha
- Centre de Recherche Scientifique et Technique en Analyses Physico—Chimiques CRAPC, Bou Ismail 42004, Algeria; (M.A.); (M.A.M.)
| | - El-Hafid Nabti
- Laboratoire de Maitrise des Energies Renouvelables, Faculté des Sciences de la Nature et de le Vie, Université de Bejaïa, Bejaïa 06000, Algeria;
| | - Rawaf Alenazy
- Department of Medical Laboratory, College of Applied Medical Sciences-Shaqra, Shaqra University, Shaqra 11961, Saudi Arabia; (M.S.A.); (A.A.I.A.); (M.A.)
| | - Mohammed Sanad Alhussaini
- Department of Medical Laboratory, College of Applied Medical Sciences-Shaqra, Shaqra University, Shaqra 11961, Saudi Arabia; (M.S.A.); (A.A.I.A.); (M.A.)
| | - Abdulrahman A. I. Alyahya
- Department of Medical Laboratory, College of Applied Medical Sciences-Shaqra, Shaqra University, Shaqra 11961, Saudi Arabia; (M.S.A.); (A.A.I.A.); (M.A.)
| | - Mohammed Alqasmi
- Department of Medical Laboratory, College of Applied Medical Sciences-Shaqra, Shaqra University, Shaqra 11961, Saudi Arabia; (M.S.A.); (A.A.I.A.); (M.A.)
| | - Maryam S. Alhumaidi
- Department of Biology, College of Science, University of Hafr Al Batin, P.O. Box 1803, Hafr Al Batin 31991, Saudi Arabia;
| | - Fawaz M. Almufarriji
- Medical Laboratories Department, College of Applied Medical Sciences in Al-Quwayiyah, Shaqra University, Shaqra 11961, Saudi Arabia;
| | - Karim Houali
- Laboratory of Analytical Biochemistry and Biotechnology, Faculty of Biological and Agronomic Sciences, Mouloud Mammeri University of Tizi-Ouzou, Tizi Ouzou 15000, Algeria; (B.S.); (K.B.); (S.S.); (Y.B.)
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5
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Gray DA, Wang B, Sidarta M, Cornejo FA, Wijnheijmer J, Rani R, Gamba P, Turgay K, Wenzel M, Strahl H, Hamoen LW. Membrane depolarization kills dormant Bacillus subtilis cells by generating a lethal dose of ROS. Nat Commun 2024; 15:6877. [PMID: 39128925 PMCID: PMC11317493 DOI: 10.1038/s41467-024-51347-0] [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: 08/12/2021] [Accepted: 08/02/2024] [Indexed: 08/13/2024] Open
Abstract
The bactericidal activity of several antibiotics partially relies on the production of reactive oxygen species (ROS), which is generally linked to enhanced respiration and requires the Fenton reaction. Bacterial persister cells, an important cause of recurring infections, are tolerant to these antibiotics because they are in a dormant state. Here, we use Bacillus subtilis cells in stationary phase, as a model system of dormant cells, to show that pharmacological induction of membrane depolarization enhances the antibiotics' bactericidal activity and also leads to ROS production. However, in contrast to previous studies, this results primarily in production of superoxide radicals and does not require the Fenton reaction. Genetic analyzes indicate that Rieske factor QcrA, the iron-sulfur subunit of respiratory complex III, seems to be a primary source of superoxide radicals. Interestingly, the membrane distribution of QcrA changes upon membrane depolarization, suggesting a dissociation of complex III. Thus, our data reveal an alternative mechanism by which antibiotics can cause lethal ROS levels, and may partially explain why membrane-targeting antibiotics are effective in eliminating persisters.
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Affiliation(s)
- Declan A Gray
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Baddiley-Clark Building, Newcastle upon Tyne, NE2 4AX, UK
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Biwen Wang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, C3.108, 1098 XH, Amsterdam, The Netherlands
| | - Margareth Sidarta
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemigården 4, 412 96, Gothenburg, Sweden
| | - Fabián A Cornejo
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany
| | - Jurian Wijnheijmer
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, C3.108, 1098 XH, Amsterdam, The Netherlands
| | - Rupa Rani
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemigården 4, 412 96, Gothenburg, Sweden
| | - Pamela Gamba
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Baddiley-Clark Building, Newcastle upon Tyne, NE2 4AX, UK
- Charles River Laboratories, Keele Science Park, Keele, ST5 5SP, UK
| | - Kürşad Turgay
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany
- Leibniz Universität Hannover, Institut für Mikrobiologie, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Michaela Wenzel
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemigården 4, 412 96, Gothenburg, Sweden
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Baddiley-Clark Building, Newcastle upon Tyne, NE2 4AX, UK
| | - Leendert W Hamoen
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Baddiley-Clark Building, Newcastle upon Tyne, NE2 4AX, UK.
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, C3.108, 1098 XH, Amsterdam, The Netherlands.
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6
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El Meouche I, Jain P, Jolly MK, Capp JP. Drug tolerance and persistence in bacteria, fungi and cancer cells: Role of non-genetic heterogeneity. Transl Oncol 2024; 49:102069. [PMID: 39121829 PMCID: PMC11364053 DOI: 10.1016/j.tranon.2024.102069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 07/17/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
A common feature of bacterial, fungal and cancer cell populations upon treatment is the presence of tolerant and persistent cells able to survive, and sometimes grow, even in the presence of usually inhibitory or lethal drug concentrations, driven by non-genetic differences among individual cells in a population. Here we review and compare data obtained on drug survival in bacteria, fungi and cancer cells to unravel common characteristics and cellular pathways, and to point their singularities. This comparative work also allows to cross-fertilize ideas across fields. We particularly focus on the role of gene expression variability in the emergence of cell-cell non-genetic heterogeneity because it represents a possible common basic molecular process at the origin of most persistence phenomena and could be monitored and tuned to help improve therapeutic interventions.
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Affiliation(s)
- Imane El Meouche
- Université Paris Cité, Université Sorbonne Paris Nord, INSERM, IAME, F-75018 Paris, France.
| | - Paras Jain
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France.
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7
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Chapartegui-González I, Stockton JL, Bowser S, Badten AJ, Torres AG. Unraveling the role of toxin-antitoxin systems in Burkholderia pseudomallei: exploring bacterial pathogenesis and interactions within the HigBA families. Microbiol Spectr 2024; 12:e0074824. [PMID: 38916327 PMCID: PMC11302019 DOI: 10.1128/spectrum.00748-24] [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: 03/21/2024] [Accepted: 05/28/2024] [Indexed: 06/26/2024] Open
Abstract
Burkholderia pseudomallei (Bpm) is a Gram-negative intracellular pathogen that causes melioidosis in humans, a neglected, underreported, and lethal disease that can reach a fatal outcome in over 50% of the cases. It can produce both acute and chronic infections, the latter being particularly challenging to eliminate because of the intracellular life cycle of the bacteria and its ability to generate a "persister" dormant state. The molecular mechanism that allows the switch between growing and persister phenotypes is not well understood but it is hypothesized to be due at least in part to the participation of toxin-antitoxin (TA) systems. We have previously studied the link between one of those systems (defined as HigBA) with specific expression patterns associated with levofloxacin antibiotic exposure. Through in silico methods, we predicted the presence of another three pairs of genes encoding for additional putative HigBA systems. Therefore, our main goal was to establish which mechanisms are conserved as well as which pathways are specific among different Bpm TA systems from the same family. We hypothesize that the high prevalence, and sometimes even redundancy of these systems in the Bpm chromosomes indicates that they can interact with each other and not function as only individual systems, as it was traditionally thought, and might be playing an undefined role in Bpm lifecycle. Here, we show that both the toxin and the antitoxin of the different systems contribute to bacterial survival and that toxins from the same family can have a cumulative effect under environmental stressful conditions. IMPORTANCE Toxin-antitoxin (TA) systems play a significant role in bacterial persistence, a phenomenon where bacterial cells enter a dormant or slow-growing state to survive adverse conditions such as nutrient deprivation, antibiotic exposure, or host immune responses. By studying TA systems in Burkholderia pseudomallei, we can gain insights into how this pathogen survives and persists in the host environment, contributing to its virulence and ability to cause melioidosis chronic infections.
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Affiliation(s)
| | - Jacob L. Stockton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Sarah Bowser
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Alexander J. Badten
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas, USA
| | - Alfredo G. Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
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8
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Niu H, Gu J, Zhang Y. Bacterial persisters: molecular mechanisms and therapeutic development. Signal Transduct Target Ther 2024; 9:174. [PMID: 39013893 PMCID: PMC11252167 DOI: 10.1038/s41392-024-01866-5] [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: 11/04/2023] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 07/18/2024] Open
Abstract
Persisters refer to genetically drug susceptible quiescent (non-growing or slow growing) bacteria that survive in stress environments such as antibiotic exposure, acidic and starvation conditions. These cells can regrow after stress removal and remain susceptible to the same stress. Persisters are underlying the problems of treating chronic and persistent infections and relapse infections after treatment, drug resistance development, and biofilm infections, and pose significant challenges for effective treatments. Understanding the characteristics and the exact mechanisms of persister formation, especially the key molecules that affect the formation and survival of the persisters is critical to more effective treatment of chronic and persistent infections. Currently, genes related to persister formation and survival are being discovered and confirmed, but the mechanisms by which bacteria form persisters are very complex, and there are still many unanswered questions. This article comprehensively summarizes the historical background of bacterial persisters, details their complex characteristics and their relationship with antibiotic tolerant and resistant bacteria, systematically elucidates the interplay between various bacterial biological processes and the formation of persister cells, as well as consolidates the diverse anti-persister compounds and treatments. We hope to provide theoretical background for in-depth research on mechanisms of persisters and suggest new ideas for choosing strategies for more effective treatment of persistent infections.
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Affiliation(s)
- Hongxia Niu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Jiaying Gu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Ying Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250022, Shandong, China.
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9
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Li B, Srivastava S, Shaikh M, Mereddy G, Garcia MR, Shah A, Ofori-Anyinam N, Chu T, Cheney N, Yang JH. Bioenergetic stress potentiates antimicrobial resistance and persistence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603336. [PMID: 39026737 PMCID: PMC11257553 DOI: 10.1101/2024.07.12.603336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Antimicrobial resistance (AMR) is a global health crisis and there is an urgent need to better understand AMR mechanisms. Antibiotic treatment alters several aspects of bacterial physiology, including increased ATP utilization, carbon metabolism, and reactive oxygen species (ROS) formation. However, how the "bioenergetic stress" induced by increased ATP utilization affects treatment outcomes is unknown. Here we utilized a synthetic biology approach to study the direct effects of bioenergetic stress on antibiotic efficacy. We engineered a genetic system that constitutively hydrolyzes ATP or NADH in Escherichia coli. We found that bioenergetic stress potentiates AMR evolution via enhanced ROS production, mutagenic break repair, and transcription-coupled repair. We also find that bioenergetic stress potentiates antimicrobial persistence via potentiated stringent response activation. We propose a unifying model that antibiotic-induced antimicrobial resistance and persistence is caused by antibiotic-induced. This has important implications for preventing or curbing the spread of AMR infections.
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10
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Jandl B, Dighe S, Gasche C, Makristathis A, Muttenthaler M. Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities. Clin Microbiol Rev 2024:e0013323. [PMID: 38995034 DOI: 10.1128/cmr.00133-23] [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: 07/13/2024] Open
Abstract
SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.
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Affiliation(s)
- Bernhard Jandl
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Satish Dighe
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Christoph Gasche
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Vienna, Vienna, Austria
- Loha for Life, Center for Gastroenterology and Iron Deficiency, Vienna, Austria
| | - Athanasios Makristathis
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Markus Muttenthaler
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
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11
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Inostroza O, Fuentes JA, Yáñez P, Espinoza G, Fica O, Queraltó C, Rodríguez J, Flores I, González R, Soto JA, Calderón IL, Gil F. Characterization of Clostridioides difficile Persister Cells and Their Role in Antibiotic Tolerance. Microorganisms 2024; 12:1394. [PMID: 39065162 PMCID: PMC11279270 DOI: 10.3390/microorganisms12071394] [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: 06/15/2024] [Revised: 07/04/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Clostridioides difficile is a Gram-positive pathogen known for its toxin production and spore formation. It is primarily responsible for most cases of antibiotic-associated diarrhea. Bacterial persisters are a small subset of the population that exhibits transient tolerance to bactericidal substances, and they are of significant medical concern due to their association with the emergence of antibiotic resistance and difficult-to-treat chronic or recurrent infections. Vancomycin, the predominant antibiotic utilized in the management of C. difficile infection, is extensively applied in the realm of clinical practice. Previous studies have demonstrated a persister-like phenotype with treatments involving this antibiotic. However, the mechanism in C. difficile remains largely unknown, primarily due to the challenge of isolating this small population at any given time. To better characterize C. difficile persister cells, we present a study that enables the enrichment and characterization of persister cells from bacterial cultures in both the exponential and stationary phases. Moreover, we could differentiate between triggered (induced using antibiotics such as vancomycin) and spontaneous (stochastic) persister cells. Additionally, we observed the involvement of toxin-antitoxin systems and Clp proteases in persister cell formation.
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Affiliation(s)
- Osvaldo Inostroza
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (O.I.); (P.Y.); (G.E.); (O.F.); camilabelen.-@hotmail.com (C.Q.); (J.R.); (I.F.); (R.G.)
| | - Juan A. Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile;
| | - Paulina Yáñez
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (O.I.); (P.Y.); (G.E.); (O.F.); camilabelen.-@hotmail.com (C.Q.); (J.R.); (I.F.); (R.G.)
| | - Giovanni Espinoza
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (O.I.); (P.Y.); (G.E.); (O.F.); camilabelen.-@hotmail.com (C.Q.); (J.R.); (I.F.); (R.G.)
| | - Omar Fica
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (O.I.); (P.Y.); (G.E.); (O.F.); camilabelen.-@hotmail.com (C.Q.); (J.R.); (I.F.); (R.G.)
| | - Camila Queraltó
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (O.I.); (P.Y.); (G.E.); (O.F.); camilabelen.-@hotmail.com (C.Q.); (J.R.); (I.F.); (R.G.)
| | - José Rodríguez
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (O.I.); (P.Y.); (G.E.); (O.F.); camilabelen.-@hotmail.com (C.Q.); (J.R.); (I.F.); (R.G.)
| | - Isidora Flores
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (O.I.); (P.Y.); (G.E.); (O.F.); camilabelen.-@hotmail.com (C.Q.); (J.R.); (I.F.); (R.G.)
| | - Ruth González
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (O.I.); (P.Y.); (G.E.); (O.F.); camilabelen.-@hotmail.com (C.Q.); (J.R.); (I.F.); (R.G.)
| | - Jorge A. Soto
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile;
| | - Iván L. Calderón
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile
| | - Fernando Gil
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (O.I.); (P.Y.); (G.E.); (O.F.); camilabelen.-@hotmail.com (C.Q.); (J.R.); (I.F.); (R.G.)
- ANID-Millennium Science Initiative Program-Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago 8370186, Chile
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12
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Greve NB, Slotved HC, Olsen JE, Thomsen LE. Identification of antibiotic induced persister cells in Streptococcus agalactiae. PLoS One 2024; 19:e0303271. [PMID: 38924011 PMCID: PMC11207178 DOI: 10.1371/journal.pone.0303271] [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: 11/24/2023] [Accepted: 04/23/2024] [Indexed: 06/28/2024] Open
Abstract
Antibiotic persistence is a phenomenon, where a small fraction of a bacterial population expresses a phenotypic variation that allows them to survive antibiotic treatment, which is lethal to the rest of the population. These cells are called persisters cells, and their occurrence has been associated with recurrent disease. Streptococcus agalactiae is a human pathobiont, able to cause invasive infections, and recurrent infections have been reported to occur in both newborns and adults. In this study, we demonstrated that S. agalactiae NEM316 can form persister cells when exposed to antibiotics from different classes. The frequency of persister cell formation was dependent on bacterial growth phase and the class of antibiotics. The ability to form persister cells in response to penicillin was shown to be a general trait among different clinical S. agalactiae isolates, independent of sero- and sequence-type. Taken together, this study shows the existence of antibiotic tolerant S. agalactiae persister cells, which may explain why this bacterial species frequently persists after treatment of invasive infection and can be associated with recurrent disease.
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Affiliation(s)
- Nanna Boll Greve
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Hans-Christian Slotved
- Department of Bacteria, Division of Infectious Disease Preparedness, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - John Elmerdahl Olsen
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Line Elnif Thomsen
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
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13
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Liu JD, Van Treeck KE, Marston WA, Papadopoulou V, Rowe SE. Ultrasound-Mediated Antibiotic Delivery to In Vivo Biofilm Infections: A Review. Chembiochem 2024:e202400181. [PMID: 38924307 DOI: 10.1002/cbic.202400181] [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: 02/28/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024]
Abstract
Bacterial biofilms are a significant concern in various medical contexts due to their resilience to our immune system as well as antibiotic therapy. Biofilms often require surgical removal and frequently lead to recurrent or chronic infections. Therefore, there is an urgent need for improved strategies to treat biofilm infections. Ultrasound-mediated drug delivery is a technique that combines ultrasound application, often with the administration of acoustically-active agents, to enhance drug delivery to specific target tissues or cells within the body. This method involves using ultrasound waves to assist in the transportation or activation of medications, improving their penetration, distribution, and efficacy at the desired site. The advantages of ultrasound-mediated drug delivery include targeted and localized delivery, reduced systemic side effects, and improved efficacy of the drug at lower doses. This review scrutinizes recent advances in the application of ultrasound-mediated drug delivery for treating biofilm infections, focusing on in vivo studies. We examine the strengths and limitations of this technology in the context of wound infections, device-associated infections, lung infections and abscesses, and discuss current gaps in knowledge and clinical translation considerations.
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Affiliation(s)
- Jamie D Liu
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
| | - Kelly E Van Treeck
- Joint Department of Biomedical Engineering, The University of North Carolina and North Carolina State University, Chapel Hill, North Carolina, 27599, USA
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - William A Marston
- Department of Surgery, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
| | - Virginie Papadopoulou
- Joint Department of Biomedical Engineering, The University of North Carolina and North Carolina State University, Chapel Hill, North Carolina, 27599, USA
- Department of Radiology, University of North Carolina, Chapel Hill, NC, USA
| | - Sarah E Rowe
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
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14
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Morrison JJ, Madden EK, Banas DA, DiBiasio EC, Hansen M, Krogfelt KA, Rowley DC, Cohen PS, Camberg JL. Metabolic flux regulates growth transitions and antibiotic tolerance in uropathogenic Escherichia coli. J Bacteriol 2024; 206:e0016224. [PMID: 38814092 PMCID: PMC11332148 DOI: 10.1128/jb.00162-24] [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: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024] Open
Abstract
Reducing growth and limiting metabolism are strategies that allow bacteria to survive exposure to environmental stress and antibiotics. During infection, uropathogenic Escherichia coli (UPEC) may enter a quiescent state that enables them to reemerge after the completion of successful antibiotic treatment. Many clinical isolates, including the well-characterized UPEC strain CFT073, also enter a metabolite-dependent, quiescent state in vitro that is reversible with cues, including peptidoglycan-derived peptides and amino acids. Here, we show that quiescent UPEC is antibiotic tolerant and demonstrate that metabolic flux in the tricarboxylic acid (TCA) cycle regulates the UPEC quiescent state via succinyl-CoA. We also demonstrate that the transcriptional regulator complex integration host factor and the FtsZ-interacting protein ZapE, which is important for E. coli division during stress, are essential for UPEC to enter the quiescent state. Notably, in addition to engaging FtsZ and late-stage cell division proteins, ZapE also interacts directly with TCA cycle enzymes in bacterial two-hybrid assays. We report direct interactions between the succinate dehydrogenase complex subunit SdhC, the late-stage cell division protein FtsN, and ZapE. These interactions may enable communication between oxidative metabolism and the cell division machinery in UPEC. Moreover, these interactions are conserved in an E. coli K-12 strain. This work suggests that there is coordination among the two fundamental and essential pathways that regulate overall growth, quiescence, and antibiotic susceptibility. IMPORTANCE Uropathogenic Escherichia coli (UPEC) are the leading cause of urinary tract infections (UTIs). Upon invasion into bladder epithelial cells, UPEC establish quiescent intracellular reservoirs that may lead to antibiotic tolerance and recurrent UTIs. Here, we demonstrate using an in vitro system that quiescent UPEC cells are tolerant to ampicillin and have decreased metabolism characterized by succinyl-CoA limitation. We identify the global regulator integration host factor complex and the cell division protein ZapE as critical modifiers of quiescence and antibiotic tolerance. Finally, we show that ZapE interacts with components of both the cell division machinery and the tricarboxylic acid cycle, and this interaction is conserved in non-pathogenic E. coli, establishing a novel link between cell division and metabolism.
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Affiliation(s)
- Josiah J. Morrison
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Ellen K. Madden
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Daniel A. Banas
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Eric C. DiBiasio
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Mads Hansen
- Department of Natural Science and Environment, Centre for Mathematical Modeling - Human Health and Disease, University of Roskilde, Roskilde, Denmark
| | - Karen A. Krogfelt
- Department of Natural Science and Environment, Centre for Mathematical Modeling - Human Health and Disease, University of Roskilde, Roskilde, Denmark
| | - David C. Rowley
- Department of Biomedical and Pharmaceutical Sciences, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Paul S. Cohen
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Jodi L. Camberg
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
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15
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Sarangi A, Singh SP, Das BS, Rajput S, Fatima S, Bhattacharya D. Mycobacterial biofilms: A therapeutic target against bacterial persistence and generation of antibiotic resistance. Heliyon 2024; 10:e32003. [PMID: 38882302 PMCID: PMC11176842 DOI: 10.1016/j.heliyon.2024.e32003] [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: 01/22/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
Mycobacterium tuberculosis (M. tb) is the causative agent of Tuberculosis, one of the deadliest infectious diseases. According to the WHO Report 2023, in 2022, approximately 10.6 million people got infected with TB, and 1.6 million died. It has multiple antibiotics for treatment, but the major drawback of anti-tuberculosis therapy (ATT) is, its prolonged treatment duration. The major contributors to the lengthy treatment period are mycobacterial persistence and drug tolerance. Persistent M. tb is phenotypically drug tolerant and metabolically slow down which makes it difficult to be eliminated during ATT. These persisting bacteria are a huge reservoir of impending disease, waiting to get reactivated upon the onset of an immune compromising state. Directly Observed Treatment Short-course, although effective against replicating bacteria; fails to eliminate the drug-tolerant persisters making TB still the second-highest killer globally. There are different mechanisms for the development of drug-tolerant mycobacterial populations being investigated. Recently, the role of biofilms in the survival and host-evasion mechanism of persisters has come to light. Therefore, it is crucial to understand the mechanism of adaptation, survival and attainment of drug tolerance by persisting M. tb-populations, in order to design better immune responses and therapeutics for the effective elimination of these bacteria by reducing the duration of treatment and also circumvent the generation of drug-resistance to achieve the goal of global eradication of TB. This review summarizes the drug-tolerance mechanism and biofilms' role in providing a niche to dormant-M.tb. We also discuss methods of targeting biofilms to achieve sterile eradication of the mycobacteria and prevent its reactivation by achieving adequate immune responses.
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Affiliation(s)
- Ashirbad Sarangi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Shashi Prakash Singh
- Vaccine and Gene Therapy Institute (VGTI) Oregon National Primate Research Centre (ONPRC) Oregon Health and Science University (OHSU) Beaverton, Oregon, USA
| | - Bhabani Shankar Das
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Sristi Rajput
- Departmental of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
| | - Samreen Fatima
- UMass Chan Medical School, University of Massachusetts, Worcester, MA, USA
| | - Debapriya Bhattacharya
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
- Departmental of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
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16
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Jandl B, Dighe S, Baumgartner M, Makristathis A, Gasche C, Muttenthaler M. Gastrointestinal Biofilms: Endoscopic Detection, Disease Relevance, and Therapeutic Strategies. Gastroenterology 2024:S0016-5085(24)05054-6. [PMID: 38876174 DOI: 10.1053/j.gastro.2024.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 06/16/2024]
Abstract
Gastrointestinal biofilms are highly heterogenic and spatially organized polymicrobial communities that can expand and cover large areas in the gastrointestinal tract. Gut microbiota dysbiosis, mucus disruption, and epithelial invasion are associated with pathogenic biofilms that have been linked to gastrointestinal disorders such as irritable bowel syndrome, inflammatory bowel diseases, gastric cancer, and colon cancer. Intestinal biofilms are highly prevalent in ulcerative colitis and irritable bowel syndrome patients, and most endoscopists will have observed such biofilms during colonoscopy, maybe without appreciating their biological and clinical importance. Gut biofilms have a protective extracellular matrix that renders them challenging to treat, and effective therapies are yet to be developed. This review covers gastrointestinal biofilm formation, growth, appearance and detection, biofilm architecture and signalling, human host defence mechanisms, disease and clinical relevance of biofilms, therapeutic approaches, and future perspectives. Critical knowledge gaps and open research questions regarding the biofilm's exact pathophysiological relevance and key hurdles in translating therapeutic advances into the clinic are discussed. Taken together, this review summarizes the status quo in gut biofilm research and provides perspectives and guidance for future research and therapeutic strategies.
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Affiliation(s)
- Bernhard Jandl
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria; University of Vienna, Vienna Doctoral School in Chemistry, Vienna, Austria; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia; Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Satish Dighe
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Maximillian Baumgartner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Athanasios Makristathis
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Christoph Gasche
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria; Loha for Life, Center for Gastroenterology and Iron Deficiency, Vienna, Austria
| | - Markus Muttenthaler
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
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Ngo HG, Mohiuddin SG, Ananda A, Orman MA. UNRAVELING CRP/cAMP-MEDIATED METABOLIC REGULATION IN ESCHERICHIA COLI PERSISTER CELLS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598332. [PMID: 38915711 PMCID: PMC11195080 DOI: 10.1101/2024.06.10.598332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
A substantial gap persists in our comprehension of how bacterial metabolism undergoes rewiring during the transition to a persistent state. Also, it remains unclear which metabolic mechanisms become indispensable for persister cell survival. To address these questions, we directed our efforts towards persister cells in Escherichia coli that emerge during the late stationary phase. These cells have been recognized for their exceptional resilience and are commonly believed to be in a dormant state. Our results demonstrate that the global metabolic regulator Crp/cAMP redirects the metabolism of these antibiotic-tolerant cells from anabolism to oxidative phosphorylation. Although our data indicates that persisters exhibit a reduced metabolic rate compared to rapidly growing exponential-phase cells, their survival still relies on energy metabolism. Extensive genomic-level analyses of metabolomics, proteomics, and single-gene deletions consistently emphasize the critical role of energy metabolism, specifically the tricarboxylic acid (TCA) cycle, electron transport chain (ETC), and ATP synthase, in sustaining the viability of persisters. Altogether, this study provides much-needed clarification regarding the role of energy metabolism in antibiotic tolerance and highlights the importance of using a multipronged approach at the genomic level to obtain a broader picture of the metabolic state of persister cells.
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Affiliation(s)
- Han G. Ngo
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
| | - Sayed Golam Mohiuddin
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
| | - Aina Ananda
- Department of Biology, Monmouth University, NJ, 07764
| | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
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18
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Guha M, Singh A, Butzin NC. Gram-positive bacteria are primed for surviving lethal doses of antibiotics and chemical stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596288. [PMID: 38895422 PMCID: PMC11185512 DOI: 10.1101/2024.05.28.596288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Antibiotic resistance kills millions worldwide yearly. However, a major contributor to recurrent infections lies in a small fraction of bacterial cells, known as persisters. These cells are not inherently antibiotic-resistant, yet they lead to increased antibiotic usage, raising the risk of developing resistant progenies. In a bacterial population, individual cells exhibit considerable fluctuations in their gene expression levels despite being cultivated under identical, stable conditions. This variability in cell-to-cell characteristics (phenotypic diversity) within an isogenic population enables persister cells to withstand antibiotic exposure by entering a non-dividing state. We recently showed the existence of "primed cells" in E. coli. Primed cells are dividing cells prepared for antibiotic stress before encountering it and are more prone to form persisters. They also pass their "prepared state" down for several generations through epigenetic memory. Here, we show that primed cells are common among distant bacterial lineages, allowing for survival against antibiotics and other chemical stress, and form in different growth phases. They are also responsible for increased persister levels in transition and stationary phases compared to the log phase. We tested and showed that the Gram-positive bacterium Bacillus megaterium, evolutionarily very distant from E. coli, forms primed cells and has a transient epigenetic memory that is maintained for 7 generations or more. We showed this using ciprofloxacin and the non-antibiotic chemical stress fluoride. It is well established that persister levels are higher in the stationary phase than in the log phase, and B. megaterium persisters levels are nearly identical from the early to late-log phase but are ~2-fold and ~4-fold higher in the transition and stationary phase, respectively. It was previously proposed that there are two distinct types of persisters: Type II forms in the log phase, while Type I forms in the stationary phase. However, we show that primed cells lead to increased persisters in the transition and stationary phase and found no evidence of Type I or II persisters with distant phenotypes. Overall, we have provided substantial evidence of the importance of primed cells and their transitory epigenetic memories to surviving stress.
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Affiliation(s)
- Manisha Guha
- Department of Biology and Microbiology; South Dakota State University; Brookings, SD, 57006; USA
| | - Abhyudai Singh
- Electrical & Computer Engineering; University of Delaware; Newark, DE 19716; USA
| | - Nicholas C. Butzin
- Department of Biology and Microbiology; South Dakota State University; Brookings, SD, 57006; USA
- Department of Chemistry and Biochemistry; South Dakota State University; Brookings, SD, 57006; USA
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19
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Cao L, Yang H, Huang Z, Lu C, Chen F, Zhang J, Ye P, Yan J, Zhang H. Direct prediction of antimicrobial resistance in Pseudomonas aeruginosa by metagenomic next-generation sequencing. Front Microbiol 2024; 15:1413434. [PMID: 38903781 PMCID: PMC11187003 DOI: 10.3389/fmicb.2024.1413434] [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: 04/07/2024] [Accepted: 05/27/2024] [Indexed: 06/22/2024] Open
Abstract
Objective Pseudomonas aeruginosa has strong drug resistance and can tolerate a variety of antibiotics, which is a major problem in the management of antibiotic-resistant infections. Direct prediction of multi-drug resistance (MDR) resistance phenotypes of P. aeruginosa isolates and clinical samples by genotype is helpful for timely antibiotic treatment. Methods In the study, whole genome sequencing (WGS) data of 494 P. aeruginosa isolates were used to screen key anti-microbial resistance (AMR)-associated genes related to imipenem (IPM), meropenem (MEM), piperacillin/tazobactam (TZP), and levofloxacin (LVFX) resistance in P. aeruginosa by comparing genes with copy number differences between resistance and sensitive strains. Subsequently, for the direct prediction of the resistance of P. aeruginosa to four antibiotics by the AMR-associated features screened, we collected 74 P. aeruginosa positive sputum samples to sequence by metagenomics next-generation sequencing (mNGS), of which 1 sample with low quality was eliminated. Then, we constructed the resistance prediction model. Results We identified 93, 88, 80, 140 AMR-associated features for IPM, MEM, TZP, and LVFX resistance in P. aeruginosa. The relative abundance of AMR-associated genes was obtained by matching mNGS and WGS data. The top 20 features with importance degree for IPM, MEM, TZP, and LVFX resistance were used to model, respectively. Then, we used the random forest algorithm to construct resistance prediction models of P. aeruginosa, in which the areas under the curves of the IPM, MEM, TZP, and LVFX resistance prediction models were all greater than 0.8, suggesting these resistance prediction models had good performance. Conclusion In summary, mNGS can predict the resistance of P. aeruginosa by directly detecting AMR-associated genes, which provides a reference for rapid clinical detection of drug resistance of pathogenic bacteria.
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Affiliation(s)
- Lichao Cao
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong Province, China
| | - Huilin Yang
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Zhigang Huang
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Chang Lu
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Fang Chen
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong Province, China
| | - Jiahao Zhang
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong Province, China
| | - Peng Ye
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Jinjin Yan
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Hezi Zhang
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong Province, China
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20
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Turner RJ. The good, the bad, and the ugly of metals as antimicrobials. Biometals 2024; 37:545-559. [PMID: 38112899 PMCID: PMC11101337 DOI: 10.1007/s10534-023-00565-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: 09/03/2023] [Accepted: 11/18/2023] [Indexed: 12/21/2023]
Abstract
We are now moving into the antimicrobial resistance (AMR) era where more antibiotic resistant bacteria are now the majority, a problem brought on by both misuse and over use of antibiotics. Unfortunately, the antibiotic development pipeline dwindled away over the past decades as they are not very profitable compounds for companies to develop. Regardless researchers over the past decade have made strides to explore alternative options and out of this we see revisiting historical infection control agents such as toxic metals. From this we now see a field of research exploring the efficacy of metal ions and metal complexes as antimicrobials. Such antimicrobials are delivered in a variety of forms from metal salts, alloys, metal complexes, organometallic compounds, and metal based nanomaterials and gives us the broad term metalloantimicrobials. We now see many effective formulations applied for various applications using metals as antimicrobials that are effective against drug resistant strains. The purpose of the document here is to step aside and begin a conversation on the issues of use of such toxic metal compounds against microbes. This critical opinion mini-review in no way aims to be comprehensive. The goal here is to understand the benefits of metalloantimicrobials, but also to consider strongly the disadvantages of using metals, and what are the potential consequences of misuse and overuse. We need to be conscious of the issues, to see the entire system and affect through a OneHealth vision.
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Affiliation(s)
- Raymond J Turner
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada.
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21
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Li M, Sun X, Zhao L, Du W, Shang D. The antibacterial activity and mechanisms of Trp-containing peptides against multidrug-resistant Pseudomonas aeruginosa persisters. Biochimie 2024; 225:133-145. [PMID: 38815647 DOI: 10.1016/j.biochi.2024.05.019] [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: 03/03/2024] [Revised: 04/27/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
Bacterial persisters avoid antibiotic-mediated death by entering a dormant state and are considered a major cause of antibiotic treatment failure. Antimicrobial peptides (AMPs) with membrane-disrupting activity are promising drugs to eradicate persister cells. In this study, carbonyl cyanide m-chlorophenylhydrazone (CCCP), ciprofloxacin (CIP), and rifampicin (RFP) were applied to induce the formation of multidrug-resistant Pseudomonas aeruginosa (MRPA0108) persisters, and the antibacterial activity and mechanisms of I1W and L12W (two Trp-containing peptides designed in our lab) against MRPA0108 persisters were investigated. The results showed that I1W and L12W displayed potent antibacterial activity against MRPA0108 persisters. Both Trp-containing peptides disturbed the inner and outer membrane of MRPA0108 persisters. In addition, I1W and L12W revealed novel antibacterial mechanisms by decreasing the enzymatic activities of superoxide dismutase (SOD) and catalase (CAT), increasing reactive oxygen species (ROS) and malondialdehyde (MDA) levels, consequently leading to oxidative stress. The transcriptome profile of I1W-treated MRPA0108 persisters revealed that the genes involved in carbon metabolism, biosynthesis of amino acids, and the TCA cycle were downregulated, indicating that I1W interfered with metabolism and energy synthesis processes. Furthermore, both Trp-containing peptides displayed synergistic activities with antibiotic tobramycin and showed additive activities with cefepime or ciprofloxacin, which revealed a potential therapeutic strategy for the eradication of MRPA0108 persisters.
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Affiliation(s)
- Mengmiao Li
- School of Life Sciences, Liaoning Normal University, Dalian, China; Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, Liaoning Normal University, Dalian, China
| | - Xiaomi Sun
- School of Life Sciences, Liaoning Normal University, Dalian, China
| | - Lei Zhao
- School of Life Sciences, Liaoning Normal University, Dalian, China
| | - Wanying Du
- School of Life Sciences, Liaoning Normal University, Dalian, China
| | - Dejing Shang
- School of Life Sciences, Liaoning Normal University, Dalian, China; Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, Liaoning Normal University, Dalian, China.
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22
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Shore SFH, Leinberger FH, Fozo EM, Berghoff BA. Type I toxin-antitoxin systems in bacteria: from regulation to biological functions. EcoSal Plus 2024:eesp00252022. [PMID: 38767346 DOI: 10.1128/ecosalplus.esp-0025-2022] [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: 09/29/2023] [Accepted: 04/11/2024] [Indexed: 05/22/2024]
Abstract
Toxin-antitoxin systems are ubiquitous in the prokaryotic world and widely distributed among chromosomes and mobile genetic elements. Several different toxin-antitoxin system types exist, but what they all have in common is that toxin activity is prevented by the cognate antitoxin. In type I toxin-antitoxin systems, toxin production is controlled by an RNA antitoxin and by structural features inherent to the toxin messenger RNA. Most type I toxins are small membrane proteins that display a variety of cellular effects. While originally discovered as modules that stabilize plasmids, chromosomal type I toxin-antitoxin systems may also stabilize prophages, or serve important functions upon certain stress conditions and contribute to population-wide survival strategies. Here, we will describe the intricate RNA-based regulation of type I toxin-antitoxin systems and discuss their potential biological functions.
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Affiliation(s)
- Selene F H Shore
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Florian H Leinberger
- Institute for Microbiology and Molecular Biology, Justus-Liebig University, Giessen, Germany
| | - Elizabeth M Fozo
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus-Liebig University, Giessen, Germany
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23
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Tang J, Herzfeld AM, Leon G, Brynildsen MP. Differential impacts of DNA repair machinery on fluoroquinolone persisters with different chromosome abundances. mBio 2024; 15:e0037424. [PMID: 38564687 PMCID: PMC11077951 DOI: 10.1128/mbio.00374-24] [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: 02/07/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
DNA repair machinery has been found to be indispensable for fluoroquinolone (FQ) persistence of Escherichia coli. Previously, we found that cells harboring two copies of the chromosome (2Chr) in stationary-phase cultures were more likely to yield FQ persisters than those with one copy of the chromosome (1Chr). Furthermore, we found that RecA and RecB were required to observe that difference, and that loss of either more significantly impacted 2Chr persisters than 1Chr persisters. To better understand the survival mechanisms of persisters with different chromosome abundances, we examined their dependencies on different DNA repair proteins. Here, we show that lexA3 and ∆recN negatively impact the abundances of 2Chr persisters to FQs, without significant impacts on 1Chr persisters. In comparison, ∆xseA, ∆xseB, and ∆uvrD preferentially depress 1Chr persistence to levels that were near the limit of detection. Collectively, these data show that the DNA repair mechanisms used by persisters vary based on chromosome number, and suggest that efforts to eradicate FQ persisters will likely have to take heterogeneity in single-cell chromosome abundance into consideration. IMPORTANCE Persisters are rare phenotypic variants in isogenic populations that survive antibiotic treatments that kill the other cells present. Evidence has accumulated that supports a role for persisters in chronic and recurrent infections. Here, we explore how an under-appreciated phenotypic variable, chromosome copy number (#Chr), influences the DNA repair systems persisters use to survive fluoroquinolone treatments. We found that #Chr significantly biases the DNA repair systems used by persisters, which suggests that #Chr heterogeneity should be considered when devising strategies to eradicate these troublesome bacterial variants.
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Affiliation(s)
- Juechun Tang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
| | - Allison M. Herzfeld
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Gabrielle Leon
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
| | - Mark P. Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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24
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Gupta A, Chandra E, Anand S, Kumar N, Arora R, Rana D, Mrigpuri P. Latent tuberculosis diagnostics: current scenario and review. Monaldi Arch Chest Dis 2024. [PMID: 38700134 DOI: 10.4081/monaldi.2024.2984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
This review presents a comprehensive examination of the contemporary landscape pertaining to latent tuberculosis infection (LTBI) diagnostics, with a particular emphasis on the global ramifications and the intricacies surrounding LTBI diagnosis and treatment. It accentuates the imperative of bolstering diagnostic, preventive, and treatment modalities for tuberculosis (TB) to fulfill the ambitious targets set forth by the World Health Organization aimed at reducing TB-related mortalities and the incidence of new TB cases. The document underscores the significance of addressing LTBI as a means of averting the progression to active TB, particularly in regions burdened with high TB prevalence, such as India. An in-depth analysis of the spectrum delineating latent and active TB disease is provided, elucidating the risk factors predisposing individuals with LTBI to progress towards active TB, including compromised immune functionality, concurrent HIV infection, and other immunosuppressive states. Furthermore, the challenges associated with LTBI diagnosis are elucidated, encompassing the absence of a definitive diagnostic assay, and the merits and demerits of tuberculin skin testing (TST) and interferon-γ release assays (IGRAs) are expounded upon. The document underscores the necessity of confronting these challenges and furnishes a meticulous examination of the advantages and limitations of TST and IGRAs, along with the intricacies involved in interpreting their outcomes across diverse demographics and settings. Additionally, attention is drawn towards the heritability of the interferon-γ response to mycobacterial antigens and the potential utility of antibodies in LTBI diagnosis.
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Affiliation(s)
- Amitesh Gupta
- Department of Pulmonary Medicine, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi.
| | - Eshutosh Chandra
- Department of Pulmonary Medicine, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi.
| | - Shipra Anand
- Department of Pulmonary Medicine, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi.
| | - Naresh Kumar
- Department of Pulmonary Medicine, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi.
| | - Richa Arora
- Department of Pulmonary Medicine, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi.
| | - Divyanshi Rana
- Department of Pulmonary Medicine, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi.
| | - Parul Mrigpuri
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi.
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25
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Ghosh S, Orman MA. Exploring the links between SOS response, mutagenesis, and resistance during the recovery period. Antimicrob Agents Chemother 2024; 68:e0146223. [PMID: 38534113 PMCID: PMC11064565 DOI: 10.1128/aac.01462-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
Although the mechanistic connections between SOS-induced mutagenesis and antibiotic resistance are well established, our current understanding of the impact of SOS response levels, recovery durations, and transcription/translation activities on mutagenesis remains relatively limited. In this study, when bacterial cells were exposed to mutagens like ultraviolet light for defined time intervals, a compelling connection between the rate of mutagenesis and the RecA-mediated SOS response levels became evident. Our observations also indicate that mutagenesis primarily occurs during the subsequent recovery phase following the removal of the mutagenic agent. When transcription/translation was inhibited or energy molecules were depleted at the onset of treatment or during the early recovery phase, there was a noticeable decrease in SOS response activation and mutagenesis. However, targeting these processes later in the recovery phase does not have the same effect in reducing mutagenesis, suggesting that the timing of inhibiting transcription/translation or depleting energy molecules is crucial for their efficacy in reducing mutagenesis. Active transcription, translation, and energy availability within the framework of SOS response and DNA repair mechanisms appear to be conserved attributes, supported by their consistent manifestation across diverse conditions, including the use of distinct mutagens such as fluoroquinolones and various bacterial strains.
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Affiliation(s)
- Sreyashi Ghosh
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
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26
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Kuczyńska-Wiśnik D, Stojowska-Swędrzyńska K, Laskowska E. Intracellular Protective Functions and Therapeutical Potential of Trehalose. Molecules 2024; 29:2088. [PMID: 38731579 PMCID: PMC11085779 DOI: 10.3390/molecules29092088] [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: 03/28/2024] [Revised: 04/28/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Trehalose is a naturally occurring, non-reducing saccharide widely distributed in nature. Over the years, research on trehalose has revealed that this initially thought simple storage molecule is a multifunctional and multitasking compound protecting cells against various stress factors. This review presents data on the role of trehalose in maintaining cellular homeostasis under stress conditions and in the virulence of bacteria and fungi. Numerous studies have demonstrated that trehalose acts in the cell as an osmoprotectant, chemical chaperone, free radical scavenger, carbon source, virulence factor, and metabolic regulator. The increasingly researched medical and therapeutic applications of trehalose are also discussed.
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Affiliation(s)
| | | | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (D.K.-W.); (K.S.-S.)
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27
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Mishra AK, Thakare RP, Santani BG, Yabaji SM, Dixit SK, Srivastava KK. Unlocking the enigma of phenotypic drug tolerance: Mechanisms and emerging therapeutic strategies. Biochimie 2024; 220:67-83. [PMID: 38168626 DOI: 10.1016/j.biochi.2023.12.009] [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: 10/11/2023] [Revised: 12/09/2023] [Accepted: 12/27/2023] [Indexed: 01/05/2024]
Abstract
In the ongoing battle against antimicrobial resistance, phenotypic drug tolerance poses a formidable challenge. This adaptive ability of microorganisms to withstand drug pressure without genetic alterations further complicating global healthcare challenges. Microbial populations employ an array of persistence mechanisms, including dormancy, biofilm formation, adaptation to intracellular environments, and the adoption of L-forms, to develop drug tolerance. Moreover, molecular mechanisms like toxin-antitoxin modules, oxidative stress responses, energy metabolism, and (p)ppGpp signaling contribute to this phenomenon. Understanding these persistence mechanisms is crucial for predicting drug efficacy, developing strategies for chronic bacterial infections, and exploring innovative therapies for refractory infections. In this comprehensive review, we dissect the intricacies of drug tolerance and persister formation, explore their role in acquired drug resistance, and highlight emerging therapeutic approaches to combat phenotypic drug tolerance. Furthermore, we outline the future landscape of interventions for persistent bacterial infections.
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Affiliation(s)
- Alok K Mishra
- Division of Microbiology, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India; Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA, 01605, USA.
| | - Ritesh P Thakare
- Division of Microbiology, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India; Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Bela G Santani
- Department of Microbiology, Sant Gadge Baba Amravati University (SGBAU), Amravati, Maharashtra, India
| | - Shivraj M Yabaji
- Division of Microbiology, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
| | - Shivendra K Dixit
- Division of Medicine ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar Bareilly, Uttar Pradesh, 243122, India.
| | - Kishore K Srivastava
- Division of Microbiology, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India.
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28
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da Silva CV, Velikkakam T, de Oliveira ECM, Silveira ACA, de Lima Júnior JP, Uombe NPI, da Silva PHR, Borges BC. Cellular dormancy: A widespread phenomenon that perpetuates infectious diseases. J Basic Microbiol 2024; 64:e2300389. [PMID: 38064123 DOI: 10.1002/jobm.202300389] [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: 07/11/2023] [Revised: 11/05/2023] [Accepted: 11/21/2023] [Indexed: 05/03/2024]
Abstract
Under adverse environmental conditions, microorganisms are able to enter a state of cellular dormancy which consists of cell cycle arrest and interruption of multiplication. This process ensures their perpetuation in the infected host organism and enables the spread of disease. Throughout biological evolution, dormancy allowed microorganisms to persist in a harsh niche until favorable conditions for their reactivation were re-established. Here, we propose to discuss the dormancy of bacteria and protozoa pathogens focusing on the potential mechanisms and components associated with dormancy.
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Affiliation(s)
- Claudio V da Silva
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Teresiama Velikkakam
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Elida C M de Oliveira
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Anna C A Silveira
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Joed P de Lima Júnior
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Nelsa P I Uombe
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Paulo H R da Silva
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Bruna C Borges
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
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29
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Ahmady L, Gothwal M, Mukkoli MM, Bari VK. Antifungal drug resistance in Candida: a special emphasis on amphotericin B. APMIS 2024; 132:291-316. [PMID: 38465406 DOI: 10.1111/apm.13389] [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: 06/16/2023] [Accepted: 02/12/2024] [Indexed: 03/12/2024]
Abstract
Invasive fungal infections in humans caused by several Candida species, increased considerably in immunocompromised or critically ill patients, resulting in substantial morbidity and mortality. Candida albicans is the most prevalent species, although the frequency of these organisms varies greatly according to geographic region. Infections with C. albicans and non-albicans Candida species have become more common, especially in the past 20 years, as a result of aging, immunosuppressive medication use, endocrine disorders, malnourishment, extended use of medical equipment, and an increase in immunogenic diseases. Despite C. albicans being the species most frequently associated with human infections, C. glabrata, C. parapsilosis, C. tropicalis, and C. krusei also have been identified. Several antifungal drugs with different modes of action are approved for use in clinical settings to treat fungal infections. However, due to the common eukaryotic structure of humans and fungi, only a limited number of antifungal drugs are available for therapeutic use. Furthermore, drug resistance in Candida species has emerged as a result of the growing use of currently available antifungal drugs against fungal infections. Amphotericin B (AmB), a polyene class of antifungal drugs, is mainly used for the treatment of serious systemic fungal infections. AmB interacts with fungal plasma membrane ergosterol, triggering cellular ion leakage via pore formation, or extracting the ergosterol from the plasma membrane inducing cellular death. AmB resistance is primarily caused by changes in the content or structure of ergosterol. This review summarizes the antifungal drug resistance exhibited by Candida species, with a special focus on AmB.
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Affiliation(s)
- Lailema Ahmady
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, India
| | - Manisha Gothwal
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, India
| | | | - Vinay Kumar Bari
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, India
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30
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Berkvens A, Salinas L, Remeijer M, Planqué R, Teusink B, Bruggeman FJ. Understanding and computational design of genetic circuits of metabolic networks. Essays Biochem 2024; 68:41-51. [PMID: 38662439 PMCID: PMC11065555 DOI: 10.1042/ebc20230045] [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: 10/30/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 05/01/2024]
Abstract
The expression of metabolic proteins is controlled by genetic circuits, matching metabolic demands and changing environmental conditions. Ideally, this regulation brings about a competitive level of metabolic fitness. Understanding how cells can achieve a robust (close-to-optimal) functioning of metabolism by appropriate control of gene expression aids synthetic biology by providing design criteria of synthetic circuits for biotechnological purposes. It also extends our understanding of the designs of genetic circuitry found in nature such as metabolite control of transcription factor activity, promoter architectures and transcription factor dependencies, and operon composition (in bacteria). Here, we review, explain and illustrate an approach that allows for the inference and design of genetic circuitry that steers metabolic networks to achieve a maximal flux per unit invested protein across dynamic conditions. We discuss how this approach and its understanding can be used to rationalize Escherichia coli's strategy to regulate the expression of its ribosomes and infer the design of circuitry controlling gene expression of amino-acid biosynthesis enzymes. The inferred regulation indeed resembles E. coli's circuits, suggesting that these have evolved to maximize amino-acid production fluxes per unit invested protein. We end by an outlook of the use of this approach in metabolic engineering applications.
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Affiliation(s)
- Alicia Berkvens
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
| | - Luis Salinas
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
| | - Maaike Remeijer
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
| | - Robert Planqué
- Department of Mathematics, Amsterdam Center for Dynamics and Computation, VU University, Amsterdam, NL
| | - Bas Teusink
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
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31
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Dirkx L, Van Acker SI, Nicolaes Y, Cunha JLR, Ahmad R, Hendrickx R, Caljon B, Imamura H, Ebo DG, Jeffares DC, Sterckx YGJ, Maes L, Hendrickx S, Caljon G. Long-term hematopoietic stem cells trigger quiescence in Leishmania parasites. PLoS Pathog 2024; 20:e1012181. [PMID: 38656959 PMCID: PMC11073788 DOI: 10.1371/journal.ppat.1012181] [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: 09/05/2023] [Revised: 05/06/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
Addressing the challenges of quiescence and post-treatment relapse is of utmost importance in the microbiology field. This study shows that Leishmania infantum and L. donovani parasites rapidly enter into quiescence after an estimated 2-3 divisions in both human and mouse bone marrow stem cells. Interestingly, this behavior is not observed in macrophages, which are the primary host cells of the Leishmania parasite. Transcriptional comparison of the quiescent and non-quiescent metabolic states confirmed the overall decrease of gene expression as a hallmark of quiescence. Quiescent amastigotes display a reduced size and signs of a rapid evolutionary adaptation response with genetic alterations. Our study provides further evidence that this quiescent state significantly enhances resistance to treatment. Moreover, transitioning through quiescence is highly compatible with sand fly transmission and increases the potential of parasites to infect cells. Collectively, this work identified stem cells in the bone marrow as a niche where Leishmania quiescence occurs, with important implications for antiparasitic treatment and acquisition of virulence traits.
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Affiliation(s)
- Laura Dirkx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Sara I. Van Acker
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Yasmine Nicolaes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - João Luís Reis Cunha
- York Biomedical Research Institute and Department of Biology, University of York, York, United Kingdom
| | - Rokaya Ahmad
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Rik Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Ben Caljon
- Brussels Interuniversity Genomics High Throughput core (BRIGHTcore) platform, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Hideo Imamura
- Brussels Interuniversity Genomics High Throughput core (BRIGHTcore) platform, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Didier G. Ebo
- Department of Immunology–Allergology–Rheumatology, Faculty of Medicine and Health Science, Infla-Med Centre of Excellence, University of Antwerp, Antwerp University Hospital, Antwerp, Belgium
| | - Daniel C. Jeffares
- York Biomedical Research Institute and Department of Biology, University of York, York, United Kingdom
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Sarah Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
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32
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Aboelnaga N, Elsayed SW, Abdelsalam NA, Salem S, Saif NA, Elsayed M, Ayman S, Nasr M, Elhadidy M. Deciphering the dynamics of methicillin-resistant Staphylococcus aureus biofilm formation: from molecular signaling to nanotherapeutic advances. Cell Commun Signal 2024; 22:188. [PMID: 38519959 PMCID: PMC10958940 DOI: 10.1186/s12964-024-01511-2] [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: 11/20/2023] [Accepted: 02/01/2024] [Indexed: 03/25/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) represents a global threat, necessitating the development of effective solutions to combat this emerging superbug. In response to selective pressures within healthcare, community, and livestock settings, MRSA has evolved increased biofilm formation as a multifaceted virulence and defensive mechanism, enabling the bacterium to thrive in harsh conditions. This review discusses the molecular mechanisms contributing to biofilm formation across its developmental stages, hence representing a step forward in developing promising strategies for impeding or eradicating biofilms. During staphylococcal biofilm development, cell wall-anchored proteins attach bacterial cells to biotic or abiotic surfaces; extracellular polymeric substances build scaffolds for biofilm formation; the cidABC operon controls cell lysis within the biofilm, and proteases facilitate dispersal. Beside the three main sequential stages of biofilm formation (attachment, maturation, and dispersal), this review unveils two unique developmental stages in the biofilm formation process for MRSA; multiplication and exodus. We also highlighted the quorum sensing as a cell-to-cell communication process, allowing distant bacterial cells to adapt to the conditions surrounding the bacterial biofilm. In S. aureus, the quorum sensing process is mediated by autoinducing peptides (AIPs) as signaling molecules, with the accessory gene regulator system playing a pivotal role in orchestrating the production of AIPs and various virulence factors. Several quorum inhibitors showed promising anti-virulence and antibiofilm effects that vary in type and function according to the targeted molecule. Disrupting the biofilm architecture and eradicating sessile bacterial cells are crucial steps to prevent colonization on other surfaces or organs. In this context, nanoparticles emerge as efficient carriers for delivering antimicrobial and antibiofilm agents throughout the biofilm architecture. Although metal-based nanoparticles have been previously used in combatting biofilms, its non-degradability and toxicity within the human body presents a real challenge. Therefore, organic nanoparticles in conjunction with quorum inhibitors have been proposed as a promising strategy against biofilms. As nanotherapeutics continue to gain recognition as an antibiofilm strategy, the development of more antibiofilm nanotherapeutics could offer a promising solution to combat biofilm-mediated resistance.
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Affiliation(s)
- Nirmeen Aboelnaga
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Salma W Elsayed
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Department of Microbiology & Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Nehal Adel Abdelsalam
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Salma Salem
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Nehal A Saif
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Manar Elsayed
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Shehab Ayman
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Maha Nasr
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohamed Elhadidy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.
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Filipić B, Ušjak D, Rambaher MH, Oljacic S, Milenković MT. Evaluation of novel compounds as anti-bacterial or anti-virulence agents. Front Cell Infect Microbiol 2024; 14:1370062. [PMID: 38510964 PMCID: PMC10951914 DOI: 10.3389/fcimb.2024.1370062] [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: 01/13/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
Antimicrobial resistance is a global threat, leading to an alarming increase in the prevalence of bacterial infections that can no longer be treated with available antibiotics. The World Health Organization estimates that by 2050 up to 10 million deaths per year could be associated with antimicrobial resistance, which would equal the annual number of cancer deaths worldwide. To overcome this emerging crisis, novel anti-bacterial compounds are urgently needed. There are two possible approaches in the fight against bacterial infections: a) targeting structures within bacterial cells, similar to existing antibiotics; and/or b) targeting virulence factors rather than bacterial growth. Here, for the first time, we provide a comprehensive overview of the key steps in the evaluation of potential new anti-bacterial and/or anti-virulence compounds. The methods described in this review include: a) in silico methods for the evaluation of novel compounds; b) anti-bacterial assays (MIC, MBC, Time-kill); b) anti-virulence assays (anti-biofilm, anti-quorum sensing, anti-adhesion); and c) evaluation of safety aspects (cytotoxicity assay and Ames test). Overall, we provide a detailed description of the methods that are an essential tool for chemists, computational chemists, microbiologists, and toxicologists in the evaluation of potential novel antimicrobial compounds. These methods are cost-effective and have high predictive value. They are widely used in preclinical studies to identify new molecular candidates, for further investigation in animal and human trials.
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Affiliation(s)
- Brankica Filipić
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Dušan Ušjak
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Martina Hrast Rambaher
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Slavica Oljacic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Marina T. Milenković
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
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Gao C, Qin S, Wang M, Li R, Ampomah-Wireko M, Chen S, Qu Y, Zhang E. Effective ciprofloxacin cationic antibacterial agent against persister bacteria with low hemolytic toxicity. Eur J Med Chem 2024; 267:116215. [PMID: 38354522 DOI: 10.1016/j.ejmech.2024.116215] [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: 01/05/2024] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
With the widespread use of antibiotics, bacterial resistance has developed rapidly. To make matters worse, infections caused by persistent bacteria and biofilms often cannot be completely eliminated, which brings great difficulties to clinical medication. In this work, three series of quinolone pyridinium quaternary ammonium small molecules were designed and synthesized. Most of the compounds showed good antibacterial activity against Gram-positive bacteria (S. aureus and E. faecalis) and Gram-negative bacteria (E. coli and S. maltophilia). The activity of the para-pyridine quaternary ammonium salt was better than that of the meta-pyridine. 3f was the optimal compound with good stability in body fluids and was unlikely to induce bacterial resistance. The hemolysis rate of erythrocytes at 1280 μg/mL for 3f was only 5.1%. Encouragingly, 3f rapidly killed bacteria within 4 h at 4 × MIC concentration and was effective in killing persistent bacteria in biofilms. The antibacterial mechanism experiments showed that 3f could cause disorder of bacterial membrane potential, increase bacterial membrane permeability, dissolve and destroy the membrane. Incomplete bacterial membranes lead to leakage of bacterial genetic material, concomitant production of ROS, and bacterial death due to these multiple effects.
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Affiliation(s)
- Chen Gao
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China Zhengzhou University, Zhengzhou 450001, PR China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China Zhengzhou University, Zhengzhou 450001, PR China
| | - Meng Wang
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China Zhengzhou University, Zhengzhou 450001, PR China
| | - Ruirui Li
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China Zhengzhou University, Zhengzhou 450001, PR China
| | - Maxwell Ampomah-Wireko
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China Zhengzhou University, Zhengzhou 450001, PR China
| | - Shengcong Chen
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China Zhengzhou University, Zhengzhou 450001, PR China
| | - Ye Qu
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China Zhengzhou University, Zhengzhou 450001, PR China
| | - En Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China Zhengzhou University, Zhengzhou 450001, PR China; Pingyuan Laboratory (Zhengzhou University), PR China.
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Murtha AN, Kazi M, Kim E, Rosch KM, Torres F, Dörr T. Multiple resistance factors collectively promote inoculum-dependent dynamic survival during antimicrobial peptide exposure in Enterobacter cloacae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583169. [PMID: 38463991 PMCID: PMC10925329 DOI: 10.1101/2024.03.03.583169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Antimicrobial peptides (AMPs) are a promising tool with which to fight rising antibiotic resistance. However, pathogenic bacteria are equipped with several AMP defense mechanisms, whose contributions to AMP resistance are often poorly defined. Here, we evaluate the genetic determinants of resistance to an insect AMP, cecropin B, in the opportunistic pathogen Enterobacter cloacae. Single-cell analysis of E. cloacae's response to cecropin revealed marked heterogeneity in cell survival, phenotypically reminiscent of heteroresistance (the ability of a subpopulation to grow in the presence of supra-MIC concentration of antimicrobial). The magnitude of this response was highly dependent on initial E. cloacae inoculum. We identified 3 genetic factors which collectively contribute to E. cloacae resistance in response to the AMP cecropin: The PhoPQ-two-component system, OmpT-mediated proteolytic cleavage of cecropin, and Rcs-mediated membrane stress response. Altogether, this evidence suggests that multiple, independent mechanisms contribute to AMP resistance in E. cloacae.
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Affiliation(s)
- Andrew N. Murtha
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Misha Kazi
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Eileen Kim
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kelly M. Rosch
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Facundo Torres
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853, USA
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Wang X, Wang D, Lu H, Wang X, Wang X, Su J, Xia G. Strategies to Promote the Journey of Nanoparticles Against Biofilm-Associated Infections. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305988. [PMID: 38178276 DOI: 10.1002/smll.202305988] [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: 07/17/2023] [Revised: 10/08/2023] [Indexed: 01/06/2024]
Abstract
Biofilm-associated infections are one of the most challenging healthcare threats for humans, accounting for 80% of bacterial infections, leading to persistent and chronic infections. The conventional antibiotics still face their dilemma of poor therapeutic effects due to the high tolerance and resistance led by bacterial biofilm barriers. Nanotechnology-based antimicrobials, nanoparticles (NPs), are paid attention extensively and considered as promising alternative. This review focuses on the whole journey of NPs against biofilm-associated infections, and to clarify it clearly, the journey is divided into four processes in sequence as 1) Targeting biofilms, 2) Penetrating biofilm barrier, 3) Attaching to bacterial cells, and 4) Translocating through bacterial cell envelope. Through outlining the compositions and properties of biofilms and bacteria cells, recent advances and present the strategies of each process are comprehensively discussed to combat biofilm-associated infections, as well as the combined strategies against these infections with drug resistance, aiming to guide the rational design and facilitate wide application of NPs in biofilm-associated infections.
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Affiliation(s)
- Xiaobo Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
| | - Dan Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
| | - Hongwei Lu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
| | - Xiaowei Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
| | - Xuelei Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
| | - Jiayi Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
| | - Guimin Xia
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, P. R. China
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Joseph I, Risener CJ, Falk K, Northington G, Quave CL. Bacterial Persistence in Urinary Tract Infection Among Postmenopausal Population. UROGYNECOLOGY (PHILADELPHIA, PA.) 2024; 30:205-213. [PMID: 38484233 PMCID: PMC10947078 DOI: 10.1097/spv.0000000000001452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
IMPORTANCE Urinary tract infections (UTIs) are common in older-aged women. Our study examined bacterial persistence with commonly prescribed antibiotics. Bacterial growth was demonstrated despite antibiotic treatment. OBJECTIVES The aims of this study were to quantify the bacterial persister phenotype in urine collected from postmenopausal women with acute and recurrent UTI and to determine the capabilities of first-line antibiotics to effectively treat persister cells. STUDY DESIGN This was an institutional review board-approved cross-sectional analysis within a large academic referral center. Uropathogens were cultured from postmenopausal women with acute or recurrent UTI and screened for persister cells using persistence assays. Demographic and clinical variables were collected and analyzed. The entire experimental process was repeated in triplicate. Data were analyzed for significance (P < 0.05) between the persister culture and antibiotic treatments using a 1-way analysis of variance with multiple comparisons in Prism 9.3.0. RESULTS Forty participants were included: 62.5% White, 22.5% Black, 3% Asian, and 2% Hispanic with a mean age of 72.3 ± 11.62 years. The persister phenotype was demonstrated in all of Escherichia coli isolates. Treatment with fosfomycin demonstrated reduced colony-forming units per milliliter compared with control (P < 0.01). Among recurrent isolates, there was a statistically significant decrease in colony-forming units per milliliter after antibiotic treatment with all 4 antibiotics (P < 0.05). CONCLUSIONS This study demonstrated in vitro bacterial persistence in uropathogens from urogynecology patients despite treatment with commonly prescribed antibiotics. Fosfomycin generated the least amount of persister cells. Results suggest that persistence may be one bacterial defense mechanism involved in UTIs. Further research is needed to understand the clinical implications.
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Zhu H, Xiong Y, Jiang Z, Liu Q, Wang J. Quantifying Dynamic Phenotypic Heterogeneity in Resistant Escherichia coli under Translation-Inhibiting Antibiotics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304548. [PMID: 38193201 PMCID: PMC10953537 DOI: 10.1002/advs.202304548] [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: 07/05/2023] [Revised: 12/20/2023] [Indexed: 01/10/2024]
Abstract
Understanding the phenotypic heterogeneity of antibiotic-resistant bacteria following treatment and the transitions between different phenotypes is crucial for developing effective infection control strategies. The study expands upon previous work by explicating chloramphenicol-induced phenotypic heterogeneities in growth rate, gene expression, and morphology of resistant Escherichia coli using time-lapse microscopy. Correlating the bacterial growth rate and cspC expression, four interchangeable phenotypic subpopulations across varying antibiotic concentrations are identified, surpassing the previously described growth rate bistability. Notably, bacterial cells exhibiting either fast or slow growth rates can concurrently harbor subpopulations characterized by high and low gene expression levels, respectively. To elucidate the mechanisms behind this enhanced heterogeneity, a concise gene expression network model is proposed and the biological significance of the four phenotypes is further explored. Additionally, by employing Hidden Markov Model fitting and integrating the non-equilibrium landscape and flux theory, the real-time data encompassing diverse bacterial traits are analyzed. This approach reveals dynamic changes and switching kinetics in different cell fates, facilitating the quantification of observable behaviors and the non-equilibrium dynamics and thermodynamics at play. The results highlight the multi-dimensional heterogeneous behaviors of antibiotic-resistant bacteria under antibiotic stress, providing new insights into the compromised antibiotic efficacy, microbial response, and associated evolution processes.
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Affiliation(s)
- Haishuang Zhu
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiAnhui230026China
| | - Yixiao Xiong
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiAnhui230026China
| | - Zhenlong Jiang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
| | - Qiong Liu
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
| | - Jin Wang
- Department of ChemistryPhysics and Applied MathematicsState University of New York at Stony Brook.Stony BrookNew York11794‐3400USA
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Wang H, Fan Q, Wang Y, Yi L, Wang Y. Rethinking the control of Streptococcus suis infection: Biofilm formation. Vet Microbiol 2024; 290:110005. [PMID: 38280304 DOI: 10.1016/j.vetmic.2024.110005] [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: 05/30/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/29/2024]
Abstract
Streptococcus suis is an emerging zoonotic pathogen that is widespread in swine populations. The control of S. suis infection and its associated diseases is a daunting challenge worldwide. Biofilm formation appears to be the main reason for the persistence of S. suis. In this review we gather existing knowledge on S. suis biofilm, describing the role of biofilm formation in S. suis virulence and drug resistance, the regulatory factors of S. suis biofilm formation, and the research progress of inhibiting S. suis biofilm formation, with the aim of providing guidance for future studies related to the field of S. suis biofilms.
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Affiliation(s)
- Haikun Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang, China
| | - Qingying Fan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang, China
| | - Yuxin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang, China
| | - Li Yi
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang, China; College of Life Science, Luoyang Normal University, Luoyang, China.
| | - Yang Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang, China.
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Roehrig C, Huemer M, Lorgé D, Arn F, Heinrich N, Selvakumar L, Gasser L, Hauswirth P, Chang CC, Schweizer TA, Eichenseher F, Lehmann S, Zinkernagel AS, Schmelcher M. MEndoB, a chimeric lysin featuring a novel domain architecture and superior activity for the treatment of staphylococcal infections. mBio 2024; 15:e0254023. [PMID: 38275913 PMCID: PMC10865858 DOI: 10.1128/mbio.02540-23] [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: 09/18/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Bacterial infections are a growing global healthcare concern, as an estimated annual 4.95 million deaths are associated with antimicrobial resistance (AMR). Methicillin-resistant Staphylococcus aureus is one of the deadliest pathogens and a high-priority pathogen according to the World Health Organization. Peptidoglycan hydrolases (PGHs) of phage origin have been postulated as a new class of antimicrobials for the treatment of bacterial infections, with a novel mechanism of action and no known resistances. The modular architecture of PGHs permits the creation of chimeric PGH libraries. In this study, the chimeric enzyme MEndoB was selected from a library of staphylococcal PGHs based on its rapid and sustained activity against staphylococci in human serum. The benefit of the presented screening approach was illustrated by the superiority of MEndoB in a head-to-head comparison with other PGHs intended for use against staphylococcal bacteremia. MEndoB displayed synergy with antibiotics and rapid killing in human whole blood with complete inhibition of re-growth over 24 h at low doses. Successful treatment of S. aureus-infected zebrafish larvae with MEndoB provided evidence for its in vivo effectiveness. This was further confirmed in a lethal systemic mouse infection model in which MEndoB significantly reduced S. aureus loads and tumor necrosis factor alpha levels in blood in a dose-dependent manner, which led to increased survival of the animals. Thus, the thorough lead candidate selection of MEndoB resulted in an outstanding second-generation PGH with in vitro, ex vivo, and in vivo results supporting further development.IMPORTANCEOne of the most pressing challenges of our era is the rising occurrence of bacteria that are resistant to antibiotics. Staphylococci are prominent pathogens in humans, which have developed multiple strategies to evade the effects of antibiotics. Infections caused by these bacteria have resulted in a high burden on the health care system and a significant loss of lives. In this study, we have successfully engineered lytic enzymes that exhibit an extraordinary ability to eradicate staphylococci. Our findings substantiate the importance of meticulous lead candidate selection to identify therapeutically promising peptidoglycan hydrolases with unprecedented activity. Hence, they offer a promising new avenue for treating staphylococcal infections.
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Affiliation(s)
- Christian Roehrig
- Micreos Pharmaceuticals AG, Baar, Zug, Switzerland
- Micreos GmbH, Wädenswil, Zurich, Switzerland
| | | | | | | | | | | | - Lynn Gasser
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences (ZHAW), Wädenswil, Zurich, Switzerland
| | - Patrick Hauswirth
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences (ZHAW), Wädenswil, Zurich, Switzerland
| | - Chun-Chi Chang
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Tiziano A. Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Steffi Lehmann
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences (ZHAW), Wädenswil, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Ke W, Xie Y, Chen Y, Ding H, Ye L, Qiu H, Li H, Zhang L, Chen L, Tian X, Shen Z, Song Z, Fan X, Zong JF, Guo Z, Ma X, Xiao M, Liao G, Liu CH, Yin WB, Dong Z, Yang F, Jiang YY, Perlin DS, Chen Y, Fu YV, Wang L. Fungicide-tolerant persister formation during cryptococcal pulmonary infection. Cell Host Microbe 2024; 32:276-289.e7. [PMID: 38215741 DOI: 10.1016/j.chom.2023.12.012] [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: 06/08/2023] [Revised: 09/25/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024]
Abstract
Bacterial persisters, a subpopulation of genetically susceptible cells that are normally dormant and tolerant to bactericides, have been studied extensively because of their clinical importance. In comparison, much less is known about the determinants underlying fungicide-tolerant fungal persister formation in vivo. Here, we report that during mouse lung infection, Cryptococcus neoformans forms persisters that are highly tolerant to amphotericin B (AmB), the standard of care for treating cryptococcosis. By exploring stationary-phase indicator molecules and developing single-cell tracking strategies, we show that in the lung, AmB persisters are enriched in cryptococcal cells that abundantly produce stationary-phase molecules. The antioxidant ergothioneine plays a specific and key role in AmB persistence, which is conserved in phylogenetically distant fungi. Furthermore, the antidepressant sertraline (SRT) shows potent activity specifically against cryptococcal AmB persisters. Our results provide evidence for and the determinant of AmB-tolerant persister formation in pulmonary cryptococcosis, which has potential clinical significance.
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Affiliation(s)
- Weixin Ke
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuyan Xie
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingying Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Ding
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leixin Ye
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haoning Qiu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Li
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Lanyue Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuyun Tian
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenghao Shen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zili Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Jian-Fa Zong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoyu Ma
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing 100730, China
| | - Guojian Liao
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Cui Hua Liu
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Yang
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yuan-Ying Jiang
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Yihua Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu V Fu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Linqi Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Mirzaei R, Campoccia D, Ravaioli S, Arciola CR. Emerging Issues and Initial Insights into Bacterial Biofilms: From Orthopedic Infection to Metabolomics. Antibiotics (Basel) 2024; 13:184. [PMID: 38391570 PMCID: PMC10885942 DOI: 10.3390/antibiotics13020184] [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: 12/19/2023] [Revised: 01/29/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
Bacterial biofilms, enigmatic communities of microorganisms enclosed in an extracellular matrix, still represent an open challenge in many clinical contexts, including orthopedics, where biofilm-associated bone and joint infections remain the main cause of implant failure. This study explores the scenario of biofilm infections, with a focus on those related to orthopedic implants, highlighting recently emerged substantial aspects of the pathogenesis and their potential repercussions on the clinic, as well as the progress and gaps that still exist in the diagnostics and management of these infections. The classic mechanisms through which biofilms form and the more recently proposed new ones are depicted. The ways in which bacteria hide, become impenetrable to antibiotics, and evade the immune defenses, creating reservoirs of bacteria difficult to detect and reach, are delineated, such as bacterial dormancy within biofilms, entry into host cells, and penetration into bone canaliculi. New findings on biofilm formation with host components are presented. The article also delves into the emerging and critical concept of immunometabolism, a key function of immune cells that biofilm interferes with. The growing potential of biofilm metabolomics in the diagnosis and therapy of biofilm infections is highlighted, referring to the latest research.
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Affiliation(s)
- Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Laboratory, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Davide Campoccia
- Laboratorio di Patologia delle Infezioni Associate all'Impianto, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy
| | - Stefano Ravaioli
- Laboratorio di Patologia delle Infezioni Associate all'Impianto, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy
| | - Carla Renata Arciola
- Laboratory of Immunorheumatology and Tissue Regeneration, Laboratory of Pathology of Implant Infections, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy
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Joshi H, Kandari D, Maitra SS, Bhatnagar R, Banerjee N. Identification of genes associated with persistence in Mycobacterium smegmatis. Front Microbiol 2024; 15:1302883. [PMID: 38410395 PMCID: PMC10894938 DOI: 10.3389/fmicb.2024.1302883] [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: 09/27/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
The prevalence of bacterial persisters is related to their phenotypic diversity and is responsible for the relapse of chronic infections. Tolerance to antibiotic therapy is the hallmark of bacterial persistence. In this study, we have screened a transposon library of Mycobacterium smegmatis mc2155 strain using antibiotic tolerance, survival in mouse macrophages, and biofilm-forming ability of the mutants. Out of 10 thousand clones screened, we selected ten mutants defective in all the three phenotypes. Six mutants showed significantly lower persister abundance under different stress conditions. Insertions in three genes belonging to the pathways of oxidative phosphorylation msmeg_3233 (cydA), biotin metabolism msmeg_3194 (bioB), and oxidative metabolism msmeg_0719, a flavoprotein monooxygenase, significantly reduced the number of live cells, suggesting their role in pathways promoting long-term survival. Another group that displayed a moderate reduction in CFU included a glycosyltransferase, msmeg_0392, a hydrogenase subunit, msmeg_2263 (hybC), and a DNA binding protein, msmeg_2211. The study has revealed potential candidates likely to facilitate the long-term survival of M. smegmatis. The findings offer new targets to develop antibiotics against persisters. Further, investigating the corresponding genes in M. tuberculosis may provide valuable leads in improving the treatment of chronic and persistent tuberculosis infections.
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Affiliation(s)
- Hemant Joshi
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Divya Kandari
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
- Divacc Research Laboratories Pvt. Ltd., incubated under Atal Incubation Centre, Jawaharlal Nehru University, New Delhi, India
| | - Subhrangsu Sundar Maitra
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Bhatnagar
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Nirupama Banerjee
- Divacc Research Laboratories Pvt. Ltd., incubated under Atal Incubation Centre, Jawaharlal Nehru University, New Delhi, India
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Li Y, Chen X, Zhang W, Fang K, Tian J, Li F, Han M, Huang J, Sun T, Bai F, Cheng M, Xu Y. The metabolic slowdown caused by the deletion of pspA accelerates protein aggregation during stationary phase facilitating antibiotic persistence. Antimicrob Agents Chemother 2024; 68:e0093723. [PMID: 38169282 PMCID: PMC10848772 DOI: 10.1128/aac.00937-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
Entering a dormant state is a prevailing mechanism used by bacterial cells to transiently evade antibiotic attacks and become persisters. The dynamic progression of bacterial dormancy depths driven by protein aggregation has been found to be critical for antibiotic persistence in recent years. However, our current understanding of the endogenous genes that affects dormancy depth remains limited. Here, we discovered a novel role of phage shock protein A (pspA) gene in modulating bacterial dormancy depth. Deletion of pspA of Escherichia coli resulted in increased bacterial dormancy depths and prolonged lag times for resuscitation during the stationary phase. ∆pspA exhibited a higher persister ratio compared to the wild type when challenged with various antibiotics. Microscopic images revealed that ∆pspA showed accelerated formation of protein aggresomes, which were collections of endogenous protein aggregates. Time-lapse imaging established the positive correlation between protein aggregation and antibiotic persistence of ∆pspA at the single-cell level. To investigate the molecular mechanism underlying accelerated protein aggregation, we performed transcriptome profiling and found the increased abundance of chaperons and a general metabolic slowdown in the absence of pspA. Consistent with the transcriptomic results, the ∆pspA strain showed a decreased cellular ATP level, which could be rescued by glucose supplementation. Then, we verified that replenishment of cellular ATP levels by adding glucose could inhibit protein aggregation and reduce persister formation in ∆pspA. This study highlights the novel role of pspA in maintaining proteostasis, regulating dormancy depth, and affecting antibiotic persistence during stationary phase.
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Affiliation(s)
- Yingxing Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Biomedical Engineering Facility of National Infrastructures for Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao Chen
- Biomedical Pioneering Innovation Centre (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Weili Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Kefan Fang
- Biomedical Pioneering Innovation Centre (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Jingjing Tian
- Biomedical Engineering Facility of National Infrastructures for Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fangyuan Li
- Clinical Biobank, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingfei Han
- National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, China
| | - Jingjing Huang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Clinical Laboratory, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Tianshu Sun
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Biobank, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Bai
- Biomedical Pioneering Innovation Centre (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Mei Cheng
- Department of Clinical Laboratory, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Chatterjee P, Chauhan N, Jain U. Confronting antibiotic-resistant pathogens: Distinctive drug delivery potentials of progressive nanoparticles. Microb Pathog 2024; 187:106499. [PMID: 38097117 DOI: 10.1016/j.micpath.2023.106499] [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: 09/26/2023] [Revised: 11/07/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
Antimicrobial resistance arises over time, usually due to genetic modifications. Global observations of high resistance rates to popular antibiotics used to treat common bacterial diseases, such as diarrhea, STIs, sepsis, and urinary tract infections, indicate that our supply of effective antibiotics is running low. The mechanisms of action of several antibiotic groups are covered in this review. Antimicrobials disrupt the development and metabolism of bacteria, leading to their eventual death. However, in recent years, microorganisms become resistant to the drugs. Bacteria encode resistant genes against antibiotics and inhibit the function of antibiotics by reducing the uptake of drugs, modifying the enzyme's active site, synthesizing enzymes to degrade antibiotics, and changing the structure of ribosomal subunits. Additionally, the methods of action of resistant bacteria against different kinds of antibiotics as well as their modes of action are discussed. Besides, the resistant pathogenic bacteria which get the most priority by World Health Organisation (WHO) for synthesizing new drugs, have also been incorporated. To overcome antimicrobial resistance, nanomaterials are used to increase the efficacy of antimicrobial drugs. Metallic, inorganic, and polymer-based nanoparticles once conjugated with antibacterial drugs, exhibit synergistic effects by increasing the efficacy of the drugs by inhibiting bacterial growth. Nanomaterial's toxic properties are proportional to their concentrations. Higher concentration nanomaterials are more toxic to the cells. In this review, the toxic properties of nanomaterials on lung cells, lymph nodes, and neuronal cells are also summarized.
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Affiliation(s)
- Pallabi Chatterjee
- School of Health Sciences & Technology (SoHST), University of Petroleum and Energy Studies (UPES), Bidholi, 248007, Dehradun, India
| | - Nidhi Chauhan
- School of Health Sciences & Technology (SoHST), University of Petroleum and Energy Studies (UPES), Bidholi, 248007, Dehradun, India
| | - Utkarsh Jain
- School of Health Sciences & Technology (SoHST), University of Petroleum and Energy Studies (UPES), Bidholi, 248007, Dehradun, India.
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Vasudevan S, David H, Chanemougam L, Ramani J, Ramesh Sangeetha M, Solomon AP. Emergence of persister cells in Staphylococcus aureus: calculated or fortuitous move? Crit Rev Microbiol 2024; 50:64-75. [PMID: 36548910 DOI: 10.1080/1040841x.2022.2159319] [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: 11/02/2021] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
A stable but reversible phenotype switch from normal to persister state is advantageous to the intracellular pathogens to cause recurrent infections and to evade the host immune system. Staphylococcus aureus is a versatile opportunistic pathogen known to cause chronic infections with significant mortality. One of the notable features is the ability to switch to a per-sisters cell, which is found in planktonic and biofilm states. This phenotypic switch is always an open question to explore the hidden fundamental science that coheres with a calculated or fortuitous move. Toxin-antitoxin modules, nutrient stress, and an erroneous translation-enabled state of dormancy entail this persistent behaviour in S. aureus. It is paramount to get a clear picture of why the cell chooses to enter a persistent condition, as it would decide the course of treatment. Analyzing the exit from a persistent state to an active state and the subsequent repercussion of this transition is essential to determine its role in chronic infections. This review attempts to provide a constructed argument discussing the most widely accepted mechanisms and identifying the various attributes of persistence.
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Affiliation(s)
- Sahana Vasudevan
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Helma David
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Lakshmi Chanemougam
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Jayalakshmi Ramani
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Maanasa Ramesh Sangeetha
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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Khaova EA, Tkachenko AG. Effects of polyamines and indole on the expression of ribosome hibernation factors in Escherichia coli at the translational level. Vavilovskii Zhurnal Genet Selektsii 2024; 28:24-32. [PMID: 38465244 PMCID: PMC10917681 DOI: 10.18699/vjgb-24-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 03/12/2024] Open
Abstract
Polyamines and indole are small regulatory molecules that are involved in the adaptation to stress in bacteria, including the regulation of gene expression. Genes, the translation of which is under the regulatory effects of polyamines, form the polyamine modulon. Previously, we showed that polyamines upregulated the transcription of genes encoding the ribosome hibernation factors RMF, RaiA, SRA, EttA and RsfS in Escherichia coli. At the same time, indole affected the expression at the transcriptional level of only the raiA and rmf genes. Ribosome hibernation factors reversibly inhibit translation under stress conditions, including exposure to antibiotics, to avoid resource waste and to conserve ribosomes for a quick restoration of their functions when favorable conditions occur. In this work, we have studied the influence of indole on the expression of the raiA and rmf genes at the translational level and regulatory effects of the polyamines putrescine, cadaverine and spermidine on the translation of the rmf, raiA, sra, ettA and rsfS genes. We have analyzed the mRNA primary structures of the studied genes and the predicted mRNA secondary structures obtained by using the RNAfold program for the availability of polyamine modulon features. We have found that all of the studied genes contain specific features typical of the polyamine modulon. Furthermore, to investigate the influence of polyamines and indole on the translation of the studied genes, we have constructed the translational reporter lacZ-fusions by using the pRS552/λRS45 system. According to the results obtained, polyamines upregulated the expression of the rmf, raiA and sra genes, the highest expression of which was observed at the stationary phase, but did not affect the translation of the ettA and rsfS genes, the highest expression of which took place during the exponential phase. The stimulatory effects were polyamine-specific and observed at the stationary phase, when bacteria are under multiple stresses. In addition, the data obtained demonstrated that indole significantly inhibited translation of the raiA and rmf genes, despite the stimulatory effect on their transcrip- tion. This can suggest the activity of a posttranscriptional regulatory mechanism of indole on gene expression.
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Affiliation(s)
- E A Khaova
- Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
| | - A G Tkachenko
- Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
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48
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Hamad M, Al-Marzooq F, Srinivasulu V, Sulaiman A, Menon V, Ramadan WS, El-Awady R, Al-Tel TH. Antimicrobial activity of nature-inspired molecules against multidrug-resistant bacteria. Front Microbiol 2024; 14:1336856. [PMID: 38318129 PMCID: PMC10838778 DOI: 10.3389/fmicb.2023.1336856] [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: 11/11/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024] Open
Abstract
Multidrug-resistant bacterial infections present a serious challenge to global health. In addition to the spread of antibiotic resistance, some bacteria can form persister cells which are tolerant to most antibiotics and can lead to treatment failure or relapse. In the present work, we report the discovery of a new class of small molecules with potent antimicrobial activity against Gram-positive bacteria and moderate activity against Gram-negative drug-resistant bacterial pathogens. The lead compound SIMR 2404 had a minimal inhibitory concentration (MIC) of 2 μg/mL against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-intermediate Staphylococcus aureus (VISA). The MIC values against Gram-negative bacteria such as Escherichia coli and Actinobacteria baumannii were between 8-32 μg/mL. Time-kill experiments show that compound SIMR 2404 can rapidly kill tested bacteria. Compound SIMR 2404 was also found to rapidly kill MRSA persisters which display high levels of tolerance to conventional antibiotics. In antibiotic evolution experiments, MRSA quickly developed resistance to ciprofloxacin but failed to develop resistance to compound SIMR 2404 even after 24 serial passages. Compound SIMR 2404 was not toxic to normal human fibroblast at a concentration of 4 μg/mL which is twice the MIC concentration against MRSA. However, at a concentration of 8 μg/mL or higher, it showed cytotoxic activity indicating that it is not ideal as a candidate against Gram-negative bacteria. The acceptable toxicity profile and rapid antibacterial activity against MRSA highlight the potential of these molecules for further studies as anti-MRSA agents.
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Affiliation(s)
- Mohamad Hamad
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Farah Al-Marzooq
- College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Ashna Sulaiman
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Varsha Menon
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Wafaa S. Ramadan
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Raafat El-Awady
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Taleb H. Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
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Bhattacharya M, Horswill AR. The role of human extracellular matrix proteins in defining Staphylococcus aureus biofilm infections. FEMS Microbiol Rev 2024; 48:fuae002. [PMID: 38337187 PMCID: PMC10873506 DOI: 10.1093/femsre/fuae002] [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: 07/19/2023] [Revised: 01/26/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
Twenty to forty one percent of the world's population is either transiently or permanently colonized by the Gram-positive bacterium, Staphylococcus aureus. In 2017, the CDC designated methicillin-resistant S. aureus (MRSA) as a serious threat, reporting ∼300 000 cases of MRSA-associated hospitalizations annually, resulting in over 19 000 deaths, surpassing that of HIV in the USA. S. aureus is a proficient biofilm-forming organism that rapidly acquires resistance to antibiotics, most commonly methicillin (MRSA). This review focuses on a large group of (>30) S. aureus adhesins, either surface-associated or secreted that are designed to specifically bind to 15 or more of the proteins that form key components of the human extracellular matrix (hECM). Importantly, this includes hECM proteins that are pivotal to the homeostasis of almost every tissue environment [collagen (skin), proteoglycans (lung), hemoglobin (blood), elastin, laminin, fibrinogen, fibronectin, and fibrin (multiple organs)]. These adhesins offer S. aureus the potential to establish an infection in every sterile tissue niche. These infections often endure repeated immune onslaught, developing into chronic, biofilm-associated conditions that are tolerant to ∼1000 times the clinically prescribed dose of antibiotics. Depending on the infection and the immune response, this allows S. aureus to seamlessly transition from colonizer to pathogen by subtly manipulating the host against itself while providing the time and stealth that it requires to establish and persist as a biofilm. This is a comprehensive discussion of the interaction between S. aureus biofilms and the hECM. We provide particular focus on the role of these interactions in pathogenesis and, consequently, the clinical implications for the prevention and treatment of S. aureus biofilm infections.
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Affiliation(s)
- Mohini Bhattacharya
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, United States
| | - Alexander R Horswill
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, United States
- Department of Veterans Affairs, Eastern Colorado Health Care System, Aurora, CO 80045, United States
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50
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Xiong X, Othmer HG, Harcombe WR. Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism. THE ISME JOURNAL 2024; 18:wrae075. [PMID: 38691424 PMCID: PMC11104777 DOI: 10.1093/ismejo/wrae075] [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: 10/09/2023] [Revised: 04/02/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024]
Abstract
Antibiotic persistence (heterotolerance) allows a subpopulation of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial mutualism of Escherichia coli and Salmonella enterica that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-to-cell heterogeneity. Tracking ampicillin-induced death for bacteria on agar surfaces, we found that E. coli forms up to 55 times more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence of S. enterica, the presence of cross-feeding, average nutrient starvation, or spontaneous resistant mutations. Time-series fluorescent microscopy revealed increased cell-to-cell variation in E. coli lag time in the mutualistic co-culture. Furthermore, we discovered that an E. coli cell can survive antibiotic killing if the nearby S. enterica cells on which it relies die first. In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially structured interactions during antibiotic treatment and understanding microbial community resilience more broadly.
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Affiliation(s)
- Xianyi Xiong
- Department of Ecology, Evolution, and Behavior, BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, United States
- Division of Community Health & Epidemiology, University of Minnesota School of Public Health, Minneapolis, MN 55454, United States
| | - Hans G Othmer
- School of Mathematics, University of Minnesota, Minneapolis, MN 55455, United States
| | - William R Harcombe
- Department of Ecology, Evolution, and Behavior, BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, United States
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