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Vijay S, Bao NLH, Vinh DN, Nhat LTH, Thu DDA, Quang NL, Trieu LPT, Nhung HN, Ha VTN, Thai PVK, Ha DTM, Lan NH, Caws M, Thwaites GE, Javid B, Thuong NT. Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates from a longitudinal study. eLife 2024; 13:RP93243. [PMID: 39250422 PMCID: PMC11383526 DOI: 10.7554/elife.93243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024] Open
Abstract
Antibiotic tolerance in Mycobacterium tuberculosis reduces bacterial killing, worsens treatment outcomes, and contributes to resistance. We studied rifampicin tolerance in isolates with or without isoniazid resistance (IR). Using a minimum duration of killing assay, we measured rifampicin survival in isoniazid-susceptible (IS, n=119) and resistant (IR, n=84) isolates, correlating tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs), and isoniazid-resistant mutations. Longitudinal IR isolates were analyzed for changes in rifampicin tolerance and genetic variant emergence. The median time for rifampicin to reduce the bacterial population by 90% (MDK90) increased from 1.23 days (IS) and 1.31 days (IR) to 2.55 days (IS) and 1.98 days (IR) over 15-60 days of incubation, indicating fast and slow-growing tolerant sub-populations. A 6 log10-fold survival fraction classified tolerance as low, medium, or high, showing that IR is linked to increased tolerance and faster growth (OR = 2.68 for low vs. medium, OR = 4.42 for low vs. high, p-trend = 0.0003). High tolerance in IR isolates was associated with rifampicin treatment in patients and genetic microvariants. These findings suggest that IR tuberculosis should be assessed for high rifampicin tolerance to optimize treatment and prevent the development of multi-drug-resistant tuberculosis.
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Affiliation(s)
- Srinivasan Vijay
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Theoretical Microbial Ecology, Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | | | - Dao Nguyen Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
| | | | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
| | - Nguyen Le Quang
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
| | | | | | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
| | | | | | | | - Maxine Caws
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Babak Javid
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, United States
| | - Nguyen Thuy Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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2
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Yamaguchi N, Otsuna H, Eisenberg-Bord M, Ramakrishnan L. An Image Processing Tool for Automated Quantification of Bacterial Burdens in Zebrafish Larvae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.16.608298. [PMID: 39229075 PMCID: PMC11370481 DOI: 10.1101/2024.08.16.608298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Zebrafish larvae are used to model the pathogenesis of multiple bacteria. This transparent model offers the unique advantage of allowing quantification of fluorescent bacterial burdens (fluorescent pixel counts: FPC) in vivo by facile microscopical methods, replacing enumeration of bacteria using time-intensive plating of lysates on bacteriological media. Accurate FPC measurements require laborious manual image processing to mark the outside borders of the animals so as to delineate the bacteria inside the animals from those in the culture medium that they are in. Here, we have developed an automated ImageJ/Fiji-based macro that accurately detect the outside borders of Mycobacterium marinum-infected larvae.
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Affiliation(s)
- Naoya Yamaguchi
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 0AW Cambridge, UK
- MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK
- Equal contributions
| | - Hideo Otsuna
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
- Equal contributions
| | - Michal Eisenberg-Bord
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 0AW Cambridge, UK
- MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK
| | - Lalita Ramakrishnan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 0AW Cambridge, UK
- MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK
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3
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Sett A, Dubey V, Bhowmik S, Pathania R. Decoding Bacterial Persistence: Mechanisms and Strategies for Effective Eradication. ACS Infect Dis 2024; 10:2525-2539. [PMID: 38940498 DOI: 10.1021/acsinfecdis.4c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
The ability of pathogenic bacteria to evade antibiotic treatment is an intricate and multifaceted phenomenon. Over the years, treatment failure among patients due to determinants of antimicrobial resistance (AMR) has been the focal point for the research and development of new therapeutic agents. However, the survival of bacteria by persisting under antibiotic stress has largely been overlooked. Bacterial persisters are a subpopulation of sensitive bacterial cells exhibiting a noninheritable drug-tolerant phenotype. They are linked to the recalcitrance of infections in healthcare settings, in turn giving rise to AMR variants. The importance of bacterial persistence in recurring infections has been firmly recognized. Fundamental work over the past decade has highlighted numerous unique tolerance factors contributing to the persister phenotype in many clinically relevant pathogens. This review summarizes contributing factors that could aid in developing new strategies against bacterial antibiotic persisters.
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Affiliation(s)
- Abhiroop Sett
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Vineet Dubey
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Somok Bhowmik
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
- Centre of Excellence in Disaster Mitigation and Management, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
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4
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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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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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6
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Habjan E, Schouten GK, Speer A, van Ulsen P, Bitter W. Diving into drug-screening: zebrafish embryos as an in vivo platform for antimicrobial drug discovery and assessment. FEMS Microbiol Rev 2024; 48:fuae011. [PMID: 38684467 PMCID: PMC11078164 DOI: 10.1093/femsre/fuae011] [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: 11/01/2023] [Revised: 02/24/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
The rise of multidrug-resistant bacteria underlines the need for innovative treatments, yet the introduction of new drugs has stagnated despite numerous antimicrobial discoveries. A major hurdle is a poor correlation between promising in vitro data and in vivo efficacy in animal models, which is essential for clinical development. Early in vivo testing is hindered by the expense and complexity of existing animal models. Therefore, there is a pressing need for cost-effective, rapid preclinical models with high translational value. To overcome these challenges, zebrafish embryos have emerged as an attractive model for infectious disease studies, offering advantages such as ethical alignment, rapid development, ease of maintenance, and genetic manipulability. The zebrafish embryo infection model, involving microinjection or immersion of pathogens and potential antibiotic hit compounds, provides a promising solution for early-stage drug screening. It offers a cost-effective and rapid means of assessing the efficacy, toxicity and mechanism of action of compounds in a whole-organism context. This review discusses the experimental design of this model, but also its benefits and challenges. Additionally, it highlights recently identified compounds in the zebrafish embryo infection model and discusses the relevance of the model in predicting the compound's clinical potential.
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Affiliation(s)
- Eva Habjan
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Gina K Schouten
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Alexander Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Peter van Ulsen
- Section Molecular Microbiology of A-LIFE, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
- Section Molecular Microbiology of A-LIFE, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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7
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Vijay S, Bao NLH, Vinh DN, Nhat LTH, Thu DDA, Quang NL, Trieu LPT, Nhung HN, Ha VTN, Thai PVK, Ha DTM, Lan NH, Caws M, Thwaites GE, Javid B, Thuong NTT. Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates: an in-vitro longitudinal study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.22.568240. [PMID: 38045287 PMCID: PMC10690245 DOI: 10.1101/2023.11.22.568240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Antibiotic tolerance in Mycobacterium tuberculosis leads to less effective bacterial killing, poor treatment responses and resistant emergence. Therefore, we investigated the rifampicin tolerance of M. tuberculosis isolates, with or without pre-existing isoniazid-resistance. We determined the in-vitro rifampicin survival fraction by minimum duration of killing assay in isoniazid susceptible (IS, n=119) and resistant (IR, n=84) M. tuberculosis isolates. Then we correlated the rifampicin tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs) and isoniazid-resistant mutations. The longitudinal IR isolates collected from patients were analyzed for changes in rifampicin tolerance and associated emergence of genetic variants. The median duration of rifampicin exposure reducing the M. tuberculosis surviving fraction by 90% (minimum duration of killing-MDK90) increased from 1.23 (95%CI 1.11; 1.37) and 1.31 (95%CI 1.14; 1.48) to 2.55 (95%CI 2.04; 2.97) and 1.98 (95%CI 1.69; 2.56) days, for IS and IR respectively, during 15 to 60 days of incubation. This indicated the presence of fast and slow growing tolerant sub-populations. A range of 6 log 10 -fold survival fraction enabled classification of tolerance as low, medium or high and revealed IR association with increased tolerance with faster growth (OR=2.68 for low vs. medium, OR=4.42 for low vs. high, P -trend=0.0003). The high tolerance in IR isolates was specific to those collected during rifampicin treatment in patients and associated with bacterial genetic microvariants. Furthermore, the high rifampicin tolerant IR isolates have survival potential similar to multi-drug resistant isolates. These findings suggest that IR tuberculosis needs to be evaluated for high rifampicin tolerance to improve treatment regimen and prevent the risk of MDR-TB emergence.
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8
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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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9
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Datta D, Jamwal S, Jyoti N, Patnaik S, Kumar D. Actionable mechanisms of drug tolerance and resistance in Mycobacterium tuberculosis. FEBS J 2024. [PMID: 38676952 DOI: 10.1111/febs.17142] [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: 09/11/2023] [Revised: 02/23/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024]
Abstract
The emergence of antimicrobial resistance (AMR) across bacterial pathogens presents a serious threat to global health. This threat is further exacerbated in tuberculosis (TB), mainly due to a protracted treatment regimen involving a combination of drugs. A diversity of factors contributes to the emergence of drug resistance in TB, which is caused by the pathogen Mycobacterium tuberculosis (Mtb). While the traditional genetic mutation-driven drug resistance mechanisms operate in Mtb, there are also several additional unique features of drug resistance in this pathogen. Research in the past decade has enriched our understanding of such unconventional factors as efflux pumps, bacterial heterogeneity, metabolic states, and host microenvironment. Given that the discovery of new antibiotics is outpaced by the emergence of drug resistance patterns displayed by the pathogen, newer strategies for combating drug resistance are desperately needed. In the context of TB, such approaches include targeting the efflux capability of the pathogen, modulating the host environment to prevent bacterial drug tolerance, and activating the host anti-mycobacterial pathways. In this review, we discuss the traditional mechanisms of drug resistance in Mtb, newer understandings and the shaping of a set of unconventional approaches to target both the emergence and treatment of drug resistance in TB.
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Affiliation(s)
- Dipanwita Datta
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Shaina Jamwal
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nishant Jyoti
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Srinivas Patnaik
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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10
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Poulton NC, DeJesus MA, Munsamy-Govender V, Kanai M, Roberts CG, Azadian ZA, Bosch B, Lin KM, Li S, Rock JM. Beyond antibiotic resistance: The whiB7 transcription factor coordinates an adaptive response to alanine starvation in mycobacteria. Cell Chem Biol 2024; 31:669-682.e7. [PMID: 38266648 PMCID: PMC11031301 DOI: 10.1016/j.chembiol.2023.12.020] [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: 06/08/2023] [Revised: 11/13/2023] [Accepted: 12/23/2023] [Indexed: 01/26/2024]
Abstract
Pathogenic mycobacteria are a significant cause of morbidity and mortality worldwide. The conserved whiB7 stress response reduces the effectiveness of antibiotic therapy by activating several intrinsic antibiotic resistance mechanisms. Despite our comprehensive biochemical understanding of WhiB7, the complex set of signals that induce whiB7 expression remain less clear. We employed a reporter-based, genome-wide CRISPRi epistasis screen to identify a diverse set of 150 mycobacterial genes whose inhibition results in constitutive whiB7 expression. We show that whiB7 expression is determined by the amino acid composition of the 5' regulatory uORF, thereby allowing whiB7 to sense amino acid starvation. Although deprivation of many amino acids can induce whiB7, whiB7 specifically coordinates an adaptive response to alanine starvation by engaging in a feedback loop with the alanine biosynthetic enzyme, aspC. These findings describe a metabolic function for whiB7 and help explain its evolutionary conservation across mycobacterial species occupying diverse ecological niches.
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Affiliation(s)
- Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | | | - Mariko Kanai
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Cameron G Roberts
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Zachary A Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Karl Matthew Lin
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA.
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11
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Tyagi S, Sadhu S, Sharma T, Paul A, Pandey M, Nain VK, Rathore DK, Chatterjee S, Awasthi A, Pandey AK. VapC12 ribonuclease toxin modulates host immune response during Mycobacterium tuberculosis infection. Front Immunol 2024; 15:1302163. [PMID: 38515752 PMCID: PMC10955575 DOI: 10.3389/fimmu.2024.1302163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/01/2024] [Indexed: 03/23/2024] Open
Abstract
Mechanistic understanding of antibiotic persistence is a prerequisite in controlling the emergence of MDR cases in Tuberculosis (TB). We have reported that the cholesterol-induced activation of VapC12 ribonuclease is critical for disease persistence in TB. In this study, we observed that relative to the wild type, mice infected with ΔvapC12 induced a pro-inflammatory response, had a higher pathogen load, and responded better to the anti-TB treatment. In a high-dose infection model, all the mice infected with ΔvapC12 succumbed early to the disease. Finally, we reported that the above phenotype of ΔvapC12 was dependent on the presence of the TLR4 receptor. Overall, the data suggests that failure of a timely resolution of the early inflammation by the ΔvapC12 infected mice led to hyperinflammation, altered T-cell response and high bacterial load. In conclusion, our findings suggest the role of the VapC12 toxin in modulating the innate immune response of the host in ways that favor the long-term survival of the pathogen inside the host.
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Affiliation(s)
- Shaifali Tyagi
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Srikanth Sadhu
- Immunobiology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Taruna Sharma
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Abhijit Paul
- Complex Analysis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Manitosh Pandey
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Vaibhav Kumar Nain
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Deepak Kumar Rathore
- Immunobiology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Samrat Chatterjee
- Complex Analysis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Immunobiology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Kumar Pandey
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
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12
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Matsuda R, Sorobetea D, Zhang J, Peterson ST, Grayczyk JP, Yost W, Apenes N, Kovalik ME, Herrmann B, O’Neill RJ, Bohrer AC, Lanza M, Assenmacher CA, Mayer-Barber KD, Shin S, Brodsky IE. A TNF-IL-1 circuit controls Yersinia within intestinal pyogranulomas. J Exp Med 2024; 221:e20230679. [PMID: 38363547 PMCID: PMC10873131 DOI: 10.1084/jem.20230679] [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: 04/20/2023] [Revised: 11/22/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024] Open
Abstract
Tumor necrosis factor (TNF) is a pleiotropic inflammatory cytokine that mediates antimicrobial defense and granuloma formation in response to infection by numerous pathogens. We previously reported that Yersinia pseudotuberculosis colonizes the intestinal mucosa and induces the recruitment of neutrophils and inflammatory monocytes into organized immune structures termed pyogranulomas (PG) that control Yersinia infection. Inflammatory monocytes are essential for the control and clearance of Yersinia within intestinal PG, but how monocytes mediate Yersinia restriction is poorly understood. Here, we demonstrate that TNF signaling in monocytes is required for bacterial containment following enteric Yersinia infection. We further show that monocyte-intrinsic TNFR1 signaling drives the production of monocyte-derived interleukin-1 (IL-1), which signals through IL-1 receptors on non-hematopoietic cells to enable PG-mediated control of intestinal Yersinia infection. Altogether, our work reveals a monocyte-intrinsic TNF-IL-1 collaborative inflammatory circuit that restricts intestinal Yersinia infection.
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Affiliation(s)
- Rina Matsuda
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Sorobetea
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jenna Zhang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stefan T. Peterson
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James P. Grayczyk
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Winslow Yost
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicolai Apenes
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria E. Kovalik
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beatrice Herrmann
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rosemary J. O’Neill
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrea C. Bohrer
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Lanza
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Charles-Antoine Assenmacher
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katrin D. Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sunny Shin
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Igor E. Brodsky
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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13
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Kumari N, Sharma R, Ali J, Chandra G, Singh S, Krishnan MY. The use of Mycobacterium tuberculosis H37Ra-infected immunocompetent mice as an in vivo model of persisters. Tuberculosis (Edinb) 2024; 145:102479. [PMID: 38262199 DOI: 10.1016/j.tube.2024.102479] [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: 10/06/2023] [Revised: 12/13/2023] [Accepted: 01/14/2024] [Indexed: 01/25/2024]
Abstract
Persistence of Mycobacterium tuberculosis (Mtb) is one of the challenges to successful treatment of tuberculosis (TB). In vitro models of non-replicating Mtb are used to test the efficacy of new molecules against Mtb persisters. The H37Ra strain is attenuated for growth in macrophages and mice. We validated H37Ra-infected immunocompetent mice for testing anti-TB molecules against slow/non-replicating Mtb in vivo. Swiss mice were infected intravenously with H37Ra and monitored for CFU burden and histopathology for a period of 12 weeks. The bacteria multiplied at a slow pace reaching a maximum load of ∼106 in 8-12 weeks depending on the infection dose, accompanied by time and dose-dependent histopathological changes in the lungs. Surprisingly, four-weeks of treatment with isoniazid-rifampicin-ethambutol-pyrazinamide combination caused only 0.4 log10 and 1 log10 reduction in CFUs in lungs and spleen respectively. The results show that ∼40 % of the H37Ra bacilli in lungs are persisters after 4 weeks of anti-TB therapy. Isoniazid/rifampicin monotherapy also showed similar results. A combination of bedaquiline and isoniazid reduced the CFU counts to <200 (limit of detection), compared to ∼5000 CFUs by isoniazid alone. The study demonstrates an in vivo model of Mtb persisters for testing new leads using a BSL-2 strain.
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Affiliation(s)
- Neetu Kumari
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226 031, India
| | - Romil Sharma
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226 031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
| | - Juned Ali
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226 031, India
| | - Gyan Chandra
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226 031, India
| | - Sarika Singh
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226 031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
| | - Manju Y Krishnan
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226 031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
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14
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Ronneau S, Michaux C, Giorgio RT, Helaine S. Intoxication of antibiotic persisters by host RNS inactivates their efflux machinery during infection. PLoS Pathog 2024; 20:e1012033. [PMID: 38421944 PMCID: PMC10903880 DOI: 10.1371/journal.ppat.1012033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
The host environment is of critical importance for antibiotic efficacy. By impacting bacterial machineries, stresses encountered by pathogens during infection promote the formation of phenotypic variants that are transiently insensitive to the action of antibiotics. It is assumed that these recalcitrant bacteria-termed persisters-contribute to antibiotic treatment failure and relapsing infections. Recently, we demonstrated that host reactive nitrogen species (RNS) transiently protect persisters against the action of β-lactam antibiotics by delaying their regrowth within host cells. Here, we discovered that RNS intoxication of persisters also collaterally sensitizing them to fluoroquinolones during infection, explaining the higher efficiency of fluoroquinolones against intramacrophage Salmonella. By reducing bacterial respiration and the proton-motive force, RNS inactivate the AcrAB efflux machinery of persisters, facilitating the accumulation of fluoroquinolones intracellularly. Our work shows that target inactivity is not the sole reason for Salmonella persisters to withstand antibiotics during infection, with active efflux being a major contributor to survival. Thus, understanding how the host environment impacts persister physiology is critical to optimize antibiotics efficacy during infection.
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Affiliation(s)
- Séverin Ronneau
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Charlotte Michaux
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rachel T. Giorgio
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sophie Helaine
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
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15
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Padmapriyadarsini C, Szumowski JD, Akbar N, Shanmugasundaram P, Jain A, Bathragiri M, Pattnaik M, Turuk J, Karunaianantham R, Balakrishnan S, Pati S, Kumar AH, Rathore MK, Raja J, Naidu KR, Horn J, Whitworth L, Sewell R, Ramakrishnan L, Swaminathan S, Edelstein PH. A Dose-Finding Study to Guide Use of Verapamil as an Adjunctive Therapy in Tuberculosis. Clin Pharmacol Ther 2024; 115:324-332. [PMID: 37983978 PMCID: PMC7615557 DOI: 10.1002/cpt.3108] [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: 07/27/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023]
Abstract
Induction of mycobacterial efflux pumps is a cause of Mycobacterium tuberculosis (Mtb) drug tolerance, a barrier to shortening antitubercular treatment. Verapamil inhibits Mtb efflux pumps that mediate tolerance to rifampin, a cornerstone of tuberculosis (TB) treatment. Verapamil's mycobacterial efflux pump inhibition also limits Mtb growth in macrophages in the absence of antibiotic treatment. These findings suggest that verapamil could be used as an adjunctive therapy for TB treatment shortening. However, verapamil is rapidly and substantially metabolized when co-administered with rifampin. We determined in a dose-escalation clinical trial of persons with pulmonary TB that rifampin-induced clearance of verapamil can be countered without toxicity by the administration of larger than usual doses of verapamil. An oral dosage of 360 mg sustained-release (SR) verapamil given every 12 hours concomitantly with rifampin achieved median verapamil exposures of 903.1 ng.h/mL (area under the curve (AUC)0-12 h ) in the 18 participants receiving this highest studied verapamil dose; these AUC findings are similar to those in persons receiving daily doses of 240 mg verapamil SR but not rifampin. Moreover, norverapamil:verapamil, R:S verapamil, and R:S norverapamil AUC ratios were all significantly greater than those of historical controls receiving SR verapamil in the absence of rifampin. Thus, rifampin administration favors the less-cardioactive verapamil metabolites and enantiomers that retain similar Mtb efflux inhibitory activity to verapamil, increasing overall benefit. Finally, rifampin exposures were 50% greater after verapamil administration, which may also be advantageous. Our findings suggest that a higher dosage of verapamil can be safely used as adjunctive treatment in rifampin-containing treatment regimens.
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Affiliation(s)
| | - John D. Szumowski
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco, USA
| | - Nabila Akbar
- National Institute for Research in Tuberculosis, Chennai, India
| | | | - Anilkumar Jain
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | | | | | | | | | | | | | | | | | | | | | - John Horn
- Department of Pharmacy, University of Washington, Seattle, USA
| | - Laura Whitworth
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Lalita Ramakrishnan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Paul H. Edelstein
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
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16
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Huang X, Lowrie DB, Fan XY, Hu Z. Natural products in anti-tuberculosis host-directed therapy. Biomed Pharmacother 2024; 171:116087. [PMID: 38171242 DOI: 10.1016/j.biopha.2023.116087] [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: 10/25/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
Given that the disease progression of tuberculosis (TB) is primarily related to the host's immune status, it has been gradually realized that chemotherapy that targets the bacteria may never, on its own, wholly eradicate Mycobacterium tuberculosis, the causative agent of TB. The concept of host-directed therapy (HDT) with immune adjuvants has emerged. HDT could potentially interfere with infection and colonization by the pathogens, enhance the protective immune responses of hosts, suppress the overwhelming inflammatory responses, and help to attain a state of homeostasis that favors treatment efficacy. However, the HDT drugs currently being assessed in combination with anti-TB chemotherapy still face the dilemmas arising from side effects and high costs. Natural products are well suited to compensate for these shortcomings by having gentle modulatory effects on the host immune responses with less immunopathological damage at a lower cost. In this review, we first summarize the profiles of anti-TB immunology and the characteristics of HDT. Then, we focus on the rationale and challenges of developing and implementing natural products-based HDT. A succinct report of the medications currently being evaluated in clinical trials and preclinical studies is provided. This review aims to promote target-based screening and accelerate novel TB drug discovery.
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Affiliation(s)
- Xuejiao Huang
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 201508, China
| | - Douglas B Lowrie
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 201508, China
| | - Xiao-Yong Fan
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 201508, China.
| | - Zhidong Hu
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 201508, China.
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17
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Singha B, Murmu S, Nair T, Rawat RS, Sharma AK, Soni V. Metabolic Rewiring of Mycobacterium tuberculosis upon Drug Treatment and Antibiotics Resistance. Metabolites 2024; 14:63. [PMID: 38248866 PMCID: PMC10820029 DOI: 10.3390/metabo14010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global health challenge, further compounded by the issue of antimicrobial resistance (AMR). AMR is a result of several system-level molecular rearrangements enabling bacteria to evolve with better survival capacities: metabolic rewiring is one of them. In this review, we present a detailed analysis of the metabolic rewiring of Mtb in response to anti-TB drugs and elucidate the dynamic mechanisms of bacterial metabolism contributing to drug efficacy and resistance. We have discussed the current state of AMR, its role in the prevalence of the disease, and the limitations of current anti-TB drug regimens. Further, the concept of metabolic rewiring is defined, underscoring its relevance in understanding drug resistance and the biotransformation of drugs by Mtb. The review proceeds to discuss the metabolic adaptations of Mtb to drug treatment, and the pleiotropic effects of anti-TB drugs on Mtb metabolism. Next, the association between metabolic changes and antimycobacterial resistance, including intrinsic and acquired drug resistance, is discussed. The review concludes by summarizing the challenges of anti-TB treatment from a metabolic viewpoint, justifying the need for this discussion in the context of novel drug discovery, repositioning, and repurposing to control AMR in TB.
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Affiliation(s)
- Biplab Singha
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA;
| | - Sumit Murmu
- Regional Centre of Biotechnology, Faridabad 121001, India;
| | - Tripti Nair
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA;
| | - Rahul Singh Rawat
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi 110067, India;
| | - Aditya Kumar Sharma
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Vijay Soni
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
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18
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Vujica L, Lončar J, Mišić L, Lučić B, Radman K, Mihaljević I, Bertoša B, Mesarić J, Horvat M, Smital T. Environmental contaminants modulate transport activity of zebrafish (Danio rerio) multidrug and toxin extrusion protein 3 (Mate3/Slc47a2.1). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:165956. [PMID: 37541507 DOI: 10.1016/j.scitotenv.2023.165956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/25/2023] [Accepted: 07/30/2023] [Indexed: 08/06/2023]
Abstract
Zebrafish Mate3 is one of six co-orthologs of human multidrug and toxin extrusion proteins. It is highly expressed in the kidneys, intestine, testes, and brain of males. Initial interaction studies showed its interaction with xenobiotic compounds, suggesting a role in the efflux of toxic compounds. In this study, we aimed to test various environmental contaminants for their interaction with zebrafish Mate3. We developed a stable zebrafish Mate3 cell line and optimized a high-throughput screening assay using DAPI and ASP+ as fluorescent model substrates. To gain insight into the structure and function of the Mate3 protein and relate these to the results of the DAPI and ASP+ transport measurements, we predicted its 3D structure using the AlphaFold2 algorithm. A 3D structure with high per residue confidence scores with 13 transmembrane segments (TMs) was obtained, with topology and mutual positioning characteristic of the Mate protein family in a shape open to the extracellular part. Molecular docking methods were used to identify DAPI and ASP+ binding sites on the surface and in the center of the protein cavity. Because our kinetics experiments combined with molecular docking indicated that there may be additional active sites in zebrafish Mate3, additional cytotoxicity experiments were performed and highly potent Mate3 interactors were identified from a set of 55 different environmental contaminants. Our results suggest that some of the identified interactors may be of environmental concern, as their interaction with Mate3 could lead to an impairment of its normal efflux function, making fish more sensitive to harmful substances commonly released into the aquatic environment. Finally, the quality of zebrafish Mate3 structures predicted by the AlphaFold2 algorithm opens up the possibility of successfully using this tool for in silico research on transport preferences of other Mate proteins.
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Affiliation(s)
- Lana Vujica
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Jovica Lončar
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Lana Mišić
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Bono Lučić
- NMR Center, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Katarina Radman
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - Ivan Mihaljević
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - Josip Mesarić
- Centre for Informatics and Computing, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Marina Horvat
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Tvrtko Smital
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
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19
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Huang X, Chu C, Shi C, Zhang J, Yan B, Shan F, Wang D, Shi Y, Peng C, Tang BZ. Seeing is believing: Efficiency evaluation of multifunctional ionic-dependent AIEgens for tuberculosis. Biomaterials 2023; 302:122301. [PMID: 37690379 DOI: 10.1016/j.biomaterials.2023.122301] [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: 06/01/2023] [Revised: 08/20/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant public health threat with high rates of infection and mortality. Rapid and reliable theranostics of TB are essential to control transmission and shorten treatment duration. In this study, we report two cationic aggregation-inducing emission luminogens (AIEgens) named TTVP and TTPy, which have different functional charged moieties, to investigate their potential for simultaneous tracing and photodynamic therapy in TB infection. TTVP and TTPy exhibit intrinsic positive charges, excellent water solubility, and near-infrared (NIR) emission. Based on ionic-function relationships, TTVP, with more positive charges, demonstrates a stronger binding affinity to Mycobacterium marinum (M.m), (a close genetic relative of Mtb), compared to TTPy. Both TTVP and TTPy exhibit high efficiency in generating reactive oxygen species (ROS) when exposed to white light irradiation, enabling effective photodynamic killing of M.m in vitro. Additionally, we achieved long-term, real-time, noninvasive, continuous tracing, and evaluated therapeutic performance in vivo. Notably, TTVP outperformed TTPy in intracellular killing of M.m, suggesting a possible correlation between the labeling and photodynamic killing abilities of AIEgens. These findings provide valuable insights and a design basis for cationic AIEgens in TB research, offering potential advancements in TB theranostics.
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Affiliation(s)
- Xueni Huang
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, 200032, China; Department of Radiology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Chengshengze Chu
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Chunzi Shi
- Department of Radiology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Jiulong Zhang
- Department of Radiology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Bo Yan
- Department of Radiology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Fei Shan
- Department of Radiology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Dong Wang
- Center for AIE Research, College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Yuxin Shi
- Department of Radiology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
| | - Chen Peng
- Department of Radiology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China.
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20
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Bai S, Song J, Pu H, Yu Y, Song W, Chen Z, Wang M, Campbell-Valois FX, Wong WL, Cai Q, Wan M, Zhang C, Bai Y, Feng X. Chemical Biology Approach to Reveal the Importance of Precise Subcellular Targeting for Intracellular Staphylococcus aureus Eradication. J Am Chem Soc 2023; 145:23372-23384. [PMID: 37838963 DOI: 10.1021/jacs.3c09587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Intracellular bacterial pathogens, such as Staphylococcus aureus, that may hide in intracellular vacuoles represent the most significant manifestation of bacterial persistence. They are critically associated with chronic infections and antibiotic resistance, as conventional antibiotics are ineffective against such intracellular persisters due to permeability issues and mechanistic reasons. Direct subcellular targeting of S. aureus vacuoles suggests an explicit opportunity for the eradication of these persisters, but a comprehensive understanding of the chemical biology nature and significance of precise S. aureus vacuole targeting remains limited. Here, we report an oligoguanidine-based peptidomimetic that effectively targets and eradicates intracellular S. aureus persisters in the phagolysosome lumen, and this oligomer was utilized to reveal the mechanistic insights linking precise targeting to intracellular antimicrobial efficacy. The oligomer has high cellular uptake via a receptor-mediated endocytosis pathway and colocalizes with S. aureus persisters in phagolysosomes as a result of endosome-lysosome interconversion and lysosome-phagosome fusion. Moreover, the observation of a bacterium's altered susceptibility to the oligomer following a modification in its intracellular localization offers direct evidence of the critical importance of precise intracellular targeting. In addition, eradication of intracellular S. aureus persisters was achieved by the oligomer's membrane/DNA dual-targeting mechanism of action; therefore, its effectiveness is not hampered by the hibernation state of the persisters. Such precise subcellular targeting of S. aureus vacuoles also increases the agent's biocompatibility by minimizing its interaction with other organelles, endowing excellent in vivo bacterial targeting and therapeutic efficacy in animal models.
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Affiliation(s)
- Silei Bai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Junfeng Song
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Huangsheng Pu
- College of Advanced Interdisciplinary Studies & Hunan Provincial Key Laboratory of Novel NanoOptoelectronic Information Materials and Devices, National University of Defense Technology, Changsha, Hunan 410073, China
- Nanhu Laser Laboratory, National University of Defense Technology, Changsha 410073, China
| | - Yue Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Wenwen Song
- College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Zhiyong Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Min Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | | | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon 999077, Hong Kong SAR, China
| | - Qingyun Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Muyang Wan
- College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Chunhui Zhang
- College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Yugang Bai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Xinxin Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
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21
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Kim H, Shin SJ. Revolutionizing control strategies against Mycobacterium tuberculosis infection through selected targeting of lipid metabolism. Cell Mol Life Sci 2023; 80:291. [PMID: 37704889 PMCID: PMC11072447 DOI: 10.1007/s00018-023-04914-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/12/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023]
Abstract
Lipid species play a critical role in the growth and virulence expression of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB). During Mtb infection, foamy macrophages accumulate lipids in granulomas, providing metabolic adaptation and survival strategies for Mtb against multiple stresses. Host-derived lipid species, including triacylglycerol and cholesterol, can also contribute to the development of drug-tolerant Mtb, leading to reduced efficacy of antibiotics targeting the bacterial cell wall or transcription. Transcriptional and metabolic analyses indicate that lipid metabolism-associated factors of Mtb are highly regulated by antibiotics and ultimately affect treatment outcomes. Despite the well-known association between major antibiotics and lipid metabolites in TB treatment, a comprehensive understanding of how altered lipid metabolites in both host and Mtb influence treatment outcomes in a drug-specific manner is necessary to overcome drug tolerance. The current review explores the controversies and correlations between lipids and drug efficacy in various Mtb infection models and proposes novel approaches to enhance the efficacy of anti-TB drugs. Moreover, the review provides insights into the efficacious control of Mtb infection by elucidating the impact of lipids on drug efficacy. This review aims to improve the effectiveness of current anti-TB drugs and facilitate the development of innovative therapeutic strategies against Mtb infection by making reverse use of Mtb-favoring lipid species.
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Affiliation(s)
- Hagyu Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea.
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22
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Padmapriyadarsini C, Szumowski JD, Akbar N, Shanmugasundaram P, Jain A, Bathragiri M, Pattnaik M, Turuk J, Karunaianantham R, Balakrishnan S, Pati S, Agibothu Kupparam HK, Rathore MK, Raja J, Naidu KR, Horn J, Whitworth L, Sewell R, Ramakrishnan L, Swaminathan S, Edelstein PH. A dose-finding study to guide use of verapamil as an adjunctive therapy in tuberculosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.28.23293316. [PMID: 37577511 PMCID: PMC10418293 DOI: 10.1101/2023.07.28.23293316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Induction of mycobacterial efflux pumps is a cause of Mycobacterium tuberculosis (Mtb) drug tolerance, a barrier to shortening antitubercular treatment. Verapamil inhibits Mtb efflux pumps that mediate tolerance to rifampin, a cornerstone of tuberculosis treatment. Verapamil's mycobacterial efflux pump inhibition also limits Mtb growth in macrophages in the absence of antibiotic treatment. These findings suggest that verapamil could be used as an adjunctive therapy for TB treatment shortening. However, verapamil is rapidly and substantially metabolized when co-administered with rifampin. We determined in a dose-escalation clinical trial that rifampin-induced clearance of verapamil can be countered without toxicity by the administration of larger than usual doses of verapamil. An oral dosage of 360 mg sustained-release (SR) verapamil given every 12 hours concomitantly with rifampin achieved median verapamil exposures of 903.1 ng.h/ml (AUC 0-12h), similar to those in persons receiving daily doses of 240 mg verapamil SR but not rifampin. Norverapamil:verapamil, R:S verapamil and R:S norverapamil AUC ratios were all significantly greater than those of historical controls receiving SR verapamil in the absence of rifampin, suggesting that rifampin administration favors the less-cardioactive verapamil metabolites and enantiomers. Finally, rifampin exposures were significantly greater after verapamil administration. Our findings suggest that a higher dosage of verapamil can be safely used as adjunctive treatment in rifampin-containing treatment regimens.
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Affiliation(s)
| | - John D Szumowski
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco, USA
| | - Nabila Akbar
- National Institute for Research in Tuberculosis, Chennai, India
| | | | - Anilkumar Jain
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | | | | | | | | | | | | | | | | | | | | | - John Horn
- Department of Pharmacy, University of Washington, Seattle, USA
| | - Laura Whitworth
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Lalita Ramakrishnan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Paul H Edelstein
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
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23
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Bollen C, Louwagie E, Verstraeten N, Michiels J, Ruelens P. Environmental, mechanistic and evolutionary landscape of antibiotic persistence. EMBO Rep 2023; 24:e57309. [PMID: 37395716 PMCID: PMC10398667 DOI: 10.15252/embr.202357309] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
Recalcitrant infections pose a serious challenge by prolonging antibiotic therapies and contributing to the spread of antibiotic resistance, thereby threatening the successful treatment of bacterial infections. One potential contributing factor in persistent infections is antibiotic persistence, which involves the survival of transiently tolerant subpopulations of bacteria. This review summarizes the current understanding of antibiotic persistence, including its clinical significance and the environmental and evolutionary factors at play. Additionally, we discuss the emerging concept of persister regrowth and potential strategies to combat persister cells. Recent advances highlight the multifaceted nature of persistence, which is controlled by deterministic and stochastic elements and shaped by genetic and environmental factors. To translate in vitro findings to in vivo settings, it is crucial to include the heterogeneity and complexity of bacterial populations in natural environments. As researchers continue to gain a more holistic understanding of this phenomenon and develop effective treatments for persistent bacterial infections, the study of antibiotic persistence is likely to become increasingly complex.
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Affiliation(s)
- Celien Bollen
- Centre of Microbial and Plant GeneticsKU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Elen Louwagie
- Centre of Microbial and Plant GeneticsKU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Natalie Verstraeten
- Centre of Microbial and Plant GeneticsKU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Jan Michiels
- Centre of Microbial and Plant GeneticsKU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Philip Ruelens
- Centre of Microbial and Plant GeneticsKU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
- Laboratory of Socioecology and Social EvolutionKU LeuvenLeuvenBelgium
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24
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Young M, Chojnacki M, Blanchard C, Cao X, Johnson WL, Flaherty D, Dunman PM. Genetic Determinants of Acinetobacter baumannii Serum-Associated Adaptive Efflux-Mediated Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1173. [PMID: 37508269 PMCID: PMC10376123 DOI: 10.3390/antibiotics12071173] [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: 06/09/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Acinetobacter baumannii is a nosocomial pathogen of serious healthcare concern that is becoming increasingly difficult to treat due to antibiotic treatment failure. Recent studies have revealed that clinically defined antibiotic-susceptible strains upregulate the expression of a repertoire of putative drug efflux pumps during their growth under biologically relevant conditions, e.g., in human serum, resulting in efflux-associated resistance to physiologically achievable antibiotic levels within a patient. This phenomenon, termed Adaptive Efflux Mediated Resistance (AEMR), has been hypothesized to account for one mechanism by which antibiotic-susceptible A. baumannii fails to respond to antibiotic treatment. In the current study, we sought to identify genetic determinants that contribute to A. baumannii serum-associated AEMR by screening a transposon mutant library for members that display a loss of the AEMR phenotype. Results revealed that mutation of a putative pirin-like protein, YhaK, results in a loss of AEMR, a phenotype that could be complemented by a wild-type copy of the yhaK gene and was verified in a second strain background. Ethidium bromide efflux assays confirmed that the loss of AEMR phenotype due to pirin-like protein mutation correlated with reduced overarching efflux capacity. Further, flow cytometry and confocal microscopy measures of a fluorophore 7-(dimethylamino)-coumarin-4-acetic acid (DMACA)-tagged levofloxacin isomer, ofloxacin, further verified that YhaK mutation reduces AEMR-mediated antibiotic efflux. RNA-sequencing studies revealed that YhaK may be required for the expression of multiple efflux-associated systems, including MATE and ABC families of efflux pumps. Collectively, the data indicate that the A. baumannii YhaK pirin-like protein plays a role in modulating the organism's adaptive efflux-mediated resistance phenotype.
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Affiliation(s)
- Mikaeel Young
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (M.Y.); (M.C.); (W.L.J.)
| | - Michaelle Chojnacki
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (M.Y.); (M.C.); (W.L.J.)
| | - Catlyn Blanchard
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (M.Y.); (M.C.); (W.L.J.)
| | - Xufeng Cao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, Lafayette, IN 47907, USA
| | - William L. Johnson
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (M.Y.); (M.C.); (W.L.J.)
| | - Daniel Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN 47907, USA
| | - Paul M. Dunman
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (M.Y.); (M.C.); (W.L.J.)
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25
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Linhares LA, Dos Santos Peixoto A, Correia de Sousa LDA, Lucena Laet JP, da Silva Santos AC, Alves Pereira VR, Carneiro Neves MM, Ferreira LFGR, Hernandes MZ, de la Vega J, Pereira-Neves A, San Feliciano A, Olmo ED, Schindler HC, Montenegro LML. In vitro bioevaluation and docking study of dihydrosphingosine and ethambutol analogues against sensitive and multi-drug resistant Mycobacterium tuberculosis. Eur J Med Chem 2023; 258:115579. [PMID: 37399709 DOI: 10.1016/j.ejmech.2023.115579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/05/2023]
Abstract
Tuberculosis remains a major public health problem and one of the top ten causes of death worldwide. The alarming increase in multidrug-resistant and extensively resistant variants (MDR, pre-XDR, and XDR) makes the disease more difficult to treat and control. New drugs that act against MDR/XDR strains are needed for programs to contain this major epidemic. The present study aimed to evaluate new compounds related to dihydro-sphingosine and ethambutol against sensitive and pre-XDR Mycobacterium strains, as well as to characterize the pharmacological activity through in vitro and in silico approaches in mmpL3 protein. Of the 48 compounds analyzed, 11 demonstrated good to moderate activity on sensitive and MDR Mycobacterium tuberculosis (Mtb), with a Minimum Inhibitory Concentration (MIC) ranging from 1.5 to 8 μM. They presented 2 to 14 times greater potency of activity when compared to ethambutol in pre-XDR strain, and demonstrated a selectivity index varying between 2.21 and 82.17. The substance 12b when combined with rifampicin, showed a synergistic effect (FICI = 0.5) on sensitive and MDR Mtb. It has also been shown to have a concentration-dependent intracellular bactericidal effect, and a time-dependent bactericidal effect in M. smegmatis and pre-XDR M. tuberculosis. The binding mode of the compounds in its cavity was identified through molecular docking and using a predicted structural model of mmpL3. Finally, we observed by transmission electron microscopy the induction of damage to the cell wall integrity of M. tuberculosis treated with the substance 12b. With these findings, we demonstrate the potential of a 2-aminoalkanol derivative to be a prototype substance and candidate for further optimization of molecular structure and anti-tubercular activity in preclinical studies.
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Affiliation(s)
- Leonardo Aquino Linhares
- Department of Immunology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (FIOCRUZ), Recife, PE, 50.740-465, Brazil.
| | - Aline Dos Santos Peixoto
- Department of Immunology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (FIOCRUZ), Recife, PE, 50.740-465, Brazil
| | | | - João Paulo Lucena Laet
- Department of Immunology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (FIOCRUZ), Recife, PE, 50.740-465, Brazil
| | | | | | | | - Luiz Felipe Gomes Rebello Ferreira
- Laboratory of Medicinal Theoretical Chemistry (LQTM), Department of Pharmaceutical Sciences, Federal University of Pernambuco, Recife, PE, Brazil
| | - Marcelo Zaldini Hernandes
- Laboratory of Medicinal Theoretical Chemistry (LQTM), Department of Pharmaceutical Sciences, Federal University of Pernambuco, Recife, PE, Brazil
| | - Jennifer de la Vega
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy-CIETUS, University of Salamanca, Salamanca, Spain
| | - Antônio Pereira-Neves
- Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (FIOCRUZ), Recife, PE, 50.740-465, Brazil
| | - Arturo San Feliciano
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy-CIETUS, University of Salamanca, Salamanca, Spain; Graduate Program in Pharmaceutical Sciences, University of Vale do Itajai, UNIVALI, Itajaí, SC, 88302-202, Brazil
| | - Esther Del Olmo
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy-CIETUS, University of Salamanca, Salamanca, Spain
| | - Haiana Charifker Schindler
- Department of Immunology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (FIOCRUZ), Recife, PE, 50.740-465, Brazil
| | - Lílian Maria Lapa Montenegro
- Department of Immunology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (FIOCRUZ), Recife, PE, 50.740-465, Brazil.
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26
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Verstraete L, Aizawa J, Govaerts M, De Vooght L, Lavigne R, Michiels J, Van den Bergh B, Cos P. In Vitro Persistence Level Reflects In Vivo Antibiotic Survival of Natural Pseudomonas aeruginosa Isolates in a Murine Lung Infection Model. Microbiol Spectr 2023; 11:e0497022. [PMID: 37140371 PMCID: PMC10269860 DOI: 10.1128/spectrum.04970-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Clinicians are increasingly confronted with the limitations of antibiotics to clear bacterial infections in patients. It has long been assumed that only antibiotic resistance plays a pivotal role in this phenomenon. Indeed, the worldwide emergence of antibiotic resistance is considered one of the major health threats of the 21st century. However, the presence of persister cells also has a significant influence on treatment outcomes. These antibiotic-tolerant cells are present in every bacterial population and are the result of the phenotypic switching of normal, antibiotic-sensitive cells. Persister cells complicate current antibiotic therapies and contribute to the development of resistance. In the past, extensive research has been performed to investigate persistence in laboratory settings; however, antibiotic tolerance under conditions that mimic the clinical setting remain poorly understood. In this study, we optimized a mouse model for lung infections with the opportunistic pathogen Pseudomonas aeruginosa. In this model, mice are intratracheally infected with P. aeruginosa embedded in seaweed alginate beads and subsequently treated with tobramycin via nasal droplets. A diverse panel of 18 P. aeruginosa strains originating from environmental, human, and animal clinical sources was selected to assess survival in the animal model. Survival levels were positively correlated with the survival levels determined via time-kill assays, a common method to study persistence in the laboratory. We showed that survival levels are comparable and thus that the classical persister assays are indicative of antibiotic tolerance in a clinical setting. The optimized animal model also enables us to test potential antipersister therapies and study persistence in relevant settings. IMPORTANCE The importance of targeting persister cells in antibiotic therapies is becoming more evident, as these antibiotic-tolerant cells underlie relapsing infections and resistance development. Here, we studied persistence in a clinically relevant pathogen, Pseudomonas aeruginosa. It is one of the six ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, P. aeruginosa, and Enterobacter spp.), which are considered major health threats. P. aeruginosa is mostly known to cause chronic lung infections in cystic fibrosis patients. We mimicked these lung infections in a mouse model to study persistence under more clinical conditions. It was shown that the survival levels of natural P. aeruginosa isolates in this model are positively correlated with the survival levels measured in classical persistence assays in vitro. These results not only validate the use of our current techniques to study persistence but also open opportunities to study new persistence mechanisms or evaluate new antipersister strategies in vivo.
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Affiliation(s)
- Laure Verstraete
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
| | - Juliana Aizawa
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Matthias Govaerts
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Linda De Vooght
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
| | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
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27
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Dierig A, Hoelscher M, Schultz S, Hoffmann L, Jarchow-MacDonald A, Svensson EM, Te Brake L, Aarnoutse R, Boeree M, McHugh TD, Wildner LM, Gong X, Phillips P, Minja LT, Ntinginya N, Mpagama S, Liyoyo A, Wallis RS, Sebe M, Mhimbira FA, Mbeya B, Rassool M, Geiter L, Cho YL, Heinrich N. A phase IIb, open-label, randomized controlled dose ranging multi-centre trial to evaluate the safety, tolerability, pharmacokinetics and exposure-response relationship of different doses of delpazolid in combination with bedaquiline delamanid moxifloxacin in adult subjects with newly diagnosed, uncomplicated, smear-positive, drug-sensitive pulmonary tuberculosis. Trials 2023; 24:382. [PMID: 37280643 DOI: 10.1186/s13063-023-07354-5] [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: 09/01/2022] [Accepted: 05/05/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Linezolid is an effective, but toxic anti-tuberculosis drug that is currently recommended for the treatment of drug-resistant tuberculosis. Improved oxazolidinones should have a better safety profile, while preserving efficacy. Delpazolid is a novel oxazolidinone developed by LegoChem Biosciences Inc. that has been evaluated up to phase 2a clinical trials. Since oxazolidinone toxicity can occur late in treatment, LegoChem Biosciences Inc. and the PanACEA Consortium designed DECODE to be an innovative dose-ranging study with long-term follow-up for determining the exposure-response and exposure-toxicity relationship of delpazolid to support dose selection for later studies. Delpazolid is administered in combination with bedaquiline, delamanid and moxifloxacin. METHODS Seventy-five participants with drug-sensitive, pulmonary tuberculosis will receive bedaquiline, delamanid and moxifloxacin, and will be randomized to delpazolid dosages of 0 mg, 400 mg, 800 mg, 1200 mg once daily, or 800 mg twice daily, for 16 weeks. The primary efficacy endpoint will be the rate of decline of bacterial load on treatment, measured by MGIT liquid culture time to detection from weekly sputum cultures. The primary safety endpoint will be the proportion of oxazolidinone class toxicities; neuropathy, myelosuppression, or tyramine pressor response. Participants who convert to negative liquid media culture by week 8 will stop treatment after the end of their 16-week course and will be observed for relapse until week 52. Participants who do not convert to negative culture will receive continuation phase treatment with rifampicin and isoniazid to complete a six-month treatment course. DISCUSSION DECODE is an innovative dose-finding trial, designed to support exposure-response modelling for safe and effective dose selection. The trial design allows assessment of occurrence of late toxicities as observed with linezolid, which is necessary in clinical evaluation of novel oxazolidinones. The primary efficacy endpoint is the change in bacterial load, an endpoint conventionally used in shorter dose-finding trials. Long-term follow-up after shortened treatment is possible through a safety rule excluding slow-and non-responders from potentially poorly performing dosages. TRIAL REGISTRATION DECODE was registered in ClinicalTrials.gov before recruitment start on 22 October 2021 (NCT04550832).
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Affiliation(s)
- A Dierig
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany
| | - M Hoelscher
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany
| | - S Schultz
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany
| | - L Hoffmann
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany
| | - A Jarchow-MacDonald
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany
- Ninewells Hospital and Medical School, NHS Tayside, Dundee, UK
| | - E M Svensson
- Department of Pharmacy, Radboud University Medical Centre, Nijmegen, The Netherlands
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - L Te Brake
- Department of Pharmacy, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - R Aarnoutse
- Department of Pharmacy, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - M Boeree
- Department of Pharmacy, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - T D McHugh
- Division of Infection & Immunity, UCL Centre for Clinical Microbiology, University College of London, London, UK
| | - L M Wildner
- Division of Infection & Immunity, UCL Centre for Clinical Microbiology, University College of London, London, UK
| | - X Gong
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, University of California San Francisco, San Francisco, USA
| | - Ppj Phillips
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, University of California San Francisco, San Francisco, USA
| | - L T Minja
- National Institute for Medical Research, Mbeya Medical Research Centre (NIMR-MMRC), Mbeya, Tanzania
| | - N Ntinginya
- National Institute for Medical Research, Mbeya Medical Research Centre (NIMR-MMRC), Mbeya, Tanzania
| | - S Mpagama
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - A Liyoyo
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - R S Wallis
- The Aurum Institute, Tembisa, South Africa
| | - M Sebe
- The Aurum Institute, Tembisa, South Africa
| | - F A Mhimbira
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - B Mbeya
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - M Rassool
- Clinical HIV Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, Helen Joseph Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | - L Geiter
- LegoChem Biosciences, Daejeon, South Korea
| | - Y L Cho
- LegoChem Biosciences, Daejeon, South Korea
| | - N Heinrich
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany.
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28
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Poulton NC, DeJesus MA, Munsamy-Govender V, Roberts CG, Azadian ZA, Bosch B, Lin KM, Li S, Rock JM. Beyond antibiotic resistance: the whiB7 transcription factor coordinates an adaptive response to alanine starvation in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543512. [PMID: 37333137 PMCID: PMC10274678 DOI: 10.1101/2023.06.02.543512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Pathogenic mycobacteria are a significant cause of morbidity and mortality worldwide. These bacteria are highly intrinsically drug resistant, making infections challenging to treat. The conserved whiB7 stress response is a key contributor to mycobacterial intrinsic drug resistance. Although we have a comprehensive structural and biochemical understanding of WhiB7, the complex set of signals that activate whiB7 expression remain less clear. It is believed that whiB7 expression is triggered by translational stalling in an upstream open reading frame (uORF) within the whiB7 5' leader, leading to antitermination and transcription into the downstream whiB7 ORF. To define the signals that activate whiB7, we employed a genome-wide CRISPRi epistasis screen and identified a diverse set of 150 mycobacterial genes whose inhibition results in constitutive whiB7 activation. Many of these genes encode amino acid biosynthetic enzymes, tRNAs, and tRNA synthetases, consistent with the proposed mechanism for whiB7 activation by translational stalling in the uORF. We show that the ability of the whiB7 5' regulatory region to sense amino acid starvation is determined by the coding sequence of the uORF. The uORF shows considerable sequence variation among different mycobacterial species, but it is universally and specifically enriched for alanine. Providing a potential rationalization for this enrichment, we find that while deprivation of many amino acids can activate whiB7 expression, whiB7 specifically coordinates an adaptive response to alanine starvation by engaging in a feedback loop with the alanine biosynthetic enzyme, aspC. Our results provide a holistic understanding of the biological pathways that influence whiB7 activation and reveal an extended role for the whiB7 pathway in mycobacterial physiology, beyond its canonical function in antibiotic resistance. These results have important implications for the design of combination drug treatments to avoid whiB7 activation, as well as help explain the conservation of this stress response across a wide range of pathogenic and environmental mycobacteria.
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Affiliation(s)
- Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Vanisha Munsamy-Govender
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Cameron G Roberts
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Zachary A Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Karl Matthew Lin
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
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29
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Matsuda R, Sorobetea D, Zhang J, Peterson ST, Grayczyk JP, Herrmann B, Yost W, O’Neill R, Bohrer AC, Lanza M, Assenmacher CA, Mayer-Barber KD, Shin S, Brodsky IE. A TNF-IL-1 circuit controls Yersinia within intestinal granulomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537749. [PMID: 37197029 PMCID: PMC10176537 DOI: 10.1101/2023.04.21.537749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Tumor necrosis factor (TNF) is a pleiotropic inflammatory cytokine that mediates antimicrobial defense and granuloma formation in response to infection by numerous pathogens. Yersinia pseudotuberculosis colonizes the intestinal mucosa and induces recruitment of neutrophils and inflammatory monocytes into organized immune structures termed pyogranulomas that control the bacterial infection. Inflammatory monocytes are essential for control and clearance of Yersinia within intestinal pyogranulomas, but how monocytes mediate Yersinia restriction is poorly understood. Here, we demonstrate that TNF signaling in monocytes is required for bacterial containment following enteric Yersinia infection. We further show that monocyte-intrinsic TNFR1 signaling drives production of monocyte-derived interleukin-1 (IL-1), which signals through IL-1 receptor on non-hematopoietic cells to enable pyogranuloma-mediated control of Yersinia infection. Altogether, our work reveals a monocyte-intrinsic TNF-IL-1 collaborative circuit as a crucial driver of intestinal granuloma function, and defines the cellular target of TNF signaling that restricts intestinal Yersinia infection.
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Affiliation(s)
- Rina Matsuda
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Daniel Sorobetea
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Jenna Zhang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Stefan T. Peterson
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - James P. Grayczyk
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Beatrice Herrmann
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Winslow Yost
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Rosemary O’Neill
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Andrea C. Bohrer
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Lanza
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Charles-Antoine Assenmacher
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Katrin D. Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sunny Shin
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Igor E. Brodsky
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
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Schrader SM, Botella H, Vaubourgeix J. Reframing antimicrobial resistance as a continuous spectrum of manifestations. Curr Opin Microbiol 2023; 72:102259. [PMID: 36608373 DOI: 10.1016/j.mib.2022.102259] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023]
Abstract
To fight antimicrobial resistance (AMR), we must recognize and target all its manifestations. In this review, we briefly summarize the history that led to recognition of the various manifestations of AMR in bacterial pathogens and the ways in which they interrelate. We emphasize the importance of distinguishing between AMR arising from genetic alterations versus induction of endogenous machinery in response to environmental triggers, including - paradoxically - stresses from host immunity and antimicrobial therapy. We present an integrated view of AMR by reframing it as a spectrum of phenotypes within a continuous three-dimensional space defined by the growth rate, prevalence, and kill rate of cells displaying AMR. Finally, we reflect on strategies that may help stem the emergence of AMR.
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Affiliation(s)
- Sarah M Schrader
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Hélène Botella
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Julien Vaubourgeix
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
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31
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Bhandari M, Soria-Carrera H, Wohlmann J, Dal NJK, de la Fuente JM, Martín-Rapún R, Griffiths G, Fenaroli F. Subcellular localization and therapeutic efficacy of polymeric micellar nanoparticles encapsulating bedaquiline for tuberculosis treatment in zebrafish. Biomater Sci 2023; 11:2103-2114. [PMID: 36723226 DOI: 10.1039/d2bm01835g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The combination drug regimens that have long been used to treat tuberculosis (TB), caused by Mycobacterium tuberculosis, are fraught with problems such as frequent administration, long duration of treatment, and harsh adverse effects, leading to the emergence of multidrug resistance. Moreover, there is no effective preventive vaccine against TB infection. In this context, nanoparticles (NPs) have emerged as a potential alternative method for drug delivery. Encapsulating antibiotics in biodegradable NPs has been shown to provide effective therapy and reduced toxicity against M. tuberculosis in different mammalian models, when compared to conventional free drug administration. Here, we evaluate the localization, therapeutic efficacy and toxic effects of polymeric micellar NPs encapsulating a promising but highly hydrophobic and toxic antitubercular drug bedaquiline (BQ) in zebrafish embryos infected with Mycobacterium marinum. Our study shows that the NP formulation of BQ improves survival and reduces bacterial burden in the infected embryos after treatment when compared to its free form. The intravenously injected BQ NPs have short circulation times due to their rapid and efficient uptake into the endothelial cells, as observed by correlative light and electron microscopy (CLEM).
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Affiliation(s)
- Madhavi Bhandari
- Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - Héctor Soria-Carrera
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, C/Mariano Esquillor s/n, 50018 Zaragoza, Spain. .,CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain.,Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Zaragoza, c/Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Jens Wohlmann
- Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | | | - Jesús M de la Fuente
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, C/Mariano Esquillor s/n, 50018 Zaragoza, Spain. .,CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rafael Martín-Rapún
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, C/Mariano Esquillor s/n, 50018 Zaragoza, Spain. .,CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain.,Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Zaragoza, c/Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Gareth Griffiths
- Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - Federico Fenaroli
- Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway.,Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4021 Stavanger, Norway.
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Ramakrishnan L. Redefining tuberculosis: an interview with Lalita Ramakrishnan. Dis Model Mech 2023; 16:dmm050189. [PMID: 36951140 PMCID: PMC10073006 DOI: 10.1242/dmm.050189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Professor Lalita Ramakrishnan is at the forefront of modern tuberculosis (TB) research. She has developed vital tools, most notably a robust zebrafish model, to study this disease, leading to seminal discoveries uncovering bacterial and host interactions throughout infection. Her group has harnessed this knowledge to develop new treatments for TB and shape clinical research. By unveiling these complex interactions, they have also improved our understanding of fundamental biology of macrophages and other infectious diseases, such as leprosy.
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Affiliation(s)
- Lalita Ramakrishnan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge CB2 OQH, UK, and MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 OQH, UK
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33
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Navigating a Path to Rifampicin Resistance in Tuberculosis. mBio 2023; 14:e0295222. [PMID: 36688640 PMCID: PMC9973358 DOI: 10.1128/mbio.02952-22] [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] [Indexed: 01/24/2023] Open
Abstract
For model bacteria, genetic drug resistance usually arises from antibiotic-tolerant subpopulations, but whether this is true for the globally important pathogen Mycobacterium tuberculosis-the cause of tuberculosis-is not known. Here, we discuss a recent article by Sebastian et al. (J. Sebastian, A. Thomas, C. Levine, R. Shrestha, et al., mBio 14:e0279522, 2023, 10.1128/mbio.02795-22) which leverages a robotic transwell microtiter experimental system coupled with deep sequencing of a barcoded library of M. tuberculosis to answer this question for rifampicin resistance. The authors investigate two distinct forms of antibiotic-tolerant subpopulations-classical tolerance, characterized by prolonged minimum duration of killing, and "differentially detectable" (DD) bacilli that are viable but can be recovered only in liquid medium as opposed to plating. They demonstrate that, indeed, resistance arises preferentially from both rifampicin-tolerant subpopulations, though earlier in the DD population. Use of barcoded libraries and parallel culture systems shows promise in investigating phenotypes mediated by minority subpopulations of bacteria such as development of antibiotic resistance.
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Mycobacterium tuberculosis Requires the Outer Membrane Lipid Phthiocerol Dimycocerosate for Starvation-Induced Antibiotic Tolerance. mSystems 2023; 8:e0069922. [PMID: 36598240 PMCID: PMC9948706 DOI: 10.1128/msystems.00699-22] [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] [Indexed: 01/05/2023] Open
Abstract
Tolerance of Mycobacterium tuberculosis to antibiotics contributes to the long duration of tuberculosis (TB) treatment and the emergence of drug-resistant strains. M. tuberculosis drug tolerance is induced by nutrient restriction, but the genetic determinants that promote antibiotic tolerance triggered by nutrient limitation have not been comprehensively identified. Here, we show that M. tuberculosis requires production of the outer membrane lipid phthiocerol dimycocerosate (PDIM) to tolerate antibiotics under nutrient-limited conditions. We developed an arrayed transposon (Tn) mutant library in M. tuberculosis Erdman and used orthogonal pooling and transposon sequencing (Tn-seq) to map the locations of individual mutants in the library. We screened a subset of the library (~1,000 mutants) by Tn-seq and identified 32 and 102 Tn mutants with altered tolerance to antibiotics under stationary-phase and phosphate-starved conditions, respectively. Two mutants recovered from the arrayed library, ppgK::Tn and clpS::Tn, showed increased susceptibility to two different drug combinations under both nutrient-limited conditions, but their phenotypes were not complemented by the Tn-disrupted gene. Whole-genome sequencing revealed single nucleotide polymorphisms in both the ppgK::Tn and clpS::Tn mutants that prevented PDIM production. Complementation of the clpS::Tn ppsD Q291* mutant with ppsD restored PDIM production and antibiotic tolerance, demonstrating that loss of PDIM sensitized M. tuberculosis to antibiotics. Our data suggest that drugs targeting production of PDIM, a critical M. tuberculosis virulence determinant, have the potential to enhance the efficacy of existing antibiotics, thereby shortening TB treatment and limiting development of drug resistance. IMPORTANCE Mycobacterium tuberculosis causes 10 million cases of active TB disease and over 1 million deaths worldwide each year. TB treatment is complex, requiring at least 6 months of therapy with a combination of antibiotics. One factor that contributes to the length of TB treatment is M. tuberculosis phenotypic antibiotic tolerance, which allows the bacteria to survive prolonged drug exposure even in the absence of genetic mutations causing drug resistance. Here, we report a genetic screen to identify M. tuberculosis genes that promote drug tolerance during nutrient starvation. Our study revealed the outer membrane lipid phthiocerol dimycocerosate (PDIM) as a key determinant of M. tuberculosis antibiotic tolerance triggered by nutrient starvation. Our study implicates PDIM synthesis as a potential target for development of new TB drugs that would sensitize M. tuberculosis to existing antibiotics to shorten TB treatment.
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Lake MA, Adams KN, Nie F, Fowler E, Verma AK, Dei S, Teodori E, Sherman DR, Edelstein PH, Spring DR, Troll M, Ramakrishnan L. The human proton pump inhibitors inhibit Mycobacterium tuberculosis rifampicin efflux and macrophage-induced rifampicin tolerance. Proc Natl Acad Sci U S A 2023; 120:e2215512120. [PMID: 36763530 PMCID: PMC7614234 DOI: 10.1073/pnas.2215512120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 01/11/2023] [Indexed: 02/11/2023] Open
Abstract
Tuberculosis treatment requires months-long combination chemotherapy with multiple drugs, with shorter treatments leading to relapses. A major impediment to shortening treatment is that Mycobacterium tuberculosis becomes tolerant to the administered drugs, starting early after infection and within days of infecting macrophages. Multiple lines of evidence suggest that macrophage-induced drug tolerance is mediated by mycobacterial drug efflux pumps. Here, using assays to directly measure drug efflux, we find that M. tuberculosis transports the first-line antitubercular drug rifampicin through a proton gradient-dependent mechanism. We show that verapamil, a known efflux pump inhibitor, which inhibits macrophage-induced rifampicin tolerance, also inhibits M.tuberculosis rifampicin efflux. As with macrophage-induced tolerance, the calcium channel-inhibiting property of verapamil is not required for its inhibition of rifampicin efflux. By testing verapamil analogs, we show that verapamil directly inhibits M. tuberculosis drug efflux pumps through its human P-glycoprotein (PGP)-like inhibitory activity. Screening commonly used drugs with incidental PGP inhibitory activity, we find many inhibit rifampicin efflux, including the proton pump inhibitors (PPIs) such as omeprazole. Like verapamil, the PPIs inhibit macrophage-induced rifampicin tolerance as well as intramacrophage growth, which has also been linked to mycobacterial efflux pump activity. Our assays provide a facile screening platform for M. tuberculosis efflux pump inhibitors that inhibit in vivo drug tolerance and growth.
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Affiliation(s)
- M. Alexandra Lake
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 0AWCambridge, UK
- Medical Research Council Laboratory of Molecular Biology, CB2 0QHCambridge, UK
| | - Kristin N. Adams
- Department of Microbiology, University of Washington, Seattle98195
| | - Feilin Nie
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, UK
| | - Elaine Fowler
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, UK
| | - Amit K. Verma
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 0AWCambridge, UK
| | - Silvia Dei
- Department of Neuroscience, Psychology, Drug Research and Child Health - Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, 50019Sesto Fiorentino (FI), Italy
| | - Elisabetta Teodori
- Department of Neuroscience, Psychology, Drug Research and Child Health - Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, 50019Sesto Fiorentino (FI), Italy
| | - David R. Sherman
- Department of Microbiology, University of Washington, Seattle98195
| | - Paul H. Edelstein
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 0AWCambridge, UK
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - David R. Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, UK
| | - Mark Troll
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 0AWCambridge, UK
- Medical Research Council Laboratory of Molecular Biology, CB2 0QHCambridge, UK
| | - Lalita Ramakrishnan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 0AWCambridge, UK
- Medical Research Council Laboratory of Molecular Biology, CB2 0QHCambridge, UK
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36
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Fan J, Hale VL, Lelieveld LT, Whitworth LJ, Busch-Nentwich EM, Troll M, Edelstein PH, Cox TM, Roca FJ, Aerts JMFG, Ramakrishnan L. Gaucher disease protects against tuberculosis. Proc Natl Acad Sci U S A 2023; 120:e2217673120. [PMID: 36745788 PMCID: PMC7614233 DOI: 10.1073/pnas.2217673120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/31/2022] [Indexed: 02/08/2023] Open
Abstract
Biallelic mutations in the glucocerebrosidase (GBA1) gene cause Gaucher disease, characterized by lysosomal accumulation of glucosylceramide and glucosylsphingosine in macrophages. Gaucher and other lysosomal diseases occur with high frequency in Ashkenazi Jews. It has been proposed that the underlying mutations confer a selective advantage, in particular conferring protection against tuberculosis. Here, using a zebrafish Gaucher disease model, we find that the mutation GBA1 N370S, predominant among Ashkenazi Jews, increases resistance to tuberculosis through the microbicidal activity of glucosylsphingosine in macrophage lysosomes. Consistent with lysosomal accumulation occurring only in homozygotes, heterozygotes remain susceptible to tuberculosis. Thus, our findings reveal a mechanistic basis for protection against tuberculosis by GBA1 N370S and provide biological plausibility for its selection if the relatively mild deleterious effects in homozygotes were offset by significant protection against tuberculosis, a rampant killer of the young in Europe through the Middle Ages into the 19th century.
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Affiliation(s)
- Jingwen Fan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CambridgeCB2 0QH, UK
- MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, UK
| | | | - Lindsey T. Lelieveld
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University2333 CC, Leiden, The Netherlands
| | - Laura J. Whitworth
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CambridgeCB2 0QH, UK
- MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, UK
| | - Elisabeth M. Busch-Nentwich
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CambridgeCB2 0QH, UK
- School of Biological and Behavioral Sciences, Queen Mary University of London, LondonE1 4NS, UK
| | - Mark Troll
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CambridgeCB2 0QH, UK
- MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, UK
| | - Paul H. Edelstein
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CambridgeCB2 0QH, UK
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PhiladelphiaPA19104
| | - Timothy M. Cox
- Department of Medicine, University of Cambridge, CambridgeCB2 0QQ, UK
| | - Francisco J. Roca
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CambridgeCB2 0QH, UK
- Department of Biochemistry and Molecular Biology B and Immunology, University of Murcia, Murcia30120, Spain
- Biomedical Research Institute of Murcia Pascual Parrilla (IMIB-Arrixaca), Murcia30120, Spain
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University2333 CC, Leiden, The Netherlands
| | - Lalita Ramakrishnan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CambridgeCB2 0QH, UK
- MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, UK
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37
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Wang Y, Yu Z, Ding P, Lu J, Mao L, Ngiam L, Yuan Z, Engelstädter J, Schembri MA, Guo J. Antidepressants can induce mutation and enhance persistence toward multiple antibiotics. Proc Natl Acad Sci U S A 2023; 120:e2208344120. [PMID: 36689653 PMCID: PMC9945972 DOI: 10.1073/pnas.2208344120] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/13/2022] [Indexed: 01/25/2023] Open
Abstract
Antibiotic resistance is an urgent threat to global health. Antidepressants are consumed in large quantities, with a similar pharmaceutical market share (4.8%) to antibiotics (5%). While antibiotics are acknowledged as the major driver of increasing antibiotic resistance, little attention is paid to the contribution of antidepressants in this process. Here, we demonstrate that antidepressants at clinically relevant concentrations induce resistance to multiple antibiotics, even following short periods of exposure. Antibiotic persistence was also enhanced. Phenotypic and genotypic analyses revealed the enhanced production of reactive oxygen species following exposure to antidepressants was directly associated with increased resistance. An enhanced stress signature response and stimulation of efflux pump expression were also associated with increased resistance and persistence. Mathematical modeling also predicted that antidepressants would accelerate the emergence of antibiotic-resistant bacteria, and persister cells would help to maintain the resistance. Overall, our findings highlight the antibiotic resistance risk caused by antidepressants.
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Affiliation(s)
- Yue Wang
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, QLD4072, Australia
- School of Environmental Science and Engineering, Tiangong University, Tianjin300387, China
| | - Zhigang Yu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, QLD4072, Australia
| | - Pengbo Ding
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, QLD4072, Australia
| | - Ji Lu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, QLD4072, Australia
| | - Likai Mao
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, QLD4072, Australia
| | - Lyman Ngiam
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, QLD4072, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, QLD4072, Australia
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD4072, Australia
| | - Mark A. Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD4072, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, QLD4072, Australia
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38
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Immune cell interactions in tuberculosis. Cell 2022; 185:4682-4702. [PMID: 36493751 DOI: 10.1016/j.cell.2022.10.025] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/15/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022]
Abstract
Despite having been identified as the organism that causes tuberculosis in 1882, Mycobacterium tuberculosis has managed to still evade our understanding of the protective immune response against it, defying the development of an effective vaccine. Technology and novel experimental models have revealed much new knowledge, particularly with respect to the heterogeneity of the bacillus and the host response. This review focuses on certain immunological elements that have recently yielded exciting data and highlights the importance of taking a holistic approach to understanding the interaction of M. tuberculosis with the many host cells that contribute to the development of protective immunity.
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Mishra S, Saito K. Clinically encountered growth phenotypes of tuberculosis-causing bacilli and their in vitro study: A review. Front Cell Infect Microbiol 2022; 12:1029111. [PMID: 36439231 PMCID: PMC9684195 DOI: 10.3389/fcimb.2022.1029111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/20/2022] [Indexed: 07/11/2024] Open
Abstract
The clinical manifestations of tuberculosis (TB) vary widely in severity, site of infection, and outcomes of treatment-leading to simultaneous efforts to individualize therapy safely and to search for shorter regimens that can be successfully used across the clinical spectrum. In these endeavors, clinicians and researchers alike employ mycobacterial culture in rich media. However, even within the same patient, individual bacilli among the population can exhibit substantial variability in their culturability. Bacilli in vitro also demonstrate substantial heterogeneity in replication rate and cultivation requirements, as well as susceptibility to killing by antimicrobials. Understanding parallels in clinical, ex vivo and in vitro growth phenotype diversity may be key to identifying those phenotypes responsible for treatment failure, relapse, and the reactivation of bacilli that progresses TB infection to disease. This review briefly summarizes the current role of mycobacterial culture in the care of patients with TB and the ex vivo evidence of variability in TB culturability. We then discuss current advances in in vitro models that study heterogenous subpopulations within a genetically identical bulk culture, with an emphasis on the effect of oxidative stress on bacillary cultivation requirements. The review highlights the complexity that heterogeneity in mycobacterial growth brings to the interpretation of culture in clinical settings and research. It also underscores the intricacies present in the interplay between growth phenotypes and antimicrobial susceptibility. Better understanding of population dynamics and growth requirements over time and space promises to aid both the attempts to individualize TB treatment and to find uniformly effective therapies.
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Affiliation(s)
- Saurabh Mishra
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, United States
| | - Kohta Saito
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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40
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Dermody R, Ali F, Popovich J, Chen S, Seo DK, Haydel SE. Modified aluminosilicates display antibacterial activity against nontuberculous mycobacteria and adsorb mycolactone and Mycobacterium ulcerans in vitro. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.1016426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Mycobacterium ulcerans (MU) infection of skin and soft tissue leads to chronic skin ulceration known as Buruli ulcer. MU releases a lipid-like toxin, mycolactone, that diffuses into the tissue, effecting disease through localized tissue necrosis and immunosuppression. Cutaneous Buruli ulcer wounds slowly advance from a painless pre-ulcerative stage to an ulcerative lesion, leading to disparities in the timing of medical intervention and treatment outcomes. Novel Buruli ulcer wound management solutions could complement and supplement systemically administered antimicrobials and reduce time to healing. Capitalizing on nanopore structure, adsorption, and exchange capacities, aluminosilicate nanozeolites (nZeos) and geopolymers (GPs) were developed and investigated in the context of therapeutics for mycobacterial disease ulcerative wound care. nZeos were ion exchanged with copper or silver to assess the antimicrobial activity against MU and Mycobacterium marinum, a rapid growing, genetic ancestor of MU that also causes skin and soft tissue infections. Silver- and copper-exchanged nZeos were bactericidal against MU, while only silver-exchanged nZeos killed M. marinum. To mediate adsorption at a biological scale, GPs with different pore sizes and altered surface modifications were generated and assessed for the ability to adsorb MU and mycolactone. Macroporous GPs with and without stearic acid modification equivalently adsorbed MU cells, while mesoporous GPs with stearic acid adsorbed mycolactone toxin significantly better than mesoporous GPs or GPs modified with phenyltriethoxysilane (PTES). In cytotoxicity assays, Cu-nZeos lacked toxicity against Detroit 551, U-937, and WM-115 cells. GPs demonstrated limited cytotoxicity in Detroit 551 and WM-115, but produced time-dependent toxicity in U-937 cells. With their large surface area and adsorptive capacities, aluminosilicates nZeos and GPs may be modified and developed to support conventional BU wound care. Topical application of nZeos and GPs could kill MU within the cutaneous wound environment and physically remove MU and mycolactone with wound dressing changes, thereby improving wound healing and overall patient outcomes.
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41
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Poulton NC, Rock JM. Unraveling the mechanisms of intrinsic drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:997283. [PMID: 36325467 PMCID: PMC9618640 DOI: 10.3389/fcimb.2022.997283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/30/2022] [Indexed: 02/03/2023] Open
Abstract
Tuberculosis (TB) is among the most difficult infections to treat, requiring several months of multidrug therapy to produce a durable cure. The reasons necessitating long treatment times are complex and multifactorial. However, one major difficulty of treating TB is the resistance of the infecting bacterium, Mycobacterium tuberculosis (Mtb), to many distinct classes of antimicrobials. This review will focus on the major gaps in our understanding of intrinsic drug resistance in Mtb and how functional and chemical-genetics can help close those gaps. A better understanding of intrinsic drug resistance will help lay the foundation for strategies to disarm and circumvent these mechanisms to develop more potent antitubercular therapies.
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Jones RM, Adams KN, Eldesouky HE, Sherman DR. The evolving biology of Mycobacterium tuberculosis drug resistance. Front Cell Infect Microbiol 2022; 12:1027394. [PMID: 36275024 PMCID: PMC9579286 DOI: 10.3389/fcimb.2022.1027394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 01/13/2023] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (Mtb) is an ancient disease that has remained a leading cause of infectious death. Mtb has evolved drug resistance to every antibiotic regimen ever introduced, greatly complicating treatment, lowering rates of cure and menacing TB control in parts of the world. As technology has advanced, our understanding of antimicrobial resistance has improved, and our models of the phenomenon have evolved. In this review, we focus on recent research progress that supports an updated model for the evolution of drug resistance in Mtb. We highlight the contribution of drug tolerance on the path to resistance, and the influence of heterogeneity on tolerance. Resistance is likely to remain an issue for as long as drugs are needed to treat TB. However, with technology driving new insights and careful management of newly developed resources, antimicrobial resistance need not continue to threaten global progress against TB, as it has done for decades.
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Affiliation(s)
| | | | | | - David R. Sherman
- Department of Microbiology, University of Washington, Seattle, WA, United States
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Parbhoo T, Mouton JM, Sampson SL. Phenotypic adaptation of Mycobacterium tuberculosis to host-associated stressors that induce persister formation. Front Cell Infect Microbiol 2022; 12:956607. [PMID: 36237425 PMCID: PMC9551238 DOI: 10.3389/fcimb.2022.956607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis exhibits a remarkable ability to interfere with the host antimicrobial response. The pathogen exploits elaborate strategies to cope with diverse host-induced stressors by modulating its metabolism and physiological state to prolong survival and promote persistence in host tissues. Elucidating the adaptive strategies that M. tuberculosis employs during infection to enhance persistence is crucial to understanding how varying physiological states may differentially drive disease progression for effective management of these populations. To improve our understanding of the phenotypic adaptation of M. tuberculosis, we review the adaptive strategies employed by M. tuberculosis to sense and coordinate a physiological response following exposure to various host-associated stressors. We further highlight the use of animal models that can be exploited to replicate and investigate different aspects of the human response to infection, to elucidate the impact of the host environment and bacterial adaptive strategies contributing to the recalcitrance of infection.
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Liebenberg D, Gordhan BG, Kana BD. Drug resistant tuberculosis: Implications for transmission, diagnosis, and disease management. Front Cell Infect Microbiol 2022; 12:943545. [PMID: 36211964 PMCID: PMC9538507 DOI: 10.3389/fcimb.2022.943545] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/06/2022] [Indexed: 01/17/2023] Open
Abstract
Drug resistant tuberculosis contributes significantly to the global burden of antimicrobial resistance, often consuming a large proportion of the healthcare budget and associated resources in many endemic countries. The rapid emergence of resistance to newer tuberculosis therapies signals the need to ensure appropriate antibiotic stewardship, together with a concerted drive to develop new regimens that are active against currently circulating drug resistant strains. Herein, we highlight that the current burden of drug resistant tuberculosis is driven by a combination of ongoing transmission and the intra-patient evolution of resistance through several mechanisms. Global control of tuberculosis will require interventions that effectively address these and related aspects. Interrupting tuberculosis transmission is dependent on the availability of novel rapid diagnostics which provide accurate results, as near-patient as is possible, together with appropriate linkage to care. Contact tracing, longitudinal follow-up for symptoms and active mapping of social contacts are essential elements to curb further community-wide spread of drug resistant strains. Appropriate prophylaxis for contacts of drug resistant index cases is imperative to limit disease progression and subsequent transmission. Preventing the evolution of drug resistant strains will require the development of shorter regimens that rapidly eliminate all populations of mycobacteria, whilst concurrently limiting bacterial metabolic processes that drive drug tolerance, mutagenesis and the ultimate emergence of resistance. Drug discovery programs that specifically target bacterial genetic determinants associated with these processes will be paramount to tuberculosis eradication. In addition, the development of appropriate clinical endpoints that quantify drug tolerant organisms in sputum, such as differentially culturable/detectable tubercle bacteria is necessary to accurately assess the potential of new therapies to effectively shorten treatment duration. When combined, this holistic approach to addressing the critical problems associated with drug resistance will support delivery of quality care to patients suffering from tuberculosis and bolster efforts to eradicate this disease.
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Novel Antibacterial Activity of Febuxostat, an FDA-Approved Antigout Drug against Mycobacterium tuberculosis Infection. Antimicrob Agents Chemother 2022; 66:e0076222. [PMID: 36040172 PMCID: PMC9487535 DOI: 10.1128/aac.00762-22] [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: 11/20/2022] Open
Abstract
Accumulating evidence suggests that drug repurposing has drawn attention as an anticipative strategy for controlling tuberculosis (TB), considering the dwindling drug discovery and development pipeline. In this study, we explored the antigout drug febuxostat and evaluated its antibacterial activity against Mycobacterium species. Based on MIC evaluation, we found that febuxostat treatment significantly inhibited mycobacterial growth, especially that of Mycobacterium tuberculosis (Mtb) and its phylogenetically close neighbors, M. bovis, M. kansasii, and M. shinjukuense, but these microorganisms were not affected by allopurinol and topiroxostat, which belong to a similar category of antigout drugs. Febuxostat concentration-dependently affected Mtb and durably mediated inhibitory functions (duration, 10 weeks maximum), as evidenced by resazurin microtiter assay, time-kill curve analysis, phenotypic susceptibility test, and the Bactec MGIT 960 system. Based on these results, we determined whether the drug shows antimycobacterial activity against Mtb inside murine bone marrow-derived macrophages (BMDMs). Notably, febuxostat markedly suppressed the intracellular growth of Mtb in a dose-dependent manner without affecting the viability of BMDMs. Moreover, orally administered febuxostat was efficacious in a murine model of TB with reduced bacterial loads in both the lung and spleen without the exacerbation of lung inflammation, which highlights the drug potency. Taken together, unexpectedly, our data demonstrated that febuxostat has the potential for treating TB.
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Miotto P, Sorrentino R, De Giorgi S, Provvedi R, Cirillo DM, Manganelli R. Transcriptional regulation and drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:990312. [PMID: 36118045 PMCID: PMC9480834 DOI: 10.3389/fcimb.2022.990312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial drug resistance is one of the major challenges to present and future human health, as the continuous selection of multidrug resistant bacteria poses at serious risk the possibility to treat infectious diseases in the near future. One of the infection at higher risk to become incurable is tuberculosis, due to the few drugs available in the market against Mycobacterium tuberculosis. Drug resistance in this species is usually due to point mutations in the drug target or in proteins required to activate prodrugs. However, another interesting and underexplored aspect of bacterial physiology with important impact on drug susceptibility is represented by the changes in transcriptional regulation following drug exposure. The main regulators involved in this phenomenon in M. tuberculosis are the sigma factors, and regulators belonging to the WhiB, GntR, XRE, Mar and TetR families. Better understanding the impact of these regulators in survival to drug treatment might contribute to identify new drug targets and/or to design new strategies of intervention.
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Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Rita Sorrentino
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Stefano De Giorgi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
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Eoh H, Liu R, Lim J, Lee JJ, Sell P. Central carbon metabolism remodeling as a mechanism to develop drug tolerance and drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:958240. [PMID: 36072228 PMCID: PMC9441700 DOI: 10.3389/fcimb.2022.958240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Suboptimal efficacy of the current antibiotic regimens and frequent emergence of antibiotic-resistant Mycobacterium tuberculosis (Mtb), an etiological agent of tuberculosis (TB), render TB the world’s deadliest infectious disease before the COVID-19 outbreak. Our outdated TB treatment method is designed to eradicate actively replicating populations of Mtb. Unfortunately, accumulating evidence suggests that a small population of Mtb can survive antimycobacterial pressure of antibiotics by entering a “persister” state (slowly replicating or non-replicating and lacking a stably heritable antibiotic resistance, termed drug tolerance). The formation of drug-tolerant Mtb persisters is associated with TB treatment failure and is thought to be an adaptive strategy for eventual development of permanent genetic mutation-mediated drug resistance. Thus, the molecular mechanisms behind persister formation and drug tolerance acquisition are a source of new antibiotic targets to eradicate both Mtb persisters and drug-resistant Mtb. As Mtb persisters are genetically identical to antibiotic susceptible populations, metabolomics has emerged as a vital biochemical tool to differentiate these populations by determining phenotypic shifts and metabolic reprogramming. Metabolomics, which provides detailed insights into the molecular basis of drug tolerance and resistance in Mtb, has unique advantages over other techniques by its ability to identify specific metabolic differences between the two genetically identical populations. This review summarizes the recent advances in our understanding of the metabolic adaptations used by Mtb persisters to achieve intrinsic drug tolerance and facilitate the emergence of drug resistance. These findings present metabolomics as a powerful tool to identify previously unexplored antibiotic targets and improved combinations of drug regimens against drug-resistant TB infection.
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Shultis MW, Mulholland CV, Berney M. Are all antibiotic persisters created equal? Front Cell Infect Microbiol 2022; 12:933458. [PMID: 36061872 PMCID: PMC9428696 DOI: 10.3389/fcimb.2022.933458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022] Open
Abstract
Antibiotic persisters are a sub-population of bacteria able to survive in the presence of bactericidal antibiotic despite the lack of heritable drug resistance mechanisms. This phenomenon exists across many bacterial species and is observed for many different antibiotics. Though these bacteria are often described as “multidrug persisters” very few experiments have been carried out to determine the homogeneity of a persister population to different drugs. Further, there is much debate in the field as to the origins of a persister cell. Is it formed spontaneously? Does it form in response to stress? These questions are particularly pressing in the field of Mycobacterium tuberculosis, where persisters may play a crucial role in the required length of treatment and the development of multidrug resistant organisms. Here we aim to interpret the known mechanisms of antibiotic persistence and how they may relate to improving treatments for M. tuberculosis, exposing the gaps in knowledge that prevent us from answering the question: Are all antibiotic persisters created equal?
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Arctic Psychrotolerant Pseudomonas sp. B14-6 Exhibits Temperature-Dependent Susceptibility to Aminoglycosides. Antibiotics (Basel) 2022; 11:antibiotics11081019. [PMID: 36009888 PMCID: PMC9405152 DOI: 10.3390/antibiotics11081019] [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: 05/18/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 12/04/2022] Open
Abstract
Bacteria can evade antibiotics by acquiring resistance genes, as well as switching to a non-growing dormant state without accompanying genetic modification. Bacteria in this quiescent state are called persisters, and this non-inheritable ability to withstand multiple antibiotics is referred to as antibiotic tolerance. Although all bacteria are considered to be able to form antibiotic-tolerant persisters, the antibiotic tolerance of extremophilic bacteria is poorly understood. Previously, we identified the psychrotolerant bacterium Pseudomonas sp. B14-6 from the glacier foreland of Midtre Lovénbreen in High Arctic Svalbard. Herein, we investigated the resistance and tolerance of Pseudomonas sp. B14-6 against aminoglycosides at various temperatures. This bacterium was resistant to streptomycin and susceptible to apramycin, gentamicin, kanamycin, and tobramycin. The two putative aminoglycoside phosphotransferase genes aph1 and aph2 were the most likely contributors to streptomycin resistance. Notably, unlike the mesophilic Pseudomonas aeruginosa PA14, this cold-adapted bacterium demonstrated reduced susceptibility to all tested aminoglycosides in a temperature-dependent manner. Pseudomonas sp. B14-6 at a lower temperature formed the persister cells that shows tolerance to the 100-fold minimum inhibitory concentration (MIC) of gentamicin, as well as the partially tolerant cells that withstand 25-fold MIC gentamicin. The temperature-dependent gentamicin tolerance appears to result from reduced metabolic activity. Lastly, the partially tolerant Pseudomonas sp. B14-6 cells could slowly proliferate under the bactericidal concentrations of aminoglycosides. Our results demonstrate that Pseudomonas sp. B14-6 has a characteristic ability to form cells with a range of tolerance, which appears to be inversely proportional to its growth rate.
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Surette MD, Waglechner N, Koteva K, Wright GD. HelR is a helicase-like protein that protects RNA polymerase from rifamycin antibiotics. Mol Cell 2022; 82:3151-3165.e9. [PMID: 35907401 DOI: 10.1016/j.molcel.2022.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 03/15/2022] [Accepted: 06/12/2022] [Indexed: 10/16/2022]
Abstract
Rifamycin antibiotics such as rifampin are potent inhibitors of prokaryotic RNA polymerase (RNAP) used to treat tuberculosis and other bacterial infections. Although resistance arises in the clinic principally through mutations in RNAP, many bacteria possess highly specific enzyme-mediated resistance mechanisms that modify and inactivate rifamycins. The expression of these enzymes is controlled by a 19-bp cis-acting rifamycin-associated element (RAE). Guided by the presence of RAE sequences, we identify a helicase-like protein, HelR, in Streptomyces venezuelae that confers broad-spectrum rifamycin resistance. We show that HelR also promotes tolerance to rifamycins, enabling bacterial evasion of the toxic properties of these antibiotics. HelR forms a complex with RNAP and rescues transcription inhibition by displacing rifamycins from RNAP, thereby providing resistance by target protection . Furthermore, HelRs are broadly distributed in Actinobacteria, including several opportunistic Mycobacterial pathogens, offering yet another challenge for developing new rifamycin antibiotics.
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Affiliation(s)
- Matthew D Surette
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Nicholas Waglechner
- Toronto Invasive Bacterial Diseases Network, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Kalinka Koteva
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Gerard D Wright
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.
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