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Helaine S, Conlon BP, Davis KM, Russell DG. Host stress drives tolerance and persistence: The bane of anti-microbial therapeutics. Cell Host Microbe 2024; 32:852-862. [PMID: 38870901 DOI: 10.1016/j.chom.2024.04.019] [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: 03/03/2024] [Revised: 04/03/2024] [Accepted: 04/25/2024] [Indexed: 06/15/2024]
Abstract
Antibiotic resistance, typically associated with genetic changes within a bacterial population, is a frequent contributor to antibiotic treatment failures. Antibiotic persistence and tolerance, which we collectively term recalcitrance, represent transient phenotypic changes in the bacterial population that prolong survival in the presence of typically lethal concentrations of antibiotics. Antibiotic recalcitrance is challenging to detect and investigate-traditionally studied under in vitro conditions, our understanding during infection and its contribution to antibiotic failure is limited. Recently, significant progress has been made in the study of antibiotic-recalcitrant populations in pathogenic species, including Mycobacterium tuberculosis, Staphylococcus aureus, Salmonella enterica, and Yersiniae, in the context of the host environment. Despite the diversity of these pathogens and infection models, shared signals and responses promote recalcitrance, and common features and vulnerabilities of persisters and tolerant bacteria have emerged. These will be discussed here, along with progress toward developing therapeutic interventions to better treat recalcitrant pathogens.
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Affiliation(s)
- Sophie Helaine
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
| | - Brian P Conlon
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
| | - Kimberly M Davis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - David G Russell
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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Davis KM. mSphere of Influence: If virulence is energetically costly, how can it be maintained? mSphere 2023; 8:e0031223. [PMID: 37676232 PMCID: PMC10597342 DOI: 10.1128/msphere.00312-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
Kimberly Davis works in the field of bacterial pathogenesis and studies heterogeneity in bacterial populations within host tissues. In this mSphere of Influence article, she reflects on how the paper "Stabilization of cooperative virulence by the expression of an avirulent phenotype" by M. Diard et al. (M. Diard et al., Nature 494:353-6, 2013, DOI: 10.1038/nature11913) impacted the way she thinks about bacterial population dynamics and the costs and benefits of producing virulence factors during infection.
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Affiliation(s)
- Kimberly Michele Davis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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Personnic N, Doublet P, Jarraud S. Intracellular persister: A stealth agent recalcitrant to antibiotics. Front Cell Infect Microbiol 2023; 13:1141868. [PMID: 37065203 PMCID: PMC10102521 DOI: 10.3389/fcimb.2023.1141868] [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: 01/10/2023] [Accepted: 03/06/2023] [Indexed: 04/03/2023] Open
Abstract
The bulk of bacteria transiently evading appropriate antibiotic regimes and recovered from non-resolutive infections are commonly refer to as persisters. In this mini-review, we discuss how antibiotic persisters stem from the interplay between the pathogen and the cellular defenses mechanisms and its underlying heterogeneity.
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Affiliation(s)
- Nicolas Personnic
- CIRI, Centre International de Recherche en Infectiologie, CNRS UMR 5308, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Group Persistence and Single-Cell Dynamics of Respiratory Pathogens, Lyon, France
- *Correspondence: Nicolas Personnic,
| | - Patricia Doublet
- CIRI, Centre International de Recherche en Infectiologie, CNRS UMR 5308, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Group Legionella Pathogenesis, Lyon, France
| | - Sophie Jarraud
- CIRI, Centre International de Recherche en Infectiologie, CNRS UMR 5308, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Group Legionella Pathogenesis, Lyon, France
- National Reference Centre for Legionella, Institute of Infectious Agents, Hospices Civils de Lyon, Lyon, France
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Braza RED, Cotten KL, Davis KM. Protocol for detecting Yersinia pseudotuberculosis nitric oxide exposure during in vitro growth. STAR Protoc 2022; 3:101760. [PMID: 36219561 PMCID: PMC9563189 DOI: 10.1016/j.xpro.2022.101760] [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: 06/30/2022] [Revised: 07/29/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
Yersinia pseudotuberculosis (Yptb) is a bacterial pathogen that causes foodborne illness. Defense against the host antimicrobial gas, nitric oxide (NO), by the bacterial NO-detoxifying gene, hmp, promotes Yptb replication in mouse models of infection. Here, we detail the use of fluorescent signals as readouts for NO exposure within individual cells and subsequent detection of heterogeneity within a population, using single-cell imaging and analysis. This protocol quantifies NO exposure in culture, without capturing the full complexity of the host environment. For complete details on the use and execution of this protocol, please refer to Patel et al. (2021).
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Affiliation(s)
- Rezia Era D. Braza
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA,Corresponding author
| | - Katherine L. Cotten
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Kimberly M. Davis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA,Corresponding author
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NO-Stressed Y. pseudotuberculosis Has Decreased Cell Division Rates in the Mouse Spleen. Infect Immun 2022; 90:e0016722. [PMID: 35862700 PMCID: PMC9387282 DOI: 10.1128/iai.00167-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Fluorescence dilution approaches can detect bacterial cell division events and can detect if there are differential rates of cell division across individual cells within a population. This approach typically involves inducing expression of a fluorescent protein and then tracking partitioning of fluorescence into daughter cells. However, fluorescence can be diluted very quickly within a rapidly replicating population, such as pathogenic bacterial populations replicating within host tissues. To overcome this limitation, we have generated two revTetR reporter constructs, where either mCherry or yellow fluorescent protein (YFP) is constitutively expressed and repressed by addition of tetracyclines, resulting in fluorescence dilution within defined time frames. We show that fluorescent signals are diluted in replicating populations and that signal accumulates in growth-inhibited populations, including during nitric oxide (NO) exposure. Furthermore, we show that tetracyclines can be delivered to the mouse spleen during Yersinia pseudotuberculosis infection and defined a drug concentration that results in even exposure of cells to tetracyclines. We then used this system to visualize bacterial cell division within defined time frames postinfection. revTetR-mCherry allowed us to detect slow-growing cells in response to NO in culture; however, this strain had a growth defect within mouse tissues, which complicated results. To address this issue, we constructed revTetR-YFP using the less toxic YFP and showed that heightened NO exposure correlated with heightened YFP signal, indicating decreased cell division rates within this subpopulation in vivo. This revTetR reporter will provide a critical tool for future studies to identify and isolate slowly replicating bacterial subpopulations from host tissues.
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Marro FC, Laurent F, Josse J, Blocker AJ. Methods to monitor bacterial growth and replicative rates at the single-cell level. FEMS Microbiol Rev 2022; 46:6623663. [PMID: 35772001 PMCID: PMC9629498 DOI: 10.1093/femsre/fuac030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 01/09/2023] Open
Abstract
The heterogeneity of bacterial growth and replicative rates within a population was proposed a century ago notably to explain the presence of bacterial persisters. The term "growth rate" at the single-cell level corresponds to the increase in size or mass of an individual bacterium while the "replicative rate" refers to its division capacity within a defined temporality. After a decades long hiatus, recent technical innovative approaches allow population growth and replicative rates heterogeneity monitoring at the single-cell level resuming in earnest. Among these techniques, the oldest and widely used is time-lapse microscopy, most recently combined with microfluidics. We also discuss recent fluorescence dilution methods informing only on replicative rates and best suited. Some new elegant single cell methods so far only sporadically used such as buoyant mass measurement and stable isotope probing have emerged. Overall, such tools are widely used to investigate and compare the growth and replicative rates of bacteria displaying drug-persistent behaviors to that of bacteria growing in specific ecological niches or collected from patients. In this review, we describe the current methods available, discussing both the type of queries these have been used to answer and the specific strengths and limitations of each method.
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Affiliation(s)
- Florian C Marro
- Evotec ID Lyon, In Vitro Biology, Infectious Diseases and Antibacterials Unit, Gerland, 69007 Lyon, France,CIRI – Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007 Lyon, France
| | - Frédéric Laurent
- CIRI – Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007 Lyon, France,Institut des Sciences Pharmaceutiques et Biologiques (ISPB), Université Claude Bernard Lyon 1, Lyon, France,Centre de Référence pour la prise en charge des Infections ostéo-articulaires complexes (CRIOAc Lyon; www.crioac-lyon.fr), Hospices Civils de Lyon, Lyon, France,Laboratoire de bactériologie, Institut des Agents Infectieux, French National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
| | - Jérôme Josse
- CIRI – Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007 Lyon, France,Institut des Sciences Pharmaceutiques et Biologiques (ISPB), Université Claude Bernard Lyon 1, Lyon, France,Centre de Référence pour la prise en charge des Infections ostéo-articulaires complexes (CRIOAc Lyon; www.crioac-lyon.fr), Hospices Civils de Lyon, Lyon, France
| | - Ariel J Blocker
- Corresponding author. Evotec ID Lyon, In Vitro Biology, Infectious Diseases and Antibacterials Unit, France. E-mail:
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Alvarez-Manzo HS, Davidson RK, Van Cauwelaert de Wyels J, Cotten KL, Nguyen BH, Xiao M, Zhu Z, Anthony J, van Opijnen T, Davis KM. Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes involved in cell permeability and tRNA modifications. PLoS Pathog 2022; 18:e1010556. [PMID: 35576231 PMCID: PMC9135342 DOI: 10.1371/journal.ppat.1010556] [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: 11/05/2021] [Revised: 05/26/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022] Open
Abstract
Antibiotic tolerance is typically associated with a phenotypic change within a bacterial population, resulting in a transient decrease in antibiotic susceptibility that can contribute to treatment failure and recurrent infections. Although tolerant cells may emerge prior to treatment, the stress of prolonged antibiotic exposure can also promote tolerance. Here, we sought to determine how Yersinia pseudotuberculosis responds to doxycycline exposure, to then verify if these gene expression changes could promote doxycycline tolerance in culture and in our mouse model of infection. Only four genes were differentially regulated in response to a physiologically-relevant dose of doxycycline: osmB and ompF were upregulated, tusB and cnfy were downregulated; differential expression also occurred during doxycycline treatment in the mouse. ompF, tusB and cnfy were also differentially regulated in response to chloramphenicol, indicating these could be general responses to ribosomal inhibition. cnfy has previously been associated with persistence and was not a major focus here. We found deletion of the OmpF porin resulted in increased antibiotic accumulation, suggesting expression may promote diffusion of doxycycline out of the cell, while OsmB lipoprotein had a minor impact on antibiotic permeability. Overexpression of tusB significantly impaired bacterial survival in culture and in the mouse, suggesting that tRNA modification by tusB, and the resulting impacts on translational machinery, promotes survival during treatment with an antibiotic classically viewed as bacteriostatic. We believe this may be the first observation of bactericidal activity of doxycycline under physiological conditions, which was revealed by reversing tusB downregulation.
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Affiliation(s)
- Hector S. Alvarez-Manzo
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Robert K. Davidson
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jasper Van Cauwelaert de Wyels
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katherine L. Cotten
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Benjamin H. Nguyen
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Melody Xiao
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Zeyu Zhu
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Jon Anthony
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Kimberly Michele Davis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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