1
|
Santi I, Dias Teixeira R, Manfredi P, Hernandez Gonzalez H, Spiess DC, Mas G, Klotz A, Kaczmarczyk A, Zamboni N, Hiller S, Jenal U. Toxin-mediated depletion of NAD and NADP drives persister formation in a human pathogen. EMBO J 2024:10.1038/s44318-024-00248-5. [PMID: 39322758 DOI: 10.1038/s44318-024-00248-5] [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: 03/08/2024] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 09/27/2024] Open
Abstract
Toxin-antitoxin (TA) systems are widespread in bacteria and implicated in genome stability, virulence, phage defense, and persistence. TA systems have diverse activities and cellular targets, but their physiological roles and regulatory mechanisms are often unclear. Here, we show that the NatR-NatT TA system, which is part of the core genome of the human pathogen Pseudomonas aeruginosa, generates drug-tolerant persisters by specifically depleting nicotinamide dinucleotides. While actively growing P. aeruginosa cells compensate for NatT-mediated NAD+ deficiency by inducing the NAD+ salvage pathway, NAD depletion generates drug-tolerant persisters under nutrient-limited conditions. Our structural and biochemical analyses propose a model for NatT toxin activation and autoregulation and indicate that NatT activity is subject to powerful metabolic feedback control by the NAD+ precursor nicotinamide. Based on the identification of natT gain-of-function alleles in patient isolates and on the observation that NatT increases P. aeruginosa virulence, we postulate that NatT modulates pathogen fitness during infections. These findings pave the way for detailed investigations into how a toxin-antitoxin system can promote pathogen persistence by disrupting essential metabolic pathways.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Alexander Klotz
- Biozentrum, University of Basel, Basel, Switzerland
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | | | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | | | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Zheng EJ, Valeri JA, Andrews IW, Krishnan A, Bandyopadhyay P, Anahtar MN, Herneisen A, Schulte F, Linnehan B, Wong F, Stokes JM, Renner LD, Lourido S, Collins JJ. Discovery of antibiotics that selectively kill metabolically dormant bacteria. Cell Chem Biol 2024; 31:712-728.e9. [PMID: 38029756 PMCID: PMC11031330 DOI: 10.1016/j.chembiol.2023.10.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 08/13/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
There is a need to discover and develop non-toxic antibiotics that are effective against metabolically dormant bacteria, which underlie chronic infections and promote antibiotic resistance. Traditional antibiotic discovery has historically favored compounds effective against actively metabolizing cells, a property that is not predictive of efficacy in metabolically inactive contexts. Here, we combine a stationary-phase screening method with deep learning-powered virtual screens and toxicity filtering to discover compounds with lethality against metabolically dormant bacteria and favorable toxicity profiles. The most potent and structurally distinct compound without any obvious mechanistic liability was semapimod, an anti-inflammatory drug effective against stationary-phase E. coli and A. baumannii. Integrating microbiological assays, biochemical measurements, and single-cell microscopy, we show that semapimod selectively disrupts and permeabilizes the bacterial outer membrane by binding lipopolysaccharide. This work illustrates the value of harnessing non-traditional screening methods and deep learning models to identify non-toxic antibacterial compounds that are effective in infection-relevant contexts.
Collapse
Affiliation(s)
- Erica J Zheng
- Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Jacqueline A Valeri
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Ian W Andrews
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aarti Krishnan
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Parijat Bandyopadhyay
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Melis N Anahtar
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Alice Herneisen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brooke Linnehan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Felix Wong
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan M Stokes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, 01062 Dresden, Germany
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - James J Collins
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
4
|
Bergkessel M, Forte B, Gilbert IH. Small-Molecule Antibiotic Drug Development: Need and Challenges. ACS Infect Dis 2023; 9:2062-2071. [PMID: 37819866 PMCID: PMC10644355 DOI: 10.1021/acsinfecdis.3c00189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Indexed: 10/13/2023]
Abstract
The need for new antibiotics is urgent. Antimicrobial resistance is rising, although currently, many more people die from drug-sensitive bacterial infections. The continued evolution of drug resistance is inevitable, fueled by pathogen population size and exposure to antibiotics. Additionally, opportunistic pathogens will always pose a threat to vulnerable patients whose immune systems cannot efficiently fight them even if they are sensitive to available antibiotics, according to clinical microbiology tests. These problems are intertwined and will worsen as human populations age, increase in density, and experience disruptions such as war, extreme weather events, or declines in standard of living. The development of appropriate drugs to treat all the world's bacterial infections should be a priority, and future success will likely require combinations of multiple approaches. However, the highest burden of bacterial infection is in Low- and Middle-Income Countries, where limited medical infrastructure is a major challenge. For effectively managing infections in these contexts, small-molecule-based treatments offer significant advantages. Unfortunately, support for ongoing small-molecule antibiotic discovery has recently suffered from significant challenges related both to the scientific difficulties in treating bacterial infections and to market barriers. Nevertheless, small-molecule antibiotics remain essential and irreplaceable tools for fighting infections, and efforts to develop novel and improved versions deserve ongoing investment. Here, we first describe the global historical context of antibiotic treatment and then highlight some of the challenges surrounding small-molecule development and potential solutions. Many of these challenges are likely to be common to all modalities of antibacterial treatment and should be addressed directly.
Collapse
Affiliation(s)
- Megan Bergkessel
- Division
of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Barbara Forte
- Drug
Discovery Unit and Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K.
| | - Ian H. Gilbert
- Drug
Discovery Unit and Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K.
| |
Collapse
|
5
|
Xia A, Thai A, Cao Z, Chen X, Chen J, Bacacao B, Bekale LA, Schiel V, Bollyky PL, Maria PLS. Chronic suppurative otitis media causes macrophage-associated sensorineural hearing loss. J Neuroinflammation 2022; 19:224. [PMID: 36096817 PMCID: PMC9465898 DOI: 10.1186/s12974-022-02585-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/23/2022] [Indexed: 11/10/2022] Open
Abstract
Background Chronic suppurative otitis media (CSOM) is the most common cause of permanent hearing loss in children in the developing world. A large component of the permanent hearing loss is sensory in nature and our understanding of the mechanism of this has so far been limited to post-mortem human specimens or acute infection models that are not representative of human CSOM. In this report, we assess cochlear injury in a validated Pseudomonas aeruginosa (PA) CSOM mouse model. Methods We generated persisters (PCs) and inoculated them into the mouse middle ear cavity. We tracked infection with IVIS and detected PA using RT-PCR. We assessed cochlear damage and innate immunity by Immunohistochemistry. Finally, we evaluated cytokines with multiplex assay and quantitative real-time PCR. Results We observed outer hair cell (OHC) loss predominantly in the basal turn of the cochlear at 14 days after bacterial inoculation. Macrophages, not neutrophils are the major immune cells in the cochlea in CSOM displaying increased numbers and a distribution correlated with the observed cochlear injury. The progression of the morphological changes suggests a transition from monocytes into tissue macrophages following infection. We also show that PA do not enter the cochlea and live bacteria are required for cochlear injury. We characterized cytokine activity in the CSOM cochlea. Conclusions Taken together, this data shows a critical role for macrophages in CSOM-mediated sensorineural hearing loss (SNHL). Supplementary Information The online version contains supplementary material available at 10.1186/s12974-022-02585-w.
Collapse
|
6
|
The polyamino-isoprenyl potentiator NV716 revives disused antibiotics against Gram-negative bacteria in broth, infected monocytes, or biofilms, by disturbing the barrier effect of their outer membrane. Eur J Med Chem 2022; 238:114496. [DOI: 10.1016/j.ejmech.2022.114496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 11/24/2022]
|
7
|
Xu L, She P, Liu Y, Liu S, Li Z, Li Y, Hussain Z, Wu Y. A novel bactericidal small molecule, STK-35, and its derivative, STK-66, as antibacterial agents against Gram-negative pathogenic bacteria in vitro and in vivo. Lett Appl Microbiol 2022; 75:655-666. [PMID: 35218030 DOI: 10.1111/lam.13682] [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: 09/30/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/29/2022]
Abstract
Due to the increasing rate of antibiotic resistance and the emergence of persister cells of Gram-negative pathogenic bacteria, the development of new antibacterial agents is urgently needed to deal with this problem. Our results indicated that both newly identified small molecule STK-35 and its derivative STK-66 exhibited effective antibacterial properties against a variety of Gram-negative pathogens including A. baumannii, E. coli, K. pneumoniae and P. aeruginosa. The minimal inhibitory concentrations (MICs) and minimal bactericidal concentrations (MBCs) ranges were 0.0625-8 μg mL-1 and 0.125-16 μg mL-1 respectively, while no hemolytic activity and mammalian cell cytotoxicity were observed. The time-killing assays showed STK-35/66 had strong bactericidal activity against Gram-negative pathogens. STK-35/66 also showed different degrees of synergistic antibacterial activity with conventional antibiotics and exhibited persister cells killing activity. Moreover, STK-35/66 effectively eradicated the pre-formed biofilms of P. aeruginosa and A. baumannii. In addition, STK-35/66 significantly increased the survival rate of E. coli infected mice and induced a decrease in bacterial load of the peritonitis model. In nutshell, these results suggested that STK-35/66 possessed antimicrobial activity against Gram-negative pathogenic bacteria in vitro and in vivo, which could be considered as potential substitutes for the treatment of Gram-negative pathogenic infections after further structure optimization.
Collapse
Affiliation(s)
- Lanlan Xu
- Department of Laboratory Medicine, Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China
| | - Pengfei She
- Department of Laboratory Medicine, Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China
| | - Yaqian Liu
- Department of Laboratory Medicine, Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China
| | - Shasha Liu
- Department of Laboratory Medicine, Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China
| | - Zehao Li
- Department of Laboratory Medicine, Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China
| | - Yimin Li
- Department of Laboratory Medicine, Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China
| | - Zubair Hussain
- Department of Laboratory Medicine, Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China
| | - Yong Wu
- Department of Laboratory Medicine, Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China.,Department of Laboratory Medicine, The First Hospital of Changsha, Changsha, 410013, Hunan, China
| |
Collapse
|
8
|
Schrank CL, Wilt IK, Monteagudo Ortiz C, Haney BA, Wuest WM. Using membrane perturbing small molecules to target chronic persistent infections. RSC Med Chem 2021; 12:1312-1324. [PMID: 34458737 PMCID: PMC8372208 DOI: 10.1039/d1md00151e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
After antibiotic treatment, a subpopulation of bacteria often remains and can lead to recalcitrant infections. This subpopulation, referred to as persisters, evades antibiotic treatment through numerous mechanisms such as decreased uptake of small molecules and slowed growth. Membrane perturbing small molecules have been shown to eradicate persisters as well as render these populations susceptible to antibiotic treatment. Chemotype similarities have emerged suggesting amphiphilic heteroaromatic compounds possess ideal properties to increase membrane fluidity and such molecules warrant further investigation as effective agents or potentiators against persister cells.
Collapse
Affiliation(s)
| | - Ingrid K Wilt
- Department of Chemistry Emory University Atlanta GA 30322 USA
| | | | | | - William M Wuest
- Department of Chemistry Emory University Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine Atlanta GA 30322 USA
| |
Collapse
|
9
|
The Polyaminoisoprenyl Potentiator NV716 Revives Old Disused Antibiotics against Intracellular Forms of Infection by Pseudomonas aeruginosa. Antimicrob Agents Chemother 2021; 65:AAC.02028-20. [PMID: 33318000 DOI: 10.1128/aac.02028-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/05/2020] [Indexed: 12/24/2022] Open
Abstract
Active efflux confers intrinsic resistance to multiple antibiotics in Pseudomonas aeruginosa, including old disused molecules. Beside resistance, intracellular survival is another reason for failure to eradicate bacteria with antibiotics. We evaluated the capacity of polyaminoisoprenyl potentiators (designed as efflux pump inhibitors [EPIs]) NV716 and NV731 compared to PAβN to restore the activity of disused antibiotics (doxycycline, chloramphenicol [substrates for efflux], and rifampin [nonsubstrate]) in comparison with ciprofloxacin against intracellular P. aeruginosa (strains with variable efflux levels) in THP-1 monocytes exposed over 24 h to antibiotics alone (0.003 to 100× MIC) or combined with EPIs. Pharmacodynamic parameters (apparent static concentrations [C s] and maximal relative efficacy [E max]) were calculated using the Hill equation of concentration-response curves. PAβN and NV731 moderately reduced (0 to 4 doubling dilutions) antibiotic MICs but did not affect their intracellular activity. NV716 markedly reduced (1 to 16 doubling dilutions) the MIC of all antibiotics (substrates or not for efflux; strains expressing efflux or not); it also improved their relative potency and maximal efficacy (i.e., lower C s; more negative E max) intracellularly. In parallel, NV716 reduced the persister fraction in stationary cultures when combined with ciprofloxacin. In contrast to PAβN and NV731, which act only as EPIs against extracellular bacteria, NV716 can resensitize P. aeruginosa to antibiotics whether they are substrates or not for efflux, both extracellularly and intracellularly. This suggests a complex mode of action that goes beyond a simple inhibition of efflux to reduce bacterial persistence. NV716 appears to be a useful adjuvant, including to disused antibiotics with low antipseudomonal activity, to improve their activity, including against intracellular P. aeruginosa.
Collapse
|
10
|
Khan F, Pham DTN, Tabassum N, Oloketuyi SF, Kim YM. Treatment strategies targeting persister cell formation in bacterial pathogens. Crit Rev Microbiol 2020; 46:665-688. [DOI: 10.1080/1040841x.2020.1822278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Fazlurrahman Khan
- Institute of Food Science, Pukyong National University, Busan, Korea
| | - Dung Thuy Nguyen Pham
- Department of Food Science and Technology, Pukyong National University, Busan, Korea
| | - Nazia Tabassum
- Industrial Convergence Bionix Engineering, Pukyong National University, Busan, Korea
| | | | - Young-Mog Kim
- Institute of Food Science, Pukyong National University, Busan, Korea
- Department of Food Science and Technology, Pukyong National University, Busan, Korea
| |
Collapse
|
11
|
Salcedo-Sora JE, Kell DB. A Quantitative Survey of Bacterial Persistence in the Presence of Antibiotics: Towards Antipersister Antimicrobial Discovery. Antibiotics (Basel) 2020; 9:E508. [PMID: 32823501 PMCID: PMC7460088 DOI: 10.3390/antibiotics9080508] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Bacterial persistence to antibiotics relates to the phenotypic ability to survive lethal concentrations of otherwise bactericidal antibiotics. The quantitative nature of the time-kill assay, which is the sector's standard for the study of antibiotic bacterial persistence, is an invaluable asset for global, unbiased, and cross-species analyses. Methods: We compiled the results of antibiotic persistence from antibiotic-sensitive bacteria during planktonic growth. The data were extracted from a sample of 187 publications over the last 50 years. The antibiotics used in this compilation were also compared in terms of structural similarity to fluorescent molecules known to accumulate in Escherichia coli. Results: We reviewed in detail data from 54 antibiotics and 36 bacterial species. Persistence varies widely as a function of the type of antibiotic (membrane-active antibiotics admit the fewest), the nature of the growth phase and medium (persistence is less common in exponential phase and rich media), and the Gram staining of the target organism (persistence is more common in Gram positives). Some antibiotics bear strong structural similarity to fluorophores known to be taken up by E. coli, potentially allowing competitive assays. Some antibiotics also, paradoxically, seem to allow more persisters at higher antibiotic concentrations. Conclusions: We consolidated an actionable knowledge base to support a rational development of antipersister antimicrobials. Persistence is seen as a step on the pathway to antimicrobial resistance, and we found no organisms that failed to exhibit it. Novel antibiotics need to have antipersister activity. Discovery strategies should include persister-specific approaches that could find antibiotics that preferably target the membrane structure and permeability of slow-growing cells.
Collapse
Affiliation(s)
- Jesus Enrique Salcedo-Sora
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK;
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
12
|
Bacterial Heterogeneity and Antibiotic Survival: Understanding and Combatting Persistence and Heteroresistance. Mol Cell 2019; 76:255-267. [DOI: 10.1016/j.molcel.2019.09.028] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022]
|
13
|
Fighting bacterial persistence: Current and emerging anti-persister strategies and therapeutics. Drug Resist Updat 2018; 38:12-26. [DOI: 10.1016/j.drup.2018.03.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/07/2018] [Accepted: 03/25/2018] [Indexed: 01/13/2023]
|
14
|
Defraine V, Liebens V, Loos E, Swings T, Weytjens B, Fierro C, Marchal K, Sharkey L, O'Neill AJ, Corbau R, Marchand A, Chaltin P, Fauvart M, Michiels J. 1-((2,4-Dichlorophenethyl)Amino)-3-Phenoxypropan-2-ol Kills Pseudomonas aeruginosa through Extensive Membrane Damage. Front Microbiol 2018; 9:129. [PMID: 29472905 PMCID: PMC5809444 DOI: 10.3389/fmicb.2018.00129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/18/2018] [Indexed: 12/31/2022] Open
Abstract
The ever increasing multidrug-resistance of clinically important pathogens and the lack of novel antibiotics have resulted in a true antibiotic crisis where many antibiotics are no longer effective. Further complicating the treatment of bacterial infections are antibiotic-tolerant persister cells. Besides being responsible for the recalcitrant nature of chronic infections, persister cells greatly contribute to the observed antibiotic tolerance in biofilms and even facilitate the emergence of antibiotic resistance. Evidently, eradication of these persister cells could greatly improve patient outcomes and targeting persistence may provide an alternative approach in combatting chronic infections. We recently characterized 1-((2,4-dichlorophenethyl)amino)-3-phenoxypropan-2-ol (SPI009), a novel anti-persister molecule capable of directly killing persisters from both Gram-negative and Gram-positive pathogens. SPI009 potentiates antibiotic activity in several in vitro and in vivo infection models and possesses promising anti-biofilm activity. Strikingly, SPI009 restores antibiotic sensitivity even in resistant strains. In this study, we investigated the mode of action of this novel compound using several parallel approaches. Genetic analyses and a macromolecular synthesis assays suggest that SPI009 acts by causing extensive membrane damage. This hypothesis was confirmed by liposome leakage assay and membrane permeability studies, demonstrating that SPI009 rapidly impairs the bacterial outer and inner membranes. Evaluation of SPI009-resistant mutants, which only could be generated under severe selection pressure, suggested a possible role for the MexCD-OprJ efflux pump. Overall, our results demonstrate the extensive membrane-damaging activity of SPI009 and confirm its clinical potential in the development of novel anti-persister therapies.
Collapse
Affiliation(s)
- Valerie Defraine
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Veerle Liebens
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Evelien Loos
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Toon Swings
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Bram Weytjens
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Carolina Fierro
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Kathleen Marchal
- Data Integration and Biological Networks, Ghent University, Ghent, Belgium
| | - Liam Sharkey
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Alex J O'Neill
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | | | | | - Patrick Chaltin
- CISTIM Leuven vzw, Leuven, Belgium.,Centre for Drug Design and Discovery, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Smart Electronics Unit, Department of Life Sciences and Imaging, imec, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| |
Collapse
|
15
|
Defraine V, Verstraete L, Van Bambeke F, Anantharajah A, Townsend EM, Ramage G, Corbau R, Marchand A, Chaltin P, Fauvart M, Michiels J. Antibacterial Activity of 1-[(2,4-Dichlorophenethyl)amino]-3-Phenoxypropan-2-ol against Antibiotic-Resistant Strains of Diverse Bacterial Pathogens, Biofilms and in Pre-clinical Infection Models. Front Microbiol 2017; 8:2585. [PMID: 29312259 PMCID: PMC5744096 DOI: 10.3389/fmicb.2017.02585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/12/2017] [Indexed: 01/13/2023] Open
Abstract
We recently described the novel anti-persister compound 1-[(2,4-dichlorophenethyl)amino]-3-phenoxypropan-2-ol (SPI009), capable of directly killing persister cells of the Gram-negative pathogen Pseudomonas aeruginosa. This compound also shows antibacterial effects against non-persister cells, suggesting that SPI009 could be used as an adjuvant for antibacterial combination therapy. Here, we demonstrate the broad-spectrum activity of SPI009, combined with different classes of antibiotics, against the clinically relevant ESKAPE pathogens Enterobacter aerogenes, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, P. aeruginosa, Enterococcus faecium and Burkholderia cenocepacia and Escherichia coli. Importantly, SPI009 re-enabled killing of antibiotic-resistant strains and effectively lowered the required antibiotic concentrations. The clinical potential was further confirmed in biofilm models of P. aeruginosa and S. aureus where SPI009 exhibited effective biofilm inhibition and eradication. Caenorhabditis elegans infected with P. aeruginosa also showed a significant improvement in survival when SPI009 was added to conventional antibiotic treatment. Overall, we demonstrate that SPI009, initially discovered as an anti-persister molecule in P. aeruginosa, possesses broad-spectrum activity and is highly suitable for the development of antibacterial combination therapies in the fight against chronic infections.
Collapse
Affiliation(s)
- Valerie Defraine
- Centre of Microbial and Plant Genetics, University of Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Laure Verstraete
- Centre of Microbial and Plant Genetics, University of Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Françoise Van Bambeke
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Ahalieyah Anantharajah
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Eleanor M. Townsend
- Oral Science Research Group, Glasgow Dental School, University of Glasgow, Glasgow, United Kingdom
- Institute of Healthcare Policy and Practice, University of West of Scotland, Paisley, United Kingdom
| | - Gordon Ramage
- Oral Science Research Group, Glasgow Dental School, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Patrick Chaltin
- CISTIM Leuven vzw, Leuven, Belgium
- Centre for Drug Design and Discovery, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, University of Leuven, Leuven, Belgium
- Department of Life Sciences and Imaging, Smart Electronics Unit, imec, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, University of Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| |
Collapse
|