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Kim JS, Wood TK. Persistent Persister Misperceptions. Front Microbiol 2016; 7:2134. [PMID: 28082974 PMCID: PMC5187198 DOI: 10.3389/fmicb.2016.02134] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 12/19/2016] [Indexed: 01/31/2023] Open
Abstract
Persister cells survive antibiotic treatment due to their lack of metabolism, rather than through genetic change, as shown via four seminal experiments conducted by the discoverers of the phenotype (Hobby et al., 1942; Bigger, 1944). Unfortunately, over seven decades of persister cell research, the literature has been populated by misperceptions that do not withstand scrutiny. This opinion piece examines some of those misunderstandings in the literature with the hope that by shining some light on these inaccuracies, the field may be advanced and subsequent manuscripts may be reviewed more critically.
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Affiliation(s)
- Jun-Seob Kim
- Department of Chemical Engineering, Pennsylvania State University, University Park PA, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park PA, USA
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202
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Lee JH, Kim YG, Gwon G, Wood TK, Lee J. Halogenated indoles eradicate bacterial persister cells and biofilms. AMB Express 2016; 6:123. [PMID: 27921270 PMCID: PMC5138170 DOI: 10.1186/s13568-016-0297-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 11/27/2016] [Indexed: 02/09/2023] Open
Abstract
The emergence of antibiotic resistance has necessitated new therapeutic approaches to combat recalcitrant bacterial infections. Persister cells, often found in biofilms, are metabolically dormant, and thus, are highly tolerant to all traditional antibiotics and represent a major drug resistance mechanism. In the present study, 36 diverse indole derivatives were investigated with the aim of identifying novel compounds that inhibit persisters and biofilm formation by Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus. 5-Iodoindole and other halogenated indoles, 4-fluoroindole, 7-chloroindole, and 7-bromoindole, eradicated persister formation by E. coli and S. aureus, and 5-iodoindole most potently inhibited biofilm formation by the two bacteria. Unlike other antibiotics, 5-iodoindole did not induce persister cell formation, and 5-iodoindole inhibited the production of the immune-evasive carotenoid staphyloxanthin in S. aureus; hence, 5-iodoindole diminished the production of virulence factors in this strain. These results demonstrate halogenated indoles are potentially useful for controlling bacterial antibiotic resistance.
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Xu T, Han J, Zhang J, Chen J, Wu N, Zhang W, Zhang Y. Absence of Protoheme IX Farnesyltransferase CtaB Causes Virulence Attenuation but Enhances Pigment Production and Persister Survival in MRSA. Front Microbiol 2016; 7:1625. [PMID: 27822202 PMCID: PMC5076432 DOI: 10.3389/fmicb.2016.01625] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/29/2016] [Indexed: 02/05/2023] Open
Abstract
The membrane protein CtaB in S. aureus is a protoheme IX farnesyltransferase involved in the synthesis of the heme containing terminal oxidases of bacterial respiratory chain. In this study, to assess the role of CtaB in S. aureus virulence, pigment production, and persister formation, we constructed a ctaB mutant in the methicillin-resistant Staphylococcus aureus (MRSA) strain USA500. We found that deletion of ctaB attenuated growth and virulence in mice but enhanced pigment production and formation of quinolone tolerant persister cells in stationary phase. RNA-seq analysis showed that deletion of ctaB caused decreased transcription of several virulence genes including RNAIII which is consistent with its virulence attenuation. In addition, transcription of 20 ribosomal genes and 24 genes involved in amino acid biosynthesis was significantly down-regulated in the ctaB knockout mutant compared with the parent strain. These findings suggest the importance of heme biosynthesis in virulence and persister formation of S. aureus.
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Affiliation(s)
- Tao Xu
- Key Laboratory of Medical Molecular Virology, Huashan Hospital, Shanghai Medical College of Fudan UniversityShanghai, China
| | - Jian Han
- Department of Pathogenic Biology, School of Basic Medical Sciences, Lanzhou UniversityLanzhou, China
| | - Jia Zhang
- Key Laboratory of Medical Molecular Virology, Huashan Hospital, Shanghai Medical College of Fudan UniversityShanghai, China
| | - Jiazhen Chen
- Key Laboratory of Medical Molecular Virology, Huashan Hospital, Shanghai Medical College of Fudan UniversityShanghai, China
| | - Nan Wu
- Key Laboratory of Medical Molecular Virology, Huashan Hospital, Shanghai Medical College of Fudan UniversityShanghai, China
| | - Wenhong Zhang
- Key Laboratory of Medical Molecular Virology, Huashan Hospital, Shanghai Medical College of Fudan UniversityShanghai, China
| | - Ying Zhang
- Key Laboratory of Medical Molecular Virology, Huashan Hospital, Shanghai Medical College of Fudan UniversityShanghai, China
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins UniversityBaltimore, MD, USA
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204
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Transposon-Sequencing Analysis Unveils Novel Genes Involved in the Generation of Persister Cells in Uropathogenic Escherichia coli. Antimicrob Agents Chemother 2016; 60:6907-6910. [PMID: 27550350 DOI: 10.1128/aac.01617-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/17/2016] [Indexed: 01/08/2023] Open
Abstract
Persister cells are highly tolerant to different antibiotics and are associated with relapsing infections. In order to understand this phenomenon further, we exposed a transposon library to a lethal concentration of ampicillin, and mutants that survived were identified by transposon sequencing (Tn-Seq). We determined that mutations related to carbon metabolism, cell envelope (cell wall generation and membrane proteins), and stress response have a role in persister cell generation.
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205
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Michiels JE, Van den Bergh B, Verstraeten N, Michiels J. Molecular mechanisms and clinical implications of bacterial persistence. Drug Resist Updat 2016; 29:76-89. [PMID: 27912845 DOI: 10.1016/j.drup.2016.10.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Any bacterial population harbors a small number of phenotypic variants that survive exposure to high concentrations of antibiotic. Importantly, these so-called 'persister cells' compromise successful antibiotic therapy of bacterial infections and are thought to contribute to the development of antibiotic resistance. Intriguingly, drug-tolerant persisters have also been identified as a factor underlying failure of chemotherapy in tumor cell populations. Recent studies have begun to unravel the complex molecular mechanisms underlying persister formation and revolve around stress responses and toxin-antitoxin modules. Additionally, in vitro evolution experiments are revealing insights into the evolutionary and adaptive aspects of this phenotype. Furthermore, ever-improving experimental techniques are stimulating efforts to investigate persisters in their natural, infection-associated, in vivo environment. This review summarizes recent insights into the molecular mechanisms of persister formation, explains how persisters complicate antibiotic treatment of infections, and outlines emerging strategies to combat these tolerant cells.
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Affiliation(s)
| | | | | | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.
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Zhao Y, McAnulty MJ, Wood TK. Toxin YafQ Reduces Escherichia coli Growth at Low Temperatures. PLoS One 2016; 11:e0161577. [PMID: 27557125 PMCID: PMC4996492 DOI: 10.1371/journal.pone.0161577] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/08/2016] [Indexed: 11/19/2022] Open
Abstract
Toxin/antitoxin (TA) systems reduce metabolism under stress; for example, toxin YafQ of the YafQ/DinJ Escherichia coli TA system reduces growth by cleaving transcripts with in-frame 5'-AAA-G/A-3' sites, and antitoxin DinJ is a global regulator that represses its locus as well as controls levels of the stationary sigma factor RpoS. Here we investigated the influence on cell growth at various temperatures and found that deletion of the antitoxin gene, dinJ, resulted in both reduced metabolism and slower growth at 18°C but not at 37°C. The reduction in growth could be complemented by producing DinJ from a plasmid. Using a transposon screen to reverse the effect of the absence of DinJ, two mutations were found that inactivated the toxin YafQ; hence, the toxin caused the slower growth only at low temperatures rather than DinJ acting as a global regulator. Corroborating this result, a clean deletion of yafQ in the ΔdinJ ΔKmR strain restored both metabolism and growth at 18°C. In addition, production of YafQ was more toxic at 18°C compared to 37°C. Furthermore, by overproducing all the E. coli proteins, the global transcription repressor Mlc was found that counteracts YafQ toxicity only at 18°C. Therefore, YafQ is more effective at reducing metabolism at low temperatures, and Mlc is its putative target.
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Affiliation(s)
- Yueju Zhao
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
- Key Laboratory of Agro-products Processing, Ministry of Agriculture, Beijing, 100193, P. R. China
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802-4400, United States of America
| | - Michael J. McAnulty
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802-4400, United States of America
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802-4400, United States of America
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802-4400, United States of America
- * E-mail:
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207
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Toxin-Antitoxin Systems in Clinical Pathogens. Toxins (Basel) 2016; 8:toxins8070227. [PMID: 27447671 PMCID: PMC4963858 DOI: 10.3390/toxins8070227] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/07/2016] [Indexed: 12/17/2022] Open
Abstract
Toxin-antitoxin (TA) systems are prevalent in bacteria and archaea. Although not essential for normal cell growth, TA systems are implicated in multiple cellular functions associated with survival under stress conditions. Clinical strains of bacteria are currently causing major human health problems as a result of their multidrug resistance, persistence and strong pathogenicity. Here, we present a review of the TA systems described to date and their biological role in human pathogens belonging to the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) and others of clinical relevance (Escherichia coli, Burkholderia spp., Streptococcus spp. and Mycobacterium tuberculosis). Better understanding of the mechanisms of action of TA systems will enable the development of new lines of treatment for infections caused by the above-mentioned pathogens.
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208
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Toxin-Antitoxin Modules Are Pliable Switches Activated by Multiple Protease Pathways. Toxins (Basel) 2016; 8:toxins8070214. [PMID: 27409636 PMCID: PMC4963847 DOI: 10.3390/toxins8070214] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 02/06/2023] Open
Abstract
Toxin-antitoxin (TA) modules are bacterial regulatory switches that facilitate conflicting outcomes for cells by promoting a pro-survival phenotypic adaptation and/or by directly mediating cell death, all through the toxin activity upon degradation of antitoxin. Intensive study has revealed specific details of TA module functions, but significant gaps remain about the molecular details of activation via antitoxin degradation used by different bacteria and in different environments. This review summarizes the current state of knowledge about the interaction of antitoxins with cellular proteases Lon and ClpP to mediate TA module activation. An understanding of these processes can answer long-standing questions regarding stochastic versus specific activation of TA modules and provide insight into the potential for manipulation of TA modules to alter bacterial growth.
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209
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Urish KL, DeMuth PW, Kwan BW, Craft DW, Ma D, Haider H, Tuan RS, Wood TK, Davis CM. Antibiotic-tolerant Staphylococcus aureus Biofilm Persists on Arthroplasty Materials. Clin Orthop Relat Res 2016; 474:1649-56. [PMID: 26831479 PMCID: PMC4887357 DOI: 10.1007/s11999-016-4720-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND The continued presence of biofilm may be one cause of the high risk of failure observed with irrigation and débridement with component retention in acute periprosthetic joint infection (PJI). There is a poor understanding of the role of biofilm antibiotic tolerance in PJI. QUESTIONS/PURPOSES (1) Do increasing doses of cefazolin result in decreased viable biofilm mass on arthroplasty materials? (2) Is cefazolin resistance phenotypic or genotypic? (3) Is biofilm viability a function of biofilm depth after treatment with cefazolin? (4) Is the toxin-antitoxin system, yoeB expression, associated with antibiotic stress? METHODS Methicillin-sensitive Staphylococcus aureus biofilm was cultured on total knee arthroplasty (TKA) materials and exposed to increasing doses of cefazolin (control, 0.5, 1.0, 10.0, 100.0 μg/mL). Quantitative confocal microscopy and quantitative culture were used to measure viable biofilm cell density. To determine if cefazolin resistance was phenotypic or genotypic, we measured minimum inhibitory concentration (MIC) after exposure to different cefazolin concentrations; changes in MIC would suggest genotypic features, whereas unchanged MIC would suggest phenotypic behavior. Finally, quantitative reverse transcription-polymerase chain reaction was used to quantify expression of yoeB levels between biofilm and planktonic bacteria after exposure to 1 μg/mL cefazolin for 3 hours. RESULTS Although live biofilm mass was reduced by exposure to cefazolin when compared with biofilm mass in controls (39.2 × 10(3) ± 26.4 × 10(3) pixels), where the level after 0.5 µg/mL exposure also showed reduced mass (20.3 × 10(3) ± 11.9 × 10(3) pixels), no further reduction was seen after higher doses (mass at 1.0 µg/mL: 5.0 × 10(3) pixels ± 1.1 × 10(3) pixels; at 10.0 µg/mL: 6.4 × 10(3) ± 9.6 × 10(3) pixels; at 100.0 µg/mL: 6.4 × 10(3) ± 3.9 × 10(3)). At the highest concentration tested (100 µg/mL), residual viable biofilm was present on all three materials, and there were no differences in percent biofilm survival among cobalt-chromium (18.5% ± 15.1%), polymethylmethacrylate (22.8% ± 20.2%), and polyethylene (14.7% ± 10.4%). We found that tolerance was a phenotypic phenomenon, because increasing cefazolin exposure did not result in changes in MIC as compared with controls (MIC in controls: 0.13 ± 0.02; at 0.5 µg/mL: 0.13 ± 0.001, p = 0.96; at 1.0 µg/m: 0.14 ± 0.04, p = 0.95; at 10.0 µg/m: 0.11 ± 0.016, p = 0.47; at 100.0 µg/m: 0.94 ± 0.047, p = 0.47). Expression of yoeB after 1 µg/mL cefazolin for 3 hours in biofilm cells was greater in biofilm but not in planktonic cells (biofilm: 62.3-fold change, planktonic cells: -78.8-fold change, p < 0.001). CONCLUSIONS Antibiotics are inadequate at complete removal of the biofilm from the surface of TKA materials. Results suggest that bacterial persisters are responsible for this phenotypic behavior allowing biofilm high tolerance to antibiotics. CLINICAL RELEVANCE Antibiotic-tolerant biofilm suggests a mechanism behind the poor results in irrigation and débridement for acute TKA PJI.
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Affiliation(s)
- Kenneth L Urish
- The Magee Bone & Joint Center, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, 15212, USA.
| | - Peter W DeMuth
- Department of Orthopaedics and Rehabilitation, Penn State Hershey Medical Center, Hershey, PA, USA
| | - Brian W Kwan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - David W Craft
- Department of Pathology, Penn State Hershey Medical Center and College of Medicine, Hershey, PA, USA
| | - Dongzhu Ma
- Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Hani Haider
- Orthopaedics Biomechanics & Advanced Surgical Technologies Laboratory, Department of Orthopaedic Surgery and Rehabilitation, University of Nebraska Medical Center, Omaha, NE, USA
| | - Rocky S Tuan
- Center for Cellular and Molecular Engineering, Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Thomas K Wood
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Charles M Davis
- Department of Orthopaedics and Rehabilitation, Penn State Hershey Medical Center, Hershey, PA, USA
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210
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Springer MT, Singh VK, Cheung AL, Donegan NP, Chamberlain NR. Effect of clpP and clpC deletion on persister cell number in Staphylococcus aureus. J Med Microbiol 2016; 65:848-857. [PMID: 27375177 DOI: 10.1099/jmm.0.000304] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Staphylococcus aureus is responsible for a wide variety of infections that include superficial skin and soft tissue infections, septicaemia, central nervous system infections, endocarditis, osteomyelitis and pneumonia. Others have demonstrated the importance of toxin-antitoxin (TA) modules in the formation of persisters and the role of the Clp proteolytic system in the regulation of these TA modules. This study was conducted to determine the effect of clpP and clpC deletion on S. aureus persister cell numbers following antibiotic treatment. Deletion of clpP resulted in a significant decrease in persister cells following treatment with oxacillin and erythromycin but not with levofloxacin and daptomycin. Deletion of clpC resulted in a decrease in persister cells following treatment with oxacillin. These differences were dependent on the antibiotic class and the CFU ml-1 in which the cells were treated. Persister revival assays for all the bacterial strains in these studies demonstrated a significant delay in resumption of growth characteristic of persister cells, indicating that the surviving organisms in this study were not likely due to spontaneous antibiotic resistance. Based on our results, ClpP and possibly ClpC play a role in persister cell formation or maintenance, and this effect is dependent on antibiotic class and the CFU ml-1 or the growth phase of the cells.
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Affiliation(s)
- Matthew T Springer
- Department of Microbiology/Immunology, A.T. Still University of Health Sciences, Kirksville College of Osteopathic Medicine, Kirksville, MO, USA
| | - Vineet K Singh
- Department of Microbiology/Immunology, A.T. Still University of Health Sciences, Kirksville College of Osteopathic Medicine, Kirksville, MO, USA
| | - Ambrose L Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Niles P Donegan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Neal R Chamberlain
- Department of Microbiology/Immunology, A.T. Still University of Health Sciences, Kirksville College of Osteopathic Medicine, Kirksville, MO, USA
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211
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Weiser J, Henke HA, Hector N, Both A, Christner M, Büttner H, Kaplan JB, Rohde H. Sub-inhibitory tigecycline concentrations induce extracellular matrix binding protein Embp dependent Staphylococcus epidermidis biofilm formation and immune evasion. Int J Med Microbiol 2016; 306:471-8. [PMID: 27292911 DOI: 10.1016/j.ijmm.2016.05.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/19/2016] [Accepted: 05/24/2016] [Indexed: 12/31/2022] Open
Abstract
Biofilm-associated Staphylococcus epidermidis implant infections are notoriously reluctant to antibiotic treatment. Here we studied the effect of sub-inhibitory concentrations of penicillin, oxacillin, vancomycin, daptomycin, linezolid and tigecycline on S. epidermidis 1585 biofilm formation, expression of extracellular matrix binding protein (Embp) and potential implications for S. epidermidis - macrophage interactions. Penicillin, vancomycin, daptomycin, and linezolid had no biofilm augmenting effect at any of the concentrations tested. In contrast, at sub-inhibitory concentrations tigecycline and oxacillin exhibited significant biofilm inducing activity. In S. epidermidis 1585, SarA is a negative regulator of giant 1 MDa Embp, and down regulation of sarA induces Embp-dependent assembly of a multi-layered biofilm architecture. Dot blot immune assays, confocal laser scanning microscopy, and qPCR showed that under biofilm inducing conditions, tigecycline augmented embp expression compared to the control grown without antibiotics. Conversely, expression of regulator sarA was suppressed, suggesting that tigecycline exerts its effects on embp expression through SarA. Tigecycline failed to induce biofilm formation in embp transposon mutant 1585-M135, proving that under these conditions Embp up-regulation is necessary for biofilm accumulation. As a functional consequence, tigecycline induced biofilm formation significantly impaired the up-take of S. epidermidis by mouse macrophage-like cell line J774A.1. Our data provide novel evidence for the molecular basis of antibiotic induced biofilm formation, a phenotype associated with inherently increased antimicrobial tolerance. While this could explain failure of antimicrobial therapies, persistence of S. epidermidis infections in the presence of sub-inhibitory antimicrobials is additionally propelled by biofilm-related impairment of macrophage-mediated pathogen eradication.
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Affiliation(s)
- Julian Weiser
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246 Hamburg, Germany
| | - Hanae A Henke
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246 Hamburg, Germany
| | - Nina Hector
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246 Hamburg, Germany
| | - Anna Both
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246 Hamburg, Germany
| | - Martin Christner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246 Hamburg, Germany
| | - Henning Büttner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246 Hamburg, Germany
| | - Jeffery B Kaplan
- Department of Biology, American University, Washington, DC 20016, USA
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246 Hamburg, Germany.
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212
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Development of Persister-FACSeq: a method to massively parallelize quantification of persister physiology and its heterogeneity. Sci Rep 2016; 6:25100. [PMID: 27142337 PMCID: PMC4855238 DOI: 10.1038/srep25100] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/07/2016] [Indexed: 01/24/2023] Open
Abstract
Bacterial persisters are thought to underlie the relapse of chronic infections. Knowledge of persister physiology would illuminate avenues for therapeutic intervention; however, such knowledge has remained elusive because persisters have yet to be segregated from other cell types to sufficient purity. This technical hurdle has stymied progress toward understanding persistence. Here we developed Persister-FACSeq, which is a method that uses fluorescence-activated cell sorting, antibiotic tolerance assays, and next generation sequencing to interrogate persister physiology and its heterogeneity. As a proof-of-concept, we used Persister-FACSeq on a library of reporters to study gene expression distributions in non-growing Escherichia coli, and found that persistence to ofloxacin is inversely correlated with the capacity of non-growing cells to synthesize protein. Since Persister-FACSeq can be applied to study persistence to any antibiotic in any environment for any bacteria that can harbor a fluorescent reporter, we anticipate that it will yield unprecedented knowledge of this detrimental phenotype.
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213
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Miquel S, Lagrafeuille R, Souweine B, Forestier C. Anti-biofilm Activity as a Health Issue. Front Microbiol 2016; 7:592. [PMID: 27199924 PMCID: PMC4845594 DOI: 10.3389/fmicb.2016.00592] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/11/2016] [Indexed: 12/13/2022] Open
Abstract
The formation and persistence of surface-attached microbial communities, known as biofilms, are responsible for 75% of human microbial infections (National Institutes of Health). Biofilm lifestyle confers several advantages to the pathogens, notably during the colonization process of medical devices and/or patients’ organs. In addition, sessile bacteria have a high tolerance to exogenous stress including anti-infectious agents. Biofilms are highly competitive communities and some microorganisms exhibit anti-biofilm capacities such as bacterial growth inhibition, exclusion or competition, which enable them to acquire advantages and become dominant. The deciphering and control of anti-biofilm properties represent future challenges in human infection control. The aim of this review is to compare and discuss the mechanisms of natural bacterial anti-biofilm strategies/mechanisms recently identified in pathogenic, commensal and probiotic bacteria and the main synthetic strategies used in clinical practice, particularly for catheter-related infections.
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Affiliation(s)
- Sylvie Miquel
- Laboratoire Microorganismes : Génome et Environnement - UMR, CNRS 6023, Université Clermont Auvergne Clermont-Ferrand, France
| | - Rosyne Lagrafeuille
- Laboratoire Microorganismes : Génome et Environnement - UMR, CNRS 6023, Université Clermont Auvergne Clermont-Ferrand, France
| | - Bertrand Souweine
- Laboratoire Microorganismes : Génome et Environnement - UMR, CNRS 6023, Université Clermont AuvergneClermont-Ferrand, France; Service de Réanimation Médicale Polyvalente, CHU de Clermont-Ferrand, Clermont-FerrandFrance
| | - Christiane Forestier
- Laboratoire Microorganismes : Génome et Environnement - UMR, CNRS 6023, Université Clermont Auvergne Clermont-Ferrand, France
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214
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Conlon BP, Rowe SE, Gandt AB, Nuxoll AS, Donegan NP, Zalis EA, Clair G, Adkins JN, Cheung AL, Lewis K. Persister formation in Staphylococcus aureus is associated with ATP depletion. Nat Microbiol 2016; 1:16051. [PMID: 27398229 PMCID: PMC4932909 DOI: 10.1038/nmicrobiol.2016.51] [Citation(s) in RCA: 414] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 03/15/2016] [Indexed: 01/06/2023]
Abstract
Persisters are dormant phenotypic variants of bacterial cells that are tolerant to killing by antibiotics1. Persisters are associated with chronic infections and antibiotic treatment failure1-3. In Escherichia coli, toxin/antitoxin (TA) modules have been linked to persister formation4-6. The mechanism of persister formation in Gram-positive bacteria is unknown. Staphylococcus aureus is a major human pathogen, responsible for a variety of chronic and relapsing infections such as osteomyelitis, endocarditis and infections of implanted devices. Deleting TA modules in S. aureus did not affect the level of persisters. Here we show that S. aureus persisters are produced due to a stochastic entrance into stationary phase accompanied by a drop in intracellular ATP. Cells expressing stationary state markers are present throughout the growth phase, increasing in frequency with cell density. Cell sorting revealed that expression of stationary markers is associated with a 100-1000 fold increase in the likelihood of survival to antibiotic challenge. The ATP level of the cell is predictive of bactericidal antibiotic efficacy and explains bacterial tolerance to antibiotics.
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Affiliation(s)
- Brian P. Conlon
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Massachusetts 02115
| | - Sarah E. Rowe
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Massachusetts 02115
- Synlogic, Cambridge, Massachusetts 02139
| | - Autumn Brown Gandt
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Massachusetts 02115
| | - Austin S. Nuxoll
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Massachusetts 02115
| | - Niles P. Donegan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, 03755
| | - Eliza A. Zalis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Massachusetts 02115
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Joshua N. Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Ambrose L. Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, 03755
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Massachusetts 02115
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215
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Wood TL, Wood TK. The HigB/HigA toxin/antitoxin system of Pseudomonas aeruginosa influences the virulence factors pyochelin, pyocyanin, and biofilm formation. Microbiologyopen 2016; 5:499-511. [PMID: 26987441 PMCID: PMC4906001 DOI: 10.1002/mbo3.346] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/27/2016] [Accepted: 02/04/2016] [Indexed: 01/30/2023] Open
Abstract
Toxin/antitoxin (TA) systems are prevalent in most bacterial and archaeal genomes, and one of the emerging physiological roles of TA systems is to help regulate pathogenicity. Although TA systems have been studied in several model organisms, few studies have investigated the role of TA systems in pseudomonads. Here, we demonstrate that the previously uncharacterized proteins HigB (unannotated) and HigA (PA4674) of Pseudomonas aeruginosa PA14 form a type II TA system in which antitoxin HigA masks the RNase activity of toxin HigB through direct binding. Furthermore, toxin HigB reduces production of the virulence factors pyochelin, pyocyanin, swarming, and biofilm formation; hence, this system affects the pathogencity of this strain in a manner that has not been demonstrated previously for TA systems.
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Affiliation(s)
- Thammajun L Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, 16802
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802
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216
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Chowdhury N, Wood TL, Martínez-Vázquez M, García-Contreras R, Wood TK. DNA-crosslinker cisplatin eradicates bacterial persister cells. Biotechnol Bioeng 2016; 113:1984-92. [PMID: 26914280 DOI: 10.1002/bit.25963] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/11/2016] [Accepted: 02/15/2016] [Indexed: 11/05/2022]
Abstract
For all bacteria, nearly every antimicrobial fails since a subpopulation of the bacteria enter a dormant state known as persistence, in which the antimicrobials are rendered ineffective due to the lack of metabolism. This tolerance to antibiotics makes microbial infections the leading cause of death worldwide and makes treating chronic infections, including those of wounds problematic. Here, we show that the FDA-approved anti-cancer drug cisplatin [cis-diamminodichloroplatinum(II)], which mainly forms intra-strand DNA crosslinks, eradicates Escherichia coli K-12 persister cells through a growth-independent mechanism. Additionally, cisplatin is more effective at killing Pseudomonas aeruginosa persister cells than mitomycin C, which forms inter-strand DNA crosslinks, and cisplatin eradicates the persister cells of several pathogens including enterohemorrhagic E. coli, Staphylococcus aureus, and P. aeruginosa. Cisplatin was also highly effective against clinical isolates of S. aureus and P. aeruginosa. Therefore, cisplatin has broad spectrum activity against persister cells. Biotechnol. Bioeng. 2016;113: 1984-1992. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nityananda Chowdhury
- Department of Chemical Engineering, Pennsylvania State University, University Park, 16802-4400, Pennsylvania
| | - Thammajun L Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, 16802-4400, Pennsylvania
| | - Mariano Martínez-Vázquez
- Laboratorio de Productos Naturales, Instituto de Química, Universidad Nacional Autónoma de México, México
| | - Rodolfo García-Contreras
- Faculty of Medicine, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de México, México
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, 16802-4400, Pennsylvania. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania.
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217
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Prax M, Mechler L, Weidenmaier C, Bertram R. Glucose Augments Killing Efficiency of Daptomycin Challenged Staphylococcus aureus Persisters. PLoS One 2016; 11:e0150907. [PMID: 26960193 PMCID: PMC4784881 DOI: 10.1371/journal.pone.0150907] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 02/21/2016] [Indexed: 02/05/2023] Open
Abstract
Treatment of Staphylococcus aureus in stationary growth phase with high doses of the antibiotic daptomycin (DAP) eradicates the vast majority of the culture and leaves persister cells behind. Despite resting in a drug-tolerant and dormant state, persister cells exhibit metabolic activity which might be exploited for their elimination. We here report that the addition of glucose to S. aureus persisters treated with DAP increased killing by up to five-fold within one hour. This glucose-DAP effect also occurred with strains less sensitive to the drug. The underlying mechanism is independent of the proton motive force and was not observed with non-metabolizable 2-deoxy-glucose. Our results are consistent with two hypotheses on the glucose-DAP interplay. The first is based upon glucose-induced carbohydrate transport proteins that may influence DAP and the second suggests that glucose may trigger the release or activity of cell-lytic proteins to augment DAP’s mode of action.
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Affiliation(s)
- Marcel Prax
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Lehrbereich Mikrobielle Genetik, Auf der Morgenstelle 28, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
- Paul-Ehrlich-Institut, Mikrobiologische Sicherheit, Paul-Ehrlich-Str. 51–59, 63225 Langen, Germany
| | - Lukas Mechler
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Lehrbereich Mikrobielle Genetik, Auf der Morgenstelle 28, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Christopher Weidenmaier
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Medizinische Mikrobiologie und Hygiene, Elfriede-Aulhorn-Str. 6, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Ralph Bertram
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Lehrbereich Mikrobielle Genetik, Auf der Morgenstelle 28, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
- Klinikum Nürnberg Medical School GmbH, Research Department, Paracelsus Medical University, Nuremberg, Germany
- * E-mail:
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218
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Chowdhury N, Kwan BW, McGibbon LC, Babitzke P, Wood TK. Toxin MqsR cleaves single-stranded mRNA with various 5' ends. Microbiologyopen 2016; 5:370-7. [PMID: 26846703 PMCID: PMC4905990 DOI: 10.1002/mbo3.335] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/29/2015] [Accepted: 12/11/2015] [Indexed: 11/06/2022] Open
Abstract
Toxin/antitoxin (TA) systems are the means by which bacterial cells become persistent; that is, those cells that are tolerant to multiple environmental stresses such as antibiotics by becoming metabolically dormant. These persister cells are responsible for recalcitrant infections. Once toxins are activated by the inactivation of antitoxins (e.g., stress-triggered Lon degradation of the antitoxin), many toxins reduce metabolism by inhibiting translation (e.g., cleaving mRNA, reducing ATP). The MqsR/MqsA TA system of Escherichia coli cleaves mRNA to help the cell withstand oxidative and bile acid stress. Here, we investigated the role of secondary structure and 5' mRNA processing on MqsR degradation of mRNA and found that MqsR cleaves only single-stranded RNA at 5'-GCU sites and that MqsR is equally active against RNA with 5'-triphosphate, 5'-monophosphate, and 5'-hydroxyl groups.
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Affiliation(s)
- Nityananda Chowdhury
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802-4400
| | - Brian W Kwan
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802-4400
| | - Louise C McGibbon
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802-4400.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802-4400
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802-4400.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802-4400
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802-4400.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802-4400.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802-4400
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219
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Persistence Increases in the Absence of the Alarmone Guanosine Tetraphosphate by Reducing Cell Growth. Sci Rep 2016; 6:20519. [PMID: 26837570 PMCID: PMC4738310 DOI: 10.1038/srep20519] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/07/2016] [Indexed: 11/09/2022] Open
Abstract
Most bacterial cells are stressed, and as a result, some become tolerant to antibiotics by entering a dormant state known as persistence. The key intracellular metabolite that has been linked to this persister state is guanosine tetraphosphate (ppGpp), the alarmone that was first linked to nutrient stress. In Escherichia coli, ppGpp redirects protein production during nutrient stress by interacting with RNA polymerase directly and by inhibiting several proteins. Consistently, increased levels of ppGpp lead to increased persistence; but, the mechanism by which elevated ppGpp translates into persistence has not been determined. Hence, we explored persistence in the absence of ppGpp so that the underlying mechanism of persister cell formation could be explored. We found that persister cells still form, although at lower levels, in the absence of ppGpp. Additionally, the toxin/antitoxin systems that we investigated (MqsR, MazF, GhoT, and YafQ) remain able to increase persistence dramatically in the absence of ppGpp. By overproducing each E. coli protein from the 4287 plasmid vectors of the ASKA library and selecting for increased persistence in the absence of ppGpp (via a relA spoT mutant), we identified five new proteins, YihS, PntA, YqjE, FocA, and Zur, that increase persistence simply by reducing cell growth.
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220
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Kayigire XA, Friedrich SO, van der Merwe L, Donald PR, Diacon AH. Simultaneous staining of sputum smears for acid-fast and lipid-containing Myobacterium tuberculosis can enhance the clinical evaluation of antituberculosis treatments. Tuberculosis (Edinb) 2015; 95:770-779. [DOI: 10.1016/j.tube.2015.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/24/2015] [Accepted: 08/02/2015] [Indexed: 10/23/2022]
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221
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Control of Biofilms with the Fatty Acid Signaling Molecule cis-2-Decenoic Acid. Pharmaceuticals (Basel) 2015; 8:816-35. [PMID: 26610524 PMCID: PMC4695811 DOI: 10.3390/ph8040816] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/11/2015] [Accepted: 11/18/2015] [Indexed: 12/26/2022] Open
Abstract
Biofilms are complex communities of microorganisms in organized structures attached to surfaces. Importantly, biofilms are a major cause of bacterial infections in humans, and remain one of the most significant challenges to modern medical practice. Unfortunately, conventional therapies have shown to be inadequate in the treatment of most chronic biofilm infections based on the extraordinary innate tolerance of biofilms to antibiotics. Antagonists of quorum sensing signaling molecules have been used as means to control biofilms. QS and other cell-cell communication molecules are able to revert biofilm tolerance, prevent biofilm formation and disrupt fully developed biofilms, albeit with restricted effectiveness. Recently however, it has been demonstrated that Pseudomonas aeruginosa produces a small messenger molecule cis-2-decenoic acid (cis-DA) that shows significant promise as an effective adjunctive to antimicrobial treatment of biofilms. This molecule is responsible for induction of the native biofilm dispersion response in a range of Gram-negative and Gram-positive bacteria and in yeast, and has been shown to reverse persistence, increase microbial metabolic activity and significantly enhance the cidal effects of conventional antimicrobial agents. In this manuscript, the use of cis-2-decenoic acid as a novel agent for biofilm control is discussed. Stimulating the biofilm dispersion response as a novel antimicrobial strategy holds significant promise for enhanced treatment of infections and in the prevention of biofilm formation.
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222
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Mulyukin AL, Kozlova AN, Sorokin VV, Suzina NE, Cherdyntseva TA, Kotova IB, Gaponov AM, Tutel’yan AV, El’-Registan GI. Surviving forms in antibiotic-treated Pseudomonas aeruginosa. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715060077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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223
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Demkina EV, Loiko NG, Mulyukin AL, Smirnova TA, Gaponov AM, Pisarev VM, Tutel’yan AV, Nikolaev YA, El’-Registan GI. Effect of inherent immunity factors on development of antibiotic tolerance and survival of bacterial populations under antibiotic attack. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715060028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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224
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Mok WWK, Park JO, Rabinowitz JD, Brynildsen MP. RNA Futile Cycling in Model Persisters Derived from MazF Accumulation. mBio 2015; 6:e01588-15. [PMID: 26578677 PMCID: PMC4659464 DOI: 10.1128/mbio.01588-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 10/19/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Metabolism plays an important role in the persister phenotype, as evidenced by the number of strategies that perturb metabolism to sabotage this troublesome subpopulation. However, the absence of techniques to isolate high-purity populations of native persisters has precluded direct measurement of persister metabolism. To address this technical challenge, we studied Escherichia coli populations whose growth had been inhibited by the accumulation of the MazF toxin, which catalyzes RNA cleavage, as a model system for persistence. Using chromosomally integrated, orthogonally inducible promoters to express MazF and its antitoxin MazE, bacterial populations that were almost entirely tolerant to fluoroquinolone and β-lactam antibiotics were obtained upon MazF accumulation, and these were subjected to direct metabolic measurements. While MazF model persisters were nonreplicative, they maintained substantial oxygen and glucose consumption. Metabolomic analysis revealed accumulation of all four ribonucleotide monophosphates (NMPs). These results are consistent with a MazF-catalyzed RNA futile cycle, where the energy derived from catabolism is dissipated through continuous transcription and MazF-mediated RNA degradation. When transcription was inhibited, oxygen consumption and glucose uptake decreased, and nucleotide triphosphates (NTPs) and NTP/NMP ratios increased. Interestingly, the MazF-inhibited cells were sensitive to aminoglycosides, and this sensitivity was blocked by inhibition of transcription. Thus, in MazF model persisters, futile cycles of RNA synthesis and degradation result in both significant metabolic demands and aminoglycoside sensitivity. IMPORTANCE Metabolism plays a critical role in controlling each stage of bacterial persistence (shutdown, stasis, and reawakening). In this work, we generated an E. coli strain in which the MazE antitoxin and MazF toxin were artificially and independently inducible, and we used this strain to generate model persisters and study their metabolism. We found that even though growth of the model persisters was inhibited, they remained highly metabolically active. We further uncovered a futile cycle driven by continued transcription and MazF-mediated transcript degradation that dissipated the energy derived from carbon catabolism. Interestingly, the existence of this futile cycle acted as an Achilles' heel for MazF model persisters, rendering them vulnerable to killing by aminoglycosides.
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Affiliation(s)
- Wendy W K Mok
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
| | - Junyoung O Park
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA Department of Chemistry, Princeton University, Princeton, New Jersey, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
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225
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Sun J, Li Z, Chu H, Guo J, Jiang G, Qi Q. Candida albicans Amphotericin B-Tolerant Persister Formation is Closely Related to Surface Adhesion. Mycopathologia 2015; 181:41-9. [PMID: 26381156 DOI: 10.1007/s11046-015-9894-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 04/19/2015] [Indexed: 11/25/2022]
Abstract
Candida albicans persisters have so far been observed only in biofilm environment; the biofilm element(s) that trigger(s) persister formation are still unknown. In this study, we tried to further elucidate the possible relationship between C. albicans persisters and the early phases of biofilm formation, especially the surface adhesion phase. Three C. albicans strains were surveyed for the formation of persisters. We tested C. albicans persister formation dynamically at different time points during the process of adhesion and biofilm formation. The number of persister cells was determined based on an assessment of cell viability after amphotericin B treatment and colony-forming unit assay. None of the planktonic cultures contained persisters. Immediately following adhesion of C. albicans cells to the surface, persister cells emerged and the proportion of persisters reached a peak of 0.2-0.69 % in approximately 2-h biofilm. As the biofilm matured, the proportion of persisters decreased and was only 0.01-0.02 % by 24 h, while the number of persisters remained stable with no significant change. Persisters were not detected in the absence of an attachment surface which was pre-coated. Persisters were also absent in biofilms that were scraped to disrupt surface adhesion prior to amphotericin B treatment. These results indicate that C. albicans antifungal-tolerant persisters are produced mainly in surface adhesion phase and surface adhesion is required for the emergence and maintenance of C. albicans persisters.
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Affiliation(s)
- Jing Sun
- Shandong Provincial Hospital Affiliated to Shandong University, 324 Jingwu Road, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Oral Biomedicine, 44-1 Wenhuaxi Road, Jinan, Shandong, China
- School of Stomatology, Shandong University, 44-1 Wenhuaxi Road, Jinan, Shandong, China
| | - Zhigang Li
- Qianfoshan Hospital Shandong Province, 16766 Jingshi Road, Jinan, Shandong, China
| | - Haoyue Chu
- Shandong Provincial Key Laboratory of Oral Biomedicine, 44-1 Wenhuaxi Road, Jinan, Shandong, China
- School of Stomatology, Shandong University, 44-1 Wenhuaxi Road, Jinan, Shandong, China
| | - Jing Guo
- Shandong Provincial Key Laboratory of Oral Biomedicine, 44-1 Wenhuaxi Road, Jinan, Shandong, China
- School of Stomatology, Shandong University, 44-1 Wenhuaxi Road, Jinan, Shandong, China
| | - Guangshui Jiang
- Shandong Provincial Key Laboratory of Oral Biomedicine, 44-1 Wenhuaxi Road, Jinan, Shandong, China.
- School of Stomatology, Shandong University, 44-1 Wenhuaxi Road, Jinan, Shandong, China.
| | - Qingguo Qi
- Shandong Provincial Key Laboratory of Oral Biomedicine, 44-1 Wenhuaxi Road, Jinan, Shandong, China.
- School of Stomatology, Shandong University, 44-1 Wenhuaxi Road, Jinan, Shandong, China.
- Cheeloo Health Science Center, Shandong University, Jinan, 250012, Shandong, China.
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226
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Wood TK. Combatting bacterial persister cells. Biotechnol Bioeng 2015; 113:476-83. [DOI: 10.1002/bit.25721] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Thomas K. Wood
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPennsylvania
- Department Biochemistry, Molecular BiologyPennsylvania State UniversityUniversity ParkPennsylvania16802‐4400
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227
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Delicate Metabolic Control and Coordinated Stress Response Critically Determine Antifungal Tolerance of Candida albicans Biofilm Persisters. Antimicrob Agents Chemother 2015. [PMID: 26195524 DOI: 10.1128/aac.00543-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Candida infection has emerged as a critical health care burden worldwide, owing to the formation of robust biofilms against common antifungals. Recent evidence shows that multidrug-tolerant persisters critically account for biofilm recalcitrance, but their underlying biological mechanisms are poorly understood. Here, we first investigated the phenotypic characteristics of Candida biofilm persisters under consecutive harsh treatments of amphotericin B. The prolonged treatments effectively killed the majority of the cells of biofilms derived from representative strains of Candida albicans, Candida glabrata, and Candida tropicalis but failed to eradicate a small fraction of persisters. Next, we explored the tolerance mechanisms of the persisters through an investigation of the proteomic profiles of C. albicans biofilm persister fractions by liquid chromatography-tandem mass spectrometry. The C. albicans biofilm persisters displayed a specific proteomic signature, with an array of 205 differentially expressed proteins. The crucial enzymes involved in glycolysis, the tricarboxylic acid cycle, and protein synthesis were markedly downregulated, indicating that major metabolic activities are subdued in the persisters. It is noteworthy that certain metabolic pathways, such as the glyoxylate cycle, were able to be activated with significantly increased levels of isocitrate lyase and malate synthase. Moreover, a number of important proteins responsible for Candida growth, virulence, and the stress response were greatly upregulated. Interestingly, the persisters were tolerant to oxidative stress, despite highly induced intracellular superoxide. The current findings suggest that delicate metabolic control and a coordinated stress response may play a crucial role in mediating the survival and antifungal tolerance of Candida biofilm persisters.
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228
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Kwan BW, Chowdhury N, Wood TK. Combatting bacterial infections by killing persister cells with mitomycin C. Environ Microbiol 2015; 17:4406-14. [PMID: 25858802 DOI: 10.1111/1462-2920.12873] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 04/04/2015] [Indexed: 11/29/2022]
Abstract
Persister cells are a multi-drug tolerant subpopulation of bacteria that contribute to chronic and recalcitrant clinical infections such as cystic fibrosis and tuberculosis. Persisters are metabolically dormant, so they are highly tolerant to all traditional antibiotics which are mainly effective against actively growing cells. Here, we show that the FDA-approved anti-cancer drug mitomycin C (MMC) eradicates persister cells through a growth-independent mechanism. MMC is passively transported and bioreductively activated, leading to spontaneous cross-linking of DNA, which we verify in both active and dormant cells. We find MMC effectively eradicates cells grown in numerous different growth states (e.g. planktonic cultures and highly robust biofilm cultures) in both rich and minimal media. Additionally, MMC is a potent bactericide for a broad range of bacterial persisters, including commensal Escherichia coli K-12 as well as pathogenic species of E. coli, Staphylococcus aureus and Pseudomonas aeruginosa. We also demonstrate the efficacy of MMC in an animal model and a wound model, substantiating the clinical applicability of MMC against bacterial infections. Therefore, MMC is the first broad-spectrum compound capable of eliminating persister cells, meriting investigation as a new approach for the treatment of recalcitrant infections.
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Affiliation(s)
- Brian W Kwan
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Nityananda Chowdhury
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802-4400, USA
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229
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Islam S, Benedik MJ, Wood TK. Orphan toxin OrtT (YdcX) of Escherichia coli reduces growth during the stringent response. Toxins (Basel) 2015; 7:299-321. [PMID: 25643179 PMCID: PMC4344625 DOI: 10.3390/toxins7020299] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 01/20/2015] [Indexed: 01/23/2023] Open
Abstract
Toxin/antitoxin (TA) systems are nearly universal in prokaryotes; toxins are paired with antitoxins which inactivate them until the toxins are utilized. Here we explore whether toxins may function alone; i.e., whether a toxin which lacks a corresponding antitoxin (orphan toxin) is physiologically relevant. By focusing on a homologous protein of the membrane-damaging toxin GhoT of the Escherichia coli GhoT/GhoS type V TA system, we found that YdcX (renamed OrtT for orphan toxin related to tetrahydrofolate) is toxic but is not part of TA pair. OrtT is not inactivated by neighboring YdcY (which is demonstrated to be a protein), nor is it inactivated by antitoxin GhoS. Also, OrtT is not inactivated by small RNA upstream or downstream of ortT. Moreover, screening a genomic library did not identify an antitoxin partner for OrtT. OrtT is a protein and its toxicity stems from membrane damage as evidenced by transmission electron microscopy and cell lysis. Furthermore, OrtT reduces cell growth and metabolism in the presence of both antimicrobials trimethoprim and sulfamethoxazole; these antimicrobials induce the stringent response by inhibiting tetrahydrofolate synthesis. Therefore, we demonstrate that OrtT acts as an independent toxin to reduce growth during stress related to amino acid and DNA synthesis.
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Affiliation(s)
- Sabina Islam
- Department of Chemical Engineering, the Pennsylvania State University, University Park, PA 16802-4400, USA.
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA.
| | - Thomas K Wood
- Department of Chemical Engineering, the Pennsylvania State University, University Park, PA 16802-4400, USA.
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230
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Inhibition of nucleic acid biosynthesis makes little difference to formation of amphotericin B-tolerant persisters in Candida albicans biofilm. Antimicrob Agents Chemother 2014; 59:1627-33. [PMID: 25547355 DOI: 10.1128/aac.03765-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Candida albicans persisters constitute a small subpopulation of biofilm cells and play a major role in recalcitrant chronic candidiasis; however, the mechanism underlying persister formation remains unclear. Persisters are often described as dormant, multidrug-tolerant, nongrowing cells. Persister cells are difficult to isolate and study not only due to their low levels in C. albicans biofilms but also due to their transient, reversible phenotype. In this study, we tried to induce persister formation by inducing C. albicans cells into a dormant state. C. albicans cells were pretreated with 5-fluorocytosine (planktonic cells, 0.8 μg ml(-1); biofilm cells, 1 μg ml(-1)) for 6 h at 37°C, which inhibits nucleic acid and protein synthesis. Biofilms and planktonic cultures of eight C. albicans strains were surveyed for persisters after amphotericin B treatment (100 μg ml(-1) for 24 h) and CFU assay. None of the planktonic cultures, with or without 5-fluorocytosine pretreatment, contained persisters. Persister cells were found in biofilms of all tested C. albicans strains, representing approximately 0.01 to 1.93% of the total population. However, the persister levels were not significantly increased in C. albicans biofilms pretreated with 5-fluorocytosine. These results suggest that inhibition of nucleic acid synthesis did not seem to increase the formation of amphotericin B-tolerant persisters in C. albicans biofilms.
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231
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Kuczyńska-Wiśnik D, Stojowska K, Matuszewska E, Leszczyńska D, Algara MM, Augustynowicz M, Laskowska E. Lack of intracellular trehalose affects formation of Escherichia coli persister cells. MICROBIOLOGY-SGM 2014; 161:786-96. [PMID: 25500492 DOI: 10.1099/mic.0.000012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/09/2014] [Indexed: 01/06/2023]
Abstract
Persisters are dormant antibiotic-tolerant cells that usually compose a small fraction of bacterial populations. In this work, we focused on the role of trehalose in persister formation. We found that the ΔotsA mutant, which is unable to synthesize trehalose, produced increased levels of persisters in the early stationary phase and under heat stress conditions. The lack of trehalose in the ΔotsA mutant resulted in oxidative stress, manifested by increased membrane lipid peroxidation after heat shock. Stationary ΔotsA cells additionally exhibited increased levels of oxidized proteins and apurinic/apyrimidinic sites in DNA as compared to WT cells. Oxidative stress caused by the lack of trehalose was accompanied by the overproduction of extracellular indole, a signal molecule that has been shown to stimulate persister formation. Our major conclusion is that intracellular trehalose protects E. coli cells against oxidative stress and limits indole synthesis, which in turn inhibits the formation of persisters.
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Affiliation(s)
- Dorota Kuczyńska-Wiśnik
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Karolina Stojowska
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Ewelina Matuszewska
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Daria Leszczyńska
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - María Moruno Algara
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Mateusz Augustynowicz
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Ewa Laskowska
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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233
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Prax M, Bertram R. Metabolic aspects of bacterial persisters. Front Cell Infect Microbiol 2014; 4:148. [PMID: 25374846 PMCID: PMC4205924 DOI: 10.3389/fcimb.2014.00148] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 10/05/2014] [Indexed: 12/23/2022] Open
Abstract
Persister cells form a multi-drug tolerant subpopulation within an isogenic culture of bacteria that are genetically susceptible to antibiotics. Studies with different Gram negative and Gram positive bacteria have identified a large number of genes associated with the persister state. In contrast, the revelation of persister metabolism has only been addressed recently. We here summarize metabolic aspects of persisters, which includes an overview about the bifunctional role of selected carbohydrates as both triggers for the exit from the drug tolerant state and metabolites which persisters feed on. Also alarmones as indicators for starvation have been shown to influence persister levels via different signaling cascades involving the activation of toxin-antitoxin systems and other regulatory factors. Finally, recent data obtained by (13)C-isotopolog profiling demonstrated an active amino acid anabolism in Staphylococcus aureus cultures challenged with high drug concentrations. Understanding the metabolism of persister cells poses challenges but also paves the way for the development of anti-persister compounds.
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Affiliation(s)
- Marcel Prax
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen Tübingen, Germany
| | - Ralph Bertram
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen Tübingen, Germany
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234
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Kwan BW, Osbourne DO, Hu Y, Benedik MJ, Wood TK. Phosphodiesterase DosP increases persistence by reducing cAMP which reduces the signal indole. Biotechnol Bioeng 2014; 112:588-600. [PMID: 25219496 DOI: 10.1002/bit.25456] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/25/2014] [Accepted: 09/02/2014] [Indexed: 12/18/2022]
Abstract
Persisters are bacteria that are highly tolerant to antibiotics due to their dormant state and are of clinical significance owing to their role in infections. Given that the population of persisters increases in biofilms and that cyclic diguanylate (c-di-GMP) is an intracellular signal that increases biofilm formation, we sought to determine whether c-di-GMP has a role in bacterial persistence. By examining the effect of 30 genes from Escherichia coli, including diguanylate cyclases that synthesize c-di-GMP and phosphodiesterases that breakdown c-di-GMP, we determined that DosP (direct oxygen sensing phosphodiesterase) increases persistence by over a thousand fold. Using both transcriptomic and proteomic approaches, we determined that DosP increases persistence by decreasing tryptophanase activity and thus indole. Corroborating this effect, addition of indole reduced persistence. Despite the role of DosP as a c-di-GMP phosphodiesterase, the decrease in tryptophanase activity was found to be a result of cyclic adenosine monophosphate (cAMP) phosphodiesterase activity. Corroborating this result, the reduction of cAMP via CpdA, a cAMP-specific phosphodiesterase, increased persistence and reduced indole levels similarly to DosP. Therefore, phosphodiesterase DosP increases persistence by reducing the interkingdom signal indole via reduction of the global regulator cAMP.
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Affiliation(s)
- Brian W Kwan
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania
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235
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The fatty acid signaling molecule cis-2-decenoic acid increases metabolic activity and reverts persister cells to an antimicrobial-susceptible state. Appl Environ Microbiol 2014; 80:6976-91. [PMID: 25192989 DOI: 10.1128/aem.01576-14] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Persister cells, which are tolerant to antimicrobials, contribute to biofilm recalcitrance to therapeutic agents. In turn, the ability to kill persister cells is believed to significantly improve efforts in eradicating biofilm-related, chronic infections. While much research has focused on elucidating the mechanism(s) by which persister cells form, little is known about the mechanism or factors that enable persister cells to revert to an active and susceptible state. Here, we demonstrate that cis-2-decenoic acid (cis-DA), a fatty acid signaling molecule, is able to change the status of Pseudomonas aeruginosa and Escherichia coli persister cells from a dormant to a metabolically active state without an increase in cell number. This cell awakening is supported by an increase of the persister cells' respiratory activity together with changes in protein abundance and increases of the transcript expression levels of several metabolic markers, including acpP, 16S rRNA, atpH, and ppx. Given that most antimicrobials target actively growing cells, we also explored the effect of cis-DA on enhancing antibiotic efficacy in killing persister cells due to their inability to keep a persister cell state. Compared to antimicrobial treatment alone, combinational treatments of persister cell subpopulations with antimicrobials and cis-DA resulted in a significantly greater decrease in cell viability. In addition, the presence of cis-DA led to a decrease in the number of persister cells isolated. We thus demonstrate the ability of a fatty acid signaling molecule to revert bacterial cells from a tolerant phenotype to a metabolically active, antimicrobial-sensitive state.
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236
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Hu Y, Kwan BW, Osbourne DO, Benedik MJ, Wood TK. Toxin YafQ increases persister cell formation by reducing indole signalling. Environ Microbiol 2014; 17:1275-85. [PMID: 25041421 DOI: 10.1111/1462-2920.12567] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 07/05/2014] [Indexed: 01/04/2023]
Abstract
Persister cells survive antibiotic and other environmental stresses by slowing metabolism. Since toxins of toxin/antitoxin (TA) systems have been postulated to be responsible for persister cell formation, we investigated the influence of toxin YafQ of the YafQ/DinJ Escherichia coli TA system on persister cell formation. Under stress, YafQ alters metabolism by cleaving transcripts with in-frame 5'-AAA-G/A-3' sites. Production of YafQ increased persister cell formation with multiple antibiotics, and by investigating changes in protein expression, we found that YafQ reduced tryptophanase levels (TnaA mRNA has 16 putative YafQ cleavage sites). Consistently, TnaA mRNA levels were also reduced by YafQ. Tryptophanase is activated in the stationary phase by the stationary-phase sigma factor RpoS, which was also reduced dramatically upon production of YafQ. Tryptophanase converts tryptophan into indole, and as expected, indole levels were reduced by the production of YafQ. Corroborating the effect of YafQ on persistence, addition of indole reduced persistence. Furthermore, persistence increased upon deleting tnaA, and persistence decreased upon adding tryptophan to the medium to increase indole levels. Also, YafQ production had a much smaller effect on persistence in a strain unable to produce indole. Therefore, YafQ increases persistence by reducing indole, and TA systems are related to cell signalling.
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Affiliation(s)
- Ying Hu
- Department of Chemical Engineering and, Pennsylvania State University, University Park, PA, 16802-4400, USA
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237
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Wen J, Fozo EM. sRNA antitoxins: more than one way to repress a toxin. Toxins (Basel) 2014; 6:2310-35. [PMID: 25093388 PMCID: PMC4147584 DOI: 10.3390/toxins6082310] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 07/15/2014] [Accepted: 07/17/2014] [Indexed: 11/16/2022] Open
Abstract
Bacterial toxin-antitoxin loci consist of two genes: one encodes a potentially toxic protein, and the second, an antitoxin to repress its function or expression. The antitoxin can either be an RNA or a protein. For type I and type III loci, the antitoxins are RNAs; however, they have very different modes of action. Type I antitoxins repress toxin protein expression through interacting with the toxin mRNA, thereby targeting the mRNA for degradation or preventing its translation or both; type III antitoxins directly bind to the toxin protein, sequestering it. Along with these two very different modes of action for the antitoxin, there are differences in the functions of the toxin proteins and the mobility of these loci between species. Within this review, we discuss the major differences as to how the RNAs repress toxin activity, the potential consequences for utilizing different regulatory strategies, as well as the confirmed and potential biological roles for these loci across bacterial species.
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Affiliation(s)
- Jia Wen
- Department of Microbiology, University of Tennessee, M409 Walters Life Sciences, Knoxville, TN 37996, USA.
| | - Elizabeth M Fozo
- Department of Microbiology, University of Tennessee, M409 Walters Life Sciences, Knoxville, TN 37996, USA.
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238
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Bacterial drug tolerance under clinical conditions is governed by anaerobic adaptation but not anaerobic respiration. Antimicrob Agents Chemother 2014; 58:5775-83. [PMID: 25049258 PMCID: PMC4187911 DOI: 10.1128/aac.02793-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Noninherited antibiotic resistance is a phenomenon whereby a subpopulation of genetically identical bacteria displays phenotypic tolerance to antibiotics. We show here that compared to Escherichia coli, the clinically relevant genus Burkholderia displays much higher levels of cells that tolerate ceftazidime. By measuring the dynamics of the formation of drug-tolerant cells under conditions that mimic in vivo infections, we show that in Burkholderia bacteria, oxygen levels affect the formation of these cells. The drug-tolerant cells are characterized by an anaerobic metabolic signature and can be eliminated by oxygenating the system or adding nitrate. The transcriptome profile suggests that these cells are not dormant persister cells and are likely to be drug tolerant as a consequence of the upregulation of anaerobic nitrate respiration, efflux pumps, β-lactamases, and stress response proteins. These findings have important implications for the treatment of chronic bacterial infections and the methodologies and conditions that are used to study drug-tolerant and persister cells in vitro.
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239
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Helaine S, Kugelberg E. Bacterial persisters: formation, eradication, and experimental systems. Trends Microbiol 2014; 22:417-24. [PMID: 24768561 DOI: 10.1016/j.tim.2014.03.008] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/16/2014] [Accepted: 03/21/2014] [Indexed: 01/02/2023]
Abstract
Persisters are multidrug-tolerant bacteria that could account for the relapse of infections. For a long time, persisters have been assumed to be nonreplicating dormant bacteria, but the growth status of these recalcitrant cells is still debated. Toxin-antitoxin (TA) modules have an important role in the formation of persisters and several studies show that they can form in response to different triggers. These findings, together with the invention of new tools to study persisters, could have important implications for the development of novel therapeutics to eradicate persisting subpopulations.
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Affiliation(s)
- Sophie Helaine
- Section of Microbiology, Medical Research Council (MRC) Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK.
| | - Elisabeth Kugelberg
- Section of Microbiology, Medical Research Council (MRC) Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
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240
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Wen Y, Behiels E, Devreese B. Toxin-Antitoxin systems: their role in persistence, biofilm formation, and pathogenicity. Pathog Dis 2014; 70:240-9. [DOI: 10.1111/2049-632x.12145] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/15/2014] [Accepted: 01/15/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Yurong Wen
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
| | - Ester Behiels
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
| | - Bart Devreese
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
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241
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Santi L, Beys-da-Silva WO, Berger M, Calzolari D, Guimarães JA, Moresco JJ, Yates JR. Proteomic profile of Cryptococcus neoformans biofilm reveals changes in metabolic processes. J Proteome Res 2014; 13:1545-59. [PMID: 24467693 PMCID: PMC3993910 DOI: 10.1021/pr401075f] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Cryptococcus neoformans, a pathogenic yeast, causes
meningoencephalitis, especially in immunocompromised patients, leading
in some cases to death. Microbes in biofilms can cause persistent
infections, which are harder to treat. Cryptococcal biofilms are becoming
common due to the growing use of brain valves and other medical devices.
Using shotgun proteomics we determine the differences in protein abundance
between biofilm and planktonic cells. Applying bioinformatic tools,
we also evaluated the metabolic pathways involved in biofilm maintenance
and protein interactions. Our proteomic data suggest general changes
in metabolism, protein turnover, and global stress responses. Biofilm
cells show an increase in proteins related to oxidation–reduction,
proteolysis, and response to stress and a reduction in proteins related
to metabolic process, transport, and translation. An increase in pyruvate-utilizing
enzymes was detected, suggesting a shift from the TCA cycle to fermentation-derived
energy acquisition. Additionally, we assign putative roles to 33 proteins
previously categorized as hypothetical. Many changes in metabolic
enzymes were identified in studies of bacterial biofilm, potentially
revealing a conserved strategy in biofilm lifestyle.
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Affiliation(s)
- Lucélia Santi
- Department of Chemical Physiology, The Scripps Research Institute , North Torrey Pines Road, Suite 11, La Jolla, California 92037, United States
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242
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Cheng HY, Soo VWC, Islam S, McAnulty MJ, Benedik MJ, Wood TK. Toxin GhoT of the GhoT/GhoS toxin/antitoxin system damages the cell membrane to reduce adenosine triphosphate and to reduce growth under stress. Environ Microbiol 2014; 16:1741-54. [PMID: 24373067 DOI: 10.1111/1462-2920.12373] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/04/2013] [Accepted: 12/14/2013] [Indexed: 11/27/2022]
Abstract
Toxin/antitoxin (TA) systems perhaps enable cells to reduce their metabolism to weather environmental challenges although there is little evidence to support this hypothesis. Escherichia coli GhoT/GhoS is a TA system in which toxin GhoT expression is reduced by cleavage of its messenger RNA (mRNA) by antitoxin GhoS, and TA system MqsR/MqsA controls GhoT/GhoS through differential mRNA decay. However, the physiological role of GhoT has not been determined. We show here through transmission electron microscopy, confocal microscopy and fluorescent stains that GhoT reduces metabolism by damaging the membrane and that toxin MqsR (a 5'-GCU-specific endoribonuclease) causes membrane damage in a GhoT-dependent manner. This membrane damage results in reduced cellular levels of ATP and the disruption of proton motive force (PMF). Normally, GhoT is localized to the pole and does not cause cell lysis under physiological conditions. Introduction of an F38R substitution results in loss of GhoT toxicity, ghost cell production and membrane damage while retaining the pole localization. Also, deletion of ghoST or ghoT results in significantly greater initial growth in the presence of antimicrobials. Collectively, these results demonstrate that GhoT reduces metabolism by reducing ATP and PMF and that this reduction in metabolism is important for growth with various antimicrobials.
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Affiliation(s)
- Hsin-Yao Cheng
- Department of Chemical Engineering, Pennsylvania State University, State College, PA, 16802, USA
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243
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Selective target inactivation rather than global metabolic dormancy causes antibiotic tolerance in uropathogens. Antimicrob Agents Chemother 2014; 58:2089-97. [PMID: 24449771 DOI: 10.1128/aac.02552-13] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Persister cells represent a multidrug-tolerant (MDT), physiologically distinct subpopulation of bacteria. The ability of these organisms to survive lethal antibiotic doses raises concern over their potential role in chronic disease, such as recurrent urinary tract infection (RUTI). Persistence is believed to be conveyed through global metabolic dormancy, which yields organisms unresponsive to external stimuli. However, recent studies have contested this stance. Here, various antibiotics that target different cellular processes were used to dissect the activity of transcription, translation, and peptidoglycan turnover in persister cells. Differential susceptibility patterns were found in type I and type II persisters, and responses differed between Staphylococcus saprophyticus and Escherichia coli uropathogens. Further, SOS-deficient strains were sensitized to ciprofloxacin, suggesting DNA gyrase activity in persisters and indicating the importance of active DNA repair systems for ciprofloxacin tolerance. These results indicate that global dormancy per se cannot sufficiently account for antibiotic tolerance. Rather, the activity of individual cellular processes dictates multidrug tolerance in an antibiotic-specific fashion. Furthermore, the susceptibility patterns of persisters depended on their mechanisms of onset, with subinhibitory antibiotic pretreatments selectively shutting down cognate targets and increasing the persister fraction against the same agent. Interestingly, antibiotics targeting transcription and translation enhanced persistence against multiple agents indirectly related to these processes. Conducting these assays with uropathogenic E. coli isolated from RUTI patients revealed an enriched persister fraction compared to organisms cleared with standard antibiotic therapy. This finding suggests that persister traits are either selected for during prolonged antibiotic treatment or initially contribute to therapy failure.
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244
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Persisters, persistent infections and the Yin-Yang model. Emerg Microbes Infect 2014; 3:e3. [PMID: 26038493 PMCID: PMC3913823 DOI: 10.1038/emi.2014.3] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/30/2013] [Accepted: 11/26/2013] [Indexed: 12/15/2022]
Abstract
Persisters are a small fraction of quiescent bacterial cells that survive lethal antibiotics or stresses but can regrow under appropriate conditions. Persisters underlie persistent and latent infections and post-treatment relapse, posing significant challenges for the treatment of many bacterial infections. The current definition of persisters has drawbacks, and a Yin–Yang model is proposed to describe the heterogeneous nature of persisters that have to be defined in highly specific conditions. Despite their discovery more than 70 years ago, the mechanisms of persisters are poorly understood. Recent studies have identified a number of genes and pathways that shed light on the mechanisms of persister formation or survival. These include toxin–antitoxin modules, stringent response, DNA repair or protection, phosphate metabolism, alternative energy production, efflux, anti-oxidative defense and macromolecule degradation. More sensitive single-cell techniques are required for a better understanding of persister mechanisms. Studies of bacterial persisters have parallels in other microbes (fungi, parasites, viruses) and cancer stem cells in terms of mechanisms and treatment approaches. New drugs and vaccines targeting persisters are critical for improved treatment of persistent infections and perhaps cancers. Novel treatment strategies for persisters and persistent infections are discussed.
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245
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Tripathi A, Dewan PC, Siddique SA, Varadarajan R. MazF-induced growth inhibition and persister generation in Escherichia coli. J Biol Chem 2013; 289:4191-205. [PMID: 24375411 DOI: 10.1074/jbc.m113.510511] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Toxin-antitoxin systems are ubiquitous in nature and present on the chromosomes of both bacteria and archaea. MazEF is a type II toxin-antitoxin system present on the chromosome of Escherichia coli and other bacteria. Whether MazEF is involved in programmed cell death or reversible growth inhibition and bacterial persistence is a matter of debate. In the present work the role of MazF in bacterial physiology was studied by using an inactive, active-site mutant of MazF, E24A, to activate WT MazF expression from its own promoter. The ectopic expression of E24A MazF in a strain containing WT mazEF resulted in reversible growth arrest. Normal growth resumed on inhibiting the expression of E24A MazF. MazF-mediated growth arrest resulted in an increase in survival of bacterial cells during antibiotic stress. This was studied by activation of mazEF either by overexpression of an inactive, active-site mutant or pre-exposure to a sublethal dose of antibiotic. The MazF-mediated persistence phenotype was found to be independent of RecA and dependent on the presence of the ClpP and Lon proteases. This study confirms the role of MazEF in reversible growth inhibition and persistence.
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Affiliation(s)
- Arti Tripathi
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India and
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246
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Kester JC, Fortune SM. Persisters and beyond: mechanisms of phenotypic drug resistance and drug tolerance in bacteria. Crit Rev Biochem Mol Biol 2013; 49:91-101. [PMID: 24328927 DOI: 10.3109/10409238.2013.869543] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
One of the challenges in clinical infectious diseases is the problem of chronic infections, which can require long durations of antibiotic treatment and often recur. An emerging explanation for the refractoriness of some infections to treatment is the existence of subpopulations of drug tolerant cells. While typically discussed as "persister" cells, it is becoming increasingly clear that there is significant heterogeneity in drug responses within a bacterial population and that multiple mechanisms underlie the emergence of drug tolerant and drug-resistant subpopulations. Many of these parallel mechanisms have been shown to affect drug susceptibility at the level of a whole population. Here we review mechanisms of phenotypic drug tolerance and resistance in bacteria with the goal of providing a framework for understanding the similarities and differences in these cells.
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Affiliation(s)
- Jemila C Kester
- Department of Immunology and Infectious Diseases, Harvard School of Public Health , Boston, MA , USA
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247
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Abstract
Bacterial cells may escape the effects of antibiotics without undergoing genetic change; these cells are known as persisters. Unlike resistant cells that grow in the presence of antibiotics, persister cells do not grow in the presence of antibiotics. These persister cells are a small fraction of exponentially growing cells (due to carryover from the inoculum) but become a significant fraction in the stationary phase and in biofilms (up to 1%). Critically, persister cells may be a major cause of chronic infections. The mechanism of persister cell formation is not well understood, and even the metabolic state of these cells is debated. Here, we review studies relevant to the formation of persister cells and their metabolic state and conclude that the best model for persister cells is still dormancy, with the latest mechanistic studies shedding light on how cells reach this dormant state.
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248
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In vitro activities of amoxicillin-clavulanate, doxycycline, ceftazidime, imipenem, and trimethoprim-sulfamethoxazole against biofilm of Brazilian strains of Burkholderia pseudomallei. Antimicrob Agents Chemother 2013; 57:5771-3. [PMID: 24002089 DOI: 10.1128/aac.00721-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study aimed at investigating the in vitro activities of amoxicillin-clavulanate, doxycycline, ceftazidime, imipenem, and trimethoprim-sulfamethoxazole against Burkholderia pseudomallei in planktonic and biofilm forms, through broth microdilution and resazurin-based viability staining, respectively. In planktonic growth, the strains were susceptible to the drugs, while in biofilm growth, significantly higher antimicrobial concentrations were required, especially for ceftazidime and imipenem, surpassing the resistance breakpoints. These results highlight the importance of the routine evaluation of biofilm antimicrobial susceptibility.
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249
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Establishment of a method to rapidly assay bacterial persister metabolism. Antimicrob Agents Chemother 2013; 57:4398-409. [PMID: 23817376 DOI: 10.1128/aac.00372-13] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial persisters exhibit an extraordinary tolerance to antibiotics that is dependent on their metabolic state. Although persister metabolism promises to be a rich source of antipersister strategies, there is relatively little known about the metabolism of these rare and transient phenotypic variants. To address this knowledge gap, we explored the use of several techniques, and we found that only one measured persister metabolism. This assay was based on the phenomenon of metabolite-enabled aminoglycoside killing of persisters, and we used it to characterize the metabolic heterogeneity of different persister populations. From these investigations, we determined that glycerol and glucose are the most ubiquitously used carbon sources by various types of Escherichia coli persisters, suggesting that these metabolites might prove beneficial to deliver in conjunction with aminoglycosides for the treatment of chronic and recurrent infections. In addition, we demonstrated that the persister metabolic assay developed here is amenable to high-throughput screening with the use of phenotype arrays.
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250
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Dormancy is not necessary or sufficient for bacterial persistence. Antimicrob Agents Chemother 2013; 57:3230-9. [PMID: 23629720 DOI: 10.1128/aac.00243-13] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The antibiotic tolerances of bacterial persisters have been attributed to transient dormancy. While persisters have been observed to be growth inhibited prior to antibiotic exposure, we sought to determine whether such a trait was essential to the phenotype. Furthermore, we sought to provide direct experimental evidence of the persister metabolic state so as to determine whether the common assumption of metabolic inactivity was valid. Using fluorescence-activated cell sorting (FACS), a fluorescent indicator of cell division, a fluorescent measure of metabolic activity, and persistence assays, we found that bacteria that are rapidly growing prior to antibiotic exposure can give rise to persisters and that a lack of replication or low metabolic activity prior to antibiotic treatment simply increases the likelihood that a cell is a persister. Interestingly, a lack of significant growth or metabolic activity does not guarantee persistence, as the majority of even "dormant" subpopulations (>99%) were not persisters. These data suggest that persistence is far more complex than dormancy and point to additional characteristics needed to define the persister phenotype.
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