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Sett A, Dubey V, Bhowmik S, Pathania R. Decoding Bacterial Persistence: Mechanisms and Strategies for Effective Eradication. ACS Infect Dis 2024; 10:2525-2539. [PMID: 38940498 DOI: 10.1021/acsinfecdis.4c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
The ability of pathogenic bacteria to evade antibiotic treatment is an intricate and multifaceted phenomenon. Over the years, treatment failure among patients due to determinants of antimicrobial resistance (AMR) has been the focal point for the research and development of new therapeutic agents. However, the survival of bacteria by persisting under antibiotic stress has largely been overlooked. Bacterial persisters are a subpopulation of sensitive bacterial cells exhibiting a noninheritable drug-tolerant phenotype. They are linked to the recalcitrance of infections in healthcare settings, in turn giving rise to AMR variants. The importance of bacterial persistence in recurring infections has been firmly recognized. Fundamental work over the past decade has highlighted numerous unique tolerance factors contributing to the persister phenotype in many clinically relevant pathogens. This review summarizes contributing factors that could aid in developing new strategies against bacterial antibiotic persisters.
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Affiliation(s)
- Abhiroop Sett
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Vineet Dubey
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Somok Bhowmik
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
- Centre of Excellence in Disaster Mitigation and Management, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
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Ngo HG, Mohiuddin SG, Ananda A, Orman MA. UNRAVELING CRP/cAMP-MEDIATED METABOLIC REGULATION IN ESCHERICHIA COLI PERSISTER CELLS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598332. [PMID: 38915711 PMCID: PMC11195080 DOI: 10.1101/2024.06.10.598332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
A substantial gap persists in our comprehension of how bacterial metabolism undergoes rewiring during the transition to a persistent state. Also, it remains unclear which metabolic mechanisms become indispensable for persister cell survival. To address these questions, we directed our efforts towards persister cells in Escherichia coli that emerge during the late stationary phase. These cells have been recognized for their exceptional resilience and are commonly believed to be in a dormant state. Our results demonstrate that the global metabolic regulator Crp/cAMP redirects the metabolism of these antibiotic-tolerant cells from anabolism to oxidative phosphorylation. Although our data indicates that persisters exhibit a reduced metabolic rate compared to rapidly growing exponential-phase cells, their survival still relies on energy metabolism. Extensive genomic-level analyses of metabolomics, proteomics, and single-gene deletions consistently emphasize the critical role of energy metabolism, specifically the tricarboxylic acid (TCA) cycle, electron transport chain (ETC), and ATP synthase, in sustaining the viability of persisters. Altogether, this study provides much-needed clarification regarding the role of energy metabolism in antibiotic tolerance and highlights the importance of using a multipronged approach at the genomic level to obtain a broader picture of the metabolic state of persister cells.
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Affiliation(s)
- Han G. Ngo
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
| | - Sayed Golam Mohiuddin
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
| | - Aina Ananda
- Department of Biology, Monmouth University, NJ, 07764
| | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
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Kamiya Y, Mishima K, Tanaka T, Sawamura K, Matsushita M, Imagama S. Acute osteomyelitis of the patella due to Pseudomonas aeruginosa in an immunocompetent child: A case report. Medicine (Baltimore) 2023; 102:e33012. [PMID: 36800616 PMCID: PMC9936032 DOI: 10.1097/md.0000000000033012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
RATIONALE Plentiful vascularity and lack of the physis are thought to render the patella less vulnerable to osteomyelitis. Pseudomonas aeruginosa (PA) is an opportunistic pathogen predominantly affecting immunocompromised hosts. Despite the ubiquitous nature of PA, osteomyelitis of the patella caused by PA has been rarely reported in children. PATIENT CONCERNS A 5-year-old boy who had presented with a prolonged history of the left anterior knee pain following minor trauma was diagnosed with prepatellar bacterial cellulitis and bursitis. Afterward, a focal osteolytic lesion emerged at the ventral surface of the patella despite oral and intravenous antibiotic therapy lasting for weeks. We described clinical presentation as well as medical and surgical management of pediatric patellar osteomyelitis secondary to prepatellar septic bursitis. DIAGNOSES Pseudomonas aeruginosa-associated osteomyelitis of the patella. Magnetic resonance imaging of the left knee showed a focal destructive change of the ventral half of the cartilaginous patella and a suprapatellar joint effusion. Bacterial culture from the bursa revealed Pseudomonas aeruginosa. INTERVENTIONS Systemic inflammation, patellar osteochondral destruction, and purulent synovial fluid of the knee were prolonged for 6 weeks despite antibiotics use deemed appropriate and reparative surgical debridement, whereas they were eventually resolved with a 6-week course of intravenous ceftazidime and cessation of continuous intracapsular irrigation. OUTCOMES He was clinically asymptomatic at the latest follow-up but exhibited a minor leg length discrepancy <2 cm associated with overgrowth of the affected femur. LESSONS This is a rare case of Pseudomonas osteomyelitis of the patella in a healthy pediatric patient. Uncommon osteochondral sequelae occurred probably because of a protracted arthritis of the affected knee. We would like to emphasize the ineffectiveness of continuous irrigation without antibiotics for Pseudomonas aeruginosa-associated osteomyelitis.
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Affiliation(s)
- Yasunari Kamiya
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kenichi Mishima
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- * Correspondence: Kenichi Mishima, Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan (e-mail: )
| | - Tetsuji Tanaka
- Department of Orthopaedic Surgery, Holy Spirit Hospital, Nagoya, Aichi, Japan
| | - Kenta Sawamura
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masaki Matsushita
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Shiro Imagama
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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Food for Thought: Proteomics for Meat Safety. Life (Basel) 2023; 13:life13020255. [PMID: 36836616 PMCID: PMC9966529 DOI: 10.3390/life13020255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
Foodborne bacteria interconnect food and human health. Despite significant progress in food safety regulation, bacterial contamination is still a serious public health concern and the reason for significant commercial losses. The screening of the microbiome in meals is one of the main aspects of food production safety influencing the health of the end-consumers. Our research provides an overview of proteomics findings in the field of food safety made over the last decade. It was believed that proteomics offered an accurate snapshot of the complex networks of the major biological machines called proteins. The proteomic methods for the detection of pathogens were armed with bioinformatics algorithms, allowing us to map the data onto the genome and transcriptome. The mechanisms of the interaction between bacteria and their environment were elucidated with unprecedented sensitivity, specificity, and depth. Using our web-based tool ScanBious for automated publication analysis, we analyzed over 48,000 scientific articles on antibiotic and disinfectant resistance and highlighted the benefits of proteomics for the food safety field. The most promising approach to studying safety in food production is the combination of classical genomic and metagenomic approaches and the advantages provided by proteomic methods with the use of panoramic and targeted mass spectrometry.
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Kaushik V, Tiwari M, Tiwari V. Interaction of RecA mediated SOS response with bacterial persistence, biofilm formation, and host response. Int J Biol Macromol 2022; 217:931-943. [PMID: 35905765 DOI: 10.1016/j.ijbiomac.2022.07.176] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Abstract
Antibiotics have a primary mode of actions, and most of them have a common secondary mode of action via reactive species (ROS and RNS) mediated DNA damage. Bacteria have been able to tolerate this DNA damage by SOS (Save-Our-Soul) response. RecA is the universal essential key protein of the DNA damage mediated SOS repair in various bacteria including ESKAPE pathogens. In addition, antibiotics also triggers activation of various other bacterial mechanisms such as biofilm formation, host dependent responses, persister subpopulation formation. These supporting the survival of bacteria in unfriendly natural conditions i.e. antibiotic presence. This review highlights the detailed mechanism of RecA mediated SOS response as well as role of RecA-LexA interaction in SOS response. The review also focuses on inter-connection between DNA damage repair pathway (like SOS response) with other survival mechanisms of bacteria such as host mediated RecA induction, persister-SOS interplay, and biofilm-SOS interplay. This understanding of inter-connection of SOS response with different other survival mechanisms will prove beneficial in targeting the SOS response for prevention and development of therapeutics against recalcitrant bacterial infections. The review also covers the significance of RecA as a promising potent therapeutic target for hindering bacterial SOS response in prevailing successful treatments of bacterial infections and enhancing the conventional antibiotic efficiency.
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Affiliation(s)
- Vaishali Kaushik
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India.
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Hartline CJ, Zhang R, Zhang F. Transient Antibiotic Tolerance Triggered by Nutrient Shifts From Gluconeogenic Carbon Sources to Fatty Acid. Front Microbiol 2022; 13:854272. [PMID: 35359720 PMCID: PMC8963472 DOI: 10.3389/fmicb.2022.854272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/22/2022] [Indexed: 12/04/2022] Open
Abstract
Nutrient shifts from glycolytic-to-gluconeogenic carbon sources can create large sub-populations of extremely antibiotic tolerant bacteria, called persisters. Positive feedback in Escherichia coli central metabolism was believed to play a key role in the formation of persister cells. To examine whether positive feedback in nutrient transport can also support high persistence to β-lactams, we performed nutrient shifts for E. coli from gluconeogenic carbon sources to fatty acid (FA). We observed tri-phasic antibiotic killing kinetics characterized by a transient period of high antibiotic tolerance, followed by rapid killing then a slower persister-killing phase. The duration of transient tolerance (3-44 h) varies with pre-shift carbon source and correlates strongly with the time needed to accumulate the FA degradation enzyme FadD after the shift. Additionally, FadD accumulation time and thus transient tolerance time can be reduced by induction of the glyoxylate bypass prior to switching, highlighting that two interacting feedback loops simultaneously control the length of transient tolerance. Our results demonstrate that nutrient switches along with positive feedback are not sufficient to trigger persistence in a majority of the population but instead triggers only a temporary tolerance. Additionally, our results demonstrate that the pre-shift metabolic state determines the duration of transient tolerance and that supplying glyoxylate can facilitate antibiotic killing of bacteria.
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Affiliation(s)
- Christopher J. Hartline
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, United States
| | - Ruixue Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, United States
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, United States
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO, United States
- Institute of Materials Science and Engineering, Washington University in St. Louis, Saint Louis, MO, United States
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Pleiotropic actions of phenothiazine drugs are detrimental to Gram-negative bacterial persister cells. Commun Biol 2022; 5:217. [PMID: 35264714 PMCID: PMC8907348 DOI: 10.1038/s42003-022-03172-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/15/2022] [Indexed: 12/28/2022] Open
Abstract
Bacterial persister cells are temporarily tolerant to bactericidal antibiotics but are not necessarily dormant and may exhibit physiological activities leading to cell damage. Based on the link between fluoroquinolone-mediated SOS responses and persister cell recovery, we screened chemicals that target fluoroquinolone persisters. Metabolic inhibitors (e.g., phenothiazines) combined with ofloxacin (OFX) perturbed persister levels in metabolically active cell populations. When metabolically stimulated, intrinsically tolerant stationary phase cells also became OFX-sensitive in the presence of phenothiazines. The effects of phenothiazines on cell metabolism and physiology are highly pleiotropic: at sublethal concentrations, phenothiazines reduce cellular metabolic, transcriptional, and translational activities; impair cell repair and recovery mechanisms; transiently perturb membrane integrity; and disrupt proton motive force by dissipating the proton concentration gradient across the cell membrane. Screening a subset of mutant strains lacking membrane-bound proteins revealed the pleiotropic effects of phenothiazines potentially rely on their ability to inhibit a wide range of critical metabolic proteins. Altogether, our study further highlights the complex roles of metabolism in persister cell formation, survival and recovery, and suggests metabolic inhibitors such as phenothiazines can be selectively detrimental to persister cells.
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Kaushik V, Sharma S, Tiwari M, Tiwari V. Anti-persister strategies against stress induced bacterial persistence. Microb Pathog 2022; 164:105423. [PMID: 35092834 DOI: 10.1016/j.micpath.2022.105423] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/17/2022] [Accepted: 01/24/2022] [Indexed: 01/22/2023]
Abstract
The increase in antibiotic non-responsive bacteria is the leading concern in current research-oriented to eliminate pathogens. Nowadays, the excess use of antibiotics without specifically understanding the potentiality of killing pathogens and bacterial survival patterns has helped bacteria emerge indefatigably. Bacteria use various mechanisms such as resistance, persistence, and tolerance to ensure survival. Among these, persistence is a mechanism by which bacteria reside in their dormant state, bypassing the effects of treatments, making it crucial for bacterial survival. Persistent bacterial cells arise from the normal bacterial population as a slow-growing subset of bacteria with no metabolic flux. This behavior renders it to survive for a longer duration and at higher concentrations of antibiotics. They are one of the underlying causes of recurrence of bacterial infections. The present article explains the detailed molecular mechanisms and strategies of bacterial persistence, including the toxin-antitoxin modules, DNA damage, the formation of inactive ribosomal complexes, (p)ppGpp network, antibiotic-induced persistence, which are triggered by drug-induced stress. The article also comprehensively covers the epigenetic memory of persistence in bacteria, and anti-persistent therapeutics like antimicrobial molecules, synthetic peptides, acyldepsipeptide antibiotics, and endolysin therapy to reduce persister cell formation and control their frequency. These strategies could be utilized in combating the pathogenic bacteria undergoing persistence.
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Affiliation(s)
- Vaishali Kaushik
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Saroj Sharma
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India.
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β-lactam Resistance in Pseudomonas aeruginosa: Current Status, Future Prospects. Pathogens 2021; 10:pathogens10121638. [PMID: 34959593 PMCID: PMC8706265 DOI: 10.3390/pathogens10121638] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is a major opportunistic pathogen, causing a wide range of acute and chronic infections. β-lactam antibiotics including penicillins, carbapenems, monobactams, and cephalosporins play a key role in the treatment of P. aeruginosa infections. However, a significant number of isolates of these bacteria are resistant to β-lactams, complicating treatment of infections and leading to worse outcomes for patients. In this review, we summarize studies demonstrating the health and economic impacts associated with β-lactam-resistant P. aeruginosa. We then describe how β-lactams bind to and inhibit P. aeruginosa penicillin-binding proteins that are required for synthesis and remodelling of peptidoglycan. Resistance to β-lactams is multifactorial and can involve changes to a key target protein, penicillin-binding protein 3, that is essential for cell division; reduced uptake or increased efflux of β-lactams; degradation of β-lactam antibiotics by increased expression or altered substrate specificity of an AmpC β-lactamase, or by the acquisition of β-lactamases through horizontal gene transfer; and changes to biofilm formation and metabolism. The current understanding of these mechanisms is discussed. Lastly, important knowledge gaps are identified, and possible strategies for enhancing the effectiveness of β-lactam antibiotics in treating P. aeruginosa infections are considered.
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Nguyen TK, Peyrusson F, Siala W, Pham NH, Nguyen HA, Tulkens PM, Van Bambeke F. Activity of Moxifloxacin Against Biofilms Formed by Clinical Isolates of Staphylococcus aureus Differing by Their Resistant or Persister Character to Fluoroquinolones. Front Microbiol 2021; 12:785573. [PMID: 34975808 PMCID: PMC8715871 DOI: 10.3389/fmicb.2021.785573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus biofilms are poorly responsive to antibiotics. Underlying reasons include a matrix effect preventing drug access to embedded bacteria, or the presence of dormant bacteria with reduced growth rate. Using 18 clinical isolates previously characterized for their moxifloxacin-resistant and moxifloxacin-persister character in stationary-phase culture, we studied their biofilm production and matrix composition and the anti-biofilm activity of moxifloxacin. Biofilms were grown in microtiter plates and their abundance quantified by crystal violet staining and colony counting; their content in polysaccharides, extracellular DNA and proteins was measured. Moxifloxacin activity was assessed after 24 h of incubation with a broad range of concentrations to establish full concentration-response curves. All clinical isolates produced more biofilm biomass than the reference strain ATCC 25923, the difference being more important for those with high relative persister fractions to moxifloxacin, most of which being also resistant. High biofilm producers expressed icaA to higher levels, enriching the matrix in polysaccharides. Moxifloxacin was less potent against biofilms from clinical isolates than from ATCC 25923, especially against moxifloxacin-resistant isolates with high persister fractions, which was ascribed to a lower concentration of moxifloxacin in these biofilms. Time-kill curves in biofilms revealed the presence of a moxifloxacin-tolerant subpopulation, with low multiplication capacity, whatever the persister character of the isolate. Thus, moxifloxacin activity depends on its local concentration in biofilm, which is reduced in most isolates with high-relative persister fractions due to matrix effects, and insufficient to kill resistant isolates due to their high MIC.
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Affiliation(s)
- Tiep K. Nguyen
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
- Department of Pharmaceutical Industry, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Frédéric Peyrusson
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Wafi Siala
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Nhung H. Pham
- Department of Microbiology, Bach Mai Hospital, Hanoi, Vietnam
| | - Hoang A. Nguyen
- The National Center for Drug Information and Adverse Drug Reactions Monitoring, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Paul M. Tulkens
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Françoise Van Bambeke
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
- *Correspondence: Françoise Van Bambeke,
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Žiemytė M, Carda-Diéguez M, Rodríguez-Díaz JC, Ventero MP, Mira A, Ferrer MD. Real-time monitoring of Pseudomonas aeruginosa biofilm growth dynamics and persister cells' eradication. Emerg Microbes Infect 2021; 10:2062-2075. [PMID: 34663186 PMCID: PMC8583918 DOI: 10.1080/22221751.2021.1994355] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 01/11/2023]
Abstract
Biofilm formation and the appearance of persister cells with low metabolic rates are key factors affecting conventional treatment failure and antibiotic resistance. Using impedance-based measurements, crystal violet staining and traditional culture we have studied the biofilm growth dynamics of 13 Pseudomonas aeruginosa strains under the effect of seven conventional antibiotics. Real-time growth quantifications revealed that the exposure of established P. aeruginosa biofilms to certain concentrations of ciprofloxacin, ceftazidime and tobramycin induced the emergence of persister cells, that showed different morphology and pigmentation, as well increased antibiotic resistance. Whole-genome sequencing of wildtype and persister cells identified several SNPs, a genomic inversion and a genomic duplication in one of the strains. However, these mutations were not uniquely associated with persisters, suggesting that the persistent phenotype may be related to metabolic and transcriptional changes. Given that mannitol has been proposed to activate bacterial metabolism, the synergistic combination of mannitol and ciprofloxacin was evaluated on clinical 48 h P. aeruginosa biofilms. When administered at doses ≥320 mg/L, mannitol was capable of preventing persister cell formation by efficiently activating dormant bacteria and making them susceptible to the antibiotic. These results were confirmed using viable colony counting. As the tested ciprofloxacin-mannitol combination appeared to fully eradicate mature biofilms, we conclude that impedance-based biofilm diagnostics, which permits antibiotic susceptibility testing and the identification of persister cells, is of great potential for the clinical practice and could aid in establishing treatment breakpoints for emerging biofilm-related infections.
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Affiliation(s)
- Miglė Žiemytė
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain
| | | | - Juan C. Rodríguez-Díaz
- Servicio de Microbiología, Hospital General Universitario de Alicante, ISABIAL, Alicante, Spain
| | - Maria P. Ventero
- Servicio de Microbiología, Hospital General Universitario de Alicante, ISABIAL, Alicante, Spain
| | - Alex Mira
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain
| | - María D. Ferrer
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain
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Li Z, Ding Z, Liu Y, Jin X, Xie J, Li T, Zeng Z, Wang Z, Liu J. Phenotypic and Genotypic Characteristics of Biofilm Formation in Clinical Isolates of Acinetobacter baumannii. Infect Drug Resist 2021; 14:2613-2624. [PMID: 34262306 PMCID: PMC8274629 DOI: 10.2147/idr.s310081] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/17/2021] [Indexed: 12/14/2022] Open
Abstract
Background Acinetobacter baumannii is an important pathogen in clinical infections, and biofilm formation is an effective way for A. baumannii to survive under external pressures. In this study, the aims were to examine the antimicrobial resistance, biofilm formation, and biofilm-specific resistance in clinical isolates of A. baumannii. Materials and Methods A total of 104 clinical A. baumannii isolates were collected from a large teaching hospital in Southwest China. The antibiotics susceptibilities were tested, and biofilm-forming ability was evaluated by crystal violet staining by confocal laser scanning microscopy (CLSM). Minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), minimum biofilm inhibitory concentration (MBIC), and minimum biofilm eradication concentration (MBEC) of ciprofloxacin, meropenem, and ceftazidime were tested on selected strains by broth microdilution method. Biofilm-associated genes were detected by polymerase chain reaction (PCR), and expression of genes at planktonic stage and biofilm stage were analyzed by real-time reverse transcription PCR (RT-PCR). Results Multidrug-resistant (MDR) isolates accounted for 65.4%, but no strain was resistant to tigecycline and polymyxin B. Moreover, non-MDR strains tended to form stronger biofilms than MDR strains, and a negative correlation between biofilm-forming ability and resistance profiles to each of tested antimicrobials were observed. The MBECs and MBICs of ciprofloxacin, ceftazidime, and meropenem were evidently increased compared with MICs and MBCs among all tested strains. Additionally, the biofilm formation ability of the csuD-positive strains was stronger than that of the csuD-negative strains. The strains in MDR group had higher carrying rate of csuA and csuD genes than non-MDR group, while non-MDR strains possessed more ompA gene than MDR group. Finally, abaI gene was significantly up-regulated after biofilm formation. Conclusion These results revealed valuable data for the negative correlation between antimicrobial resistance and biofilm formation, as well as phenotypic and genotypic characteristics of biofilm formation in A. baumannii.
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Affiliation(s)
- Zhaoyinqian Li
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Zixuan Ding
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Yao Liu
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Xinrui Jin
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Jingling Xie
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Tingting Li
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Zhangrui Zeng
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Zhibin Wang
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Jinbo Liu
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
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Werner N, Petersen K, Vollstedt C, Garcia PP, Chow J, Ferrer M, Fernandez-Lopez L, Falke S, Perbandt M, Hinrichs W, Betzel C, Streit WR. The Komagataeibacter europaeus GqqA is the prototype of a novel bifunctional N-Acyl-homoserine lactone acylase with prephenate dehydratase activity. Sci Rep 2021; 11:12255. [PMID: 34112823 PMCID: PMC8192741 DOI: 10.1038/s41598-021-91536-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/24/2021] [Indexed: 11/09/2022] Open
Abstract
Previously, we reported the isolation of a quorum quenching protein (QQ), designated GqqA, from Komagataeibacter europaeus CECT 8546 that is highly homologous to prephenate dehydratases (PDT) (Valera et al. in Microb Cell Fact 15, 88. https://doi.org/10.1186/s12934-016-0482-y , 2016). GqqA strongly interfered with N-acyl-homoserine lactone (AHL) quorum sensing signals from Gram-negative bacteria and affected biofilm formation in its native host strain Komagataeibacter europaeus. Here we present and discuss data identifying GqqA as a novel acylase. ESI-MS-MS data showed unambiguously that GqqA hydrolyzes the amide bond of the acyl side-chain of AHL molecules, but not the lactone ring. Consistent with this observation the protein sequence does not carry a conserved Zn2+ binding motif, known to be essential for metal-dependent lactonases, but in fact harboring the typical periplasmatic binding protein domain (PBP domain), acting as catalytic domain. We report structural details for the native structure at 2.5 Å resolution and for a truncated GqqA structure at 1.7 Å. The structures obtained highlight that GqqA acts as a dimer and complementary docking studies indicate that the lactone ring of the substrate binds within a cleft of the PBP domain and interacts with polar residues Y16, S17 and T174. The biochemical and phylogenetic analyses imply that GqqA represents the first member of a novel type of QQ family enzymes.
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Affiliation(s)
- Nadine Werner
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University Hamburg, C/O DESY, 22607, Hamburg, Germany
| | - Katrin Petersen
- Microbiology and Biotechnology, University Hamburg, 22609, Hamburg, Germany
| | - Christel Vollstedt
- Microbiology and Biotechnology, University Hamburg, 22609, Hamburg, Germany
| | - Pablo Perez Garcia
- Microbiology and Biotechnology, University Hamburg, 22609, Hamburg, Germany
| | - Jennifer Chow
- Microbiology and Biotechnology, University Hamburg, 22609, Hamburg, Germany
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Laura Fernandez-Lopez
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University Hamburg, C/O DESY, 22607, Hamburg, Germany
| | - Markus Perbandt
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University Hamburg, C/O DESY, 22607, Hamburg, Germany
| | - Winfried Hinrichs
- Institute for Biochemistry, University Greifswald, 17487, Greifswald, Germany
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University Hamburg, C/O DESY, 22607, Hamburg, Germany.
| | - Wolfgang R Streit
- Microbiology and Biotechnology, University Hamburg, 22609, Hamburg, Germany.
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14
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Furusawa G, Diyana T, Lau NS. Metabolic strategies of dormancy of a marine bacterium Microbulbifer aggregans CCB-MM1: Its alternative electron transfer chain and sulfate-reducing pathway. Genomics 2021; 114:443-455. [PMID: 33689784 DOI: 10.1016/j.ygeno.2021.02.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/26/2021] [Accepted: 02/28/2021] [Indexed: 12/26/2022]
Abstract
Bacterial dormancy plays a crucial role in maintaining the functioning and diversity of microbial communities in natural environments. However, the metabolic regulations of the dormancy of bacteria in natural habitats, especially marine habitats, have remained largely unknown. A marine bacterium, Microbulbifer aggregans CCB-MM1 exhibits rod-to-coccus cell shape change during the dormant state. Therefore, to clarify the metabolic regulation of the dormancy, differential gene expression analysis based on RNA-Seq was performed between rod- (vegetative), intermediate, and coccus-shaped cells (dormancy). The RNA-Seq data revealed that one of two distinct electron transfer chains was upregulated in the dormancy. Dissimilatory sulfite reductase and soluble hydrogenase were also highly upregulated in the dormancy. In addition, induction of the dormancy of MM1 in the absence of MgSO4 was slower than that in the presence of MgSO4. These results indicate that the sulfate-reducing pathway plays an important role in entering the dormancy of MM1.
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Affiliation(s)
- Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.
| | - Tarmizi Diyana
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
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15
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The Polyaminoisoprenyl Potentiator NV716 Revives Old Disused Antibiotics against Intracellular Forms of Infection by Pseudomonas aeruginosa. Antimicrob Agents Chemother 2021; 65:AAC.02028-20. [PMID: 33318000 DOI: 10.1128/aac.02028-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/05/2020] [Indexed: 12/24/2022] Open
Abstract
Active efflux confers intrinsic resistance to multiple antibiotics in Pseudomonas aeruginosa, including old disused molecules. Beside resistance, intracellular survival is another reason for failure to eradicate bacteria with antibiotics. We evaluated the capacity of polyaminoisoprenyl potentiators (designed as efflux pump inhibitors [EPIs]) NV716 and NV731 compared to PAβN to restore the activity of disused antibiotics (doxycycline, chloramphenicol [substrates for efflux], and rifampin [nonsubstrate]) in comparison with ciprofloxacin against intracellular P. aeruginosa (strains with variable efflux levels) in THP-1 monocytes exposed over 24 h to antibiotics alone (0.003 to 100× MIC) or combined with EPIs. Pharmacodynamic parameters (apparent static concentrations [C s] and maximal relative efficacy [E max]) were calculated using the Hill equation of concentration-response curves. PAβN and NV731 moderately reduced (0 to 4 doubling dilutions) antibiotic MICs but did not affect their intracellular activity. NV716 markedly reduced (1 to 16 doubling dilutions) the MIC of all antibiotics (substrates or not for efflux; strains expressing efflux or not); it also improved their relative potency and maximal efficacy (i.e., lower C s; more negative E max) intracellularly. In parallel, NV716 reduced the persister fraction in stationary cultures when combined with ciprofloxacin. In contrast to PAβN and NV731, which act only as EPIs against extracellular bacteria, NV716 can resensitize P. aeruginosa to antibiotics whether they are substrates or not for efflux, both extracellularly and intracellularly. This suggests a complex mode of action that goes beyond a simple inhibition of efflux to reduce bacterial persistence. NV716 appears to be a useful adjuvant, including to disused antibiotics with low antipseudomonal activity, to improve their activity, including against intracellular P. aeruginosa.
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16
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Nguyen TK, Peyrusson F, Dodémont M, Pham NH, Nguyen HA, Tulkens PM, Van Bambeke F. The Persister Character of Clinical Isolates of Staphylococcus aureus Contributes to Faster Evolution to Resistance and Higher Survival in THP-1 Monocytes: A Study With Moxifloxacin. Front Microbiol 2020; 11:587364. [PMID: 33329458 PMCID: PMC7719683 DOI: 10.3389/fmicb.2020.587364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/16/2020] [Indexed: 12/26/2022] Open
Abstract
Staphylococcus aureus may cause relapsing infections. We previously showed that S. aureus SH1000 surviving intracellularly to bactericidal antibiotics are persisters. Here, we used 54 non-duplicate clinical isolates to assess links between persistence, resistance evolution, and intracellular survival, using moxifloxacin throughout as test bactericidal antibiotic. The relative persister fraction (RPF: percentage of inoculum surviving to 100× MIC moxifloxacin in stationary phase culture for each isolate relative to ATCC 25923) was determined to categorize isolates with low (≤10) or high (>10) RPF. Evolution to resistance (moxifloxacin MIC ≥ 0.5 mg/L) was triggered by serial passages at 0.5× MIC (with daily concentration readjustments). Intracellular moxifloxacin maximal efficacy (Emax) was determined by 24 h concentration-response experiments [pharmacodynamic model (Hill-Langmuir)] with infected THP-1 monocytes exposed to moxifloxacin (0.01 to 100× MIC) after phagocytosis. Division of intracellular survivors was followed by green fluorescence protein dilution (FACS). Most (30/36) moxifloxacin-susceptible isolates showed low RPF but all moxifloxacin-resistant (n = 18) isolates harbored high RPF. Evolution to resistance of susceptible isolates was faster for those with high vs. low RPF (with SOS response and topoisomerase-encoding genes overexpression). Intracellularly, moxifloxacin Emax was decreased (less negative) for isolates with high vs. low RPF, independently from resistance. Moxifloxacin intracellular survivors were non-dividing. The data demonstrate and quantitate persisters in clinical isolates of S. aureus, and show that this phenotype accelerates resistance evolution and is associated with intracellular survival in spite of high antibiotic concentrations. Isolates with high RPF may represent a possible cause of treatment failure not directly related to resistance in patients receiving active antibiotics.
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Affiliation(s)
- Tiep K Nguyen
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium.,Department of Pharmaceutical Industry, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Frédéric Peyrusson
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Magali Dodémont
- Centre National de Référence des Staphylocoques, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB) Site Anderlecht, Hôpital Erasme - Cliniques Universitaires de Bruxelles, Brussels, Belgium
| | - Nhung H Pham
- Department of Microbiology, Bach Mai Hospital, Hanoi, Vietnam.,Microbiology Department, Hanoi Medical University, Hanoi, Vietnam
| | - Hoang A Nguyen
- The National Center for Drug Information and Adverse Drug Reactions Monitoring, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Paul M Tulkens
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Françoise Van Bambeke
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
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17
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Memar MY, Yekani M, Celenza G, Poortahmasebi V, Naghili B, Bellio P, Baghi HB. The central role of the SOS DNA repair system in antibiotics resistance: A new target for a new infectious treatment strategy. Life Sci 2020; 262:118562. [PMID: 33038378 DOI: 10.1016/j.lfs.2020.118562] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/15/2020] [Accepted: 10/01/2020] [Indexed: 01/19/2023]
Abstract
Bacteria have a considerable ability and potential to acquire resistance against antimicrobial agents by acting diverse mechanisms such as target modification or overexpression, multidrug transporter systems, and acquisition of drug hydrolyzing enzymes. Studying the mechanisms of bacterial cell physiology is mandatory for the development of novel strategies to control the antimicrobial resistance phenomenon, as well as for the control of infections in clinics. The SOS response is a cellular DNA repair mechanism that has an essential role in the bacterial biologic process involved in resistance to antibiotics. The activation of the SOS network increases the resistance and tolerance of bacteria to stress and, as a consequence, to antimicrobial agents. Therefore, SOS can be an applicable target for the discovery of new antimicrobial drugs. In the present review, we focus on the central role of SOS response in bacterial resistance mechanisms and its potential as a new target for control of resistant pathogens.
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Affiliation(s)
- Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Vahdat Poortahmasebi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrooz Naghili
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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18
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Soares A, Alexandre K, Etienne M. Tolerance and Persistence of Pseudomonas aeruginosa in Biofilms Exposed to Antibiotics: Molecular Mechanisms, Antibiotic Strategies and Therapeutic Perspectives. Front Microbiol 2020; 11:2057. [PMID: 32973737 PMCID: PMC7481396 DOI: 10.3389/fmicb.2020.02057] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/05/2020] [Indexed: 01/19/2023] Open
Abstract
Pseudomonas aeruginosa biofilm-related infections are difficult to treat with antibiotics. Along the different layers of the biofilm, the P. aeruginosa population is heterogeneous, exhibiting an extreme ability to adapt his metabolic activity to the local microenvironment. At the deepest layers of the biofilm is a subset of dormant cells, called persister cells. Though antimicrobial failure might be multifactorial, it is now demonstrated that these persister cells, genetically identical to a fully susceptible strain, but phenotypically divergent, are highly tolerant to antibiotics, and contribute to antimicrobial failure. By eradicating susceptible, metabolically active cells, antibiotics bring out pre-existing persister cells. The biofilm mode of growth creates microenvironment conditions that activate stringent response mechanisms, SOS response and toxin-antitoxin systems that render the bacterial population highly tolerant to antibiotics. Using diverse, not standardized, models of biofilm infection, a large panel of antibiotic regimen has been evaluated. They demonstrated that biofilm growth had an unequal impact of antibiotic activity, colistin and meropenem being the less impacted antibiotics. Different combination and sequential antimicrobial therapies were also evaluated, and could be partially efficient, but none succeeded in eradicating persister cells, so that non-antibiotic alternative strategies are currently under development. This article reviews the molecular mechanisms involved in antibiotic tolerance and persistence in P. aeruginosa biofilm infections. A review of the antimicrobial regimen evaluated for the treatment of P. aeruginosa biofilm infection is also presented. While tremendous progress has been made in the understanding of biofilm-related infections, alternative non-antibiotic strategies are now urgently needed.
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Affiliation(s)
- Anaïs Soares
- GRAM 2.0, EA 2656, Normandie University, UNIROUEN, Rouen, France
| | - Kévin Alexandre
- GRAM 2.0, EA 2656, Normandie University, UNIROUEN, Rouen, France.,Infectious Diseases Department, Rouen University Hospital, Rouen, France
| | - Manuel Etienne
- GRAM 2.0, EA 2656, Normandie University, UNIROUEN, Rouen, France.,Infectious Diseases Department, Rouen University Hospital, Rouen, France
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19
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Mohiuddin SG, Hoang T, Saba A, Karki P, Orman MA. Identifying Metabolic Inhibitors to Reduce Bacterial Persistence. Front Microbiol 2020; 11:472. [PMID: 32292393 PMCID: PMC7118205 DOI: 10.3389/fmicb.2020.00472] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 03/04/2020] [Indexed: 01/08/2023] Open
Abstract
Bacterial persisters are rare phenotypic variants that are temporarily tolerant to high concentrations of antibiotics. We have previously discovered that stationary-phase-cell subpopulations exhibiting high redox activities were less capable of producing proteins and resuming growth upon their dilution into fresh media. The redox activities of these cells were maintained by endogenous protein and RNA degradation, resulting in self-inflicted damage that transiently repressed the cellular functions targeted by antibiotics. Here, we showed that pretreatment of stationary-phase cells with an ATP synthase inhibitor, chlorpromazine hydrochloride (CPZ), significantly reduced stationary-phase-redox activities and protein degradation, and yielded cells that were more susceptible to cell death when exposed to antibiotics in fresh media. Leveraging this knowledge, we developed an assay integrating a degradable fluorescent protein system and a small library, containing FDA-approved drugs and antibiotics, to detect medically relevant drugs that potentially target persister metabolism. We identified a subset of chemical inhibitors, including polymyxin B, poly-L-lysine and phenothiazine anti-psychotic drugs, that were able to reduce the persistence phenotype in Escherichia coli. These chemical inhibitors also reduced Pseudomonas aeruginosa persistence, potentially verifying the existence of similar mechanisms in a medically relevant organism.
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Affiliation(s)
- Sayed Golam Mohiuddin
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Thuy Hoang
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Adesola Saba
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Prashant Karki
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Mehmet A Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
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20
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Verstraeten N, Gkekas S, Kint CI, Deckers B, Van den Bergh B, Herpels P, Louwagie E, Knapen W, Wilmaerts D, Dewachter L, Fauvart M, Singh RK, Michiels J, Versées W. Biochemical determinants of ObgE-mediated persistence. Mol Microbiol 2019; 112:1593-1608. [PMID: 31498933 DOI: 10.1111/mmi.14382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2019] [Indexed: 11/30/2022]
Abstract
Obg is a versatile GTPase that plays a pivotal role in bacterial persistence. We previously showed that the Escherichia coli homolog ObgE exerts this activity through transcriptional activation of a toxin-antitoxin module and subsequent membrane depolarization. Here, we assessed the role of G-domain functionality in ObgE-mediated persistence. Through screening of a mutant library, we identified five obgE alleles (with substitutions G166V, D246G, S270I, N283I and I313N) that have lost their persistence function and no longer activate hokB expression. These alleles support viability of a strain otherwise deprived of ObgE, indicating that ObgE's persistence function can be uncoupled from its essential role. Based on the ObgE crystal structure, we designed two additional mutant proteins (T193A and D286Y), one of which (D286Y) no longer affects persistence. Using isothermal titration calorimetry, stopped-flow experiments and kinetics, we subsequently assessed nucleotide binding and GTPase activity in all mutants. With the exception of the S270I mutant that is possibly affected in protein-protein interactions, all mutants that have lost their persistence function display severely reduced binding to GDP or the alarmone ppGpp. However, we find no clear relation between persistence and GTP or pppGpp binding nor with GTP hydrolysis. Combined, our results signify an important step toward understanding biochemical determinants underlying persistence.
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Affiliation(s)
- Natalie Verstraeten
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium
| | - Sotirios Gkekas
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
| | - Cyrielle Ines Kint
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium
| | - Babette Deckers
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
| | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium
| | - Pauline Herpels
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium
| | - Elen Louwagie
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium
| | - Wouter Knapen
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium
| | - Dorien Wilmaerts
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium
| | - Liselot Dewachter
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium.,Department of Life Science Technologies, Smart Systems and Emerging Technologies Unit, IMEC, Kapeldreef 75, 3001, Leuven, Belgium
| | - Ranjan Kumar Singh
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 20 Box 2460, 3001, Leuven, Belgium
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
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21
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Ciofu O, Tolker-Nielsen T. Tolerance and Resistance of Pseudomonas aeruginosa Biofilms to Antimicrobial Agents-How P. aeruginosa Can Escape Antibiotics. Front Microbiol 2019; 10:913. [PMID: 31130925 PMCID: PMC6509751 DOI: 10.3389/fmicb.2019.00913] [Citation(s) in RCA: 371] [Impact Index Per Article: 74.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/10/2019] [Indexed: 11/24/2022] Open
Abstract
Pseudomonas aeruginosa is one of the six bacterial pathogens, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp., which are commonly associated with antimicrobial resistance, and denoted by their acronym ESKAPE. P. aeruginosa is also recognized as an important cause of chronic infections due to its ability to form biofilms, where the bacteria are present in aggregates encased in a self-produced extracellular matrix and are difficult or impossible to eradicate with antibiotic treatment. P. aeruginosa causes chronic infections in the lungs of patients with cystic fibrosis and chronic obstructive lung disease, as well as chronic urinary tract infections in patients with permanent bladder catheter, and ventilator-associated pneumonia in intubated patients, and is also an important pathogen in chronic wounds. Antibiotic treatment cannot eradicate these biofilm infections due to their intrinsic antibiotic tolerance and the development of mutational antibiotic resistance. The tolerance of biofilms to antibiotics is multifactorial involving physical, physiological, and genetic determinants, whereas the antibiotic resistance of bacteria in biofilms is caused by mutations and driven by the repeated exposure of the bacteria to high levels of antibiotics. In this review, both the antimicrobial tolerance and the development of resistance to antibiotics in P. aeruginosa biofilms are discussed. Possible therapeutic approaches based on the understanding of the mechanisms involved in the tolerance and resistances of biofilms to antibiotics are also addressed.
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Affiliation(s)
- Oana Ciofu
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
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22
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Mandal S, Njikan S, Kumar A, Early JV, Parish T. The relevance of persisters in tuberculosis drug discovery. MICROBIOLOGY-SGM 2019; 165:492-499. [PMID: 30775961 DOI: 10.1099/mic.0.000760] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Bacterial persisters are a subpopulation of cells that exhibit phenotypic resistance during exposure to a lethal dose of antibiotics. They are difficult to target and thought to contribute to the long treatment duration required for tuberculosis. Understanding the molecular and cellular biology of persisters is critical to finding new tuberculosis drugs that shorten treatment. This review focuses on mycobacterial persisters and describes the challenges they pose in tuberculosis therapy, their characteristics and formation, how persistence leads to resistance, and the current approaches being used to target persisters within mycobacterial drug discovery.
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Affiliation(s)
- Soma Mandal
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Samuel Njikan
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Anuradha Kumar
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Julie V Early
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
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23
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Sulaiman JE, Lam H. Application of proteomics in studying bacterial persistence. Expert Rev Proteomics 2019; 16:227-239. [DOI: 10.1080/14789450.2019.1575207] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Jordy Evan Sulaiman
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Kowloon, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Kowloon, Hong Kong
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24
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Lewenza S, Abboud J, Poon K, Kobryn M, Humplik I, Bell JR, Mardan L, Reckseidler-Zenteno S. Pseudomonas aeruginosa displays a dormancy phenotype during long-term survival in water. PLoS One 2018; 13:e0198384. [PMID: 30235203 PMCID: PMC6147739 DOI: 10.1371/journal.pone.0198384] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/28/2018] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas aeruginosa is capable of long-term survival in water, which may serve as a reservoir for infection. Although viable cell counts of PAO1 incubated in water remain stable throughout 8 weeks, LIVE/DEAD staining indicated a high proportion of cells stained with propidium iodide (PI). The proportion of PI-stained cells increased by 4 weeks, then decreased again by 8 weeks, suggesting an adaptive response. This was also evident in an observed shift in cell morphology from a rod to a coccoid shape after 8 weeks. Fluorescence-activated cell sorting (FACS) was used to recover PI-stained cells, which were plated and shown to be viable, indicating that PI-stained cells were membrane-compromised but still cultivable. PAO1 mid-log cells in water were labeled with the dsDNA-binding dye PicoGreen to monitor viability as well as DNA integrity, which demonstrated that the population remains viable and transitions towards increased dsDNA staining. Metabolic activity was found to decrease significantly in water by 4 weeks. The PAO1 outer membrane became less permeable and more resistant to polymyxin B damage in water, and the profile of total membrane lipids changed over time. Among the ~1400 transcriptional lux fusions, gene expression in water revealed that the majority of genes were repressed, but subsets of genes were induced at particular time points. In summary, these results indicate that P. aeruginosa is dormant in water and this adaptation involves a complex pattern of gene regulation and changes to the cell to promote long-term survival and antibiotic tolerance. The approach of P. aeruginosa incubated in water may be useful to study antibiotic tolerance and the mechanisms of dormancy and survival in nutrient limiting conditions.
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Affiliation(s)
- Shawn Lewenza
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada.,Department of Microbiology, Immunology, and Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jason Abboud
- Department of Microbiology, Immunology, and Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Karen Poon
- Department of Microbiology, Immunology, and Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Madison Kobryn
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada
| | - Istvan Humplik
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada
| | - John Rainer Bell
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada.,Department of Microbiology, Immunology, and Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Laura Mardan
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada
| | - Shauna Reckseidler-Zenteno
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada.,Department of Microbiology, Immunology, and Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
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25
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Gaviard C, Jouenne T, Hardouin J. Proteomics ofPseudomonas aeruginosa: the increasing role of post-translational modifications. Expert Rev Proteomics 2018; 15:757-772. [DOI: 10.1080/14789450.2018.1516550] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Charlotte Gaviard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
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26
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Khandekar S, Liebens V, Fauvart M, Tulkens PM, Michiels J, Van Bambeke F. The Putative De- N-acetylase DnpA Contributes to Intracellular and Biofilm-Associated Persistence of Pseudomonas aeruginosa Exposed to Fluoroquinolones. Front Microbiol 2018; 9:1455. [PMID: 30042739 PMCID: PMC6048251 DOI: 10.3389/fmicb.2018.01455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 06/12/2018] [Indexed: 11/30/2022] Open
Abstract
Persisters are the fraction of antibiotic-exposed bacteria transiently refractory to killing and are recognized as a cause of antibiotic treatment failure. The putative de-N-acetylase DnpA increases persister levels in Pseudomonas aeruginosa upon exposure to fluoroquinolones in broth. In this study the wild-type PAO1 and its dnpA insertion mutant (dnpA::Tn) were used in parallel and compared for their capacity to generate persisters in broth (surviving fraction after exposure to high antibiotic concentrations) and their susceptibility to antibiotics in models of intracellular infection of THP-1 monocytes and of biofilms grown in microtiter plates. Multiplication in monocytes was evaluated by fluorescence dilution of GFP (expressed under the control of an inducible promoter) using flow cytometry. Gene expression was measured by quantitative RT-PCR. When exposed to fluoroquinolones (ciprofloxacin or levofloxacin) but not to meropenem or amikacin, the dnpA::Tn mutant showed a 3- to 10-fold lower persister fraction in broth. In infected monocytes, fluoroquinolones (but not the other antibiotics) were more effective (difference in Emax: 1.5 log cfu) against the dnpA::Tn mutant than against the wild-type PAO1. Dividing intracellular bacteria were more frequently seen (1.5 to 1.9-fold) with the fluoroquinolone-exposed dnpA::Tn mutant than with its parental strain. Fluoroquinolones (but not the other antibiotics) were also 3-fold more potent to prevent biofilm formation by the dnpA::Tn mutant than by PAO1 as well as to act upon biofilms (1–3 days of maturity) formed by the mutant than by the parental strain. Fluoroquinolones induced the expression of gyrA (4.5–7 fold) and mexX (3.6–5.4 fold) in the parental strain but to a lower extent (3–4-fold for gyrA and 1.8–2.8-fold for mexX, respectively) in the dnpA::Tn mutant. Thus, our data show that a dnpA insertion mutant of P. aeruginosa is more receptive to fluoroquinolone antibacterial effects than its parental strain in infected monocytes or in biofilms. The mechanism of this higher responsiveness could involve a reduced overexpression of the fluoroquinolone target.
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Affiliation(s)
- Shaunak Khandekar
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Veerle Liebens
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium.,imec, Leuven, Belgium
| | - Paul M Tulkens
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Françoise Van Bambeke
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
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27
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Gaviard C, Broutin I, Cosette P, Dé E, Jouenne T, Hardouin J. Lysine Succinylation and Acetylation in Pseudomonas aeruginosa. J Proteome Res 2018; 17:2449-2459. [DOI: 10.1021/acs.jproteome.8b00210] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Charlotte Gaviard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Isabelle Broutin
- LCRB, UMR 8015, CNRS, University Paris Descartes, Sorbonne Paris City, 75270 Paris Cedex 06, France
| | - Pascal Cosette
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Emmanuelle Dé
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
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28
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Fighting bacterial persistence: Current and emerging anti-persister strategies and therapeutics. Drug Resist Updat 2018; 38:12-26. [DOI: 10.1016/j.drup.2018.03.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/07/2018] [Accepted: 03/25/2018] [Indexed: 01/13/2023]
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29
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Reduction in adaptor amounts establishes degradation hierarchy among protease substrates. Proc Natl Acad Sci U S A 2018; 115:E4483-E4492. [PMID: 29686082 DOI: 10.1073/pnas.1722246115] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
ATP-dependent proteases control critical cellular processes, including development, physiology, and virulence. A given protease may recognize a substrate directly via an unfoldase domain or subunit or indirectly via an adaptor that delivers the substrate to the unfoldase. We now report that cells achieve differential stability among substrates of a given protease by modulating adaptor amounts. We establish that the regulatory protein PhoP represses transcription of the gene specifying the ClpAP protease adaptor ClpS when the bacteria Salmonella enterica and Escherichia coli experience low cytoplasmic Mg2+ The resulting decrease in ClpS amounts diminishes proteolysis of several ClpSAP-dependent substrates, including the putrescine aminotransferase Oat, which heightens the formation of antibiotic persisters, and the transcriptional regulators UvrY and PhoP, which alter the expression of genes controlled by these proteins. By contrast, the decrease in ClpS amounts did not impact the abundance of the ClpSAP substrate FtsA, reflecting that FtsA binds to ClpS more tightly than to UvrY and PhoP. Our findings show how physiological conditions that reduce adaptor amounts modify the abundance of selected substrates of a given protease.
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30
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Identification of 1-((2,4-Dichlorophenethyl)Amino)-3-Phenoxypropan-2-ol, a Novel Antibacterial Compound Active against Persisters of Pseudomonas aeruginosa. Antimicrob Agents Chemother 2017. [PMID: 28630188 DOI: 10.1128/aac.00836-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antibiotics typically fail to completely eradicate a bacterial population, leaving a small fraction of transiently antibiotic-tolerant persister cells intact. Persisters are therefore seen to be a major cause of treatment failure and greatly contribute to the recalcitrant nature of chronic infections. The current study focused on Pseudomonas aeruginosa, a Gram-negative pathogen belonging to the notorious ESKAPE group of pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and, due to increasing resistance against most conventional antibiotics, posing a serious threat to human health. Greatly contributing to the difficult treatment of P. aeruginosa infections is the presence of persister cells, and elimination of these cells would therefore significantly improve patient outcomes. In this study, a small-molecule library was screened for compounds that, in combination with the fluoroquinolone antibiotic ofloxacin, reduced the number of P. aeruginosa persisters compared to the number achieved with treatment with the antibiotic alone. Based on the early structure-activity relationship, 1-((2,4-dichlorophenethyl)amino)-3-phenoxypropan-2-ol (SPI009) was selected for further characterization. Combination of SPI009 with mechanistically distinct classes of antibiotics reduced the number of persisters up to 106-fold in both lab strains and clinical isolates of P. aeruginosa Further characterization of the compound revealed a direct and efficient killing of persister cells. SPI009 caused no erythrocyte damage and demonstrated minor cytotoxicity. In conclusion, we identified a novel antipersister compound active against P. aeruginosa with promising applications for the design of novel, case-specific combination therapies in the fight against chronic infections.
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31
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Harms A, Maisonneuve E, Gerdes K. Mechanisms of bacterial persistence during stress and antibiotic exposure. Science 2017; 354:354/6318/aaf4268. [PMID: 27980159 DOI: 10.1126/science.aaf4268] [Citation(s) in RCA: 516] [Impact Index Per Article: 73.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bacterial persister cells avoid antibiotic-induced death by entering a physiologically dormant state and are considered a major cause of antibiotic treatment failure and relapsing infections. Such dormant cells form stochastically, but also in response to environmental cues, by various pathways that are usually controlled by the second messenger (p)ppGpp. For example, toxin-antitoxin modules have been shown to play a major role in persister formation in many model systems. More generally, the diversity of molecular mechanisms driving persister formation is increasingly recognized as the cause of physiological heterogeneity that underlies collective multistress and multidrug tolerance of persister subpopulations. In this Review, we summarize the current state of the field and highlight recent findings, with a focus on the molecular basis of persister formation and heterogeneity.
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Affiliation(s)
- Alexander Harms
- Center of Excellence for Bacterial Stress Response and Persistence (BASP), Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Etienne Maisonneuve
- Center of Excellence for Bacterial Stress Response and Persistence (BASP), Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Kenn Gerdes
- Center of Excellence for Bacterial Stress Response and Persistence (BASP), Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
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32
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Ciofu O, Rojo-Molinero E, Macià MD, Oliver A. Antibiotic treatment of biofilm infections. APMIS 2017; 125:304-319. [PMID: 28407419 DOI: 10.1111/apm.12673] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 01/10/2017] [Indexed: 12/24/2022]
Abstract
Bacterial biofilms are associated with a wide range of infections, from those related to exogenous devices, such as catheters or prosthetic joints, to chronic tissue infections such as those occurring in the lungs of cystic fibrosis patients. Biofilms are recalcitrant to antibiotic treatment due to multiple tolerance mechanisms (phenotypic resistance). This causes persistence of biofilm infections in spite of antibiotic exposure which predisposes to antibiotic resistance development (genetic resistance). Understanding the interplay between phenotypic and genetic resistance mechanisms acting on biofilms, as well as appreciating the diversity of environmental conditions of biofilm infections which influence the effect of antibiotics are required in order to optimize the antibiotic treatment of biofilm infections. Here, we review the current knowledge on phenotypic and genetic resistance in biofilms and describe the potential strategies for the antibiotic treatment of biofilm infections. Of note is the optimization of PK/PD parameters in biofilms, high-dose topical treatments, combined and sequential/alternate therapies or the use antibiotic adjuvants.
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Affiliation(s)
- Oana Ciofu
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Estrella Rojo-Molinero
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain
| | - María D Macià
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain
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33
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Van den Bergh B, Fauvart M, Michiels J. Formation, physiology, ecology, evolution and clinical importance of bacterial persisters. FEMS Microbiol Rev 2017; 41:219-251. [DOI: 10.1093/femsre/fux001] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/12/2017] [Indexed: 12/19/2022] Open
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Abstract
Persisters are dormant variants that form a subpopulation of cells tolerant to antibiotics. Persisters are largely responsible for the recalcitrance of chronic infections to therapy. In Escherichia coli, one widely accepted model of persister formation holds that stochastic accumulation of ppGpp causes activation of the Lon protease that degrades antitoxins; active toxins then inhibit translation, resulting in dormant, drug-tolerant persisters. We found that various stresses induce toxin-antitoxin (TA) expression but that induction of TAs does not necessarily increase persisters. The 16S rRNA promoter rrnB P1 was proposed to be a persister reporter and an indicator of toxin activation regulated by ppGpp. Using fluorescence-activated cell sorting (FACS), we confirmed the enrichment for persisters in the fraction of rrnB P1-gfp dim cells; however, this is independent of toxin-antitoxins. rrnB P1 is coregulated by ppGpp and ATP. We show that rrnB P1 can report persisters in a relA/spoT deletion background, suggesting that rrnB P1 is a persister marker responding to ATP. Consistent with this finding, decreasing the level of ATP by arsenate treatment causes drug tolerance. Lowering ATP slows translation and prevents the formation of DNA double-strand breaks upon fluoroquinolone treatment. We conclude that variation in ATP levels leads to persister formation by decreasing the activity of antibiotic targets. Persisters are a subpopulation of antibiotic-tolerant cells responsible for the recalcitrance of chronic infections. Our current understanding of persister formation is primarily based on studies of E. coli. The activation of toxin-antitoxin systems by ppGpp has become a widely accepted model for persister formation. In this study, we found that stress-induced activation of mRNA interferase-type toxins does not necessarily cause persister formation. We also found that the persister marker rrnB P1 reports persister cells because it detects a drop in cellular ATP levels. Consistent with this, lowering the ATP level decreases antibiotic target activity and, thus, leads to persister formation. We conclude that stochastic variation in ATP is the main mechanism of persister formation. A decrease in ATP provides a satisfactory explanation for the drug tolerance of persisters, since bactericidal antibiotics act by corrupting energy-dependent targets.
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35
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Active efflux in dormant bacterial cells - New insights into antibiotic persistence. Drug Resist Updat 2016; 30:7-14. [PMID: 28363336 DOI: 10.1016/j.drup.2016.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/14/2016] [Accepted: 11/02/2016] [Indexed: 01/07/2023]
Abstract
Bacterial persisters are phenotypic variants of an isogenic cell population that can survive antibiotic treatment and resume growth after the antibiotics have been removed. Cell dormancy has long been considered the principle mechanism underlying persister formation. However, dormancy alone is insufficient to explain the full range of bacterial persistence. Our recent work revealed that in addition to 'passive defense' via dormancy, persister cells employ 'active defense' via enhanced efflux activity to expel drugs. This finding suggests that persisters combine two seemingly contradictory mechanisms to tolerate antibiotic attack. Here, we review the passive and active aspects of persister formation, discuss new insights into the process, and propose new techniques that can facilitate the study of bacterial persistence.
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36
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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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37
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Michiels JE, Van den Bergh B, Verstraeten N, Fauvart M, Michiels J. In Vitro Emergence of High Persistence upon Periodic Aminoglycoside Challenge in the ESKAPE Pathogens. Antimicrob Agents Chemother 2016; 60:4630-7. [PMID: 27185802 PMCID: PMC4958152 DOI: 10.1128/aac.00757-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/10/2016] [Indexed: 12/31/2022] Open
Abstract
Health care-associated infections present a major threat to modern medical care. Six worrisome nosocomial pathogens-Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.-are collectively referred to as the "ESKAPE bugs." They are notorious for extensive multidrug resistance, yet persistence, or the phenotypic tolerance displayed by a variant subpopulation, remains underappreciated in these pathogens. Importantly, persistence can prevent eradication of antibiotic-sensitive bacterial populations and is thought to act as a catalyst for the development of genetic resistance. Concentration- and time-dependent aminoglycoside killing experiments were used to investigate persistence in the ESKAPE pathogens. Additionally, a recently developed method for the experimental evolution of persistence was employed to investigate adaptation to high-dose, extended-interval aminoglycoside therapy in vitro We show that ESKAPE pathogens exhibit biphasic killing kinetics, indicative of persister formation. In vitro cycling between aminoglycoside killing and persister cell regrowth, evocative of clinical high-dose extended-interval therapy, caused a 37- to 213-fold increase in persistence without the emergence of resistance. Increased persistence also manifested in biofilms and provided cross-tolerance to different clinically important antibiotics. Together, our results highlight a possible drawback of intermittent, high-dose antibiotic therapy and suggest that clinical diagnostics might benefit from taking into account persistence.
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Affiliation(s)
| | | | | | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium Smart Systems and Emerging Technologies Unit, Department of Life Science Technologies, imec, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
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38
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Experimental Evolution of Escherichia coli Persister Levels Using Cyclic Antibiotic Treatments. Methods Mol Biol 2016; 1333:131-43. [PMID: 26468106 DOI: 10.1007/978-1-4939-2854-5_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Persister cells are difficult to study owing to their transient nature and their usually small number in bacterial populations. In the past, numerous attempts have been made to elucidate persistence mechanisms. However, because of the challenges involved in studying persisters and the clear redundancy in mechanisms underlying their generation, our knowledge of molecular pathways to persistence remains incomplete. Here, we describe how to use experimental evolution with cyclic antibiotic treatments to generate mutants with an increased persister level in stationary phase, ranging from the initial ancestral level up to 100 %. This method will help to unravel molecular pathways to persistence, and opens up a myriad of new possibilities in persister research, such as the convenient study of nearly pure persister cultures and the possibility to investigate the role of time and environmental aspects in the evolution of persistence.
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39
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Kaldalu N, Hauryliuk V, Tenson T. Persisters-as elusive as ever. Appl Microbiol Biotechnol 2016; 100:6545-6553. [PMID: 27262568 PMCID: PMC4939303 DOI: 10.1007/s00253-016-7648-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/23/2016] [Accepted: 05/25/2016] [Indexed: 12/27/2022]
Abstract
Persisters—a drug-tolerant sub-population in an isogenic bacterial culture—have been featured throughout the last decade due to their important role in recurrent bacterial infections. Numerous investigations detail the mechanisms responsible for the formation of persisters and suggest exciting strategies for their eradication. In this review, we argue that the very term “persistence” is currently used to describe a large and heterogeneous set of physiological phenomena that are functions of bacterial species, strains, growth conditions, and antibiotics used in the experiments. We caution against the oversimplification of the mechanisms of persistence and urge for a more rigorous validation of the applicability of these mechanisms in each case.
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Affiliation(s)
- Niilo Kaldalu
- University of Tartu, Institute of Technology, Nooruse 1, 50411, Tartu, Estonia
| | - Vasili Hauryliuk
- University of Tartu, Institute of Technology, Nooruse 1, 50411, Tartu, Estonia
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, SE-901 87, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, SE-901 87, Umeå, Sweden
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411, Tartu, Estonia.
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40
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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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41
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A PhoPQ-Regulated ABC Transporter System Exports Tetracycline in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2016; 60:3016-24. [PMID: 26953208 DOI: 10.1128/aac.02986-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/29/2016] [Indexed: 12/21/2022] Open
Abstract
Pseudomonas aeruginosa is an important human pathogen whose infections are difficult to treat due to its high intrinsic resistance to many antibiotics. Here, we show that the disruption of PA4456, encoding the ATP binding component of a putative ATP-binding cassette (ABC) transporter, increased the bacterium's susceptible to tetracycline and other antibiotics or toxic chemicals. Fluorescence spectroscopy and antibiotic accumulation tests showed that the interruption of the ABC transporter caused increased intracellular accumulation of tetracycline, demonstrating a role of the ABC transporter in tetracycline expulsion. Site-directed mutagenesis proved that the conserved residues of E170 in the Walker B motif and H203 in the H-loop, which are important for ATP hydrolysis, were essential for the function of PA4456. Through a genome-wide search, the PhoPQ two-component system was identified as a regulator of the computationally predicted PA4456-4452 operon that encodes the ABC transporter system. A >5-fold increase of the expression of this operon was observed in the phoQ mutant. The results obtained also show that the expression of the phzA1B1C1D1E1 operon and the production of pyocyanin were significantly higher in the ABC transporter mutant, signifying a connection between the ABC transporter and pyocyanin production. These results indicated that the PhoPQ-regulated ABC transporter is associated with intrinsic resistance to antibiotics and other adverse compounds in P. aeruginosa, probably by extruding them out of the cell.
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Van Acker H, Coenye T. The Role of Efflux and Physiological Adaptation in Biofilm Tolerance and Resistance. J Biol Chem 2016; 291:12565-12572. [PMID: 27129224 DOI: 10.1074/jbc.r115.707257] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Microbial biofilms demonstrate a decreased susceptibility to antimicrobial agents. Various mechanisms have been proposed to be involved in this recalcitrance. We focus on two of these factors. Firstly, the ability of sessile cells to actively mediate efflux of antimicrobial compounds has a profound impact on resistance and tolerance, and several studies point to the existence of biofilm-specific efflux systems. Secondly, biofilm-specific stress responses have a marked influence on cellular physiology, and contribute to the occurrence of persister cells. We provide an overview of the data that demonstrate that both processes are important for survival following exposure to antimicrobial agents.
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Affiliation(s)
- Heleen Van Acker
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium.
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Gonçalves FDA, de Carvalho CCCR. Phenotypic Modifications in Staphylococcus aureus Cells Exposed to High Concentrations of Vancomycin and Teicoplanin. Front Microbiol 2016; 7:13. [PMID: 26834731 PMCID: PMC4724715 DOI: 10.3389/fmicb.2016.00013] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 01/08/2016] [Indexed: 12/31/2022] Open
Abstract
Bacterial cells are known to change the fatty acid (FA) composition of the phospholipids as a phenotypic response to environmental conditions and to the presence of toxic compounds such as antibiotics. In the present study, Staphylococcus aureus cells collected during the exponential growth phase were challenged with 50 and 100 mg/L of vancomycin and teicoplanin, which are concentrations high enough to kill the large majority of the cell population. Colony-forming unit counts showed biphasic killing kinetics, typical for persister cell enrichment, in both antibiotics and concentrations tested. However, fluorescence microscopy showed the existence of viable but non-culturable (VBNC) cells in a larger number than that of possible persister cells. The analysis of the FA composition of the cells showed that, following antibiotic exposure up to 6 h, the survivor cells have an increased percentage of saturated FAs, a significant reduced percentage of branched FAs and an increased iso/anteiso branched FA ratio when compared to cells exhibiting a regular phenotype. This should result in lower membrane fluidity. However, cells exposed for 8-24 h presented an increased branched/saturated and lower iso/anteiso branched FA ratios, and thus increased membrane fluidity. Furthermore, the phenotypic changes were transmitted to daughter cells grown in drug-free media. The fact that VBNC cells presented nearly the same FA composition as those obtained after cell growth in drug-free media, which could only be the result of growth of persister cells, suggest that VBNC and persister phenotypes share the same type of response to antibiotics at the lipid level.
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Affiliation(s)
- Fábio D A Gonçalves
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa Lisbon, Portugal
| | - Carla C C R de Carvalho
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa Lisbon, Portugal
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Roberfroid S, Vanderleyden J, Steenackers H. Gene expression variability in clonal populations: Causes and consequences. Crit Rev Microbiol 2016; 42:969-84. [PMID: 26731119 DOI: 10.3109/1040841x.2015.1122571] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
During the last decade it has been shown that among cell variation in gene expression plays an important role within clonal populations. Here, we provide an overview of the different mechanisms contributing to gene expression variability in clonal populations. These are ranging from inherent variations in the biochemical process of gene expression itself, such as intrinsic noise, extrinsic noise and bistability to individual responses to variations in the local micro-environment, a phenomenon called phenotypic plasticity. Also genotypic variations caused by clonal evolution and phase variation can contribute to gene expression variability. Consequently, gene expression studies need to take these fluctuations in expression into account. However, frequently used techniques for expression quantification, such as microarrays, RNA sequencing, quantitative PCR and gene reporter fusions classically determine the population average of gene expression. Here, we discuss how these techniques can be adapted towards single cell analysis by integration with single cell isolation, RNA amplification and microscopy. Alternatively more qualitative selection-based techniques, such as mutant screenings, in vivo expression technology (IVET) and recombination-based IVET (RIVET) can be applied for detection of genes expressed only within a subpopulation. Finally, differential fluorescence induction (DFI), a protocol specially designed for single cell expression is discussed.
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Affiliation(s)
- Stefanie Roberfroid
- a Department of Microbial and Molecular Systems , Centre of Microbial and Plant Genetics, KU Leuven , Leuven , Belgium
| | - Jos Vanderleyden
- a Department of Microbial and Molecular Systems , Centre of Microbial and Plant Genetics, KU Leuven , Leuven , Belgium
| | - Hans Steenackers
- a Department of Microbial and Molecular Systems , Centre of Microbial and Plant Genetics, KU Leuven , Leuven , Belgium
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Rowe SE, Conlon BP, Keren I, Lewis K. Persisters: Methods for Isolation and Identifying Contributing Factors--A Review. Methods Mol Biol 2016; 1333:17-28. [PMID: 26468096 DOI: 10.1007/978-1-4939-2854-5_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Persister cells are phenotypic variants surviving a lethal dose of antibiotic, sufficient to kill the bulk of an exponential phase population. In this chapter we summarize current techniques to isolate persisters and discuss limitations associated with identifying mechanisms of persister formation.
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Affiliation(s)
- Sarah E Rowe
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Brian P Conlon
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Iris Keren
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave., Boston, MA, 02115, USA.
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Liebens V, Defraine V, Fauvart M. A Whole-Cell-Based High-Throughput Screening Method to Identify Molecules Targeting Pseudomonas aeruginosa Persister Cells. Methods Mol Biol 2016; 1333:113-120. [PMID: 26468104 DOI: 10.1007/978-1-4939-2854-5_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Despite its clinical relevance and the fact that the phenomenon of persistence was discovered in the 1940s, little is known about the mechanisms behind persister cell formation. Research in this field has mainly focused on the model organism Escherichia coli and few genetic determinants of persistence have been described in other bacterial species, impairing the development of target-based strategies to combat these antibiotic-tolerant cells. In this chapter we describe a top-down large-scale screening method capable of specifically identifying small molecule compounds that, in combination with conventional antibiotics, significantly reduce the persister fraction in Pseudomonas aeruginosa. The method is readily adaptable for other species. Further characterization and analysis of the mode of action of the identified compounds can provide additional insight into the mechanisms behind persister formation and can guide the development of future anti-persister therapies.
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Affiliation(s)
- Veerle Liebens
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven - University of Leuven, Kasteelpark Arenberg 20, Box 2460, Leuven, 3001, Belgium
| | - Valerie Defraine
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven - University of Leuven, Kasteelpark Arenberg 20, Box 2460, Leuven, 3001, Belgium
| | - Maarten Fauvart
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven - University of Leuven, Kasteelpark Arenberg 20, Box 2460, Leuven, 3001, Belgium.
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Orman MA, Brynildsen MP. Inhibition of stationary phase respiration impairs persister formation in E. coli. Nat Commun 2015; 6:7983. [PMID: 26246187 PMCID: PMC4530465 DOI: 10.1038/ncomms8983] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 07/02/2015] [Indexed: 12/15/2022] Open
Abstract
Bacterial persisters are rare phenotypic variants that temporarily tolerate high antibiotic concentrations. Persisters have been hypothesized to underlie the recalcitrance of biofilm infections, and strategies to eliminate these cells have the potential to improve treatment outcomes for many hospital-treated infections. Here we investigate the role of stationary phase metabolism in generation of type I persisters in Escherichia coli, which are those that are formed by passage through stationary phase. We find that persisters are unlikely to derive from bacteria with low redox activity, and that inhibition of respiration during stationary phase reduces persister levels by up to ∼1,000-fold. Loss of stationary phase respiratory activity prevents digestion of endogenous proteins and RNA, which yields bacteria that are more capable of translation, replication and concomitantly cell death when exposed to antibiotics. These findings establish bacterial respiration as a prime target for reducing the number of persisters formed in nutrient-depleted, non-growing populations. A few bacterial cells within a genetically homogeneous population can become ‘persisters', or temporarily tolerant to antibiotics. Here Orman and Brynildsen show that development of persisters among growth-arrested E. coli cells can be prevented by inhibiting bacterial respiration.
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Affiliation(s)
- Mehmet A Orman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersy 08544, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersy 08544, USA
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Verstraeten N, Knapen W, Kint C, Liebens V, Van den Bergh B, Dewachter L, Michiels J, Fu Q, David C, Fierro A, Marchal K, Beirlant J, Versées W, Hofkens J, Jansen M, Fauvart M, Michiels J. Obg and Membrane Depolarization Are Part of a Microbial Bet-Hedging Strategy that Leads to Antibiotic Tolerance. Mol Cell 2015; 59:9-21. [DOI: 10.1016/j.molcel.2015.05.011] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 03/20/2015] [Accepted: 05/01/2015] [Indexed: 10/25/2022]
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Ciofu O, Tolker-Nielsen T, Jensen PØ, Wang H, Høiby N. Antimicrobial resistance, respiratory tract infections and role of biofilms in lung infections in cystic fibrosis patients. Adv Drug Deliv Rev 2015; 85:7-23. [PMID: 25477303 DOI: 10.1016/j.addr.2014.11.017] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/11/2014] [Accepted: 11/23/2014] [Indexed: 02/08/2023]
Abstract
Lung infection is the main cause of morbidity and mortality in patients with cystic fibrosis and is mainly dominated by Pseudomonas aeruginosa. The biofilm mode of growth makes eradication of the infection impossible, and it causes a chronic inflammation in the airways. The general mechanisms of biofilm formation and antimicrobial tolerance and resistance are reviewed. Potential anti-biofilm therapeutic targets such as weakening of biofilms by quorum-sensing inhibitors or antibiotic killing guided by pharmacokinetics and pharmacodynamics of antibiotics are presented. The vicious circle of adaptive evolution of the persisting bacteria imposes important therapeutic challenges and requires development of new drug delivery systems able to reach the different niches occupied by the bacteria in the lung of cystic fibrosis patients.
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50
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Stepanyan K, Wenseleers T, Duéñez-Guzmán EA, Muratori F, Van den Bergh B, Verstraeten N, De Meester L, Verstrepen KJ, Fauvart M, Michiels J. Fitness trade-offs explain low levels of persister cells in the opportunistic pathogen Pseudomonas aeruginosa. Mol Ecol 2015; 24:1572-83. [PMID: 25721227 DOI: 10.1111/mec.13127] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 01/09/2015] [Accepted: 02/13/2015] [Indexed: 02/03/2023]
Abstract
Microbial populations often contain a fraction of slow-growing persister cells that withstand antibiotics and other stress factors. Current theoretical models predict that persistence levels should reflect a stable state in which the survival advantage of persisters under adverse conditions is balanced with the direct growth cost impaired under favourable growth conditions, caused by the nonreplication of persister cells. Based on this direct growth cost alone, however, it remains challenging to explain the observed low levels of persistence (<<1%) seen in the populations of many species. Here, we present data from the opportunistic human pathogen Pseudomonas aeruginosa that can explain this discrepancy by revealing various previously unknown costs of persistence. In particular, we show that in the absence of antibiotic stress, increased persistence is traded off against a lengthened lag phase as well as a reduced survival ability during stationary phase. We argue that these pleiotropic costs contribute to the very low proportions of persister cells observed among natural P. aeruginosa isolates (3 × 10(-8) -3 × 10(-4)) and that they can explain why strains with higher proportions of persister cells lose out very quickly in competition assays under favourable growth conditions, despite a negligible difference in maximal growth rate. We discuss how incorporating these trade-offs could lead to models that can better explain the evolution of persistence in nature and facilitate the rational design of alternative therapeutic strategies for treating infectious diseases.
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Affiliation(s)
- Kristine Stepanyan
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Kasteelpark Arenberg 20 bus 2460, 3001 Leuven, Belgium
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