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Stojowska-Swędrzyńska K, Kuczyńska-Wiśnik D, Laskowska E. Influence of N ε-Lysine Acetylation on the Formation of Protein Aggregates and Antibiotic Persistence in E. coli. Molecules 2024; 29:383. [PMID: 38257296 PMCID: PMC10819833 DOI: 10.3390/molecules29020383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/07/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Numerous studies indicate that reversible Nε-lysine acetylation in bacteria may play a key role in the regulation of metabolic processes, transcription and translation, biofilm formation, virulence, and drug resistance. Using appropriate mutant strains deficient in non-enzymatic acetylation and enzymatic acetylation or deacetylation pathways, we investigated the influence of protein acetylation on cell viability, protein aggregation, and persister formation in Escherichia coli. Lysine acetylation was found to increase protein aggregation and cell viability under the late stationary phase. Moreover, increased lysine acetylation stimulated the formation of persisters. These results suggest that acetylation-dependent aggregation may improve the survival of bacteria under adverse conditions (such as the late stationary phase) and during antibiotic treatment. Further experiments revealed that acetylation-favorable conditions may increase persister formation in Klebsiella pneumoniae clinical isolate. However, the exact mechanisms underlying the relationship between acetylation and persistence in this pathogen remain to be elucidated.
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Affiliation(s)
| | | | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (K.S.-S.); (D.K.-W.)
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2
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Liu S, Huang Y, Jensen S, Laman P, Kramer G, Zaat SAJ, Brul S. Molecular physiological characterization of the dynamics of persister formation in Staphylococcus aureus. Antimicrob Agents Chemother 2024; 68:e0085023. [PMID: 38051079 PMCID: PMC10777834 DOI: 10.1128/aac.00850-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023] Open
Abstract
Bacteria possess the ability to enter a growth-arrested state known as persistence in order to survive antibiotic exposure. Clinically, persisters are regarded as the main causative agents for chronic and recurrent infectious diseases. To combat this antibiotic-tolerant population, a better understanding of the molecular physiology of persisters is required. In this study, we collected samples at different stages of the biphasic kill curve to reveal the dynamics of the cellular molecular changes that occur in the process of persister formation. After exposure to antibiotics with different modes of action, namely, vancomycin and enrofloxacin, similar persister levels were obtained. Both shared and distinct stress responses were enriched for the respective persister populations. However, the dynamics of the presence of proteins linked to the persister phenotype throughout the biphasic kill curve and the molecular profiles in a stable persistent population did show large differences, depending on the antibiotic used. This suggests that persisters at the molecular level are highly stress specific, emphasizing the importance of characterizing persisters generated under different stress conditions. Additionally, although generated persisters exhibited cross-tolerance toward tested antibiotics, combined therapies were demonstrated to be a promising approach to reduce persister levels. In conclusion, this investigation sheds light on the stress-specific nature of persisters, highlighting the necessity of tailored treatment approaches and the potential of combined therapy.
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Affiliation(s)
- Shiqi Liu
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Yixuan Huang
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Sean Jensen
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Paul Laman
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Gertjan Kramer
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Sebastian A. J. Zaat
- Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
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3
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Laulund AS, Schwartz FA, Høiby N, Thomsen K, Moser C. Hyperbaric oxygen therapy counteracts Pseudomonas aeruginosa biofilm micro-compartment phenomenon in murine thermal wounds. Biofilm 2023; 6:100159. [PMID: 37928621 PMCID: PMC10622832 DOI: 10.1016/j.bioflm.2023.100159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/20/2023] [Accepted: 09/24/2023] [Indexed: 11/07/2023] Open
Abstract
Background Biofilm antibiotic tolerance is partly explained by the behavior of a biofilm as an independent pharmacokinetic micro-compartment. Hyperbaric oxygen therapy has been shown to potentiate antibiotic effects in biofilms. The present study investigates the effect of hyperbaric oxygen therapy (HBOT) on the biofilm micro-pharmacokinetic/pharmacodynamic behavior of tobramycin in an animal biofilm model. Methods Full-thickness necroses were created mid-scapular on mice by means of a thermal lesion. After four days, three 16 h seaweed alginate biofilm beads containing Pseudomonas aeruginosa PAO1 were inserted under the necrosis, and three beads were inserted under the adjacent non-affected skin. The mice were randomized to three groups I) HBOT for 1.5 h at 2.8 atm and 0.8 mg tobramycin/mouse subcutaneously; II) Tobramycin as monotherapy, same dose; III) Saline control group. Half the number of mice from group 1 and 2 were sacrificed, and beads were recovered in toto after 3 h and the other half and the placebo mice were sacrificed and beads collected after 4.5 h. Results Lower CFUs were seen in the burned group receiving HBOT at 3 and 4.5 h compared to beads in the atmospheric environment (p = 0.043 and p = 0.0089). At 3 h, no CFU difference was observed in the non-burned skin (HBOT vs atmospheric). At 4.5 h, CFU in the non-burned skin had lower CFUs in the group receiving HBOT compared to the corresponding atmospheric group (p = 0.02). CFU was higher in the burned skin than in the non-burned skin at 3 h when HBOT was applied (p = 0.04), effect faded out at 4.5 h.At both time points, the tobramycin content in the beads under burned skin were higher in the HBOT group than in the atmospheric groups (p = 0.031 and p = 0.0078). Only at 4.5 h a higher tobramycin content was seen in the beads under the HBOT-treated burned skin than the beads under the corresponding non-burned skin (p = 0.006). Conclusion HBOT, as an anti-biofilm adjuvant treatment of chronic wounds, counteracts biofilm pharmacokinetic micro-compartmentalization through increased available tobramycin and augmented bacterial killing.
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Affiliation(s)
- Anne Sofie Laulund
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Henrik Harpestrengs Vej 4A, 2100, Copenhagen, Denmark
| | | | - Niels Høiby
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital and Department of Immunology and Microbiology (ISIM), University of Copenhagen, Denmark
| | - Kim Thomsen
- Department of Clinical Microbiology, Zealand University Hospital, Denmark
| | - Claus Moser
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet and Department of Immunology and Microbiology (ISIM), University of Copenhagen, Denmark
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4
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Durrani B, Mohammad A, Ljubetic BM, Dobberfuhl AD. The Potential Role of Persister Cells in Urinary Tract Infections. Curr Urol Rep 2023; 24:541-551. [PMID: 37907771 DOI: 10.1007/s11934-023-01182-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2023] [Indexed: 11/02/2023]
Abstract
PURPOSE OF REVIEW This review explores the role of persister cells in urinary tract infections (UTIs). UTIs are one of the most common bacterial infections, affecting millions of people worldwide. Persister cells are a subpopulation of bacteria with dormant metabolic activity which allows survival in the presence of antibiotics. RECENT FINDINGS This review summarizes recent research on the pathogenesis of persister cell formation in UTIs, the impact of persister cells on the effectiveness of antibiotics, the challenges they pose for treatment, and the need for new strategies to target these cells. Furthermore, this review examines the current state of research on the identification and characterization of persister cells in UTIs, as well as the future directions for investigations in this field. This review highlights the importance of understanding the role of persister cells in UTIs and the potential impact of targeting these cells in the development of new treatments.
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Affiliation(s)
- Butool Durrani
- Department of Internal Medicine, Aga Khan University Hospital, National Stadium Rd, Karachi, Karachi City, Pakistan
| | - Ashu Mohammad
- Department of Urology, Center for Academic Medicine, Stanford University School of Medicine, 453 Quarry Road, Urology-5656, Palo Alto, CA, 94304, USA
| | - Bernardita M Ljubetic
- Department of Urology, Center for Academic Medicine, Stanford University School of Medicine, 453 Quarry Road, Urology-5656, Palo Alto, CA, 94304, USA
| | - Amy D Dobberfuhl
- Department of Urology, Center for Academic Medicine, Stanford University School of Medicine, 453 Quarry Road, Urology-5656, Palo Alto, CA, 94304, USA.
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Rousseau CJ, Fraikin N, Zedek S, Van Melderen L. Are envelope stress responses essential for persistence to β-lactams in Escherichia coli? Antimicrob Agents Chemother 2023; 67:e0032923. [PMID: 37787525 PMCID: PMC10583663 DOI: 10.1128/aac.00329-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/05/2023] [Indexed: 10/04/2023] Open
Abstract
Bacterial persistence to antibiotics defines the ability of small sub-populations of sensitive cells within an isogenic population to survive high doses of bactericidal antibiotics. Here, we investigated the importance of the five main envelope stress responses (ESRs) of Escherichia coli in persistence to five bactericidal β-lactam antibiotics by combining classical time-kill curve experiments and single-cell analysis using time-lapse microscopy. We showed that the survival frequency of mutants for the Bae, Cpx, Psp, and Rcs systems treated with different β-lactams is comparable to that of the wild-type strain, indicating that these ESRs do not play a direct role in persistence to β-lactams. Since the σE-encoding gene is essential, we could not directly test its role. Using fluorescent reporters to monitor the activation of ESRs, we observed that σE is induced by high doses of meropenem. However, the dynamics of σE activation during meropenem treatment did not reveal any difference in persister cells compared to the bulk of the population, indicating that σE activation is not a hallmark of persistence. The Bae, Cpx, Psp, and Rcs responses were neither induced by ampicillin nor by meropenem. However, pre-induction of the Rcs system by polymyxin B increased survival to meropenem in an Rcs-dependent manner, suggesting that this ESR might confer some yet uncharacterized advantages during meropenem treatment or at the post-antibiotic recovery step. Altogether, our data suggest that ESRs are not key actors in E. coli persistence to β-lactams in the conditions we tested.
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Affiliation(s)
- Clothilde J. Rousseau
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Nathan Fraikin
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Safia Zedek
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Laurence Van Melderen
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
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Marrocco I, Yarden Y. Resistance of Lung Cancer to EGFR-Specific Kinase Inhibitors: Activation of Bypass Pathways and Endogenous Mutators. Cancers (Basel) 2023; 15:5009. [PMID: 37894376 PMCID: PMC10605519 DOI: 10.3390/cancers15205009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Epidermal growth factor receptor (EGFR)-specific tyrosine kinase inhibitors (TKIs) have changed the landscape of lung cancer therapy. For patients who are treated with the new TKIs, the current median survival exceeds 3 years, substantially better than the average 20 month survival rate only a decade ago. Unfortunately, despite initial efficacy, nearly all treated patients evolve drug resistance due to the emergence of either new mutations or rewired signaling pathways that engage other receptor tyrosine kinases (RTKs), such as MET, HER3 and AXL. Apparently, the emergence of mutations is preceded by a phase of epigenetic alterations that finely regulate the cell cycle, bias a mesenchymal phenotype and activate antioxidants. Concomitantly, cells that evade TKI-induced apoptosis (i.e., drug-tolerant persister cells) activate an intrinsic mutagenic program reminiscent of the SOS system deployed when bacteria are exposed to antibiotics. This mammalian system imbalances the purine-to-pyrimidine ratio, inhibits DNA repair and boosts expression of mutation-prone DNA polymerases. Thus, the net outcome of the SOS response is a greater probability to evolve new mutations. Deeper understanding of the persister-to-resister transformation, along with the development of next-generation TKIs, EGFR-specific proteolysis targeting chimeras (PROTACs), as well as bispecific antibodies, will permit delaying the onset of relapses and prolonging survival of patients with EGFR+ lung cancer.
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Affiliation(s)
- Ilaria Marrocco
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Yosef Yarden
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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Pizzolato-Cezar LR, Spira B, Machini MT. Bacterial toxin-antitoxin systems: Novel insights on toxin activation across populations and experimental shortcomings. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 5:100204. [PMID: 38024808 PMCID: PMC10643148 DOI: 10.1016/j.crmicr.2023.100204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
The alarming rise in hard-to-treat bacterial infections is of great concern to human health. Thus, the identification of molecular mechanisms that enable the survival and growth of pathogens is of utmost urgency for the development of more efficient antimicrobial therapies. In challenging environments, such as presence of antibiotics, or during host infection, metabolic adjustments are essential for microorganism survival and competitiveness. Toxin-antitoxin systems (TASs) consisting of a toxin with metabolic modulating activity and a cognate antitoxin that antagonizes that toxin are important elements in the arsenal of bacterial stress defense. However, the exact physiological function of TA systems is highly debatable and with the exception of stabilization of mobile genetic elements and phage inhibition, other proposed biological functions lack a broad consensus. This review aims at gaining new insights into the physiological effects of TASs in bacteria and exploring the experimental shortcomings that lead to discrepant results in TAS research. Distinct control mechanisms ensure that only subsets of cells within isogenic cultures transiently develop moderate levels of toxin activity. As a result, TASs cause phenotypic growth heterogeneity rather than cell stasis in the entire population. It is this feature that allows bacteria to thrive in diverse environments through the creation of subpopulations with different metabolic rates and stress tolerance programs.
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Affiliation(s)
- Luis R. Pizzolato-Cezar
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Beny Spira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - M. Teresa Machini
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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8
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Dufour D, Li H, Gong SG, Lévesque CM. Transcriptome Analysis of Streptococcus mutans Quorum Sensing-Mediated Persisters Reveals an Enrichment in Genes Related to Stress Defense Mechanisms. Genes (Basel) 2023; 14:1887. [PMID: 37895236 PMCID: PMC10606796 DOI: 10.3390/genes14101887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Persisters are a small fraction of growth-arrested phenotypic variants that can survive lethal concentrations of antibiotics but are able to resume growth once antibiotics are stopped. Their formation can be a stochastic process or one triggered by environmental cues. In the human pathogen Streptococcus mutans, the canonical peptide-based quorum-sensing system is an inducible DNA repair system that is pivotal for bacterial survival. Previous work has shown that the CSP-signaling peptide is a stress-signaling alarmone that promotes the formation of stress-induced persisters. In this study, we exposed S. mutans to the CSP pheromone to mimic DNA damage conditions and isolated the antibiotic persisters by treating the cultures with ofloxacin. A transcriptome analysis was then performed to evaluate the differential gene expression between the normal stationary-phase cells and the persisters. RNA sequencing revealed that triggered persistence was associated with the upregulation of genes related to several stress defense mechanisms, notably, multidrug efflux pumps, the arginine deaminase pathway, and the Opu/Opc system. In addition, we showed that inactivation of the VicK kinase of the YycFG essential two-component regulatory system abolished the formation of triggered persisters via the CSP pheromone. These data contribute to the understanding of the triggered persistence phenotype and may suggest new therapeutic strategies for treating persistent streptococcal infections.
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Affiliation(s)
| | | | | | - Céline M. Lévesque
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada; (D.D.); (H.L.); (S.-G.G.)
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9
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Mancini L, Pilizota T. Environmental conditions define the energetics of bacterial dormancy and its antibiotic susceptibility. Biophys J 2023; 122:3207-3218. [PMID: 37403359 PMCID: PMC10465703 DOI: 10.1016/j.bpj.2023.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/17/2023] [Accepted: 06/30/2023] [Indexed: 07/06/2023] Open
Abstract
Bacterial cells that stop growing but maintain viability and the capability to regrow are termed dormant and have been shown to transiently tolerate high concentrations of antimicrobials. Links between tolerance and cellular energetics as a possible explanation for the tolerance, have been investigated and have produced mixed and seemingly contradictory results. Because dormancy merely indicates growth arrest, which can be induced by various stimuli, we hypothesize that dormant cells may exist in a range of energetic states that depend on the environment. To energetically characterize different dormancies, we first induce them in a way that results in dormant populations and subsequently measure both of their main energy sources, the proton motive force magnitude and the concentration of ATP. We find that different types of dormancy exhibit characteristic energetic profiles that vary in level and dynamics. The energetic makeup was associated with survival to some antibiotics but not others. Our findings portray dormancy as a state that is rich in phenotypes with various stress survival capabilities. Because environmental conditions outside of the lab often halt or limit microbial growth, a typologization of dormant states may yield relevant insights on the survival and evolutionary strategies of these organisms.
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Affiliation(s)
- Leonardo Mancini
- School of Biological Sciences, Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Teuta Pilizota
- School of Biological Sciences, Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom.
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10
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Marrocco I, Giri S, Simoni-Nieves A, Gupta N, Rudnitsky A, Haga Y, Romaniello D, Sekar A, Zerbib M, Oren R, Lindzen M, Fard D, Tsutsumi Y, Lauriola M, Tamagnone L, Yarden Y. L858R emerges as a potential biomarker predicting response of lung cancer models to anti-EGFR antibodies: Comparison of osimertinib vs. cetuximab. Cell Rep Med 2023; 4:101142. [PMID: 37557179 PMCID: PMC10439256 DOI: 10.1016/j.xcrm.2023.101142] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/21/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
EGFR-specific tyrosine kinase inhibitors (TKIs), especially osimertinib, have changed lung cancer therapy, but secondary mutations confer drug resistance. Because other EGFR mutations promote dimerization-independent active conformations but L858R strictly depends on receptor dimerization, we herein evaluate the therapeutic potential of dimerization-inhibitory monoclonal antibodies (mAbs), including cetuximab. This mAb reduces viability of cells expressing L858R-EGFR and blocks the FOXM1-aurora survival pathway, but other mutants show no responses. Unlike TKI-treated patient-derived xenografts, which relapse post osimertinib treatment, cetuximab completely prevents relapses of L858R+ tumors. We report that osimertinib's inferiority associates with induction of mutagenic reactive oxygen species, whereas cetuximab's superiority is due to downregulation of adaptive survival pathways (e.g., HER2) and avoidance of mutation-prone mechanisms that engage AXL, RAD18, and the proliferating cell nuclear antigen. These results identify L858R as a predictive biomarker, which may pave the way for relapse-free mAb monotherapy relevant to a large fraction of patients with lung cancer.
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Affiliation(s)
- Ilaria Marrocco
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Suvendu Giri
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Arturo Simoni-Nieves
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nitin Gupta
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anna Rudnitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yuya Haga
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Donatella Romaniello
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Arunachalam Sekar
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mirie Zerbib
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roni Oren
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moshit Lindzen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Damon Fard
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Yasuo Tsutsumi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan
| | - Mattia Lauriola
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Luca Tamagnone
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Gemelli - IRCCS, 00168 Rome, Italy
| | - Yosef Yarden
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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11
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Zhou Y, Liao H, Pei L, Pu Y. Combatting persister cells: The daunting task in post-antibiotics era. CELL INSIGHT 2023; 2:100104. [PMID: 37304393 PMCID: PMC10250163 DOI: 10.1016/j.cellin.2023.100104] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/25/2023] [Accepted: 04/21/2023] [Indexed: 06/13/2023]
Abstract
Over the years, much attention has been drawn to antibiotic resistance bacteria, but drug inefficacy caused by a subgroup of special phenotypic variants - persisters - has been largely neglected in both scientific and clinical field. Interestingly, this subgroup of phenotypic variants displayed their power of withstanding sufficient antibiotics exposure in a mechanism different from antibiotic resistance. In this review, we summarized the clinical importance of bacterial persisters, the evolutionary link between resistance, tolerance, and persistence, redundant mechanisms of persister formation as well as methods of studying persister cells. In the light of our recent findings of membrane-less organelle aggresome and its important roles in regulating bacterial dormancy depth, we propose an alternative approach for anti-persister therapy. That is, to force a persister into a deeper dormancy state to become a VBNC (viable but non-culturable) cell that is incapable of regrowth. We hope to provide the latest insights on persister studies and call upon more research interest into this field.
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Affiliation(s)
- Yidan Zhou
- Department of Clinical Laboratory, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
| | - Hebin Liao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
| | - Linsen Pei
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
| | - Yingying Pu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
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12
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Tang J, Brynildsen MP. Genome-wide mapping of fluoroquinolone-stabilized DNA gyrase cleavage sites displays drug specific effects that correlate with bacterial persistence. Nucleic Acids Res 2023; 51:1208-1228. [PMID: 36631985 PMCID: PMC9943676 DOI: 10.1093/nar/gkac1223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/03/2022] [Accepted: 12/12/2022] [Indexed: 01/13/2023] Open
Abstract
Bacterial persisters are rare phenotypic variants that are suspected to be culprits of recurrent infections. Fluoroquinolones (FQs) are a class of antibiotics that facilitate bacterial killing by stabilizing bacterial type II topoisomerases when they are in a complex with cleaved DNA. In Escherichia coli, DNA gyrase is the primary FQ target, and previous work has demonstrated that persisters are not spared from FQ-induced DNA damage. Since DNA gyrase cleavage sites (GCSs) largely govern the sites of DNA damage from FQ treatment, we hypothesized that GCS characteristics (e.g. number, strength, location) may influence persistence. To test this hypothesis, we measured genome-wide GCS distributions after treatment with a panel of FQs in stationary-phase cultures. We found drug-specific effects on the GCS distribution and discovered a strong negative correlation between the genomic cleavage strength and FQ persister levels. Further experiments and analyses suggested that persistence was unlikely to be governed by cleavage to individual sites, but rather survival was a function of the genomic GCS distribution. Together, these findings demonstrate FQ-specific differences in GCS distribution that correlate with persister levels and suggest that FQs that better stabilize DNA gyrase in cleaved complexes with DNA will lead to lower levels of persistence.
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Affiliation(s)
- Juechun Tang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
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13
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Geerts N, De Vooght L, Passaris I, Delputte P, Van den Bergh B, Cos P. Antibiotic Tolerance Indicative of Persistence Is Pervasive among Clinical Streptococcus pneumoniae Isolates and Shows Strong Condition Dependence. Microbiol Spectr 2022; 10:e0270122. [PMID: 36374111 PMCID: PMC9769776 DOI: 10.1128/spectrum.02701-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Streptococcus pneumoniae is an important human pathogen, being one of the most common causes of community-acquired pneumonia and otitis media. Antibiotic resistance in S. pneumoniae is an emerging problem, as it depletes our arsenal of effective drugs. In addition, persistence also contributes to the antibiotic crisis in many other pathogens, yet for S. pneumoniae, little is known about antibiotic-tolerant persisters and robust experimental means are lacking. Persister cells are phenotypic variants that exist as a subpopulation within a clonal culture. Being tolerant to lethal antibiotics, they underly the chronic nature of a variety of infections and even help in acquiring genetic resistance. In this study, we set out to identify and characterize persistence in S. pneumoniae. Specifically, we followed different strategies to overcome the self-limiting nature of S. pneumoniae as a confounding factor in the prolonged monitoring of antibiotic survival needed to study persistence. Under optimized conditions, we identified genuine persisters in various growth phases and for four relevant antibiotics through biphasic survival dynamics and heritability assays. Finally, we detected a high variety in antibiotic survival levels across a diverse collection of S. pneumoniae clinical isolates, which assumes that a high natural diversity in persistence is widely present in S. pneumoniae. Collectively, this proof of concept significantly progresses the understanding of the importance of antibiotic persistence in S. pneumoniae infections, which will set the stage for characterizing its relevance to clinical outcomes and advocates for increased attention to the phenotype in both fundamental and clinical research. IMPORTANCE S. pneumoniae is considered a serious threat by the Centers for Disease Control and Prevention because of rising antibiotic resistance. In addition to resistance, bacteria can also survive lethal antibiotic treatment by developing antibiotic tolerance, more specifically, antibiotic tolerance through persistence. This phenotypic variation seems omnipresent among bacterial life, is linked to therapy failure, and acts as a catalyst for resistance development. This study gives the first proof of the presence of persister cells in S. pneumoniae and shows a high variety in persistence levels among diverse strains, suggesting that persistence is a general trait in S. pneumoniae cultures. Our work advocates for higher interest for persistence in S. pneumoniae as a contributing factor for therapy failure and resistance development.
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Affiliation(s)
- Nele Geerts
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
| | - Linda De Vooght
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
| | | | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
| | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
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14
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Dawan J, Ahn J. Variability in Adaptive Resistance of Salmonella Typhimurium to Sublethal Levels of Antibiotics. Antibiotics (Basel) 2022; 11:antibiotics11121725. [PMID: 36551382 PMCID: PMC9774383 DOI: 10.3390/antibiotics11121725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
This study was designed to evaluate the adaptive resistance of Salmonella Typhimurium under continuous sublethal selective pressure. Salmonella Typhimurium ATCC 19585 (STATCC) and S. Typhimurium CCARM 8009 (STCCARM) were sequentially cultured for 3 days at 37 °C in trypticase soy broth containing 1/2 × MICs of cefotaxime (CEF1/2), chloramphenicol (CHL1/2), gentamicin (GEN1/2), and polymyxin B (POL1/2). The STATCC and STCCARM exposed to CEF1/2, CHL1/2, GEN1/2, and POL1/2 were evaluated using antibiotic susceptibility, cross-resistance, and relative fitness. The susceptibilities of STATCC exposed to GEN1/2 and POL1/2 were increased by a 2-fold (gentamicin) and 8-fold (polymyxin B) increase in minimum inhibitory concentration (MIC) values, respectively. The MIC values of STCCARM exposed to CEF1/2, CHL1/2, GEN1/2, and POL1/2 were increased by 4-fold (cefotaxime), 2-fold (chloramphenicol), 2-fold (gentamicin), and 8-fold (polymyxin B). The highest heterogeneous fractions were observed for the STATCC exposed to CEF1/2 (38%) and POL1/2 (82%). The STCCARM exposed to GEN1/2 was cross-resistant to cefotaxime (p < 0.05), chloramphenicol (p < 0.01), and polymyxin B (p < 0.05). The highest relative fitness levels were 0.92 and 0.96, respectively, in STATCC exposed to CEF1/2 and STCCARM exposed to POL1/2. This study provides new insight into the fate of persistent cells and also guidance for antibiotic use.
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Affiliation(s)
- Jirapat Dawan
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
- Correspondence: ; Tel.: +82-33-250-6564
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15
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A DNA-Damage Inducible Gene Promotes the Formation of Antibiotic Persisters in Response to the Quorum Sensing Signaling Peptide in Streptococcus mutans. Genes (Basel) 2022; 13:genes13081434. [PMID: 36011345 PMCID: PMC9408444 DOI: 10.3390/genes13081434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022] Open
Abstract
Bacteria use quorum sensing (QS) to communicate with each other via secreted small autoinducers produced by individuals. QS allows bacteria to display a unified response that benefits the species during adaptation to environment, colonization, and defense against competitors. In oral streptococci, the CSP-ComDE QS is an inducible DNA damage repair system that is pivotal for bacterial survival. In the oral pathogen Streptococcus mutans, the QS system positively influences the formation of antibiotic persisters, cells that can survive antibiotic attack by entering a non-proliferative state. We recently identified a novel gene, pep299, that is activated in the persister cell fraction induced by QS. In this study, we focused our investigation on the role of pep299, a gene encoding a bacteriocin-like peptide, in the formation of antibiotic persisters. Mutant Δ299, unable to produce Pep299, showed a dramatic reduction in the number of stress-induced persisters. Using a co-culture assay, we showed that cells overproducing pep299 induced the formation of persisters in the mutant, suggesting that Pep299 was actively secreted and detected by neighboring cells. Cells exposed to DNA damage conditions activated the gene expression of pep299. Interestingly, our results suggested that the pep299 gene was also involved in the regulation of a QS-inducible toxin−antitoxin system. Our study suggests that the pep299 gene is at the core of the triggered persistence phenotype in S. mutans, allowing cells to transition into a state of reduced metabolic activity and antibiotic tolerance.
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16
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Verschuuren TD, Bosch T, Mascaro V, Willems RJL, Kluytmans JAJW. External validation of WGS-based antimicrobial susceptibility prediction tools, KOVER-AMR and ResFinder 4.1 for Escherichia coli clinical isolates. Clin Microbiol Infect 2022; 28:1465-1470. [PMID: 35662642 DOI: 10.1016/j.cmi.2022.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 05/08/2022] [Accepted: 05/14/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To externally validate whole genome sequence-antimicrobial susceptibility testing (WGS-AST) phenotype prediction tools KOVER-AMR and ResFinder 4.1 for Escherichia coli clinical isolates from Dutch routine care. METHODS A random sample of 234 E. coli, and 283 3rd generation cephalosporin-resistant E. coli isolates from urine and blood were collected (2014-17). Culture-AST was performed using VITEK 2 and BD Phoenix. Sequences were used as input for KOVER-AMR-SCM, KOVER-AMR-CART and ResFinder 4.1. The concordance, major error rate (MER), and very major error rate (VMER) were calculated, with subsequent comparison to U.S. Food and Drug Administration (FDA) criteria (MER ≤3%, and VMER with a 95% confidence interval (CI) ≤1.5%-≤7.5%). RESULTS ResFinder 4.1 performed better than KOVER-AMR-models, however, neither tools achieved overall (V)MERs below FDA criteria. KOVER-AMR-SCM, KOVER-AMR-CART, and ResFinder 4.1, MER (cumulative all antimicrobials) were: 5.1% (4.4-5.9), 4.3% (3.6-5.0), and 5.1% (4.5-5.8), respectively. MERs ≤3% were achieved for 6 (SCM) and 5 (CART) of the 11 tested antimicrobials for KOVER-AMR-models, and for 9/13 antimicrobials tested with ResFinder 4.1. KOVER-AMR-SCM, KOVER-AMR-CART, and ResFinder 4.1, cumulative VMERs were: 26% (24-28), 29% (27-31), and 11% (9.2-12). VMERs with a 95%CI ≤1.5-≤7.5 were only achieved for 4/13 tested antimicrobials with ResFinder 4.1. CONCLUSION In this study, WGS-AST phenotype prediction tools, KOVER-AMR and ResFinder 4.1, did not meet the FDA criteria needed for clinical diagnostic use in 517 E. coli clinical isolates from Dutch routine care. The tested tools should be further improved before they can be used for clinical decision making.
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Affiliation(s)
- T D Verschuuren
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, the Netherlands.
| | - T Bosch
- the Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - V Mascaro
- ASST Rhodense, G. Salvini Hospital, Garbagnate Milanese, Italy
| | - R J L Willems
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - J A J W Kluytmans
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, the Netherlands; Amphia Hospital Breda, Breda, the Netherlands
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17
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Quorum quenching of Streptococcus mutans via the nano-quercetin-based antimicrobial photodynamic therapy as a potential target for cariogenic biofilm. BMC Microbiol 2022; 22:125. [PMID: 35538403 PMCID: PMC9088123 DOI: 10.1186/s12866-022-02544-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
Background Quorum sensing (QS) system can regulate the expression of virulence factors and biofilm formation in Streptococcus mutans. Antimicrobial photodynamic therapy (aPDT) inhibits quorum quenching (QQ), and can be used to prevent microbial biofilm. We thereby aimed to evaluate the anti-biofilm potency and anti-metabolic activity of nano-quercetin (N-QCT)-mediated aPDT against S. mutans. Also, in silico evaluation of the inhibitory effect of N-QCT on the competence-stimulating peptide (CSP) of S. mutans was performed to elucidate the impact of aPDT on various QS-regulated genes. Methods Cytotoxicity and intracellular reactive oxygen species (ROS) generation were assessed following synthesis and confirmation of N-QCT. Subsequently, the minimum biofilm inhibitory concentration (MBIC) of N-QCT against S. mutans and anti-biofilm effects of aPDT were assessed using colorimetric assay and plate counting. Molecular modeling and docking analysis were performed to confirm the connection of QCT to CSP. The metabolic activity of S. mutans and the expression level of various genes involved in QS were evaluated by flow cytometry and reverse transcription quantitative real-time PCR, respectively. Results Successful synthesis of non-toxic N-QCT was confirmed through several characterization tests. The MBIC value of N-QCT against S. mutans was 128 μg/mL. Similar to the crystal violet staining, the results log10 CFU/mL showed a significant degradation of preformed biofilms in the group treated with aPDT compared to the control group (P < 0.05). Following aPDT, metabolic activity of S. mutans also decreased by 85.7% (1/2 × MBIC of N-QCT) and 77.3% (1/4 × MBIC of N-QCT), as compared to the control values (P < 0.05). In silico analysis showed that the QCT molecule was located in the site formed by polypeptide helices of CSP. The relative expression levels of the virulence genes were significantly decreased in the presence of N-QCT-mediated aPDT (P < 0.05). Conclusions The combination of N-QCT with blue laser as a QQ-strategy leads to maximum ROS generation, disrupts the microbial biofilm of S. mutans, reduces metabolic activity, and downregulates the expression of genes involved in the QS pathway by targeting genes of the QS signaling system of S. mutans.
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18
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19
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Hemeg HA. Combatting persisted and biofilm antimicrobial resistant bacterial by using nanoparticles. Z NATURFORSCH C 2022; 77:365-378. [PMID: 35234019 DOI: 10.1515/znc-2021-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/04/2022] [Indexed: 11/15/2022]
Abstract
Some bacteria can withstand the existence of an antibiotic without undergoing any genetic changes. They are neither cysts nor spores and are one of the causes of disease recurrence, accounting for about 1% of the biofilm. There are numerous approaches to eradication and combating biofilm-forming organisms. Nanotechnology is one of them, and it has shown promising results against persister cells. In the review, we go over the persister cell and biofilm in extensive detail. This includes the biofilm formation cycle, antibiotic resistance, and treatment with various nanoparticles. Furthermore, the gene-level mechanism of persister cell formation and its therapeutic interventions with nanoparticles were discussed.
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Affiliation(s)
- Hassan A Hemeg
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, P.O. Box 344, Al-Madinah Al-Monawra 41411, Saudi Arabia
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20
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Van den Bergh B, Schramke H, Michiels JE, Kimkes TEP, Radzikowski JL, Schimpf J, Vedelaar SR, Burschel S, Dewachter L, Lončar N, Schmidt A, Meijer T, Fauvart M, Friedrich T, Michiels J, Heinemann M. Mutations in respiratory complex I promote antibiotic persistence through alterations in intracellular acidity and protein synthesis. Nat Commun 2022; 13:546. [PMID: 35087069 PMCID: PMC8795404 DOI: 10.1038/s41467-022-28141-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 01/04/2022] [Indexed: 11/28/2022] Open
Abstract
Antibiotic persistence describes the presence of phenotypic variants within an isogenic bacterial population that are transiently tolerant to antibiotic treatment. Perturbations of metabolic homeostasis can promote antibiotic persistence, but the precise mechanisms are not well understood. Here, we use laboratory evolution, population-wide sequencing and biochemical characterizations to identify mutations in respiratory complex I and discover how they promote persistence in Escherichia coli. We show that persistence-inducing perturbations of metabolic homeostasis are associated with cytoplasmic acidification. Such cytoplasmic acidification is further strengthened by compromised proton pumping in the complex I mutants. While RpoS regulon activation induces persistence in the wild type, the aggravated cytoplasmic acidification in the complex I mutants leads to increased persistence via global shutdown of protein synthesis. Thus, we propose that cytoplasmic acidification, amplified by a compromised complex I, can act as a signaling hub for perturbed metabolic homeostasis in antibiotic persisters.
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Affiliation(s)
- Bram Van den Bergh
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Hannah Schramke
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Joran Elie Michiels
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
| | - Tom E P Kimkes
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Jakub Leszek Radzikowski
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Johannes Schimpf
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Silke R Vedelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Sabrina Burschel
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Liselot Dewachter
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
| | - Nikola Lončar
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Tim Meijer
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Thorsten Friedrich
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium.
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium.
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands.
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21
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Mohiuddin SG, Ghosh S, Ngo HG, Sensenbach S, Karki P, Dewangan NK, Angardi V, Orman MA. Cellular Self-Digestion and Persistence in Bacteria. Microorganisms 2021; 9:2269. [PMID: 34835393 PMCID: PMC8626048 DOI: 10.3390/microorganisms9112269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/30/2022] Open
Abstract
Cellular self-digestion is an evolutionarily conserved process occurring in prokaryotic cells that enables survival under stressful conditions by recycling essential energy molecules. Self-digestion, which is triggered by extracellular stress conditions, such as nutrient depletion and overpopulation, induces degradation of intracellular components. This self-inflicted damage renders the bacterium less fit to produce building blocks and resume growth upon exposure to fresh nutrients. However, self-digestion may also provide temporary protection from antibiotics until the self-digestion-mediated damage is repaired. In fact, many persistence mechanisms identified to date may be directly or indirectly related to self-digestion, as these processes are also mediated by many degradative enzymes, including proteases and ribonucleases (RNases). In this review article, we will discuss the potential roles of self-digestion in bacterial persistence.
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Affiliation(s)
| | | | | | | | | | | | | | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77004, USA; (S.G.M.); (S.G.); (H.G.N.); (S.S.); (P.K.); (N.K.D.); (V.A.)
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22
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Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021; 478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.
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Abstract
Mediators of the initiation, development, and recurrence of periodontitis include the oral microbiome embedded in subgingival plaque and the host immune response to a dysbiosis within this dynamic and complex microbial community. Although mediators have been studied extensively, researchers in the field have been unable to fully ascribe certain clinical presentations of periodontitis to their nature. Emergence of high-throughput sequencing technologies has resulted in better characterization of the microbial oral dysbiosis that extends beyond the extensively studied putative bacterial periodontopathogens to a shift in the oral virome composition during disease conditions. Although the biological dark matter inserted by retroviruses was once believed to be nonfunctional, research has revealed that it encodes historical viral-eukaryotic interactions and influences host development. The objective of this review is to evaluate the proposed association of herpesviruses to the etiology and pathogenesis of periodontal disease and survey the highly abundant prokaryotic viruses to delineate their potential roles in biofilm dynamics, as well as their interactions with putative bacterial periodontopathogens and eukaryotic cells. The findings suggest that potential novel periodontal therapies targeting or utilizing the oral virome can alleviate certain clinical presentations of periodontitis. Perhaps it is time to embrace the viral dark matter within the periodontal environment to fully comprehend the pathogenesis and systemic implications of periodontitis.
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Affiliation(s)
- April Martínez
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Ryutaro Kuraji
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Department of Life Science DentistryThe Nippon Dental UniversityTokyoJapan
- Department of PeriodontologyThe Nippon Dental University School of Life Dentistry at TokyoTokyoJapan
| | - Yvonne L. Kapila
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
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24
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Santa Maria PL, Kaufman AC, Bacacao B, Thai A, Chen X, Xia A, Cao Z, Fouad A, Bekale LA. Topical Therapy Failure in Chronic Suppurative Otitis Media is Due to Persister Cells in Biofilms. Otol Neurotol 2021; 42:e1263-e1272. [PMID: 34149028 DOI: 10.1097/mao.0000000000003222] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Chronic suppurative otitis media (CSOM) is characterized by a chronically draining middle ear. CSOM is typically treated with multiple courses of antibiotics or antiseptics which are successful in achieving quiescence; however, the disease is prone to relapse. Understanding why these treatment failures occur is essential. STUDY DESIGN The minimum inhibitory concentration (MIC), minimal biofilm eradication concentration, and the inhibitory zone were determined for ototopicals and ofloxacin for the laboratory strains and CSOM-derived isolates. The percentage of persister cells and bacterial biofilm formation were measured. Disease eradication was tested in a validated in-vivo model of CSOM after treatment with ofloxacin. SETTING Microbiology Laboratory. METHODS Basic science experiments were performed to measure the effectiveness of a number of compounds against CSOM bacteria in a number of distinct settings. RESULTS The minimal biofilm eradication concentration is higher than is physiologically achievable with commercial preparations, except for povo-iodine. Clincial isolates of CSOM have equivalent biofilm-forming ability but increased proportions of persister cells. Ofloxacin can convert to inactive disease temporarily but fails to eradicate disease in an in-vivo model. CONCLUSIONS Higher percentages of persister cells in clinical CSOM isolates are associated with resistance to ototopicals. Current ototopicals, except povo-iodine, have limited clinical effectiveness; however, it is unknown what the maximum achievable concentration is and there are ototoxicity concerns. Fluoroquinolones, while successful in producing inactive disease in the short term, have the potential to encourage antimicrobial resistance and disease recalcitrance and do not achieve a permanent remission. Given these limitations, clinicians should consider surgery earlier or use of clinically safe concentrations of povo-iodine earlier into the treatment algorithm.
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Affiliation(s)
- Peter L Santa Maria
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Adam C Kaufman
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Brian Bacacao
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Anthony Thai
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Xiaohua Chen
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
- Department of Otolaryngology, Head and Neck Surgery, First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Anping Xia
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Zhixin Cao
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong University, Ji'nan, China
| | - Ayman Fouad
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
- Department of Otolaryngology, Head and Neck Surgery, Tanta University, Tanta, Eqypt
| | - Laurent A Bekale
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
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25
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Toxin Induction or Inhibition of Transcription or Translation Posttreatment Increases Persistence to Fluoroquinolones. mBio 2021; 12:e0198321. [PMID: 34399616 PMCID: PMC8406316 DOI: 10.1128/mbio.01983-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Toxin-antitoxin modules are widespread in prokaryotes, and the capacity of toxin accumulation to increase the tolerances of bacteria to antibiotics has been well documented. The conventional model for this functionality implies that an overabundance of toxin arrests bacterial growth, which inhibits processes targeted by antibiotics and thereby limits their corruption and the lethal damage that would ensue. Implicit in this model is that toxins exert their influence on antibiotic lethality before and/or during treatment, even though they are also present and functional after treatment concludes. Given recent evidence establishing that the period following antibiotic treatment (recovery) is important for the survival of nongrowing bacterial populations treated with fluoroquinolones (FQs), we assayed to what extent toxins influence bacterial survival during the recovery period. With both LdrD and MazF, toxins of type I and II systems, respectively, controlling accumulation to occur only after FQ treatment of nongrowing cultures resulted in significant increases in persisters. Further genetic investigation revealed important roles for homologous recombination and nucleotide excision repair machinery. Focusing on the wild type, we did not observe any SOS-induced toxin functioning in this manner; however, an analogous phenomenon was observed for wild-type Escherichia coli as well as uropathogenic E. coli (UPEC) when transcription or translation was inhibited during the post-FQ recovery period. Collectively, these data reveal the capacity of toxins to thwart FQ killing even after the treatment has concluded and show that FQ treatment of nongrowing bacteria can be rendered largely ineffective if bacteria cannot readily resume translation and growth at the conclusion of treatment.
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26
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Schrank CL, Wilt IK, Monteagudo Ortiz C, Haney BA, Wuest WM. Using membrane perturbing small molecules to target chronic persistent infections. RSC Med Chem 2021; 12:1312-1324. [PMID: 34458737 PMCID: PMC8372208 DOI: 10.1039/d1md00151e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
After antibiotic treatment, a subpopulation of bacteria often remains and can lead to recalcitrant infections. This subpopulation, referred to as persisters, evades antibiotic treatment through numerous mechanisms such as decreased uptake of small molecules and slowed growth. Membrane perturbing small molecules have been shown to eradicate persisters as well as render these populations susceptible to antibiotic treatment. Chemotype similarities have emerged suggesting amphiphilic heteroaromatic compounds possess ideal properties to increase membrane fluidity and such molecules warrant further investigation as effective agents or potentiators against persister cells.
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Affiliation(s)
| | - Ingrid K Wilt
- Department of Chemistry Emory University Atlanta GA 30322 USA
| | | | | | - William M Wuest
- Department of Chemistry Emory University Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine Atlanta GA 30322 USA
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27
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Xia K, Ma J, Liang X. Impacts of type II toxin-antitoxin systems on cell physiology and environmental behavior in acetic acid bacteria. Appl Microbiol Biotechnol 2021; 105:4357-4367. [PMID: 34021811 DOI: 10.1007/s00253-021-11357-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/08/2021] [Accepted: 05/16/2021] [Indexed: 12/19/2022]
Abstract
Acetic acid bacteria (AAB) are a group of Gram-negative and strictly aerobic microorganisms widely used in vinegar industry, especially the species belonging to the genera Acetobacter and Komagataeibacter. The environments inhabited by AAB during the vinegar fermentation, in particular those natural traditional bioprocesses, are complex and dynamically changed, usually accompanied by diverse microorganisms, bacteriophages, and the increasing acetic acid concentration. For this reason, how AAB survive to such harsh niches has always been an interesting research field. Previous omic analyses (e.g., genomics, proteomics, and transcriptomics) have provided abundant clues for the metabolic pathways and bioprocesses indispensable for the acid stress adaptation of AAB. Nevertheless, it is far from fully understanding what factors regulate these modular mechanisms overtly and covertly upon shifting environments. Bacterial toxin-antitoxin systems (TAS), usually consisting of a pair of genes encoding a stable toxin and an unstable antitoxin that is capable of counteracting the toxin, have been uncovered to have a variety of biological functions. Recent studies focusing on the role of TAS in Acetobacter pasteurianus suggest that TAS contribute substantially to the acid stress resistance. In this mini review, we discuss the biological functions of type II TAS in the context of AAB with regard to the acid stress resistance, persister formation and resuscitation, genome stability, and phage immunity. KEY POINTS: • Type II TAS act as regulators in the acid stress resistance of AAB. • Type II TAS are implicated in the formation of acid-tolerant persister cells in AAB. • Type II TAS are potential factors responsible for phage immunity and genome stability.
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Affiliation(s)
- Kai Xia
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Jiawen Ma
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.,Institute of Food Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Xinle Liang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China. .,Institute of Food Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
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28
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Hossain T, Deter HS, Peters EJ, Butzin NC. Antibiotic tolerance, persistence, and resistance of the evolved minimal cell, Mycoplasma mycoides JCVI-Syn3B. iScience 2021; 24:102391. [PMID: 33997676 PMCID: PMC8091054 DOI: 10.1016/j.isci.2021.102391] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 02/01/2021] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
Antibiotic resistance is a growing problem, but bacteria can evade antibiotic treatment via tolerance and persistence. Antibiotic persisters are a small subpopulation of bacteria that tolerate antibiotics due to a physiologically dormant state. Hence, persistence is considered a major contributor to the evolution of antibiotic-resistant and relapsing infections. Here, we used the synthetically developed minimal cell Mycoplasma mycoides JCVI-Syn3B to examine essential mechanisms of antibiotic survival. The minimal cell contains only 473 genes, and most genes are essential. Its reduced complexity helps to reveal hidden phenomenon and fundamental biological principles can be explored because of less redundancy and feedback between systems compared to natural cells. We found that Syn3B evolves antibiotic resistance to different types of antibiotics expeditiously. The minimal cell also tolerates and persists against multiple antibiotics. It contains a few already identified persister-related genes, although lacking many systems previously linked to persistence (e.g. toxin-antitoxin systems, ribosome hibernation genes).
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Affiliation(s)
- Tahmina Hossain
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
| | - Heather S. Deter
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Eliza J. Peters
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
| | - Nicholas C. Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
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29
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Haga Y, Marrocco I, Noronha A, Uribe ML, Nataraj NB, Sekar A, Drago-Garcia D, Borgoni S, Lindzen M, Giri S, Wiemann S, Tsutsumi Y, Yarden Y. Host-Dependent Phenotypic Resistance to EGFR Tyrosine Kinase Inhibitors. Cancer Res 2021; 81:3862-3875. [PMID: 33941614 DOI: 10.1158/0008-5472.can-20-3555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/01/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022]
Abstract
Lung cancers driven by mutant forms of EGFR invariably develop resistance to kinase inhibitors, often due to secondary mutations. Here we describe an unconventional mechanism of resistance to dacomitinib, a newly approved covalent EGFR kinase inhibitor, and uncover a previously unknown step of resistance acquisition. Dacomitinib-resistant (DR) derivatives of lung cancer cells were established by means of gradually increasing dacomitinib concentrations. These DR cells acquired no secondary mutations in the kinase or other domains of EGFR. Along with resistance to other EGFR inhibitors, DR cells acquired features characteristic to epithelial-mesenchymal transition, including an expanded population of aldehyde dehydrogenase-positive cells and upregulation of AXL, a receptor previously implicated in drug resistance. Unexpectedly, when implanted in animals, DR cells reverted to a dacomitinib-sensitive state. Nevertheless, cell lines derived from regressing tumors displayed renewed resistance when cultured in vitro. Three-dimensional and cocultures along with additional analyses indicated lack of involvement of hypoxia, fibroblasts, and immune cells in phenotype reversal, implying that other host-dependent mechanisms might nullify nonmutational modes of resistance. Thus, similar to the phenotypic resistance of bacteria treated with antibiotics, the reversible resisters described here likely evolve from drug-tolerant persisters and give rise to the irreversible, secondary mutation-driven nonreversible resister state. SIGNIFICANCE: This study reports that stepwise acquisition of kinase inhibitor resistance in lung cancers driven by mutant EGFR comprises a nonmutational, reversible resister state. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/14/3862/F1.large.jpg.
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Affiliation(s)
- Yuya Haga
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Ilaria Marrocco
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Ashish Noronha
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Mary Luz Uribe
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Arunachalam Sekar
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Diana Drago-Garcia
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Simone Borgoni
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Moshit Lindzen
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Suvendu Giri
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yasuo Tsutsumi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Global Center for Medical Engineering and Informatics, Osaka University, Osaka, Japan
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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30
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Khan F, Park SK, Bamunuarachchi NI, Oh D, Kim YM. Caffeine-loaded gold nanoparticles: antibiofilm and anti-persister activities against pathogenic bacteria. Appl Microbiol Biotechnol 2021; 105:3717-3731. [PMID: 33900427 DOI: 10.1007/s00253-021-11300-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/31/2021] [Accepted: 04/17/2021] [Indexed: 01/18/2023]
Abstract
The formation of biofilms by bacterial pathogens and the presence of persister cells in biofilms have become major concerns in the health sector, owing to their antibiotic resistance and tolerance. The transformation of bacterial pathogens into persister cells, either stochastically or due to stressful environmental factors, results in recalcitrant and recurring infections. Here, we sought to prepare gold nanoparticles from naturally occurring caffeine and explore their inhibitory action against biofilm formation and persister cells. Fourier transform infrared spectroscopy, UV-visible absorption spectroscopy, field emission transmission electron microscopy, energy-dispersive X-ray diffraction, and dynamic light scattering were used to characterize the gold nanoparticles obtained from caffeine (Caff-AuNPs). The Caff-AuNPs were found to exhibit a number of properties, including the ability to prevent biofilm formation, disperse mature biofilms, and kill different types of persister of gram-positive (Staphylococcus aureus and Listeria monocytogenes) and gram-negative (Pseudomonas aeruginosa and Escherichia coli) pathogenic bacteria. Microscopic analysis of the aforementioned bacterial cells, treated with Caff-AuNPs, revealed the bactericidal effect of Caff-AuNPs, although the underlying mechanism remains unknown. Collectively, the Caff-AuNPs synthesized in this study may be used as potential drugs to combat chronic infections caused by biofilm-forming pathogenic bacteria. KEY POINTS: • Biofilm and persister cells are clinically relevant, as they either prolong or completely resist antibiotic treatments. • Caffeine is used in the green synthesis of Caff-AuNPs, which have antibacterial and antibiofilm properties. • Caff-AuNPs are effective against various pathogenic bacterial persister cells.
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Affiliation(s)
- Fazlurrahman Khan
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, South Korea
| | - Seul-Ki Park
- Institute of Food Science, Pukyong National University, Busan, 48513, South Korea
| | | | - DoKyung Oh
- Department of Food Science and Technology, Pukyong National University, Busan, 48513, South Korea
| | - Young-Mog Kim
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, South Korea. .,Institute of Food Science, Pukyong National University, Busan, 48513, South Korea. .,Department of Food Science and Technology, Pukyong National University, Busan, 48513, South Korea.
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31
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França A, Gaio V, Lopes N, Melo LDR. Virulence Factors in Coagulase-Negative Staphylococci. Pathogens 2021; 10:170. [PMID: 33557202 PMCID: PMC7913919 DOI: 10.3390/pathogens10020170] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 12/13/2022] Open
Abstract
Coagulase-negative staphylococci (CoNS) have emerged as major pathogens in healthcare-associated facilities, being S. epidermidis, S. haemolyticus and, more recently, S. lugdunensis, the most clinically relevant species. Despite being less virulent than the well-studied pathogen S. aureus, the number of CoNS strains sequenced is constantly increasing and, with that, the number of virulence factors identified in those strains. In this regard, biofilm formation is considered the most important. Besides virulence factors, the presence of several antibiotic-resistance genes identified in CoNS is worrisome and makes treatment very challenging. In this review, we analyzed the different aspects involved in CoNS virulence and their impact on health and food.
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Affiliation(s)
- Angela França
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (V.G.); (N.L.)
| | | | | | - Luís D. R. Melo
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (V.G.); (N.L.)
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32
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Eisenreich W, Rudel T, Heesemann J, Goebel W. Persistence of Intracellular Bacterial Pathogens-With a Focus on the Metabolic Perspective. Front Cell Infect Microbiol 2021; 10:615450. [PMID: 33520740 PMCID: PMC7841308 DOI: 10.3389/fcimb.2020.615450] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022] Open
Abstract
Persistence has evolved as a potent survival strategy to overcome adverse environmental conditions. This capability is common to almost all bacteria, including all human bacterial pathogens and likely connected to chronic infections caused by some of these pathogens. Although the majority of a bacterial cell population will be killed by the particular stressors, like antibiotics, oxygen and nitrogen radicals, nutrient starvation and others, a varying subpopulation (termed persisters) will withstand the stress situation and will be able to revive once the stress is removed. Several factors and pathways have been identified in the past that apparently favor the formation of persistence, such as various toxin/antitoxin modules or stringent response together with the alarmone (p)ppGpp. However, persistence can occur stochastically in few cells even of stress-free bacterial populations. Growth of these cells could then be induced by the stress conditions. In this review, we focus on the persister formation of human intracellular bacterial pathogens, some of which belong to the most successful persister producers but lack some or even all of the assumed persistence-triggering factors and pathways. We propose a mechanism for the persister formation of these bacterial pathogens which is based on their specific intracellular bipartite metabolism. We postulate that this mode of metabolism ultimately leads, under certain starvation conditions, to the stalling of DNA replication initiation which may be causative for the persister state.
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Affiliation(s)
- Wolfgang Eisenreich
- Department of Chemistry, Chair of Biochemistry, Technische Universität München, Garching, Germany
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
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33
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Riber L, Hansen LH. Epigenetic Memories: The Hidden Drivers of Bacterial Persistence? Trends Microbiol 2021; 29:190-194. [PMID: 33414017 DOI: 10.1016/j.tim.2020.12.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 11/25/2022]
Abstract
Epigenetic modifications, including DNA methylation, stably alter gene expression without modifying genomic sequences. Recent evidence suggests that epigenetic regulation coupled with a long-term 'memory' effect plays a major role within bacterial persistence formation. Today, emerging high-resolution, single-molecule sequencing technologies allow an increased focus on DNA modifications as regulatory epigenetic marks, which presents a unique opportunity to identify possible epigenetic drivers of bacterial persistence.
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Affiliation(s)
- Leise Riber
- Section of Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark.
| | - Lars Hestbjerg Hansen
- Section of Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
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34
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Maffei E, Fino C, Harms A. Antibiotic Tolerance and Persistence Studied Throughout Bacterial Growth Phases. Methods Mol Biol 2021; 2357:23-40. [PMID: 34590249 DOI: 10.1007/978-1-0716-1621-5_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Antibiotic tolerance and persistence allow bacteria to survive lethal doses of antibiotic drugs in the absence of genetic resistance. Despite the urgent need to address these phenomena as a cause of clinical antibiotic treatment failure, studies on antibiotic tolerance and persistence are notorious for contradictory and inconsistent findings. Many of these problems are likely caused by differences in the methodology used to study antibiotic tolerance and persistence in the laboratory. Standardized experimental procedures would therefore greatly promote research in this field by facilitating the integrated analysis of results obtained by different research groups. Here, we present a robust and adaptable methodology to study antibiotic tolerance/persistence in broth cultures of Escherichia coli and Pseudomonas aeruginosa . The hallmark of this methodology is that the formation and disappearance of antibiotic-tolerant cells is recorded throughout all bacterial growth phases from lag after inoculation over exponential growth into early and then late stationary phase. In addition, all relevant experimental conditions are rigorously controlled to obtain highly reproducible results. We anticipate that this methodology will promote research on antibiotic tolerance and persistence by enabling a deeper view at the growth-dependent dynamics of this phenomenon and by contributing to the standardization or at least comparability of experimental procedures used in the field.
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Affiliation(s)
- Enea Maffei
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Cinzia Fino
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Harms
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland.
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35
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Chen H, Green A, Martz K, Wu X, Alzahrani A, Warriner K. The progress of type II persisters of Escherichia coli O157:H7 to a non-culturable state during prolonged exposure to antibiotic stress with revival being aided through acid-shock treatment and provision of methyl pyruvate. Can J Microbiol 2020; 67:518-528. [PMID: 33125853 DOI: 10.1139/cjm-2020-0339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Persisters are a form of dormancy in bacteria that provide temporary resistance to antibiotics. The following reports on the formation of Escherichia coli O157:H7 E318 type II persisters from a protracted (8 days) challenge with ampicillin. Escherichia coli O157:H7 followed a multiphasic die-off pattern with an initial rapid decline (Phase I) of susceptible cells that transitioned to a slower rate representing tolerant cells (Phase II). After 24 h post-antibiotic challenge, the E. coli O157:H7 levels remained relatively constant at 2 log CFU/mL (Phase III), but became non-culturable within 8-days (Phase IV). The revival of persisters in Phase III could be achieved by the removal of antibiotic stress, although those in Phase IV required an extended incubation period or application of acid-shock. The carbon utilization profile of persister cells was less diverse compared with non-persisters, with only methyl pyruvate being utilized from the range tested. Inclusion of methyl pyruvate in tryptic soy agar revived non-cultural persisters, presumably by stimulating metabolism. The results suggest that persisters could be subdivided into culturable or non-culturable cells, with the former representing a transition state to the latter. The study provided insights into how to revive cells from dormancy to aid enumeration and control.
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Affiliation(s)
- Heather Chen
- Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada.,Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Andrew Green
- Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada.,Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Kailey Martz
- Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada.,Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Xueyang Wu
- Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada.,Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Abdulhakeem Alzahrani
- Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada.,Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Keith Warriner
- Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada.,Center of Public Health and Zoonosis, Department of Food Science, University of Guelph, Guelph, Ontario, Canada
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36
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Ovsepian A, Larsen MH, Vegge CS, Ingmer H. Ciprofloxacin-induced persister-cells in Campylobacter jejuni. MICROBIOLOGY-SGM 2020; 166:849-853. [PMID: 32697188 DOI: 10.1099/mic.0.000953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Campylobacter jejuni is a major bacterial foodborne-pathogen. Ciprofloxacin is an important antibiotic for the treatment of C. jejuni, albeit high rates of fluoroquinolone resistance have limited its usefulness. Persister-cells are transiently antibiotic-tolerant fractions of bacterial populations and their occurrence has been associated with recalcitrant and persistent bacterial infections. Here, time-kill assays with ciprofloxacin (200×MIC, 25 µg ml-1) were performed in C. jejuni strains 81-176 and RM1221 and persister-cells were found. The frequency of survivors after 8 h of ciprofloxacin exposure was approx. 10-3 for both strains, while after 22 h the frequency was between 10-5-10-7, depending on the strain and growth-phase. Interestingly, the stationary-phase cultures did not display more persister-cells compared to exponential-phase cultures, in contrast to what has been observed in other bacterial species. Persister-cells after ampicillin exposure (100×MIC, 200 µg ml-1) were not detected, implying that persister-cell formation in C. jejuni is antibiotic-specific. In attempts to identify the mechanism of ciprofloxacin persister-cell formation, stringent or SOS responses were not found to play major roles. Overall, this study reports ciprofloxacin persister-cells in C. jejuni and challenges the notion of persister-cells as plainly dormant non-growing cells.
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Affiliation(s)
- Armen Ovsepian
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, DK-1870 Frederiksberg C, Denmark
| | - Marianne Halberg Larsen
- Present address: Chr. Hansen, Hørsholm, Denmark.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, DK-1870 Frederiksberg C, Denmark
| | - Christina Skovgaard Vegge
- Present address: Bacthera, Hørsholm, Denmark.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, DK-1870 Frederiksberg C, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, DK-1870 Frederiksberg C, Denmark
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37
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Vlazaki M, Rossi O, Price DJ, McLean C, Grant AJ, Mastroeni P, Restif O. A data-based mathematical modelling study to quantify the effects of ciprofloxacin and ampicillin on the within-host dynamics of Salmonella enterica during treatment and relapse. J R Soc Interface 2020; 17:20200299. [PMID: 32634369 DOI: 10.1098/rsif.2020.0299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Antibiotic therapy has drastically reduced the mortality and sequelae of bacterial infections. From naturally occurring to chemically synthesized, different classes of antibiotics have been successfully used without detailed knowledge of how they affect bacterial dynamics in vivo. However, a proportion of patients receiving antimicrobial therapy develop recrudescent infections post-treatment. Relapsing infections are attributable to incomplete clearance of bacterial populations following antibiotic administration; the metabolic profile of this antibiotic-recalcitrant bacterial subpopulation, the spatio-temporal context of its emergence and the variance of antibiotic-bacterial interactions in vivo remain unclear. Here, we develop and apply a mechanistic mathematical model to data from a study comparing the effects of ciprofloxacin and ampicillin on the within-host dynamics of Salmonella enterica serovar Typhimurium in murine infections. Using the inferential capacity of our model, we show that the antibiotic-recalcitrant bacteria following ampicillin, but not ciprofloxacin, treatment belong to a non-replicating phenotype. Aligning with previous studies, we independently estimate that the lymphoid tissues and spleen are important reservoirs of non-replicating bacteria. Finally, we predict that post-treatment, the progenitors of the non-growing and growing bacterial populations replicate and die at different rates. Ultimately, the liver, spleen and mesenteric lymph nodes are all repopulated by progenitors of the previously non-growing phenotype in ampicillin-treated mice.
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Affiliation(s)
- Myrto Vlazaki
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Omar Rossi
- GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy
| | - David J Price
- Centre of Epidemiology and Biostatistics, University of Melbourne, Grattan Street, Parkville, Victoria 3010, Australia.,The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Callum McLean
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Pietro Mastroeni
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
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38
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Song S, Wood TK. Combatting Persister Cells With Substituted Indoles. Front Microbiol 2020; 11:1565. [PMID: 32733426 PMCID: PMC7358577 DOI: 10.3389/fmicb.2020.01565] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Given that a subpopulation of most bacterial cells becomes dormant due to stress, and that the resting cells of pathogens can revive and reconstitute infections, it is imperative to find methods to treat dormant cells to eradicate infections. The dormant bacteria that are not spores or cysts are known as persister cells. Remarkably, in contrast to the original report that incorrectly indicated indole increases persistence, a large number of indole-related compounds have been found in the last few years that kill persister cells. Hence, in this review, along with a summary of recent results related to persister cell formation and resuscitation, we focus on the ability of indole and substituted indoles to combat the persister cells of both pathogens and non-pathogens.
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Affiliation(s)
- Sooyeon Song
- Department of Animal Science, Jeonbuk National University, Jeonju, South Korea
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, United States
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39
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Chang J, Lee RE, Lee W. A pursuit of Staphylococcus aureus continues: a role of persister cells. Arch Pharm Res 2020; 43:630-638. [PMID: 32627141 DOI: 10.1007/s12272-020-01246-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 06/29/2020] [Indexed: 11/29/2022]
Abstract
Staphylococcus aureus is a pathogen that causes critical diseases, such as pneumonia, endocarditis, and bacteremia, upon gaining access to the bloodstream of the host. Because host innate immunity alone cannot fight against this rapidly expanding pathogen, the use of antibiotic agents is necessary to clear out S. aureus. However, sub-populations of S. aureus fail to respond to the antibiotics resulting in ineffective clearance of the bacteria. One mechanism by which S. aureus does not respond to the antibiotics is by developing resistance through alterations in its genetic makeup, and genetic studies have revealed a major portion of mechanisms that are responsible for the rise of these antibiotic-resistant strains. Another sub-population that fails to respond to the antibiotics is called persister cells. There is a mounting clinical evidence that these persister cells significantly contribute to the antibiotic failure and persistent infection, but a clear mechanistic picture of the formation of the S. aureus persister cells is unavailable. This review focuses on drawing out a mechanistic map of factors that contribute to the formation of S. aureus persister cells. Understanding the mechanism will provide future direction for the development of novel antibiotic strategies to more efficiently tackle infections caused by S. aureus.
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Affiliation(s)
- JuOae Chang
- School of Pharmacy, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, 16419, Gyeonggi-do, South Korea
| | - Rho-Eun Lee
- School of Pharmacy, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, 16419, Gyeonggi-do, South Korea
| | - Wonsik Lee
- School of Pharmacy, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, 16419, Gyeonggi-do, South Korea.
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40
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Fodor A, Abate BA, Deák P, Fodor L, Gyenge E, Klein MG, Koncz Z, Muvevi J, Ötvös L, Székely G, Vozik D, Makrai L. Multidrug Resistance (MDR) and Collateral Sensitivity in Bacteria, with Special Attention to Genetic and Evolutionary Aspects and to the Perspectives of Antimicrobial Peptides-A Review. Pathogens 2020; 9:pathogens9070522. [PMID: 32610480 PMCID: PMC7399985 DOI: 10.3390/pathogens9070522] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic poly-resistance (multidrug-, extreme-, and pan-drug resistance) is controlled by adaptive evolution. Darwinian and Lamarckian interpretations of resistance evolution are discussed. Arguments for, and against, pessimistic forecasts on a fatal “post-antibiotic era” are evaluated. In commensal niches, the appearance of a new antibiotic resistance often reduces fitness, but compensatory mutations may counteract this tendency. The appearance of new antibiotic resistance is frequently accompanied by a collateral sensitivity to other resistances. Organisms with an expanding open pan-genome, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, can withstand an increased number of resistances by exploiting their evolutionary plasticity and disseminating clonally or poly-clonally. Multidrug-resistant pathogen clones can become predominant under antibiotic stress conditions but, under the influence of negative frequency-dependent selection, are prevented from rising to dominance in a population in a commensal niche. Antimicrobial peptides have a great potential to combat multidrug resistance, since antibiotic-resistant bacteria have shown a high frequency of collateral sensitivity to antimicrobial peptides. In addition, the mobility patterns of antibiotic resistance, and antimicrobial peptide resistance, genes are completely different. The integron trade in commensal niches is fortunately limited by the species-specificity of resistance genes. Hence, we theorize that the suggested post-antibiotic era has not yet come, and indeed might never come.
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Affiliation(s)
- András Fodor
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
| | - Birhan Addisie Abate
- Ethiopian Biotechnology Institute, Agricultural Biotechnology Directorate, Addis Ababa 5954, Ethiopia;
| | - Péter Deák
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
| | - Ervin Gyenge
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
| | - Michael G. Klein
- Department of Entomology, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA;
| | - Zsuzsanna Koncz
- Max-Planck Institut für Pflanzenzüchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Köln, Germany;
| | | | - László Ötvös
- OLPE, LLC, Audubon, PA 19403-1965, USA;
- Institute of Medical Microbiology, Semmelweis University, H-1085 Budapest, Hungary
- Arrevus, Inc., Raleigh, NC 27612, USA
| | - Gyöngyi Székely
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania
| | - Dávid Vozik
- Research Institute on Bioengineering, Membrane Technology and Energetics, Faculty of Engineering, University of Veszprem, H-8200 Veszprém, Hungary; or or
| | - László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
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41
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Zhang D, Hu Y, Zhu Q, Huang J, Chen Y. Proteomic interrogation of antibiotic resistance and persistence in Escherichia coli - progress and potential for medical research. Expert Rev Proteomics 2020; 17:393-409. [PMID: 32567419 DOI: 10.1080/14789450.2020.1784731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction Escherichia coli strains possess two survival strategies to endure lethal antibiotic exposure including antibiotic resistance and persistence, in which persistence can contribute to the emergence of antibiotic resistance and increasing the risk of multidrug resistance. Using high-throughput proteomics for the comprehensive understanding of mechanisms of antibiotic resistance and persistence is an effective strategy for development of target-based anti-bacterial therapies. Areas covered In this review, we summarize a comprehensive proteomic perspective of antibiotic resistance and persistence in E. coli, and overview of anti-antibiotic resistance and anti-persister molecules and strategies for the development of potential therapies. Expert opinion Proteomics allows us to globally identify the critical proteins and pathways involved in antibiotic resistance and persistence. Advancements in methodologies of proteomics and multi-omic strategies are required to overcome the limitations of proteomics and better understand mechanisms of antibiotic resistance and persistence in E. coli, and to open the possibility for identification of new targets for alternative strategies in therapeutics.
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Affiliation(s)
- Danfeng Zhang
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Yuanqing Hu
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Qiuqiang Zhu
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Jiafu Huang
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China.,Engineering Technological Center of Mushroom Industry , Zhangzhou, China
| | - Yiyun Chen
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
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42
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Kandel PP, Baltrus DA, Hockett KL. Pseudomonas Can Survive Tailocin Killing via Persistence-Like and Heterogenous Resistance Mechanisms. J Bacteriol 2020; 202:e00142-20. [PMID: 32312747 PMCID: PMC7283598 DOI: 10.1128/jb.00142-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
Phage tail-like bacteriocins (tailocins) are bacterially produced protein toxins that mediate competitive interactions between cocolonizing bacteria. Both theoretical and experimental research has shown there are intransitive interactions between bacteriocin-producing, bacteriocin-sensitive, and bacteriocin-resistant populations, whereby producers outcompete sensitive cells, sensitive cells outcompete resistant cells, and resistant cells outcompete producers. These so-called rock-paper-scissors dynamics explain how all three populations occupy the same environment, without one driving the others extinct. Using Pseudomonas syringae as a model, we demonstrate that otherwise sensitive cells survive bacteriocin exposure through a physiological mechanism. This mechanism allows cells to survive bacteriocin killing without acquiring resistance. We show that a significant fraction of the target cells that survive a lethal dose of tailocin did not exhibit any detectable increase in survival during a subsequent exposure. Tailocin persister cells were more prevalent in stationary- rather than log-phase cultures. Of the fraction of cells that gained detectable resistance, there was a range from complete (insensitive) to incomplete (partially sensitive) resistance. By using genomic sequencing and genetic engineering, we showed that a mutation in a hypothetical gene containing 8 to 10 transmembrane domains causes tailocin high persistence and that genes of various glycosyltransferases cause incomplete and complete tailocin resistance. Importantly, of the several classes of mutations, only those causing complete tailocin resistance compromised host fitness. This result indicates that bacteria likely utilize persistence to survive bacteriocin-mediated killing without suffering the costs associated with resistance. This research provides important insight into how bacteria can escape the trap of fitness trade-offs associated with gaining de novo tailocin resistance.IMPORTANCE Bacteriocins are bacterially produced protein toxins that are proposed as antibiotic alternatives. However, a deeper understanding of the responses of target bacteria to bacteriocin exposure is lacking. Here, we show that target cells of Pseudomonas syringae survive lethal bacteriocin exposure through both physiological persistence and genetic resistance mechanisms. Cells that are not growing rapidly rely primarily on persistence, whereas those growing rapidly are more likely to survive via resistance. We identified various mutations in lipopolysaccharide biogenesis-related regions involved in tailocin persistence and resistance. By assessing host fitness of various classes of mutants, we showed that persistence and subtle resistance are mechanisms P. syringae uses to survive competition and preserve host fitness. These results have important implications for developing bacteriocins as alternative therapeutic agents.
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Affiliation(s)
- Prem P Kandel
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Kevin L Hockett
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
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43
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Ferreira MA, Pereira ML, Dos Santos KV. Drug-induced tolerance: the effects of antibiotic pre-exposure in Stenotrophomonas maltophilia. Future Microbiol 2020; 15:497-508. [PMID: 32478618 DOI: 10.2217/fmb-2019-0253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Aim: To investigate if the prior use of nontargeted antibiotics induces cross-tolerance in Stenotrophomonas maltophilia. Methods: Antibiotic induction was performed to evaluate daptomycin and vancomycin as possible tolerance-inducing drugs measured by minimum bactericidal concentration/minimum inhibitory concentration (MIC) ratio, adapted disk-diffusion tests and time-kill curves. Results: After antibiotic exposure, three potentially tolerant strains were isolated, maintaining the same MIC value of levofloxacin, with minimum bactericidal concentration/MIC ratio slightly higher than the parental. In the adapted disk-diffusion test, one strain (D25) showed high tolerance level for levofloxacin, ceftazidime and ticarcillin-clavulanate. In time-kill activity of levofloxacin, D25 presented a subpopulation of persisters with survival rate higher (1.6-fold) than the parental. Conclusion: Previous exposure of S. maltophilia to daptomycin can induce cross-tolerance to ceftazidime and ticarcillin-clavulanate and cross-persistence to levofloxacin.
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Affiliation(s)
- Mariana Am Ferreira
- Department of Pathology, Health Sciences Center, Universidade Federal do Espírito Santo (UFES), Av. Marechal Campos, 1468, 29040-090 Vitória, Espírito Santo, Brazil
| | - Maria Ls Pereira
- Department of Pathology, Health Sciences Center, Universidade Federal do Espírito Santo (UFES), Av. Marechal Campos, 1468, 29040-090 Vitória, Espírito Santo, Brazil
| | - Kênia V Dos Santos
- Department of Pathology, Health Sciences Center, Universidade Federal do Espírito Santo (UFES), Av. Marechal Campos, 1468, 29040-090 Vitória, Espírito Santo, Brazil
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44
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Abokhalil RN, Elkhatib WF, Aboulwafa MM, Hassouna NA. Persisters of Klebsiella pneumoniae and Proteus mirabilis: A Common Phenomenon and Different Behavior Profiles. Curr Microbiol 2020; 77:1233-1244. [PMID: 32123985 DOI: 10.1007/s00284-020-01926-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/17/2020] [Indexed: 12/12/2022]
Abstract
Persisters of infectious agents are capable of surviving antibiotic treatment so the emergence of these subpopulations need to be overcome. In this study, we aimed to isolate, characterize and inhibit persister subpopulation in two clinical isolates Klebsiella pneumoniae and Proteus mirabilis. Different behavior profiles between the two isolates could be observed. The results of dose-dependent killing curve revealed that 2.3% (Klebsiella pneumoniae) versus 1.3% (Proteus mirabilis) persister cells could be recovered using 500 and 30 ug/ml ciprofloxacin, respectively. Upon resuscitation, persister cells exhibited only 65% versus 30% percentage growth and 5 versus 7 times cell elongation relative to Klebsiella pneumoniae and Proteus mirabilis, respectively. The levels of persister cells to ciprofloxacin of Klebsiella pneumoniae were dramatically decreased by about 79, 92, 97 and 83% in average by pre-exposure to hyperosmotic stress, temperature, different pHs, and hydrogen peroxide, respectively, while those of Proteus mirabilis were minimally decreased with corresponding reduction percentages of about 12%, 24 & 25%, and 0%. Regarding combating persisters, Klebsiella pneumoniae showed different response as compared to Proteus mirabilis. Among the tested sugars, the highest reduction of Klebsiella pneumoniae persister cells was obtained with pre-priming with sucrose while for Proteus mirabilis persister cells, the highest reduction was obtained with pre-priming with glucose. Using sodium salicylate with ciprofloxacin could eradicate persisters of Klebsiella pneumoniae at any tested concentration while for Proteus mirabilis it caused some reduction in persister cells at certain concentrations. Complete eradication of persisters was obtained by combining silver nitrate with ciprofloxacin for each test isolate.
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Affiliation(s)
- Rana N Abokhalil
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Abbassia, POB: 11566, Cairo, Egypt
| | - Walid F Elkhatib
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Abbassia, POB: 11566, Cairo, Egypt
- Department of Microbiology and Immunology, School of Pharmacy & Pharmaceutical Industries, Badr University in Cairo (BUC), Entertainment Area, Badr City, Cairo, Egypt
| | - Mohammad M Aboulwafa
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Abbassia, POB: 11566, Cairo, Egypt.
| | - Nadia A Hassouna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Abbassia, POB: 11566, Cairo, Egypt
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45
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A ParDE-family toxin antitoxin system in major resistance plasmids of Enterobacteriaceae confers antibiotic and heat tolerance. Sci Rep 2019; 9:9872. [PMID: 31285520 PMCID: PMC6614396 DOI: 10.1038/s41598-019-46318-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/26/2019] [Indexed: 11/16/2022] Open
Abstract
Toxin-antitoxin (TA) systems were initially discovered as plasmid addiction systems on low-copy-number plasmids. Thousands of TA loci have since been identified on chromosomes, plasmids and mobile elements in bacteria and archaea with diverse roles in bacterial physiology and in maintenance of genetic elements. Here, we identified and characterised a plasmid mediated type II TA system in Enterobacteriaceae as a member of the ParDE super family. This system (hereafter, ParDEI) is distributed among IncI and IncF-type antibiotic resistance and virulence plasmids found in avian and human-source Escherichia coli and Salmonella. It is found that ParDEI is a plasmid stability and stress response module that increases tolerance of aminoglycoside, quinolone and β-lactam antibiotics in E. coli by ~100–1,000-fold, and thus to levels beyond those achievable in the course of antibiotic therapy for human infections. ParDEI also confers a clear survival advantage at 42 °C and expression of the ParEI toxin in trans induces the SOS response, inhibits cell division and promotes biofilm formation. This transmissible high-level antibiotic tolerance is likely to be an important factor in the success of the IncI and IncF plasmids which carry it and the important pathogens in which these are resident.
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46
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Goormaghtigh F, Van Melderen L. Single-cell imaging and characterization of Escherichia coli persister cells to ofloxacin in exponential cultures. SCIENCE ADVANCES 2019; 5:eaav9462. [PMID: 31223653 PMCID: PMC6584399 DOI: 10.1126/sciadv.aav9462] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/10/2019] [Indexed: 06/02/2023]
Abstract
Bacterial persistence refers to the capacity of small subpopulations within clonal populations to tolerate antibiotics. Persisters are thought to originate from dormant cells in which antibiotic targets are less active and cannot be corrupted. Here, we report that in exponentially growing cultures, ofloxacin persisters originate from metabolically active cells: These cells are dividing before the addition of ofloxacin and do endure DNA damages during the treatment, similar to their nonpersister siblings. We observed that growth rate, DNA content, and SOS induction vary among persisters, as in the bulk of the population and therefore do not constitute predictive markers for persistence. Persister cells typically form long polynucleoid filaments and reach maximum SOS induction after removal of ofloxacin. Eventually, cell division resumes, giving rise to a new population. Our findings highlight the heterogeneity of persister cells and therefore the need to analyze these low-frequency phenotypic variants on a case-by-case basis at the single-cell level.
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Affiliation(s)
- Frédéric Goormaghtigh
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
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47
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Garrigues GE, Zmistowski B, Cooper AM, Green A. Proceedings from the 2018 International Consensus Meeting on Orthopedic Infections: management of periprosthetic shoulder infection. J Shoulder Elbow Surg 2019; 28:S67-S99. [PMID: 31196516 DOI: 10.1016/j.jse.2019.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 04/20/2019] [Indexed: 02/05/2023]
Abstract
The Second International Consensus Meeting on Orthopedic Infections was held in Philadelphia, Pennsylvania, in July 2018. A multidisciplinary team of international experts from all 9 subspecialties of orthopedic surgery and allied fields of infectious disease, microbiology, and epidemiology was assembled to form the International Consensus Group. The following consensus proceedings from the International Consensus Meeting involve 30 questions pertaining to the management of periprosthetic shoulder infection.
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Affiliation(s)
- Grant E Garrigues
- Division of Sports Medicine, Midwest Orthopaedics at Rush, Rush University Medical Center, Chicago, IL, USA.
| | - Benjamin Zmistowski
- Department of Orthopaedic Surgery, Rothman Institute at Thomas Jefferson University, Philadelphia, PA, USA
| | - Alexus M Cooper
- Department of Orthopaedic Surgery, Rothman Institute at Thomas Jefferson University, Philadelphia, PA, USA
| | - Andrew Green
- Division of Shoulder and Elbow Surgery, Department of Orthopaedic Surgery, Warren Alpert Medical School, Brown University, Providence, RI, USA
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48
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Abstract
Systemic Salmonella enterica infections are a major cause of mortality worldwide and are becoming increasingly untreatable. Recent single-cell data from a mouse model of typhoid fever show that the host immune system actually eradicates many Salmonella cells, while other Salmonella organisms thrive at the same time in the same tissue, causing lethal disease progression. The surviving Salmonella cells have highly heterogeneous metabolism, growth rates, and exposure to various stresses. Emerging evidence suggests that similarly heterogeneous host-pathogen encounters might be a key feature of many infectious diseases. This heterogeneity offers fascinating opportunities for research and application. If we understand the mechanisms that determine the disparate local outcomes, we might be able to develop entirely novel strategies for infection control by broadening successful host antimicrobial attacks and closing permissive niches in which pathogens can thrive. This review describes suitable technologies, a current working model of heterogeneous host-Salmonella interactions, the impact of diverse Salmonella subsets on antimicrobial chemotherapy, and major open questions and challenges.
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49
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Barrett TC, Mok WWK, Murawski AM, Brynildsen MP. Enhanced antibiotic resistance development from fluoroquinolone persisters after a single exposure to antibiotic. Nat Commun 2019; 10:1177. [PMID: 30862812 PMCID: PMC6414640 DOI: 10.1038/s41467-019-09058-4] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 02/12/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial persisters are able to tolerate high levels of antibiotics and give rise to new populations. Persister tolerance is generally attributed to minimally active cellular processes that prevent antibiotic-induced damage, which has led to the supposition that persister offspring give rise to antibiotic-resistant mutants at comparable rates to normal cells. Using time-lapse microscopy to monitor Escherichia coli populations following ofloxacin treatment, we find that persisters filament extensively and induce impressive SOS responses before returning to a normal appearance. Further, populations derived from fluoroquinolone persisters contain significantly greater quantities of antibiotic-resistant mutants than those from untreated controls. We confirm that resistance is heritable and that the enhancement requires RecA, SOS induction, an opportunity to recover from treatment, and the involvement of error-prone DNA polymerase V (UmuDC). These findings show that fluoroquinolones damage DNA in persisters and that the ensuing SOS response accelerates the development of antibiotic resistance from these survivors. Fluoroquinolone (FQ)-induced DNA damage in persisters could promote antibiotic resistance. Here, using time-lapse microscopy and genetic analyses, the authors show that after a single round of FQ treatment, SOS response in persisters accelerates the development of resistance to unrelated antibiotics.
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Affiliation(s)
- Theresa C Barrett
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Wendy W K Mok
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.,Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, 06032-3305, USA
| | - Allison M Murawski
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Mark P Brynildsen
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA. .,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
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50
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Regrowth-delay body as a bacterial subcellular structure marking multidrug-tolerant persisters. Cell Discov 2019; 5:8. [PMID: 30675381 PMCID: PMC6341109 DOI: 10.1038/s41421-019-0080-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/28/2018] [Accepted: 01/01/2019] [Indexed: 02/08/2023] Open
Abstract
Bacteria have long been recognized to be capable of entering a phenotypically non-growing persister state, in which the cells exhibit an extended regrowth lag and a multidrug tolerance, thus posing a great challenge in treating infectious diseases. Owing to their non-inheritability, low abundance of existence, lack of metabolic activities, and high heterogeneity, properties of persisters remain poorly understood. Here, we report our accidental discovery of a subcellular structure that we term the regrowth-delay body, which is formed only in non-growing bacterial cells and sequesters multiple key proteins. This structure, that dissolves when the cell resumes growth, is able to be viewed as a marker of persisters. Our studies also indicate that persisters exhibit different depth of persistence, as determined by the status of their regrowth-delay bodies. Our findings imply that suppressing the formation and/or promoting the dissolution of regrowth-delay bodies could be viable strategies for eradicating persisters.
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