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da Cruz Nizer WS, Adams ME, Allison KN, Montgomery MC, Mosher H, Cassol E, Overhage J. Oxidative stress responses in biofilms. Biofilm 2024; 7:100203. [PMID: 38827632 PMCID: PMC11139773 DOI: 10.1016/j.bioflm.2024.100203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024] Open
Abstract
Oxidizing agents are low-molecular-weight molecules that oxidize other substances by accepting electrons from them. They include reactive oxygen species (ROS), such as superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (HO-), and reactive chlorine species (RCS) including sodium hypochlorite (NaOCl) and its active ingredient hypochlorous acid (HOCl), and chloramines. Bacteria encounter oxidizing agents in many different environments and from diverse sources. Among them, they can be produced endogenously by aerobic respiration or exogenously by the use of disinfectants and cleaning agents, as well as by the mammalian immune system. Furthermore, human activities like industrial effluent pollution, agricultural runoff, and environmental activities like volcanic eruptions and photosynthesis are also sources of oxidants. Despite their antimicrobial effects, bacteria have developed many mechanisms to resist the damage caused by these toxic molecules. Previous research has demonstrated that growing as a biofilm particularly enhances bacterial survival against oxidizing agents. This review aims to summarize the current knowledge on the resistance mechanisms employed by bacterial biofilms against ROS and RCS, focussing on the most important mechanisms, including the formation of biofilms in response to oxidative stressors, the biofilm matrix as a protective barrier, the importance of detoxifying enzymes, and increased protection within multi-species biofilm communities. Understanding the complexity of bacterial responses against oxidative stress will provide valuable insights for potential therapeutic interventions and biofilm control strategies in diverse bacterial species.
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Affiliation(s)
| | - Madison Elisabeth Adams
- Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, ON, Canada
| | - Kira Noelle Allison
- Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, ON, Canada
| | | | - Hailey Mosher
- Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, ON, Canada
| | - Edana Cassol
- Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, ON, Canada
| | - Joerg Overhage
- Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, ON, Canada
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2
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Kumari K, Sharma PK, Singh RP. The transcriptome response of Enterobacter sp. S-33 is modulated by low pH-stress. Genes Genomics 2024; 46:671-687. [PMID: 38687436 DOI: 10.1007/s13258-024-01513-x] [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: 06/13/2023] [Accepted: 03/26/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Acidic environments naturally occur worldwide and uncontrolled use of agricultural practices may also cause acidification of soils. The development of acidic conditions disturbs the establishment of efficient microbial populations in their natural niches. The survival of Enterobacter species under acidic stress remains poorly understood. OBJECTIVE This study aimed to investigate the survival of an environmental isolate Enterobacter sp. S-33 under acidic stress and to identify the various genes involved in stress protection at the global gene transcription level. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to environmental pH changes. METHODS We used the next-generation sequencing (NGS) method to analyze the expression (up-regulation & down-regulation) of genes under varying pH conditions. RESULTS A total of 4214 genes were differentially expressed under acidic conditions (pH 5.0), with 294 up-regulated and 167 down-regulated. At pH 6.0, 50 genes were significantly expressed, of which 34 and 16 were identified as up-regulated and down-regulated, respectively. Many of the up-regulated genes were involved in carbohydrate metabolism, amino acid transport & metabolism, and the most down-regulated genes were related to post-translational modification, lipid transport & metabolism, etc. The observed transcriptomic regulation of genes and pathways identified that Enterobacter reduced its post-translational modification, lipid transport & metabolism, and increased carbohydrate metabolism, amino acid metabolism & transport, energy production & conversion to adapt and grow in acidic stress. CONCLUSIONS The present work provides in-depth information on the characterization of genes associated with tolerance or adaptation to acidic stress of Enterobacter bacterium.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Rajnish Prakash Singh
- Department of Biotechnlogy, Jaypee Insttute of Information Technology, Noida, 201309, India.
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3
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Prakash A, Dutta D. Bicyclomycin generates ROS and blocks cell division in Escherichia coli. PLoS One 2024; 19:e0293858. [PMID: 38551933 PMCID: PMC10980228 DOI: 10.1371/journal.pone.0293858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/27/2024] [Indexed: 04/01/2024] Open
Abstract
The role of reactive oxygen species (ROS) in the killing exerted by antibiotics on bacteria is debated. Evidence attributes part of toxicity of many antibiotics to their ability to generate ROS by interfering with cellular metabolism, but some studies dismiss the role of ROS. Bicyclomycin (BCM) is a broad-spectrum antibiotic that is the only known compound to inhibit E. coli transcription terminator factor Rho with no known other cellular targets. In the present study, we addressed this question by checking whether the induction of oxidative stress could explain the increased sensitivity to Bicyclomycin in the hns deleted strain even in Δkil background in E. coli. BCM evoked the generation of ROS in E. coli cells. BCM is known to cause the cell filamentation phenotype in E. coli. Performing fluorescence microscopic analysis, we show that bicyclomycin-dependent cell filamentation is associated with SOS response. RecA-GFP filaments were found to colocalize with the damaged DNA sites in the cell. Further analysis revealed that the genomic DNA was partitioned but the cell septum formation was severely affected under BCM treatment. Furthermore, we observed biofilm formation by E. coli after BCM treatment. We hypothesize that ROS production after BCM treatment could lead to cell filamentation in bacteria. A better understanding of the mode of toxicity of BCM will help us design better antibiotic treatment regimes for clinical practices, including combinatorial drug therapies. The cell filamentation phenotype observed after BCM treatment makes this antibiotic a promising drug for phage-antibiotic synergy (PAS) therapy.
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Affiliation(s)
- Anand Prakash
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Dipak Dutta
- CSIR-Institute of Microbial Technology, Chandigarh, India
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4
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Kimijima M, Narisawa N, Hori E, Mandokoro K, Ito T, Ota Y, Sashida M, Kawai Y, Takenaga F. Nattokinase, a Subtilisin-like Alkaline-Serine Protease, Reduces Mutacin Activity by Inactivating the Competence-Stimulating Peptide in Streptococcus mutans. Pathogens 2024; 13:286. [PMID: 38668241 PMCID: PMC11054032 DOI: 10.3390/pathogens13040286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024] Open
Abstract
Streptococcus mutans is a major cariogenic organism because of its ability to form biofilms on tooth surfaces. Bacteriocins produced by S. mutans (known as mutacins) are indirect pathogenic factors that play a role in the persistence of this microbe in the oral environment. Nattokinase, a subtilisin-like alkaline serine protease, potently inhibits biofilm formation without affecting S. mutans growth. However, effective strategies utilizing nattokinase to control mutacin production by S. mutans are lacking. In this study, we evaluated the effect of nattokinase on mutacin activity in 46 strains of S. mutans with different mutacin genotypes isolated from the dental plaques of pediatric patients with caries. Nattokinase reduced the activity of mutacin against oral streptococci at a concentration of 1 mg/mL in all clinical isolates. Furthermore, nattokinase reduced the expression of non-lantibiotic mutacin structural genes (nlmABCD) and inactivated the extracellular competence-stimulating peptide involved in comDE activation, which regulates non-lantibiotic mutacin gene expression. These results suggest that nattokinase may reduce the virulence of S. mutans and could potentially be used as a new caries-preventive agent as an alternative to conventional drug treatments.
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Affiliation(s)
- Manami Kimijima
- Bioresource Utilization Sciences, Nihon University Graduate School of Bioresource Sciences, Fujisawa 252-0880, Kanagawa, Japan; (M.K.)
| | - Naoki Narisawa
- Bioresource Utilization Sciences, Nihon University Graduate School of Bioresource Sciences, Fujisawa 252-0880, Kanagawa, Japan; (M.K.)
| | - Eiji Hori
- Bioresource Utilization Sciences, Nihon University Graduate School of Bioresource Sciences, Fujisawa 252-0880, Kanagawa, Japan; (M.K.)
| | - Kengo Mandokoro
- Bioresource Utilization Sciences, Nihon University Graduate School of Bioresource Sciences, Fujisawa 252-0880, Kanagawa, Japan; (M.K.)
| | - Tatsuro Ito
- Department of Pediatric Dentistry, Nihon University School of Dentistry at Matsudo, Matsudo 271-8587, Chiba, Japan
- Research Institute of Oral Science, Nihon University School of Dentistry at Matsudo, Matsudo 271-8587, Chiba, Japan
| | - Yukina Ota
- Nihon University Graduate School of Dentistry at Matsudo, Pediatric Dentistry, Matsudo 271-8587, Chiba, Japan
| | - Momoko Sashida
- Department of Pediatric Dentistry, Nihon University School of Dentistry at Matsudo, Matsudo 271-8587, Chiba, Japan
| | - Yasushi Kawai
- Bioresource Utilization Sciences, Nihon University Graduate School of Bioresource Sciences, Fujisawa 252-0880, Kanagawa, Japan; (M.K.)
| | - Fumio Takenaga
- Bioresource Utilization Sciences, Nihon University Graduate School of Bioresource Sciences, Fujisawa 252-0880, Kanagawa, Japan; (M.K.)
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5
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Yu S, Ma Q, Huang J, Liu Y, Li J, Wang Y, Gong T, Zhang Q, Zou J, Li Y. SMU_1361c regulates the oxidative stress response of Streptococcus mutans. Appl Environ Microbiol 2024; 90:e0187123. [PMID: 38299814 PMCID: PMC10880606 DOI: 10.1128/aem.01871-23] [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: 10/19/2023] [Accepted: 12/22/2023] [Indexed: 02/02/2024] Open
Abstract
Dental caries is the most common chronic infectious disease around the world and disproportionately affects the marginalized socioeconomic group. Streptococcus mutans, considered a primary etiological agent of caries, depends on the coordinated physiological response to tolerate the oxidative stress generated by commensal species within dental plaque, which is a critical aspect of its pathogenicity. Here, we identified and characterized a novel tetracycline repressor family regulator, SMU_1361c, which appears to be acquired by the bacteria via horizontal gene transfer. Surprisingly, smu_1361c functions as a negative transcriptional regulator to regulate gene expression outside its operon and is involved in the oxidative stress response of S. mutans. The smu_1361c overexpression strain UA159/pDL278-1361c was more susceptible to oxidative stress and less competitive against hydrogen peroxide generated by commensal species Streptococcus gordonii and Streptococcus sanguinis. Transcriptomics analysis revealed that smu_1361c overexpression resulted in the significant downregulation of 22 genes, mainly belonging to three gene clusters responsible for the oxidative stress response. The conversed DNA binding motif of SMU_1361c was determined by electrophoretic mobility shift and DNase I footprinting assay with purified SMU_1361c protein; therefore, smu_1361c is directly involved in gene transcription related to the oxidative stress response. Crucially, our finding provides a new understanding of how S. mutans deals with the oxidative stress that is required for pathogenesis and will facilitate the development of new and improved therapeutic approaches for dental caries.IMPORTANCEStreptococcus mutans is the major organism associated with the development of dental caries, which globally is the most common chronic disease. To persist and survive in biofilms, S. mutans must compete with commensal species that occupy the same ecological niche. Here, we uncover a novel molecular mechanism of how tetracycline repressor family regulator smu_1361c is involved in the oxidative stress response through transcriptomics analysis, electrophoretic mobility shift assay, and DNase I footprinting assay. Furthermore, we demonstrated that smu_1361c mediates S. mutans sensitivity to oxidative stress and competitiveness with commensal streptococci. Therefore, this study has revealed a previously unknown regulation between smu_1361c and genes outside its operon and demonstrated the importance of smu_1361c in the oxidative stress response and the fitness of S. mutans within the plaque biofilms, which can be exploited as a new therapy to modulate ecological homeostasis and prevent dental caries.
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Affiliation(s)
- Shuxing Yu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qizhao Ma
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jun Huang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yaqi Liu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yan Wang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qiong Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jing Zou
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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6
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Ciarlantini C, Lacolla E, Francolini I, Fernández-García M, Muñoz-Núñez C, Muñoz-Bonilla A, Piozzi A. Development of Antioxidant and Antimicrobial Membranes Based on Functionalized and Crosslinked Chitosan for Tissue Regeneration. Int J Mol Sci 2024; 25:1961. [PMID: 38396645 PMCID: PMC10888599 DOI: 10.3390/ijms25041961] [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: 12/24/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Tissue engineering is an interdisciplinary field that develops new methods to enhance the regeneration of damaged tissues, including those of wounds. Polymer systems containing bioactive molecules can play an important role in accelerating tissue regeneration, mitigating inflammation process, and fighting bacterial infection. Chitosan (CS) has attracted much attention regarding its use in wound healing system fabrication thanks to its biocompatibility, biodegradability, and the presence of functional groups in its structure. In this work, bioactive chitosan-based membranes were obtained by both chemical and physical modifications of the polymer with glycidyl methacrylate and glycerol (GLY), respectively. The most suitable GLY concentration to obtain wound healing systems with good elongation at break, a good water vapor transmission rate (WVTR), and good wettability values was 20% (w/w). Afterwards, the membranes were crosslinked with different concentrations of ethylene glycol dimethacrylate (EGDMA). By using a concentration of 0.05 mM EGDMA, membranes with a contact angle and WVTR values suitable for the application were obtained. To make the system bioactive, 3,4-dihydrocinnamic acid (HCAF) was introduced into the membranes, either by imbibition or chemical reaction, using laccase as a catalyst. Thermal and mechanical analyses confirmed the formation of a cohesive network, which limited the plasticizing effect of GLY, particularly when HCAF was chemically bound. The HCAF-imbibed membrane showed a good antioxidant and antimicrobial activity, highlighting the potential of this system for the treatment of wound healing.
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Affiliation(s)
- Clarissa Ciarlantini
- Department of Chemistry, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (C.C.); (E.L.); (I.F.)
| | - Elisabetta Lacolla
- Department of Chemistry, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (C.C.); (E.L.); (I.F.)
| | - Iolanda Francolini
- Department of Chemistry, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (C.C.); (E.L.); (I.F.)
| | - Marta Fernández-García
- Institute of Polymer Science and Technology (ICTP-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (M.F.-G.); (C.M.-N.); (A.M.-B.)
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), 28006 Madrid, Spain
| | - Carolina Muñoz-Núñez
- Institute of Polymer Science and Technology (ICTP-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (M.F.-G.); (C.M.-N.); (A.M.-B.)
| | - Alexandra Muñoz-Bonilla
- Institute of Polymer Science and Technology (ICTP-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (M.F.-G.); (C.M.-N.); (A.M.-B.)
| | - Antonella Piozzi
- Department of Chemistry, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (C.C.); (E.L.); (I.F.)
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7
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Long CM, Beare PA, Cockrell D, Binette P, Tesfamariam M, Richards C, Anderson M, McCormick-Ell J, Brose M, Anderson R, Omsland A, Pearson T, Heinzen RA. Natural reversion promotes LPS elongation in an attenuated Coxiella burnetii strain. Nat Commun 2024; 15:697. [PMID: 38267444 PMCID: PMC10808227 DOI: 10.1038/s41467-023-43972-y] [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: 07/27/2023] [Accepted: 11/24/2023] [Indexed: 01/26/2024] Open
Abstract
Lipopolysaccharide (LPS) phase variation is a critical aspect of virulence in many Gram-negative bacteria. It is of particular importance to Coxiella burnetii, the biothreat pathogen that causes Q fever, as in vitro propagation of this organism leads to LPS truncation, which is associated with an attenuated and exempted from select agent status (Nine Mile II, NMII). Here, we demonstrate that NMII was recovered from the spleens of infected guinea pigs. Moreover, these strains exhibit a previously unrecognized form of elongated LPS and display increased virulence in comparison with the initial NMII strain. The reversion of a 3-bp mutation in the gene cbu0533 directly leads to LPS elongation. To address potential safety concerns, we introduce a modified NMII strain unable to produce elongated LPS.
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Affiliation(s)
- Carrie M Long
- Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, MT, 59840, USA.
| | - Paul A Beare
- Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Diane Cockrell
- Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Picabo Binette
- Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Mahelat Tesfamariam
- Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Crystal Richards
- Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Matthew Anderson
- Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Jessica McCormick-Ell
- Office of the Director, Office of Research Services, Division of Occupational Health and Safety, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Megan Brose
- Office of the Director, Office of Research Services, Division of Occupational Health and Safety, National Institutes of Health, Hamilton, 59840, USA
| | - Rebecca Anderson
- Office of the Director, Office of Research Services, Division of Occupational Health and Safety, National Institutes of Health, Hamilton, 59840, USA
| | - Anders Omsland
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, WA, 99164, USA
| | - Talima Pearson
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Robert A Heinzen
- Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, MT, 59840, USA
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8
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Fernández-Billón M, Llambías-Cabot AE, Jordana-Lluch E, Oliver A, Macià MD. Mechanisms of antibiotic resistance in Pseudomonas aeruginosa biofilms. Biofilm 2023; 5:100129. [PMID: 37205903 PMCID: PMC10189392 DOI: 10.1016/j.bioflm.2023.100129] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023] Open
Abstract
Pseudomonas aeruginosa is a major cause of life-threatening acute infections and life-long lasting chronic infections. The characteristic biofilm mode of life in P. aeruginosa chronic infections severely limits the efficacy of antimicrobial therapies, as it leads to intrinsic tolerance, involving physical and physiological factors in addition to biofilm-specific genes that can confer a transient protection against antibiotics promoting the development of resistance. Indeed, a striking feature of this pathogen is the extraordinary capacity to develop resistance to nearly all available antibiotics through the selection of chromosomal mutations, evidenced by its outstanding and versatile mutational resistome. This threat is dramatically amplified in chronic infections, driven by the frequent emergence of mutator variants with enhanced spontaneous mutation rates. Thus, this mini review is focused on describing the complex interplay of antibiotic resistance mechanisms in P. aeruginosa biofilms, to provide potentially useful information for the design of effective therapeutic strategies.
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Affiliation(s)
- María Fernández-Billón
- Department of Microbiology, Hospital Universitario Son Espases, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma de Mallorca, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), 28029, Madrid, Spain
| | - Aina E. Llambías-Cabot
- Department of Microbiology, Hospital Universitario Son Espases, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma de Mallorca, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), 28029, Madrid, Spain
| | - Elena Jordana-Lluch
- Department of Microbiology, Hospital Universitario Son Espases, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma de Mallorca, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), 28029, Madrid, Spain
| | - Antonio Oliver
- Department of Microbiology, Hospital Universitario Son Espases, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma de Mallorca, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), 28029, Madrid, Spain
| | - María D. Macià
- Department of Microbiology, Hospital Universitario Son Espases, Health Research Institute of the Balearic Islands (IdISBa), 07120, Palma de Mallorca, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), 28029, Madrid, Spain
- Corresponding author. Department of Microbiology, Hospital Universitario Son Espases, Crta. Vallemossa 79, 07120, Palma de Mallorca, Spain.
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He J, Cheng L, Rastelli ANDS, Deng D. Oral Bacteria: Friends and Foes? Pathogens 2023; 12:1319. [PMID: 38003784 PMCID: PMC10675697 DOI: 10.3390/pathogens12111319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The oral cavity is an ideal niche for microbial prosperity due to its stable temperature, suitable pH, and continuous nutrient supply [...].
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Affiliation(s)
- Jinzhi He
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Lei Cheng
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | | | - Dongmei Deng
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, 1081 LA Amsterdam, The Netherlands
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10
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Perullini M, Dulhoste S, Ribot F, Pehau-Arnaudet G, Bouvet OMM, Livage J, Nassif N. Bacteria metabolic adaptation to oxidative stress: the case of silica. J Biotechnol 2023; 374:80-89. [PMID: 37567503 DOI: 10.1016/j.jbiotec.2023.08.002] [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: 05/18/2023] [Revised: 07/25/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Although the presence of silica in many living organisms offers advanced properties including cell protection, the different in vitro attempts to build living materials in pure silica never favoured the cells viability. Thus, little attention has been paid to host-guest interactions to modify the expected biologic response. Here we report the physiological changes undergone by Escherichia coli K-12 in silica from colloidal solution to gel confinement. We show that the physiological alterations in growing cultures are not triggered by the initial oxidative Reactive Oxygen Species (ROS) response. Silica promotes the induction of alternative metabolic pathways along with an increase of growth suggesting the existence of rpoS polymorphisms. Since the functionality of hybrid materials depends on the specific biologic responses of their guests, such cell physiological adaptation opens perspectives in the design of bioactive devices attracting for a large field of sciences.
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Affiliation(s)
- Mercedes Perullini
- CONICET - Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Laboratorio de materiales funcionales con actividad biológica, Buenos Aires, Argentina.
| | - Sophie Dulhoste
- CONICET - Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Laboratorio de materiales funcionales con actividad biológica, Buenos Aires, Argentina
| | - François Ribot
- Sorbonne Université, CNRS, Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), F-75252 Paris Cedex 05, France
| | | | - Odile M M Bouvet
- IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France
| | - Jacques Livage
- Sorbonne Université, CNRS, Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), F-75252 Paris Cedex 05, France.
| | - Nadine Nassif
- Sorbonne Université, CNRS, Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), F-75252 Paris Cedex 05, France
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11
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Michael HSR, Subiramanian SR, Thyagarajan D, Mohammed NB, Saravanakumar VK, Govindaraj M, Maheswari KM, Karthikeyan N, Ramesh Kumar C. Melanin biopolymers from microbial world with future perspectives-a review. Arch Microbiol 2023; 205:306. [PMID: 37580645 DOI: 10.1007/s00203-023-03642-5] [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: 05/30/2023] [Revised: 07/10/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023]
Abstract
Melanin is an amorphous polymer made of heterogeneous functional groups synthesized by diverse organisms including fungi, bacteria, animals, and plants. It was widely acknowledged for its biological processes and its key role in the protection of organisms from environmental stress. Recently, melanin clutches attention in the field of nanobiotechnology, drug delivery, organic semiconductors and bioelectronics, environmental bioremediation, photoprotection, etc., Furthermore, melanin from natural sources like microbial community shows antimicrobial, fighting cancer, radical scavenging, cosmeceuticals, and many therapeutic areas as well. Though the multipotentiality nature of melanin has been put forth, real-world applications still flag fall behind, which might be anticipated to the inadequate and high price essence of natural melanin. However, current bioprocess technologies have paved for the large-scale or industrial production of microbial melanin, which could help in the replacement of synthetic melanin. Thus, this review emphasizes the various sources for melanin, i.e., types-based on its pathways and its chemical structures, functional efficiency, physical properties, and conventional and modern methods of both extraction and characterization. Moreover, an outlook on how it works in the field of medicine, bioremediation, and other related areas provides perspectives on the complete exploitation of melanin in practical applications of medicine and the environment.
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Affiliation(s)
| | - Shri Ranjani Subiramanian
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Nava India, Coimbatore, India
| | - Divyavaahini Thyagarajan
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Nava India, Coimbatore, India
| | - Nazneen Bobby Mohammed
- Department of Biotechnology, Vignan's Foundation for Science Technology and Research, Vadlamudi, Guntur Dist, Andhra Pradesh, India
| | | | - Mageswari Govindaraj
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Nava India, Coimbatore, India
| | | | - Naresh Karthikeyan
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Nava India, Coimbatore, India
| | - Charu Ramesh Kumar
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Nava India, Coimbatore, India
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12
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Cremin K, Duxbury SJN, Rosko J, Soyer OS. Formation and emergent dynamics of spatially organized microbial systems. Interface Focus 2023; 13:20220062. [PMID: 36789239 PMCID: PMC9912014 DOI: 10.1098/rsfs.2022.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/19/2022] [Indexed: 02/12/2023] Open
Abstract
Spatial organization is the norm rather than the exception in the microbial world. While the study of microbial physiology has been dominated by studies in well-mixed cultures, there is now increasing interest in understanding the role of spatial organization in microbial physiology, coexistence and evolution. Where studied, spatial organization has been shown to influence all three of these aspects. In this mini review and perspective article, we emphasize that the dynamics within spatially organized microbial systems (SOMS) are governed by feedbacks between local physico-chemical conditions, cell physiology and movement, and evolution. These feedbacks can give rise to emergent dynamics, which need to be studied through a combination of spatio-temporal measurements and mathematical models. We highlight the initial formation of SOMS and their emergent dynamics as two open areas of investigation for future studies. These studies will benefit from the development of model systems that can mimic natural ones in terms of species composition and spatial structure.
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Affiliation(s)
- Kelsey Cremin
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Jerko Rosko
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Orkun S. Soyer
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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13
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Sazykin IS, Sazykina MA. The role of oxidative stress in genome destabilization and adaptive evolution of bacteria. Gene X 2023; 857:147170. [PMID: 36623672 DOI: 10.1016/j.gene.2023.147170] [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: 08/09/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.
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Affiliation(s)
- I S Sazykin
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
| | - M A Sazykina
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation.
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14
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Usui M, Yoshii Y, Thiriet-Rupert S, Ghigo JM, Beloin C. Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance. Commun Biol 2023; 6:275. [PMID: 36928386 PMCID: PMC10020551 DOI: 10.1038/s42003-023-04601-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial antibiotic resistance is a global health concern of increasing importance and intensive study. Although biofilms are a common source of infections in clinical settings, little is known about the development of antibiotic resistance within biofilms. Here, we use experimental evolution to compare selection of resistance mutations in planktonic and biofilm Escherichia coli populations exposed to clinically relevant cycles of lethal treatment with the aminoglycoside amikacin. Consistently, mutations in sbmA, encoding an inner membrane peptide transporter, and fusA, encoding the essential elongation factor G, are rapidly selected in biofilms, but not in planktonic cells. This is due to a combination of enhanced mutation rate, increased adhesion capacity and protective biofilm-associated tolerance. These results show that the biofilm environment favors rapid evolution of resistance and provide new insights into the dynamic evolution of antibiotic resistance in biofilms.
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Affiliation(s)
- Masaru Usui
- Laboratory of Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan.
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France.
| | - Yutaka Yoshii
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Stanislas Thiriet-Rupert
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Christophe Beloin
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France.
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15
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Abedon ST. Ecology and Evolutionary Biology of Hindering Phage Therapy: The Phage Tolerance vs. Phage Resistance of Bacterial Biofilms. Antibiotics (Basel) 2023; 12:245. [PMID: 36830158 PMCID: PMC9952518 DOI: 10.3390/antibiotics12020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
As with antibiotics, we can differentiate various acquired mechanisms of bacteria-mediated inhibition of the action of bacterial viruses (phages or bacteriophages) into ones of tolerance vs. resistance. These also, respectively, may be distinguished as physiological insensitivities (or protections) vs. resistance mutations, phenotypic resistance vs. genotypic resistance, temporary vs. more permanent mechanisms, and ecologically vs. also near-term evolutionarily motivated functions. These phenomena can result from multiple distinct molecular mechanisms, many of which for bacterial tolerance of phages are associated with bacterial biofilms (as is also the case for the bacterial tolerance of antibiotics). The resulting inhibitions are relevant from an applied perspective because of their potential to thwart phage-based treatments of bacterial infections, i.e., phage therapies, as well as their potential to interfere more generally with approaches to the phage-based biological control of bacterial biofilms. In other words, given the generally low toxicity of properly chosen therapeutic phages, it is a combination of phage tolerance and phage resistance, as displayed by targeted bacteria, that seems to represent the greatest impediments to phage therapy's success. Here I explore general concepts of bacterial tolerance of vs. bacterial resistance to phages, particularly as they may be considered in association with bacterial biofilms.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
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16
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Azhogina T, Sazykina M, Konstantinova E, Khmelevtsova L, Minkina T, Antonenko E, Sushkova S, Khammami M, Mandzhieva S, Sazykin I. Bioaccessible PAH influence on distribution of antibiotic resistance genes and soil toxicity of different types of land use. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:12695-12713. [PMID: 36114974 DOI: 10.1007/s11356-022-23028-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
For a better understanding of the dissemination of antibiotic resistance genes (ARGs) in natural microbial communities, it is necessary to study the factors influencing it. There are not enough studies showing the connection of some pollutants with the dissemination of ARGs and especially few works on the effect of polycyclic aromatic compounds (PAHs) on the spread of resistance in microbiocenosis. In this respect, the aim of the study was to determine the effect of bioaccessible PAHs on soil resistome. The toxicity and the content of bioaccessible PAHs and ARGs were studied in 64 samples of soils of different types of land use in the Rostov Region of Russia. In most soils, a close positive correlation was demonstrated between different ARGs and bioaccessible PAHs with different content of rings in the structure. Six of the seven studied ARGs correlated with the content of 2-, 3-, 4-, 5- or 6-ring PAHs. The greatest number of close correlations was found between the content of PAHs and ARGs in the soils of protected areas, for agricultural purposes, and in soils of hospitals. The diverse composition of microbial communities in these soils might greatly facilitate this process. A close correlation between various toxic effects identified with a battery of whole-cell bacterial biosensors and bioaccessible PAHs of various compositions was established. This correlation showed possible mechanisms of PAHs' influence on microorganisms (DNA damage, oxidative stress, etc.), which led to a significant increase in horizontal gene transfer and spread of some ARGs in soil microbial communities. All this information, taken together, suggests that bioaccessible PAHs can enhance the spread of antibiotic resistance genes.
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Affiliation(s)
- Tatiana Azhogina
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don, 344090, Russian Federation
| | - Marina Sazykina
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don, 344090, Russian Federation.
| | - Elizaveta Konstantinova
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don, 344090, Russian Federation
| | - Ludmila Khmelevtsova
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don, 344090, Russian Federation
| | - Tatiana Minkina
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don, 344090, Russian Federation
| | - Elena Antonenko
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don, 344090, Russian Federation
| | - Svetlana Sushkova
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don, 344090, Russian Federation
| | - Margarita Khammami
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don, 344090, Russian Federation
| | - Saglara Mandzhieva
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don, 344090, Russian Federation
| | - Ivan Sazykin
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don, 344090, Russian Federation
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17
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Wang H, Feng Y, Lu H. Low-Level Cefepime Exposure Induces High-Level Resistance in Environmental Bacteria: Molecular Mechanism and Evolutionary Dynamics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15074-15083. [PMID: 35608924 DOI: 10.1021/acs.est.2c00793] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antibiotics exert selective pressures on clinically relevant antibiotic resistance. It is critical to understand how antibiotic resistance evolves in environmental microbes exposed to subinhibitory concentrations of antibiotics and whether evolutionary dynamics and emergence of resistance are predictable. In this study, Comamonas testosteroni isolated from wastewater activated sludge were subcultured in a medium containing 10 ng/mL cefepime for 40 days (∼300 generations). Stepwise mutations were accumulated, leading to an ultimate 200-fold increase in the minimum inhibitory concentration (MIC) of cefepime. Early stage mutation in DNA polymerase-encoding gene dnaE2 played an important role in antibiotic resistance evolution. Diverse resistance mechanisms were employed and validated experimentally, including increased efflux, biofilm formation, reduced antibiotic uptake, and drug inactivation. The cefepime minimal selective concentrations (MSCs) and relative fitness of susceptible, intermediate, and resistant mutants were determined. Agent-based modeling of the modified Moran process enabled simulations of resistance evolution and predictions of the emergence time and frequency of resistant mutants. The unraveled cefepime resistance mechanisms could be employed by broader bacteria, and the newly developed model is applicable to the predictions of general resistance evolution. The improved knowledge facilitates the assessment, prediction, and mitigation of antibiotic resistance progression in antibiotic-polluted environments.
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Affiliation(s)
- Hanqing Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Youjun Feng
- Departments of Microbiology & General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Huijie Lu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Academy of Ecological Civilization, Zhejiang University, Hangzhou, Zhejiang 310058, China
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18
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Biofilm antimicrobial susceptibility through an experimental evolutionary lens. NPJ Biofilms Microbiomes 2022; 8:82. [PMID: 36257971 PMCID: PMC9579162 DOI: 10.1038/s41522-022-00346-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/04/2022] [Indexed: 11/19/2022] Open
Abstract
Experimental evolution experiments in which bacterial populations are repeatedly exposed to an antimicrobial treatment, and examination of the genotype and phenotype of the resulting evolved bacteria, can help shed light on mechanisms behind reduced susceptibility. In this review we present an overview of why it is important to include biofilms in experimental evolution, which approaches are available to study experimental evolution in biofilms and what experimental evolution has taught us about tolerance and resistance in biofilms. Finally, we present an emerging consensus view on biofilm antimicrobial susceptibility supported by data obtained during experimental evolution studies.
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19
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Dostert M, Belanger CR, Pedraz L, Alford MA, Blimkie TM, Falsafi RF, Bains M, Dhillon BK, Haney CH, Lee AH, Hancock REW. BosR: A novel biofilm-specific regulator in Pseudomonas aeruginosa. Front Microbiol 2022; 13:1021021. [PMID: 36312952 PMCID: PMC9611778 DOI: 10.3389/fmicb.2022.1021021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Biofilms are the most common cause of bacterial infections in humans and notoriously hard to treat due to their ability to withstand antibiotics and host immune defenses. To overcome the current lack of effective antibiofilm therapies and guide future design, the identification of novel biofilm-specific gene targets is crucial. In this regard, transcriptional regulators have been proposed as promising targets for antimicrobial drug design. Therefore, a Transposon insertion sequencing approach was employed to systematically identify regulators phenotypically affecting biofilm growth in Pseudomonas aeruginosa PA14 using the TnSeq analysis tools Bio-TraDIS and TRANSIT. A screen of a pool of 300,000 transposon insertion mutants identified 349 genes involved in biofilm growth on hydroxyapatite, including 47 regulators. Detection of 19 regulatory genes participating in well-established biofilm pathways validated the results. An additional 28 novel prospective biofilm regulators suggested the requirement for multiple one-component transcriptional regulators. Biofilm-defective phenotypes were confirmed for five one-component transcriptional regulators and a protein kinase, which did not affect motility phenotypes. The one-component transcriptional regulator bosR displayed a conserved role in P. aeruginosa biofilm growth since its ortholog in P. aeruginosa strain PAO1 was also required for biofilm growth. Microscopic analysis of a chromosomal deletion mutant of bosR confirmed the role of this regulator in biofilm growth. Overall, our results highlighted that the gene network driving biofilm growth is complex and involves regulators beyond the primarily studied groups of two-component systems and cyclic diguanylate signaling proteins. Furthermore, biofilm-specific regulators, such as bosR, might constitute prospective new drug targets to overcome biofilm infections.
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Affiliation(s)
- Melanie Dostert
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Corrie R. Belanger
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Lucas Pedraz
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Morgan A. Alford
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Travis M. Blimkie
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Reza F. Falsafi
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Manjeet Bains
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Bhavjinder Kaur Dhillon
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Cara H. Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Amy H. Lee
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Robert E. W. Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Robert E. W. Hancock,
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20
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Hall-Stoodley L, McCoy KS. Biofilm aggregates and the host airway-microbial interface. Front Cell Infect Microbiol 2022; 12:969326. [PMID: 36081767 PMCID: PMC9445362 DOI: 10.3389/fcimb.2022.969326] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Biofilms are multicellular microbial aggregates that can be associated with host mucosal epithelia in the airway, gut, and genitourinary tract. The host environment plays a critical role in the establishment of these microbial communities in both health and disease. These host mucosal microenvironments however are distinct histologically, functionally, and regarding nutrient availability. This review discusses the specific mucosal epithelial microenvironments lining the airway, focusing on: i) biofilms in the human respiratory tract and the unique airway microenvironments that make it exquisitely suited to defend against infection, and ii) how airway pathophysiology and dysfunctional barrier/clearance mechanisms due to genetic mutations, damage, and inflammation contribute to biofilm infections. The host cellular responses to infection that contribute to resolution or exacerbation, and insights about evaluating and therapeutically targeting airway-associated biofilm infections are briefly discussed. Since so many studies have focused on Pseudomonas aeruginosa in the context of cystic fibrosis (CF) or on Haemophilus influenzae in the context of upper and lower respiratory diseases, these bacteria are used as examples. However, there are notable differences in diseased airway microenvironments and the unique pathophysiology specific to the bacterial pathogens themselves.
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Affiliation(s)
- Luanne Hall-Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, United States
- *Correspondence: Luanne Hall-Stoodley,
| | - Karen S. McCoy
- Division of Pulmonary Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
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21
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Visnapuu A, Van der Gucht M, Wagemans J, Lavigne R. Deconstructing the Phage-Bacterial Biofilm Interaction as a Basis to Establish New Antibiofilm Strategies. Viruses 2022; 14:v14051057. [PMID: 35632801 PMCID: PMC9145820 DOI: 10.3390/v14051057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 12/19/2022] Open
Abstract
The bacterial biofilm constitutes a complex environment that endows the bacterial community within with an ability to cope with biotic and abiotic stresses. Considering the interaction with bacterial viruses, these biofilms contain intrinsic defense mechanisms that protect against phage predation; these mechanisms are driven by physical, structural, and metabolic properties or governed by environment-induced mutations and bacterial diversity. In this regard, horizontal gene transfer can also be a driver of biofilm diversity and some (pro)phages can function as temporary allies in biofilm development. Conversely, as bacterial predators, phages have developed counter mechanisms to overcome the biofilm barrier. We highlight how these natural systems have previously inspired new antibiofilm design strategies, e.g., by utilizing exopolysaccharide degrading enzymes and peptidoglycan hydrolases. Next, we propose new potential approaches including phage-encoded DNases to target extracellular DNA, as well as phage-mediated inhibitors of cellular communication; these examples illustrate the relevance and importance of research aiming to elucidate novel antibiofilm mechanisms contained within the vast set of unknown ORFs from phages.
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22
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Lorquin F, Piccerelle P, Orneto C, Robin M, Lorquin J. New insights and advances on pyomelanin production: from microbial synthesis to applications. J Ind Microbiol Biotechnol 2022; 49:6575554. [PMID: 35482661 PMCID: PMC9338888 DOI: 10.1093/jimb/kuac013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/21/2022] [Indexed: 11/14/2022]
Abstract
Pyomelanin is a brown-black phenolic polymer and results from the oxidation of homogentisic acid (HGA) in the L-tyrosine pathway. As part of the research for natural and active ingredients issued from realistic bioprocesses, this work re-evaluates the HGA pigment and makes an updated inventory of its syntheses, microbial pathways, and properties, with tracks and recent advances for its large-scale production. The mechanism of the HGA polymerization is also well documented. In alkaptonuria, pyomelanin formation leads to connective tissue damages and arthritis, most probably due to the ROS issued from HGA oxidation. While UV radiation on human melanin may generate degradation products, pyomelanin is not photodegradable, is hyperthermostable, and has other properties better than the L-Dopa melanin. This review aims to raise awareness about the potential of this pigment for various applications, not only for skin coloring and protection but also for other cells, materials, and as a promising (semi)conductor for bioelectronics and energy.
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Affiliation(s)
- Faustine Lorquin
- Aix-Marseille Université, Mediterranean Institute of Oceanology (MIO), 163 avenue de Luminy, 13288 Marseille Cedex 9, France.,Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Philippe Piccerelle
- Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Caroline Orneto
- Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Maxime Robin
- Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Jean Lorquin
- Aix-Marseille Université, Mediterranean Institute of Oceanology (MIO), 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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23
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Mercolino J, Lo Sciuto A, Spinnato MC, Rampioni G, Imperi F. RecA and Specialized Error-Prone DNA Polymerases are not Required for Mutagenesis and Antibiotic Resistance Induced by Fluoroquinolones in Pseudomonas aeruginosa. Antibiotics (Basel) 2022; 11:antibiotics11030325. [PMID: 35326787 PMCID: PMC8944484 DOI: 10.3390/antibiotics11030325] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 02/05/2023] Open
Abstract
To cope with stressful conditions, including antibiotic exposure, bacteria activate the SOS response, a pathway that induces error-prone DNA repair and mutagenesis mechanisms. In most bacteria, the SOS response relies on the transcriptional repressor LexA and the co-protease RecA, the latter being also involved in homologous recombination. The role of the SOS response in stress- and antibiotic-induced mutagenesis has been characterized in detail in the model organism Escherichia coli. However, its effect on antibiotic resistance in the human pathogen Pseudomonas aeruginosa is less clear. Here, we analyzed a recA deletion mutant and confirmed, by conjugation and gene expression assays, that RecA is required for homologous recombination and SOS response induction in P. aeruginosa. MIC assays demonstrated that RecA affects P. aeruginosa resistance only towards fluoroquinolones and genotoxic agents. The comparison of antibiotic-resistant mutant frequency between treated and untreated cultures revealed that, among the antibiotics tested, only fluoroquinolones induced mutagenesis in P. aeruginosa. Notably, both RecA and error-prone DNA polymerases were found to be dispensable for this process. These data demonstrate that the SOS response is not required for antibiotic-induced mutagenesis in P. aeruginosa, suggesting that RecA inhibition is not a suitable strategy to target antibiotic-induced emergence of resistance in this pathogen.
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Affiliation(s)
- Jessica Mercolino
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Alessandra Lo Sciuto
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Maria Concetta Spinnato
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Giordano Rampioni
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
- IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
- IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
- Correspondence:
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24
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Effect of a Defective Clamp Loader Complex of DNA Polymerase III on Growth and SOS Response in Pseudomonas aeruginosa. Microorganisms 2022; 10:microorganisms10020423. [PMID: 35208877 PMCID: PMC8879598 DOI: 10.3390/microorganisms10020423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/17/2022] Open
Abstract
DNA polymerase III (Pol III) is the replicative enzyme in bacteria. It consists of three subcomplexes, the catalytic core, the β clamp, and the clamp loader. While this complex has been thoroughly characterized in the model organism Escherichia coli, much less is known about its functioning and/or its specific properties in other bacteria. Biochemical studies highlighted specific features in the clamp loader subunit ψ of Pseudomonas aeruginosa as compared to its E. coli counterpart, and transposon mutagenesis projects identified the ψ-encoding gene holD among the strictly essential core genes of P. aeruginosa. By generating a P. aeruginosa holD conditional mutant, here we demonstrate that, as previously observed for E. coli holD mutants, HolD-depleted P. aeruginosa cells show strongly decreased growth, induction of the SOS response, and emergence of suppressor mutants at high frequency. However, differently from what was observed in E. coli, the growth of P. aeruginosa cells lacking HolD cannot be rescued by the deletion of genes for specialized DNA polymerases. We also observed that the residual growth of HolD-depleted cells is strictly dependent on homologous recombination functions, suggesting that recombination-mediated rescue of stalled replication forks is crucial to support replication by a ψ-deficient Pol III enzyme in P. aeruginosa.
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25
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Combination and nanotechnology based pharmaceutical strategies for combating respiratory bacterial biofilm infections. Int J Pharm 2022; 616:121507. [PMID: 35085729 DOI: 10.1016/j.ijpharm.2022.121507] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/31/2021] [Accepted: 01/20/2022] [Indexed: 12/14/2022]
Abstract
Respiratory infections are one of the major global health problems. Among them, chronic respiratory infections caused by biofilm formation are difficult to treat because of both drug tolerance and poor drug penetration into the complex biofilm structure. A major part of the current research on combating respiratory biofilm infections have been focused on destroying the matrix of extracellular polymeric substance and eDNA of the biofilm or promoting the penetration of antibiotics through the extracellular polymeric substance via delivery technologies in order to kill the bacteria inside. There are also experimental data showing that certain inhaled antibiotics with simple formulations can effectively penetrate EPS to kill surficially located bacteria and centrally located dormant bacteria or persisters. This article aims to review recent advances in the pharmaceutical strategies for combating respiratory biofilm infections with a focus on nanotechnology-based drug delivery approaches. The formation and characteristics of bacterial biofilm infections in the airway mucus are presented, which is followed by a brief review on the current clinical approaches to treat respiratory biofilm infections by surgical removal and antimicrobial therapy, and also the emerging clinical treatment approaches. The current combination of antibiotics and non-antibiotic adjuvants to combat respiratory biofilm infections are also discussed.
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26
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Xu A, Zhang X, Wang T, Xin F, Ma LZ, Zhou J, Dong W, Jiang M. Rugose small colony variant and its hyper-biofilm in Pseudomonas aeruginosa: Adaption, evolution, and biotechnological potential. Biotechnol Adv 2021; 53:107862. [PMID: 34718136 DOI: 10.1016/j.biotechadv.2021.107862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 10/23/2021] [Accepted: 10/24/2021] [Indexed: 12/16/2022]
Abstract
One of the hallmarks of the environmental bacterium Pseudomonas aeruginosa is its excellent ecological flexibility, which can thrive in diverse ecological niches. In different ecosystems, P. aeruginosa may use different strategies to survive, such as forming biofilms in crude oil environment, converting to mucoid phenotype in the cystic fibrosis (CF) lung, or becoming persisters when treated with antibiotics. Rugose small colony variants (RSCVs) are the adaptive mutants of P. aeruginosa, which can be frequently isolated from chronic infections. During the past years, there has been a renewed interest in using P. aeruginosa as a model organism to investigate the RSCVs formation, persistence and pathogenesis, as RSCVs represent a hyper-biofilm formation, high adaptability, high-tolerance sub-population in biofilms. This review will briefly summarize recent advances regarding the phenotypic, genetic and host interaction associated with RSCVs, with an emphasis on P. aeruginosa. Meanwhile, some non-pathogenic bacteria such as Pseudomonas fluorescence, Pseudomonas putida and Bacillus subtilis will be also included. Remarkable emphasis is given on intrinsic functions of such hyper-biofilm formation characteristic as well as its potential applications in several biocatalytic transformations including wastewater treatment, microbial fermentation, and plastic degradation. Hopefully, this review will attract the interest of researchers in various fields and shape future research focused not only on evolutionary biology but also on biotechnological applications related to RSCVs.
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Affiliation(s)
- Anming Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Xiaoxiao Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Tong Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Luyan Z Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
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27
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Zhang Y, Zhang Y, Liu L, Zhou L, Zhao Z. Impacts of antibiotics on biofilm bacterial community and disinfection performance on simulated drinking water supply pipe wall. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 288:117736. [PMID: 34256291 DOI: 10.1016/j.envpol.2021.117736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/30/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Overuse of antibiotics is accelerating the spread of resistance risk in the environment. In drinking water supply systems, the effect of antibiotics on the resistance of biofilm is unclear, and there have been few studies in disinfectant-containing systems. Here, we designed a series of drinking water supply reactors to investigate the effects of antibiotics on biofilm and bacteria in the water. At low concentrations, antibiotics could promote the growth of bacteria in biofilm; among the tested antibiotics (tetracycline, sulfadiazine and chloramphenicol), tetracycline had the strongest ability to promote this. And the antibiotic resistant bacteria (ARB) could inhibit the growth of bacteria in drinking water. Results have shown that antibiotics enhanced the bacterial chlorine resistance in the effluent, but reduced that in the biofilm. Furthermore, metagenomic analysis showed that antibiotics reduced the richness of biofilm communities. The dominant phyla in the biofilm were Proteobacteria, Planctomycetes, and Firmicutes. In tetracycline-treated biofilm, the dominant phylum was Planctomycetes. In sulfadiazine- and chloramphenicol-treated groups, bacteria with complex cell structures preferentially accumulated. The dominant class in biofilm in the ARB-added group was Gammaproteobacteria. The abundance of antibiotic resistant genes (ARGs) was correlated with biofilm community structure. This study shows that antibiotics make the biofilm community structure of drinking water more resistant to chlorine. ARGs may be selective for certain bacteria in the process, and there may ultimately be enhanced chlorine and antibiotic resistance of effluent bacteria in drinking water.
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Affiliation(s)
- Yongji Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Yingyu Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Lina Liu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Lingling Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
| | - Zhiling Zhao
- College of Civil Engineering, Huaqiao University, Jimei District, Xiamen, 361021, China
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28
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Armbruster CR, Marshall CW, Garber AI, Melvin JA, Zemke AC, Moore J, Zamora PF, Li K, Fritz IL, Manko CD, Weaver ML, Gaston JR, Morris A, Methé B, DePas WH, Lee SE, Cooper VS, Bomberger JM. Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis. Cell Rep 2021; 37:109829. [PMID: 34686349 PMCID: PMC8667756 DOI: 10.1016/j.celrep.2021.109829] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022] Open
Abstract
Pseudomonas aeruginosa notoriously adapts to the airways of people with cystic fibrosis (CF), yet how infection-site biogeography and associated evolutionary processes vary as lifelong infections progress remains unclear. Here we test the hypothesis that early adaptations promoting aggregation influence evolutionary-genetic trajectories by examining longitudinal P. aeruginosa from the sinuses of six adults with CF. Highly host-adapted lineages harbored mutator genotypes displaying signatures of early genome degradation associated with recent host restriction. Using an advanced imaging technique (MiPACT-HCR [microbial identification after passive clarity technique]), we find population structure tracks with genome degradation, with the most host-adapted, genome-degraded P. aeruginosa (the mutators) residing in small, sparse aggregates. We propose that following initial adaptive evolution in larger populations under strong selection for aggregation, P. aeruginosa persists in small, fragmented populations that experience stronger effects of genetic drift. These conditions enrich for mutators and promote degenerative genome evolution. Our findings underscore the importance of infection-site biogeography to pathogen evolution.
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Affiliation(s)
- Catherine R Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | | | - Arkadiy I Garber
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jeffrey A Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Anna C Zemke
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John Moore
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Paula F Zamora
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Ian L Fritz
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Christopher D Manko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Madison L Weaver
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jordan R Gaston
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Alison Morris
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Barbara Methé
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - William H DePas
- Department of Pediatrics, Children's Hospital of Pittsburgh and University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Stella E Lee
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA.
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA; Pittsburgh Center for Evolutionary Biology & Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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29
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Moreno Osorio JH, Pollio A, Frunzo L, Lens PNL, Esposito G. A Review of Microalgal Biofilm Technologies: Definition, Applications, Settings and Analysis. FRONTIERS IN CHEMICAL ENGINEERING 2021. [DOI: 10.3389/fceng.2021.737710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Biofilm-based algal cultivation has many advantages over the conventional suspended growth methods and has received increased attention as a potential platform for algal production, wastewater treatment (nutrient removal), and a potential pathway to supply feedstock for microalgae-based biorefinery attempts. However, the attached cultivation by definition and application is a result of a complex interaction between the biotic and abiotic components involved. Therefore, the entire understanding of the biofilm nature is still a research challenge due to the need for real-time analysis of the system. In this review, the state of the art of biofilm definition, its life cycle, the proposed designs of bioreactors, screening of carrier materials, and non-destructive techniques for the study of biofilm formation and performance are summarized. Perspectives for future research needs are also discussed to provide a primary reference for the further development of microalgal biofilm systems.
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30
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Xu A, Wang D, Wang Y, Zhang L, Xie Z, Cui Y, Bhamse P, Yu H, Zhang XX, Li D, Ma LZ. Mutations in surface-sensing receptor WspA lock the Wsp signal transduction system into a constitutively active state. Environ Microbiol 2021; 24:1150-1165. [PMID: 34499799 DOI: 10.1111/1462-2920.15763] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 08/26/2021] [Accepted: 09/04/2021] [Indexed: 12/31/2022]
Abstract
Pseudomonas aeruginosa rugose small-colony variants (RSCVs) are frequently isolated from chronic infections, yet, they are rarely reported in environmental isolates. Here, during the comparative genomic analysis of two P. aeruginosa strains isolated from crude oil, we discovered a spontaneous in-frame deletion, wspAΔ280-307 , which led to hyper-biofilm and RSCV phenotypes. WspA is a homologue of methyl-accepting chemotaxis proteins (MCPs) that senses surfaces to regulate biofilm formation by stimulating cyclic-di-guanosine monophosphate (c-di-GMP) synthesis through the Wsp system. However, the methylation sites of WspA have never been identified. In this study, we identified E280 and E294 of WspA as methylation sites. The wspAΔ280-307 mutation enabled the Wsp system to lock into a constitutively active state that is independent of regulation by methylation. The result is an enhanced production of c-di-GMP. Sequence alignment revealed three conserved repeat sequences within the amino acid residues 280-313 (aa280-313) region of WspA homologues, suggesting that a spontaneous deletion within this DNA encoding region was likely a result of intragenic recombination and that similar mutations might occur in several related bacterial genera. Our results provide a plausible explanation for the selection of RSCVs and a mechanism to confer a competitive advantage for P. aeruginosa in a crude-oil environment.
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Affiliation(s)
- Anming Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yunhao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhang
- Liaoning University, Shenyang, 110136, China
| | - Zhensheng Xie
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yifan Cui
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pramod Bhamse
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xue-Xian Zhang
- School of Natural and Computational Sciences, Massey University, Auckland, 0745, New Zealand
| | - Defeng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luyan Z Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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31
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Ismail MH, Michie KA, Goh YF, Noorian P, Kjelleberg S, Duggin IG, McDougald D, Rice SA. The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression. Viruses 2021; 13:1614. [PMID: 34452479 PMCID: PMC8402870 DOI: 10.3390/v13081614] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 12/17/2022] Open
Abstract
It has been shown that the filamentous phage, Pf4, plays an important role in biofilm development, stress tolerance, genetic variant formation and virulence in Pseudomonas aeruginosa PAO1. These behaviours are linked to the appearance of superinfective phage variants. Here, we have investigated the molecular mechanism of superinfection as well as how the Pf4 phage can control host gene expression to modulate host behaviours. Pf4 exists as a prophage in PAO1 and encodes a homologue of the P2 phage repressor C and was recently named Pf4r. Through a combination of molecular techniques, ChIPseq and transcriptomic analyses, we show a critical site in repressor C (Pf4r) where a mutation in the site, 788799A>G (Ser4Pro), causes Pf4r to lose its function as the immunity factor against reinfection by Pf4. X-ray crystal structure analysis shows that Pf4r forms symmetric homo-dimers homologous to the E.coli bacteriophage P2 RepC protein. A mutation, Pf4r*, associated with the superinfective Pf4r variant, found at the dimer interface, suggests dimer formation may be disrupted, which derepresses phage replication. This is supported by multi-angle light scattering (MALS) analysis, where the Pf4r* protein only forms monomers. The loss of dimerisation also explains the loss of Pf4r's immunity function. Phenotypic assays showed that Pf4r increased LasB activity and was also associated with a slight increase in the percentage of morphotypic variants. ChIPseq and transcriptomic analyses suggest that Pf4r also likely functions as a transcriptional regulator for other host genes. Collectively, these data suggest the mechanism by which filamentous phages play such an important role in P. aeruginosa biofilm development.
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Affiliation(s)
- Muhammad Hafiz Ismail
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Katharine A. Michie
- Structural Biology Facility, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia;
| | - Yu Fen Goh
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
| | - Parisa Noorian
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Iain G. Duggin
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
| | - Diane McDougald
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
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32
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Wu Y, Wang S, Nie W, Wang P, Fu L, Ahmad I, Zhu B, Chen G. A key antisense sRNA modulates the oxidative stress response and virulence in Xanthomonas oryzae pv. oryzicola. PLoS Pathog 2021; 17:e1009762. [PMID: 34297775 PMCID: PMC8336823 DOI: 10.1371/journal.ppat.1009762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/04/2021] [Accepted: 06/27/2021] [Indexed: 11/18/2022] Open
Abstract
Pathogens integrate multiple environmental signals to navigate the host and control the expression of virulence genes. In this process, small regulatory noncoding RNAs (sRNAs) may function in gene expression as post-transcriptional regulators. In this study, the sRNA Xonc3711 functioned in the response of the rice pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), to oxidative stress. Xonc3711 repressed production of the DNA-binding protein Xoc_3982 by binding to the xoc_3982 mRNA within the coding region. Mutational analysis showed that regulation required an antisense interaction between Xonc3711 and xoc_3982 mRNA, and RNase E was needed for degradation of the xoc_3982 transcript. Deletion of Xonc3711 resulted in a lower tolerance to oxidative stress due to the repression of flagella-associated genes and reduced biofilm formation. Furthermore, ChIP-seq and electrophoretic mobility shift assays showed that Xoc_3982 repressed the transcription of effector xopC2, which contributes to virulence in Xoc BLS256. This study describes how sRNA Xonc3711 modulates multiple traits in Xoc via signals perceived from the external environment. Small, stable RNA species perform diverse functions in both prokaryotes and eukaryotes. In this study, the sRNA Xonc3711 decreased the production of DNA-binding protein Xoc_3982 in the bacterium Xanthomonas oryzae pv. oryzicola (Xoc) by base pairing with the xoc_3982 transcript. When Xonc3711 was mutated, Xoc was impaired in its ability to form flagella and produce biofilms, which reduced Xoc tolerance to oxidative stress. We also discovered that the DNA-binding protein Xoc_3982 represses the expression of xopC2, which encodes an effector protein, and reduces its expression. Our results show that Xonc3711 modulates and integrates multiple systems in Xoc to protect cells from oxidative damage.
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Affiliation(s)
- Yan Wu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenhan Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Peihong Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Luoyi Fu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Iftikhar Ahmad
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari Campus, Vehari, Pakistan
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (BZ); (GC)
| | - Gongyou Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (BZ); (GC)
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Reece E, Bettio PHDA, Renwick J. Polymicrobial Interactions in the Cystic Fibrosis Airway Microbiome Impact the Antimicrobial Susceptibility of Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10070827. [PMID: 34356747 PMCID: PMC8300716 DOI: 10.3390/antibiotics10070827] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Pseudomonas aeruginosa is one of the most dominant pathogens in cystic fibrosis (CF) airway disease and contributes to significant inflammation, airway damage, and poorer disease outcomes. The CF airway is now known to be host to a complex community of microorganisms, and polymicrobial interactions have been shown to play an important role in shaping P. aeruginosa pathogenicity and resistance. P. aeruginosa can cause chronic infections that once established are almost impossible to eradicate with antibiotics. CF patients that develop chronic P. aeruginosa infection have poorer lung function, higher morbidity, and a reduced life expectancy. P. aeruginosa adapts to the CF airway and quickly develops resistance to several antibiotics. A perplexing phenomenon is the disparity between in vitro antimicrobial sensitivity testing and clinical response. Considering the CF airway is host to a diverse community of microorganisms or 'microbiome' and that these microorganisms are known to interact, the antimicrobial resistance and progression of P. aeruginosa infection is likely influenced by these microbial relationships. This review combines the literature to date on interactions between P. aeruginosa and other airway microorganisms and the influence of these interactions on P. aeruginosa tolerance to antimicrobials.
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Yip CH, Mahalingam S, Wan KL, Nathan S. Prodigiosin inhibits bacterial growth and virulence factors as a potential physiological response to interspecies competition. PLoS One 2021; 16:e0253445. [PMID: 34161391 PMCID: PMC8221495 DOI: 10.1371/journal.pone.0253445] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/06/2021] [Indexed: 11/19/2022] Open
Abstract
Prodigiosin, a red linear tripyrrole pigment, has long been recognised for its antimicrobial property. However, the physiological contribution of prodigiosin to the survival of its producing hosts still remains undefined. Hence, the aim of this study was to investigate the biological role of prodigiosin from Serratia marcescens, particularly in microbial competition through its antimicrobial activity, towards the growth and secreted virulence factors of four clinical pathogenic bacteria (methicillin-resistant Staphylococcus aureus (MRSA), Enterococcus faecalis, Salmonella enterica serovar Typhimurium and Pseudomonas aeruginosa) as well as Staphylococcus aureus and Escherichia coli. Prodigiosin was first extracted from S. marcescens and its purity confirmed by absorption spectrum, high performance liquid chromatography (HPLC) and liquid chromatography-tandem mass spectrophotometry (LC-MS/MS). The extracted prodigiosin was antagonistic towards all the tested bacteria. A disc-diffusion assay showed that prodigiosin is more selective towards Gram-positive bacteria and inhibited the growth of MRSA, S. aureus and E. faecalis and Gram-negative E. coli. A minimum inhibitory concentration of 10 μg/μL of prodigiosin was required to inhibit the growth of S. aureus, E. coli and E. faecalis whereas > 10 μg/μL was required to inhibit MRSA growth. We further assessed the effect of prodigiosin towards bacterial virulence factors such as haemolysin and production of protease as well as on biofilm formation. Prodigiosin did not inhibit haemolysis activity of clinically associated bacteria but was able to reduce protease activity for MRSA, E. coli and E. faecalis as well as decrease E. faecalis, Salmonella Typhimurium and E. coli biofilm formation. Results of this study show that in addition to its role in inhibiting bacterial growth, prodigiosin also inhibits the bacterial virulence factor protease production and biofilm formation, two strategies employed by bacteria in response to microbial competition. As clinical pathogens were more resistant to prodigiosin, we propose that prodigiosin is physiologically important for S. marcescens to compete against other bacteria in its natural soil and surface water environments.
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Affiliation(s)
- Chee-Hoo Yip
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Sobina Mahalingam
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Kiew-Lian Wan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Sheila Nathan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
- * E-mail:
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Soto W, Nishiguchi MK. Environmental Stress Selects for Innovations That Drive Vibrio Symbiont Diversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.616973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Symbiotic bacteria in the Vibrionaceae are a dynamic group of γ-Proteobacteria that are commonly found throughout the world. Although they primarily are free-living in the environment, they can be commonly found associated with various Eukarya, either as beneficial or pathogenic symbionts. Interestingly, this dual lifestyle (free-living or in symbiosis) enables the bacteria to have enormous ecological breadth, where they can accommodate a variety of stresses in both stages. Here, we discuss some of the most common stressors that Vibrio bacteria encounter when in their free-living state or associated with an animal host, and how some of the mechanisms that are used to cope with these stressors can be used as an evolutionary advantage that increases their diversity both in the environment and within their specific hosts.
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Brauer M, Lassek C, Hinze C, Hoyer J, Becher D, Jahn D, Sievers S, Riedel K. What's a Biofilm?-How the Choice of the Biofilm Model Impacts the Protein Inventory of Clostridioides difficile. Front Microbiol 2021; 12:682111. [PMID: 34177868 PMCID: PMC8225356 DOI: 10.3389/fmicb.2021.682111] [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: 03/17/2021] [Accepted: 05/12/2021] [Indexed: 12/18/2022] Open
Abstract
The anaerobic pathogen Clostridioides difficile is perfectly equipped to survive and persist inside the mammalian intestine. When facing unfavorable conditions C. difficile is able to form highly resistant endospores. Likewise, biofilms are currently discussed as form of persistence. Here a comprehensive proteomics approach was applied to investigate the molecular processes of C. difficile strain 630Δerm underlying biofilm formation. The comparison of the proteome from two different forms of biofilm-like growth, namely aggregate biofilms and colonies on agar plates, revealed major differences in the formation of cell surface proteins, as well as enzymes of its energy and stress metabolism. For instance, while the obtained data suggest that aggregate biofilm cells express both flagella, type IV pili and enzymes required for biosynthesis of cell-surface polysaccharides, the S-layer protein SlpA and most cell wall proteins (CWPs) encoded adjacent to SlpA were detected in significantly lower amounts in aggregate biofilm cells than in colony biofilms. Moreover, the obtained data suggested that aggregate biofilm cells are rather actively growing cells while colony biofilm cells most likely severely suffer from a lack of reductive equivalents what requires induction of the Wood-Ljungdahl pathway and C. difficile’s V-type ATPase to maintain cell homeostasis. In agreement with this, aggregate biofilm cells, in contrast to colony biofilm cells, neither induced toxin nor spore production. Finally, the data revealed that the sigma factor SigL/RpoN and its dependent regulators are noticeably induced in aggregate biofilms suggesting an important role of SigL/RpoN in aggregate biofilm formation.
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Affiliation(s)
- Madita Brauer
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Lassek
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Hinze
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Juliane Hoyer
- Department for Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department for Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Susanne Sievers
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
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Alencar VC, Silva JDFDS, Vilas Boas RO, Farnézio VM, de Maria YNLF, Aciole Barbosa D, Almeida AT, de Souza EM, Müller-Santos M, Jabes DL, Menegidio FB, Costa de Oliveira R, Rodrigues T, Tersariol ILDS, Walmsley AR, Nunes LR. The Quorum Sensing Auto-Inducer 2 (AI-2) Stimulates Nitrogen Fixation and Favors Ethanol Production over Biomass Accumulation in Zymomonas mobilis. Int J Mol Sci 2021; 22:ijms22115628. [PMID: 34073173 PMCID: PMC8198075 DOI: 10.3390/ijms22115628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
Autoinducer 2 (or AI-2) is one of the molecules used by bacteria to trigger the Quorum Sensing (QS) response, which activates expression of genes involved in a series of alternative mechanisms, when cells reach high population densities (including bioluminescence, motility, biofilm formation, stress resistance, and production of public goods, or pathogenicity factors, among others). Contrary to most autoinducers, AI-2 can induce QS responses in both Gram-negative and Gram-positive bacteria, and has been suggested to constitute a trans-specific system of bacterial communication, capable of affecting even bacteria that cannot produce this autoinducer. In this work, we demonstrate that the ethanologenic Gram-negative bacterium Zymomonas mobilis (a non-AI-2 producer) responds to exogenous AI-2 by modulating expression of genes involved in mechanisms typically associated with QS in other bacteria, such as motility, DNA repair, and nitrogen fixation. Interestingly, the metabolism of AI-2-induced Z. mobilis cells seems to favor ethanol production over biomass accumulation, probably as an adaptation to the high-energy demand of N2 fixation. This opens the possibility of employing AI-2 during the industrial production of second-generation ethanol, as a way to boost N2 fixation by these bacteria, which could reduce costs associated with the use of nitrogen-based fertilizers, without compromising ethanol production in industrial plants.
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Affiliation(s)
- Valquíria Campos Alencar
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Alameda da Universidade, s/n, São Bernardo do Campo 09606-045, SP, Brazil; (V.C.A.); (J.d.F.d.S.S.); (V.M.F.); (T.R.)
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes 08780-911, SP, Brazil; (R.O.V.B.); (Y.N.L.F.d.M.); (D.A.B.); (D.L.J.); (F.B.M.); (R.C.d.O.)
| | - Juliana de Fátima dos Santos Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Alameda da Universidade, s/n, São Bernardo do Campo 09606-045, SP, Brazil; (V.C.A.); (J.d.F.d.S.S.); (V.M.F.); (T.R.)
| | - Renata Ozelami Vilas Boas
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes 08780-911, SP, Brazil; (R.O.V.B.); (Y.N.L.F.d.M.); (D.A.B.); (D.L.J.); (F.B.M.); (R.C.d.O.)
| | - Vinícius Manganaro Farnézio
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Alameda da Universidade, s/n, São Bernardo do Campo 09606-045, SP, Brazil; (V.C.A.); (J.d.F.d.S.S.); (V.M.F.); (T.R.)
| | - Yara N. L. F. de Maria
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes 08780-911, SP, Brazil; (R.O.V.B.); (Y.N.L.F.d.M.); (D.A.B.); (D.L.J.); (F.B.M.); (R.C.d.O.)
| | - David Aciole Barbosa
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes 08780-911, SP, Brazil; (R.O.V.B.); (Y.N.L.F.d.M.); (D.A.B.); (D.L.J.); (F.B.M.); (R.C.d.O.)
| | - Alex Tramontin Almeida
- Setor de Ciências Biológicas-Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Rua Cel. Francisco H. dos Santos, 100, Curitiba 81531-980, PR, Brazil; (A.T.A.); (E.M.d.S.); (M.M.-S.)
| | - Emanuel Maltempi de Souza
- Setor de Ciências Biológicas-Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Rua Cel. Francisco H. dos Santos, 100, Curitiba 81531-980, PR, Brazil; (A.T.A.); (E.M.d.S.); (M.M.-S.)
| | - Marcelo Müller-Santos
- Setor de Ciências Biológicas-Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Rua Cel. Francisco H. dos Santos, 100, Curitiba 81531-980, PR, Brazil; (A.T.A.); (E.M.d.S.); (M.M.-S.)
| | - Daniela L. Jabes
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes 08780-911, SP, Brazil; (R.O.V.B.); (Y.N.L.F.d.M.); (D.A.B.); (D.L.J.); (F.B.M.); (R.C.d.O.)
| | - Fabiano B. Menegidio
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes 08780-911, SP, Brazil; (R.O.V.B.); (Y.N.L.F.d.M.); (D.A.B.); (D.L.J.); (F.B.M.); (R.C.d.O.)
| | - Regina Costa de Oliveira
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes 08780-911, SP, Brazil; (R.O.V.B.); (Y.N.L.F.d.M.); (D.A.B.); (D.L.J.); (F.B.M.); (R.C.d.O.)
| | - Tiago Rodrigues
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Alameda da Universidade, s/n, São Bernardo do Campo 09606-045, SP, Brazil; (V.C.A.); (J.d.F.d.S.S.); (V.M.F.); (T.R.)
| | - Ivarne Luis dos Santos Tersariol
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP), Rua Três de Maio, 100, São Paulo 04044-020, SP, Brazil;
| | - Adrian R. Walmsley
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK;
| | - Luiz R. Nunes
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Alameda da Universidade, s/n, São Bernardo do Campo 09606-045, SP, Brazil; (V.C.A.); (J.d.F.d.S.S.); (V.M.F.); (T.R.)
- Correspondence: ; Tel.: +55-11-4996-8371 (ext. 4996-3166)
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Functionalization of Synthetic Bone Substitutes. Int J Mol Sci 2021; 22:ijms22094412. [PMID: 33922517 PMCID: PMC8122961 DOI: 10.3390/ijms22094412] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022] Open
Abstract
Bone substitutes have been applied to treat osseous defects for a long time. To prevent implant related infection (IRI) and enhance bone healing functionalized biomaterials, antibiotics and osteoinductive substances have been introduced. This study gives an overview of the current available surface-coated bone substitutes and provides an outlook for future perspectives.
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Wu L, Wu ZC, Todosiichuk T, Korneva O. Nosocomial Infections: Pathogenicity, Resistance and Novel Antimicrobials. INNOVATIVE BIOSYSTEMS AND BIOENGINEERING 2021. [DOI: 10.20535/ibb.2021.5.2.228970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Background. The fight against the spread of infectious diseases creates the problem of resistance to pathogens and the most resistant of them – the propagators of nosocomial infections – are formed in hospitals because of a number of reasons. The solution of the problem lies in different areas, but the search of new effective means for the treatment of such diseases remains relevant right today. The shortest way to do this is to find the "pain points" of the pathogens themselves, i.e. the factors of their pathogenicity and resistance to which the action of novel antiseptics should be directed.
Objective. We aimed to analyse and evaluate the main factors of pathogenicity and resistance of pathogens of nosocomial infections to determine modern approaches to the development of novel antimicrobials.
Methods. Search and systematization of new scientific data and results concerning pathogenic factors of microbial pathogens that can be used as targets for the action of drugs.
Results. Over the last 10–20 years, due to the development of new research methods in biology, it has become possible to clarify the features and additional conditions for the detection of pathogenic factors of nosocomial infections. Additional mechanisms of manifestation of resistance, adhesiveness, invasiveness, transmission of signs, secretion of toxins by pathogens are shownthat determines the general increase of their resistance to the action of currently used means. The general idea of creating antiseptics that will not increase the resistance of pathogens can now be implemented by using substances with multidirectional or indirect mechanisms of action that minimally affect the metabolism of the cell and significantly reduce its resistance and pathogenicity.
Conclusions. Factors of pathogenicity of propagators of nosocomial infections and mechanisms of their implementation can be considered as the main targets for the action of novel antiseptics that will inhibit the spread of pathogens without increasing their resistance. The promising substances for such drugs, among other things, are bacteriophages and their modifications, enzybiotics, immunobiotics, autoinducer inhibitors, quorum sensing-system inhibitors, b-lactamase inhibitors and others. Some of these substances in combination with the new generation of antibiotics significantly enhance their effectiveness and together they are able to overcome the resistance of even multidrug-resistant pathogens.
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Lorquin F, Ziarelli F, Amouric A, Di Giorgio C, Robin M, Piccerelle P, Lorquin J. Production and properties of non-cytotoxic pyomelanin by laccase and comparison to bacterial and synthetic pigments. Sci Rep 2021; 11:8538. [PMID: 33879803 PMCID: PMC8058095 DOI: 10.1038/s41598-021-87328-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/15/2021] [Indexed: 11/09/2022] Open
Abstract
Pyomelanin is a polymer of homogentisic acid synthesized by microorganisms. This work aimed to develop a production process and evaluate the quality of the pigment. Three procedures have been elaborated and optimized, (1) an HGA-Mn2+ chemical autoxidation (PyoCHEM yield 0.317 g/g substrate), (2) an induced bacterial culture of Halomonas titanicae through the 4-hydroxyphenylacetic acid-1-hydroxylase route (PyoBACT, 0.55 g/L), and (3) a process using a recombinant laccase extract with the highest level produced (PyoENZ, 1.25 g/g substrate) and all the criteria for a large-scale prototype. The chemical structures had been investigated by 13C solid-state NMR (CP-MAS) and FTIR. Car-Car bindings predominated in the three polymers, Car-O-Car (ether) linkages being absent, proposing mainly C3-C6 (α-bindings) and C4-C6 (β-bindings) configurations. This work highlighted a biological decarboxylation by the laccase or bacterial oxidase(s), leading to the partly formation of gentisyl alcohol and gentisaldehyde that are integral parts of the polymer. By comparison, PyoENZ exhibited an Mw of 5,400 Da, was hyperthermostable, non-cytotoxic even after irradiation, scavenged ROS induced by keratinocytes, and had a highly DPPH-antioxidant and Fe3+-reducing activity. As a representative pigment of living cells and an available standard, PyoENZ might also be useful for applications in extreme conditions and skin protection.
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Affiliation(s)
- Faustine Lorquin
- Mediterranean Institute of Oceanology (MIO), Aix-Marseille Université, 163 avenue de Luminy, 13288, Marseille Cedex 9, France.,Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Fabio Ziarelli
- Fédération Sciences Chimiques de Marseille, Aix-Marseille Université, 52 Avenue Escadrille Normandie Niemen, 13397, Marseille, France
| | - Agnès Amouric
- Mediterranean Institute of Oceanology (MIO), Aix-Marseille Université, 163 avenue de Luminy, 13288, Marseille Cedex 9, France
| | - Carole Di Giorgio
- Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Maxime Robin
- Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Philippe Piccerelle
- Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Jean Lorquin
- Mediterranean Institute of Oceanology (MIO), Aix-Marseille Université, 163 avenue de Luminy, 13288, Marseille Cedex 9, France.
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Pinilla CMB, Stincone P, Brandelli A. Proteomic analysis reveals differential responses of Listeria monocytogenes to free and nanoencapsulated nisin. Int J Food Microbiol 2021; 346:109170. [PMID: 33770680 DOI: 10.1016/j.ijfoodmicro.2021.109170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 12/18/2022]
Abstract
The ability of Listeria monocytogenes grow on ready-to-eat food is a major concern in food safety. Natural antimicrobials, such as nisin, can be used to control this pathogen, but the increasing reports of nisin tolerance and resistance make necessary novel approaches to increase its effectiveness, such as encapsulation. The goal of this study was to investigate how L. monocytogenes ATCC7644 regulates and shapes its proteome in response to sublethal doses of nisin and nisin-loaded phosphatidylcholine liposomes (lipo-nisin), compared to untreated cells growing under optimal conditions. Total proteins were extracted from L. monocytogenes cells treated for 1 h with free and lipo-nisin. As result, of 803 proteins that were initially identified, 64 and 53 proteins were differentially upregulated and downregulated respectively, in the treatments with nisin and lipo-nisin. Changes of Listeria proteome in response to treatments containing nisin were mainly related to ATP-binding cassette (ABC) transporter systems, transmembrane proteins, RNA-binding proteins and diverse stress response proteins. Some of the proteins uniquely detected in samples treated with free nisin were the membrane proteins SecD, Lmo1539 and the YfhO enzyme, which are related to translocation of L. monocytogenes virulence factors, activation of the LiaR-mediated stress defense and glycosylation of wall teichoic acid, respectively. The L. monocytogenes treated with liposome encapsulated nisin showed no expression of some stress response factors as compared with the free nisin, suggesting a reduction of stress mediated response and production of nisin-resistance factors by exposure to encapsulated nisin.
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Affiliation(s)
| | - Paolo Stincone
- Laboratório de Bioquímica e Microbiologia Aplicada, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adriano Brandelli
- Laboratório de Bioquímica e Microbiologia Aplicada, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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Rapacka-Zdonczyk A, Wozniak A, Nakonieczna J, Grinholc M. Development of Antimicrobial Phototreatment Tolerance: Why the Methodology Matters. Int J Mol Sci 2021; 22:2224. [PMID: 33672375 PMCID: PMC7926562 DOI: 10.3390/ijms22042224] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022] Open
Abstract
Due to rapidly growing antimicrobial resistance, there is an urgent need to develop alternative, non-antibiotic strategies. Recently, numerous light-based approaches, demonstrating killing efficacy regardless of microbial drug resistance, have gained wide attention and are considered some of the most promising antimicrobial modalities. These light-based therapies include five treatments for which high bactericidal activity was demonstrated using numerous in vitro and in vivo studies: antimicrobial blue light (aBL), antimicrobial photodynamic inactivation (aPDI), pulsed light (PL), cold atmospheric plasma (CAP), and ultraviolet (UV) light. Based on their multitarget activity leading to deleterious effects to numerous cell structures-i.e., cell envelopes, proteins, lipids, and genetic material-light-based treatments are considered to have a low risk for the development of tolerance and/or resistance. Nevertheless, the most recent studies indicate that repetitive sublethal phototreatment may provoke tolerance development, but there is no standard methodology for the proper evaluation of this phenomenon. The statement concerning the lack of development of resistance to these modalities seem to be justified; however, the most significant motivation for this review paper was to critically discuss existing dogma concerning the lack of tolerance development, indicating that its assessment is more complex and requires better terminology and methodology.
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Affiliation(s)
- Aleksandra Rapacka-Zdonczyk
- Laboratory of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (A.R.-Z.); (A.W.); (J.N.)
- Department of Pharmaceutical Microbiology, The Faculty of Pharmacy, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Agata Wozniak
- Laboratory of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (A.R.-Z.); (A.W.); (J.N.)
| | - Joanna Nakonieczna
- Laboratory of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (A.R.-Z.); (A.W.); (J.N.)
| | - Mariusz Grinholc
- Laboratory of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (A.R.-Z.); (A.W.); (J.N.)
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Transcriptome Analysis Reveals the Genes Involved in Bifidobacterium Longum FGSZY16M3 Biofilm Formation. Microorganisms 2021; 9:microorganisms9020385. [PMID: 33672820 PMCID: PMC7917626 DOI: 10.3390/microorganisms9020385] [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: 01/12/2021] [Revised: 01/29/2021] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Biofilm formation has evolved as an adaptive strategy for bacteria to cope with harsh environmental conditions. Currently, little is known about the molecular mechanisms of biofilm formation in bifidobacteria. A time series transcriptome sequencing analysis of both biofilm and planktonic cells of Bifidobacterium longum FGSZY16M3 was performed to identify candidate genes involved in biofilm formation. Protein–protein interaction network analysis of 1296 differentially expressed genes during biofilm formation yielded 15 clusters of highly interconnected nodes, indicating that genes related to the SOS response (dnaK, groS, guaB, ruvA, recA, radA, recN, recF, pstA, and sufD) associated with the early stage of biofilm formation. Genes involved in extracellular polymeric substances were upregulated (epsH, epsK, efp, frr, pheT, rfbA, rfbJ, rfbP, rpmF, secY and yidC) in the stage of biofilm maturation. To further investigate the genes related to biofilm formation, weighted gene co-expression network analysis (WGCNA) was performed with 2032 transcript genes, leading to the identification of nine WGCNA modules and 133 genes associated with response to stress, regulation of gene expression, quorum sensing, and two-component system. These results indicate that biofilm formation in B. longum is a multifactorial process, involving stress response, structural development, and regulatory processes.
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Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations. PLoS Pathog 2021; 17:e1009304. [PMID: 33544760 PMCID: PMC7891712 DOI: 10.1371/journal.ppat.1009304] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/18/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022] Open
Abstract
S. epidermidis is a substantial component of the human skin microbiota, but also one of the major causes of nosocomial infection in the context of implanted medical devices. We here aimed to advance the understanding of S. epidermidis genotypes and phenotypes conducive to infection establishment. Furthermore, we investigate the adaptation of individual clonal lines to the infection lifestyle based on the detailed analysis of individual S. epidermidis populations of 23 patients suffering from prosthetic joint infection. Analysis of invasive and colonizing S. epidermidis provided evidence that invasive S. epidermidis are characterized by infection-supporting phenotypes (e.g. increased biofilm formation, growth in nutrient poor media and antibiotic resistance), as well as specific genetic traits. The discriminating gene loci were almost exclusively assigned to the mobilome. Here, in addition to IS256 and SCCmec, chromosomally integrated phages was identified for the first time. These phenotypic and genotypic features were more likely present in isolates belonging to sequence type (ST) 2. By comparing seven patient-matched nasal and invasive S. epidermidis isolates belonging to identical genetic lineages, infection-associated phenotypic and genotypic changes were documented. Besides increased biofilm production, the invasive isolates were characterized by better growth in nutrient-poor media and reduced hemolysis. By examining several colonies grown in parallel from each infection, evidence for genetic within-host population heterogeneity was obtained. Importantly, subpopulations carrying IS insertions in agrC, mutations in the acetate kinase (AckA) and deletions in the SCCmec element emerged in several infections. In summary, these results shed light on the multifactorial processes of infection adaptation and demonstrate how S. epidermidis is able to flexibly repurpose and edit factors important for colonization to facilitate survival in hostile infection environments. S. epidermidis is a substantial component of the human skin microbiota, but also a major cause of nosocomial infections related to implanted medical devices. While phenotypic and genotypic determinants supporting invasion were identified, none appears to be necessary. By analysis of S. epidermidis from prosthetic joint infections, we here show that adaptive events are of importance during the transition from commensalism to infection. Adaptation to the infectious lifestyle is characterised by the development of intra-clonal heterogeneity, increased biofilm formation and enhanced growth in iron-free and nutrient-poor media, as well as reduced production of hemolysins. Importantly, during infection subpopulations emerge that carry mutations in a number of genes, most importantly the acetate kinase (ackA) and the β-subunit of the RNA polymerase (rpoB), have deleted larger chromosomal fragments (e.g. within the SCCmec element) or IS insertions in AgrC, a component of the master quorum sensing system in S. epidermidis. These results shed light on the multifactorial processes of infection adaptation and demonstrate how S. epidermidis is able to flexibly repurpose and edit factors important for colonization to facilitate survival under hostile infection conditions. While mobilome associated factors are important for S. epidermidis invasive potential, the species possesses a multi-layered and complex ability for adaptation to hostile environments, supporting the progression to chronic implant-associated infections.
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Nano-emulsification improves physical properties and bioactivities of litsea cubeba essential oil. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110361] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Pátek M, Grulich M, Nešvera J. Stress response in Rhodococcus strains. Biotechnol Adv 2021; 53:107698. [PMID: 33515672 DOI: 10.1016/j.biotechadv.2021.107698] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022]
Abstract
Rhodococci are bacteria which can survive under various extreme conditions, in the presence of toxic compounds, and in other hostile habitats. Their tolerance of unfavorable conditions is associated with the structure of their cell wall and their large array of enzymes, which degrade or detoxify harmful compounds. Their physiological and biotechnological properties, together with tools for their genetic manipulation, enable us to apply them in biotransformations, biodegradation and bioremediation. Many such biotechnological applications cause stresses that positively or negatively affect their efficiency. Whereas numerous reviews on rhodococci described their enzyme activities, the optimization of degradation or production processes, and corresponding technological solutions, only a few reviews discussed some specific effects of stresses on the physiology of rhodococci and biotechnological processes. This review aims to comprehensively describe individual stress responses in Rhodococcus strains, the interconnection of different types of stresses and their consequences for cell physiology. We examine here the responses to (1) environmental stresses (desiccation, heat, cold, osmotic and pH stress), (2) the presence of stress-inducing compounds (metals, organic compounds and antibiotics) in the environment (3) starvation and (4) stresses encountered during biotechnological applications. Adaptations of the cell envelope, the formation of multicellular structures and stresses induced by the interactions of hosts with pathogenic rhodococci are also included. The roles of sigma factors of RNA polymerase in the global regulation of stress responses in rhodococci are described as well. Although the review covers a large number of stressful conditions, our intention was to provide an overview of the selected stress responses and their possible connection to biotechnological processes, not an exhaustive survey of the scientific literature. The findings on stress responses summarized in this review and the demonstration of gaps in current knowledge may motivate researchers working to fill these gaps.
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Affiliation(s)
- Miroslav Pátek
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Michal Grulich
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Jan Nešvera
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
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Martínez SR, Durantini AM. Revealing ROS Production by Antibiotics and Photosensitizers in Biofilms: A Fluorescence Microscopy Approach. Methods Mol Biol 2021; 2202:125-135. [PMID: 32857352 DOI: 10.1007/978-1-0716-0896-8_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Reactive oxygen species (ROS) production within biofilms is studied with a simple and easy setup based on fluorescence microscopy. Herein, a biofilm is exposed to different ROS inducers: a bactericidal antibiotic (ciprofloxacin) and a BODIPY-based photosensitizer (I2B-OAc). Real-time ROS induction in the core of the biofilms is monitored utilizing two fluorescent reporters-AMDA and H2DCFDA-the first one with selectivity toward singlet oxygen (1O2) and the latest for other ROS (O2•-, H2O2, and OH•-). A point-by-point methodology is reported, starting with the sample preparation all the way through the microscope setup and, finally, processing of the images.
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Affiliation(s)
- Sol R Martínez
- IITEMA-CONICET, Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | - Andrés M Durantini
- IDAS-CONICET, Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, Argentina.
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Riquelme SA, Prince A. Airway immunometabolites fuel Pseudomonas aeruginosa infection. Respir Res 2020; 21:326. [PMID: 33302964 PMCID: PMC7731785 DOI: 10.1186/s12931-020-01591-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023] Open
Abstract
Pulmonary infections are associated with a brisk inflammatory reaction to bacterial surface components. Lipopolysaccharides (LPS) trigger macrophage activation and release of mitochondrial metabolites that control the intensity of the immune response. Whereas succinate induces oxidative stress (ROS), HIF1α stabilization, glycolysis and IL-1β release, itaconate suppresses inflammation by inhibiting succinate oxidation, glycolytic flux and promoting anti-oxidant Nrf2-HO-1 functions. P. aeruginosa is a major pathogen associated with acute and chronic lung infection. Although both secreted toxins, LPS and proteases are key factors to establish acute P. aeruginosa pneumonia, lack of these components in chronic P. aeruginosa isolates suggest these organisms exploit other mechanisms to adapt and persist in the lung. Upon inhalation, P. aeruginosa strains trigger airway macrophage reprograming and bacterial variants obtained from acutely and chronically infected subjects exhibit metabolic adaptation consistent with succinate and itaconate assimilation; namely, high expression of extracellular polysaccharides (EPS), reduced lptD-LPS function, increased glyoxylate shunt (GS) activity and substantial biofilm production. In this review we discuss recent findings illustrating how P. aeruginosa induces and adapts to macrophage metabolites in the human lung, and that catabolism of succinate and itaconate contribute to their formidable abilities to tolerate oxidative stress, phagocytosis and immune clearance.
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Affiliation(s)
| | - Alice Prince
- Department of Pediatrics, Columbia University, New York, NY, 10032, USA.
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Bidossi A, Bottagisio M, Logoluso N, De Vecchi E. In Vitro Evaluation of Gentamicin or Vancomycin Containing Bone Graft Substitute in the Prevention of Orthopedic Implant-Related Infections. Int J Mol Sci 2020; 21:ijms21239250. [PMID: 33291550 PMCID: PMC7729858 DOI: 10.3390/ijms21239250] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
Antibiotic-loaded bone graft substitutes are attractive clinical options and have been used for years either for prophylaxis or therapy for periprosthetic and fracture-related infections. Calcium sulfate and hydroxyapatite can be combined in an injectable and moldable bone graft substitute that provides dead space management with local release of high concentrations of antibiotics in a one-stage approach. With the aim to test preventive strategies against bone infections, a commercial hydroxyapatite/calcium sulfate bone graft substitute containing either gentamicin or vancomycin was tested against Staphylococcus aureus, Staphylococcus epidermidis and Pseudomonas aeruginosa, harboring different resistance determinants. The prevention of bacterial colonization and biofilm development by selected microorganisms was investigated along with the capability of the eluted antibiotics to select for antibiotic resistance. The addition of antibiotics drastically affected the ability of the selected strains to adhere to the tested compound. Furthermore, both the antibiotics eluted by the bone graft substitutes were able to negatively impair the biofilm maturation of all the staphylococcal strains. As expected, P. aeruginosa was significantly affected only by the gentamicin containing bone graft substitutes. Finally, the prolonged exposure to antibiotic-containing sulfate/hydroxyapatite discs did not lead to any stable or transient adaptations in either of the tested bacterial strains. No signs of the development of antibiotic resistance were found, which confirms the safety of this strategy for the prevention of infection in orthopedic surgery.
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Affiliation(s)
- Alessandro Bidossi
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, 20161 Milan, Italy; (A.B.); (E.D.V.)
| | - Marta Bottagisio
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, 20161 Milan, Italy; (A.B.); (E.D.V.)
- Correspondence: ; Tel.: +39-02-6621-4886
| | - Nicola Logoluso
- IRCCS Istituto Ortopedico Galeazzi, Department of Reconstructive Surgery of Osteo-Articular Infections C.R.I.O. Unit, 20161 Milan, Italy;
| | - Elena De Vecchi
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, 20161 Milan, Italy; (A.B.); (E.D.V.)
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Deciphering Streptococcal Biofilms. Microorganisms 2020; 8:microorganisms8111835. [PMID: 33233415 PMCID: PMC7700319 DOI: 10.3390/microorganisms8111835] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 12/19/2022] Open
Abstract
Streptococci are a diverse group of bacteria, which are mostly commensals but also cause a considerable proportion of life-threatening infections. They colonize many different host niches such as the oral cavity, the respiratory, gastrointestinal, and urogenital tract. While these host compartments impose different environmental conditions, many streptococci form biofilms on mucosal membranes facilitating their prolonged survival. In response to environmental conditions or stimuli, bacteria experience profound physiologic and metabolic changes during biofilm formation. While investigating bacterial cells under planktonic and biofilm conditions, various genes have been identified that are important for the initial step of biofilm formation. Expression patterns of these genes during the transition from planktonic to biofilm growth suggest a highly regulated and complex process. Biofilms as a bacterial survival strategy allow evasion of host immunity and protection against antibiotic therapy. However, the exact mechanisms by which biofilm-associated bacteria cause disease are poorly understood. Therefore, advanced molecular techniques are employed to identify gene(s) or protein(s) as targets for the development of antibiofilm therapeutic approaches. We review our current understanding of biofilm formation in different streptococci and how biofilm production may alter virulence-associated characteristics of these species. In addition, we have summarized the role of surface proteins especially pili proteins in biofilm formation. This review will provide an overview of strategies which may be exploited for developing novel approaches against biofilm-related streptococcal infections.
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