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Suarez SA, Martiny AC. Intraspecific variation in antibiotic resistance potential within E. coli. Microbiol Spectr 2024; 12:e0316223. [PMID: 38661581 PMCID: PMC11237723 DOI: 10.1128/spectrum.03162-23] [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: 08/22/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024] Open
Abstract
Intraspecific genomic diversity brings the potential for an unreported and diverse reservoir of cryptic antibiotic resistance genes in pathogens, as cryptic resistance can occur without major mutations and horizontal transmission. Here, we predicted the differences in the types of antibiotics and genes that induce cryptic and latent resistance between micro-diverse Escherichia coli strains. For example, we hypothesize that known resistance genes will be the culprit of latent resistance within clinical strains. We used a modified functional metagenomics method to induce expression in eight E. coli strains. We found a total of 66 individual genes conferring phenotypic resistance to 11 out of 16 antibiotics. A total of 14 known antibiotic resistance genes comprised 21% of total identified genes, whereas the majority (52 genes) were unclassified cryptic resistance genes. Between the eight strains, 1.2% of core orthologous genes were positive (conferred resistance in at least one strain). Sixty-four percent of positive orthologous genes conferred resistance to only one strain, demonstrating high intraspecific variability of latent resistance genes. Cryptic resistance genes comprised most resistance genes among laboratory and clinical strains as well as natural, semisynthetic, and synthetic antibiotics. Known antibiotic resistance genes primarily conferred resistance to multiple antibiotics from varying origins and within multiple strains. Hence, it is uncommon for E. coli to develop cross-cryptic resistance to antibiotics from multiple origins or within multiple strains. We have uncovered prospective and previously unknown resistance genes as well as antibiotics that have the potential to trigger latent antibiotic resistance in E. coli strains from varying origins.IMPORTANCEIntraspecific genomic diversity may be a driving force in the emergence of adaptive antibiotic resistance. Adaptive antibiotic resistance enables sensitive bacterial cells to acquire temporary antibiotic resistance, creating an optimal window for the development of permanent mutational resistance. In this study, we investigate cryptic resistance, an adaptive resistance mechanism, and unveil novel (cryptic) antibiotic resistance genes that confer resistance when amplified within eight E. coli strains derived from clinical and laboratory origins. We identify the potential of cryptic resistance genes to confer cross-resistance to antibiotics from varying origins and within multiple strains. We discern antibiotic characteristics that promote latent resistance in multiple strains, considering intraspecific diversity. This study may help detect novel resistance genes and functional genes that could become responsible for cryptic resistance among diverse strains and antibiotics, thus also identifying potential novel antibiotic targets and mechanisms.
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Affiliation(s)
- Stacy A. Suarez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Adam C. Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, California, USA
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2
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Ding J, Wang X, Liu W, Ding C, Wu J, He R, Zhang X. Biofilm Microenvironment Activated Antibiotic Adjuvant for Implant-Associated Infections by Systematic Iron Metabolism Interference. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400862. [PMID: 38408138 PMCID: PMC11077648 DOI: 10.1002/advs.202400862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Indexed: 02/28/2024]
Abstract
Hematoma, a risk factor of implant-associated infections (IAIs), creates a Fe-rich environment following implantation, which proliferates the growth of pathogenic bacteria. Fe metabolism is a major vulnerability for pathogens and is crucial for several fundamental physiological processes. Herein, a deferiprone (DFP)-loaded layered double hydroxide (LDH)-based nanomedicine (DFP@Ga-LDH) that targets the Fe-rich environments of IAIs is reported. In response to acidic changes at the infection site, DFP@Ga-LDH systematically interferes with bacterial Fe metabolism via the substitution of Ga3+ and Fe scavenging by DFP. DFP@Ga-LDH effectively reverses the Fe/Ga ratio in Pseudomonas aeruginosa, causing comprehensive interference in various Fe-associated targets, including transcription and substance metabolism. In addition to its favorable antibacterial properties, DFP@Ga-LDH functions as a nano-adjuvant capable of delaying the emergence of antibiotic resistance. Accordingly, DFP@Ga-LDH is loaded with a siderophore antibiotic (cefiderocol, Cefi) to achieve the antibacterial nanodrug DFP@Ga-LDH-Cefi. Antimicrobial and biosafety efficacies of DFP@Ga-LDH-Cefi are validated using ex vivo human skin and mouse IAI models. The pivotal role of the hematoma-created Fe-rich environment of IAIs is highlighted, and a nanoplatform that efficiently interferes with bacterial Fe metabolism is developed. The findings of the study provide promising guidance for future research on the exploration of nano-adjuvants as antibacterial agents.
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Affiliation(s)
- Jianing Ding
- Department of OrthopaedicsShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai200233P. R. China
| | - Xin Wang
- Department of OrthopaedicsShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai200233P. R. China
| | - Wei Liu
- Department of OrthopaedicsShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai200233P. R. China
| | - Cheng Ding
- Department of OrthopaedicsShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai200233P. R. China
| | - Jianrong Wu
- Shanghai Institute of Ultrasound in MedicineShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai200233P. R. China
| | - Renke He
- Department of OrthopaedicsShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai200233P. R. China
| | - Xianlong Zhang
- Department of OrthopaedicsShanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai200233P. R. China
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Dehbashi S, Tahmasebi H, Alikhani MY, Shahbazi MA, Arabestani MR. Staphopain mediated virulence and antibiotic resistance alteration in co-infection of Staphylococcus aureus and Pseudomonas aeruginosa: an animal model. BMC Biotechnol 2024; 24:10. [PMID: 38439037 PMCID: PMC10913572 DOI: 10.1186/s12896-024-00840-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: 08/19/2023] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
Polymicrobial communities lead to worsen the wound infections, due to mixed biofilms, increased antibiotic resistance, and altered virulence production. Promising approaches, including enzymes, may overcome the complicated condition of polymicrobial infections. Therefore, this study aimed to investigate Staphopain A-mediated virulence and resistance alteration in an animal model of Staphylococcus aureus and Pseudomonas aeruginosa co-infection. S. aureus and P. aeruginosa were co-cultured on the L-929 cell line and wound infection in an animal model. Then, recombinant staphopain A was purified and used to treat mono- and co-infections. Following the treatment, changes in virulence factors and resistance were investigated through phenotypic methods and RT-PCR. Staphopain A resulted in a notable reduction in the viability of S. aureus and P. aeruginosa. The biofilm formed in the wound infection in both animal model and cell culture was disrupted remarkably. Moreover, the biofilm-encoding genes, quorum sensing regulating genes, and virulence factors (hemolysin and pyocyanin) controlled by QS were down-regulated in both microorganisms. Furthermore, the resistance to vancomycin and doripenem decreased following treatment with staphopain A. According to this study, staphopain A might promote wound healing and cure co-infection. It seems to be a promising agent to combine with antibiotics to overcome hard-to-cure infections.
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Affiliation(s)
- Sanaz Dehbashi
- Department of Laboratory Sciences, Varastegan Institute of Medical Sciences, Mashhad, Iran
| | - Hamed Tahmasebi
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Mohammad Yousef Alikhani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad-Ali Shahbazi
- Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713, Groningen, AV, The Netherlands
| | - Mohammad Reza Arabestani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
- Infectious disease Research center, Hamadan University of Medical Sciences, Hamadan, Iran.
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Dehbashi S, Tahmasebi H, Alikhani MY, Vidal JE, Seifalian A, Arabestani MR. The healing effect of Pseudomonas Quinolone Signal (PQS) with co-infection of Staphylococcus aureus and Pseudomonas aeruginosa: A preclinical animal co-infection model. J Infect Public Health 2024; 17:329-338. [PMID: 38194764 DOI: 10.1016/j.jiph.2023.12.016] [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: 08/01/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Because of the rise in antibiotic resistance and the control of pathogenicity, polymicrobial bacterial biofilms exacerbate wound infections. Since bacterial quorum sensing (QS) signals can dysregulate biofilm development, they are interesting therapeutic treatments. In this study, Pseudomonas Quinolone Signal (PQS) was used to treat an animal model of a wound that had both Staphylococcus aureus and Pseudomonas aeruginosa co-infection. METHODS S. aureus and P. aeruginosa mono- and co-infection models were developed in vitro on the L-929 cell line and in an animal model of wound infection. Moreover, PQS was extracted and purified using liquid chromatography. Then, the mono- and co-infection models were treated by PQS in vitro and in vivo. RT-PCR analysis was used to look into changes in biofilm, QS, tissue regeneration, and apoptosis genes after the treatment. RESULTS PQS significantly disrupted established biofilm up to 90% in both in vitro and in vivo models. Moreover, a 93% reduction in the viability of S. aureus and P. aeruginosa was detected during the 10 days of treatment in comparison to control groups. In addition, the biofilm-encoding and QS-regulating genes were down-regulated to 75% in both microorganisms. Also, fewer epithelial cells died when treated with PQS compared to control groups in both mono- and co-infection groups. CONCLUSION According to this study, PQS may facilitate wound healing by stimulating the immune system and reducing apoptosis. It seems to be a potential medication to use in conjunction with antibiotics to treat infections that are difficult to treat.
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Affiliation(s)
- Sanaz Dehbashi
- Department of Laboratory Sciences, Varastegan Institute of Medical Sciences, Mashhad, Iran
| | - Hamed Tahmasebi
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Mohammad Yousef Alikhani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Jorge E Vidal
- Department of Cell and Molecular Biology, Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Alexander Seifalian
- Nanotechnology & Regenerative Medicine Commercialization Centre (NanoRegMed Ltd, Nanoloom Ltd, & Liberum Health Ltd), London BioScience Innovation Centre, London, United Kingdom
| | - Mohammad Reza Arabestani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Infectious Disease Research center, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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Sadeghian Y, Raeeszadeh M, Karimi Darehabi H. The Impact of Metal and Heavy Metal Concentrations on Vancomycin Resistance in Staphylococcus aureus within Milk Produced by Cattle Farms and the Health Risk Assessment in Kurdistan Province, Iran. Animals (Basel) 2024; 14:148. [PMID: 38200879 PMCID: PMC10778068 DOI: 10.3390/ani14010148] [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: 12/20/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
In today's food landscape, the paramount focus is on ensuring food safety and hygiene. Recognizing the pivotal role of the environment and its management in safeguarding animal products, this study explores vancomycin resistance in raw milk from livestock farms in the Kurdistan province and its correlation with metal and heavy metal. One hundred and sixty raw milk samples were collected from various locations, with heavy metal concentrations analyzed using ICP-MS. Identification of Staphylococcus aureus and vancomycin resistance testing were conducted through culture and the Kirby-Bauer method. This study investigates the relationship between resistance and heavy metal levels, revealing that 8.75% of milk samples contained Staphylococcus aureus, with 28.58% exhibiting vancomycin resistance. Significant variations in arsenic, iron, zinc, sodium, and aluminum concentrations were observed between resistant and sensitive samples (p < 0.01). The increase in arsenic, iron, and aluminum, along with the decrease in zinc, demonstrated a significant association with vancomycin resistance (p < 0.001). Levels of lead, cadmium, mercury, zinc, and iron exceeded permissible limits (p < 0.05). The Target Hazard Quotient (THQ) for cadmium indicated a high non-carcinogenic risk, while the Target Risk (TR) for arsenic fell within the carcinogenic range. Accumulation of heavy metals has the potential to impact antibiotic resistance in milk, underscoring the imperative to control arsenic residues for national safety.
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Affiliation(s)
- Yeganeh Sadeghian
- Graduate of Faculty of Veterinary Sciences, Sanandaj Branch, Islamic Azad University, Sanandaj 618, Iran;
| | - Mahdieh Raeeszadeh
- Department of Basic Sciences, Sanandaj Branch, Islamic Azad University, Sanandaj 618, Iran
| | - Hiva Karimi Darehabi
- Department of Food Hygiene and Public Health, Sanandaj Branch, Islamic Azad University, Sanandaj 618, Iran;
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Vanderpool EJ, Rumbaugh KP. Host-microbe interactions in chronic rhinosinusitis biofilms and models for investigation. Biofilm 2023; 6:100160. [PMID: 37928619 PMCID: PMC10622848 DOI: 10.1016/j.bioflm.2023.100160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a debilitating condition characterized by long-lasting inflammation of the paranasal sinuses. It affects a significant portion of the population, causing a considerable burden on individuals and healthcare systems. The pathogenesis of CRS is multifactorial, with bacterial infections playing a crucial role in CRS development and persistence. In recent years, the presence of biofilms has emerged as a key contributor to the chronicity of sinusitis, further complicating treatment and exacerbating symptoms. This review aims to explore the role of biofilms in CRS, focusing on the involvement of the bacterial species Staphylococcus aureus and Pseudomonas aeruginosa, their interactions in chronic infections, and model systems for studying biofilms in CRS. These species serve as an example of how microbial interplay can influence disease progression and exemplify the need for continued investigation and innovation in CRS research.
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Affiliation(s)
- Emily J. Vanderpool
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Burn Center of Research Excellence, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Kendra P. Rumbaugh
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Burn Center of Research Excellence, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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Mashayamombe M, Carda-Diéguez M, Mira A, Fitridge R, Zilm PS, Kidd SP. Subpopulations in Strains of Staphylococcus aureus Provide Antibiotic Tolerance. Antibiotics (Basel) 2023; 12:antibiotics12020406. [PMID: 36830316 PMCID: PMC9952555 DOI: 10.3390/antibiotics12020406] [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: 01/30/2023] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The ability of Staphylococcus aureus to colonise different niches across the human body is linked to an adaptable metabolic capability, as well as its ability to persist within specific tissues despite adverse conditions. In many cases, as S. aureus proliferates within an anatomical niche, there is an associated pathology. The immune response, together with medical interventions such as antibiotics, often removes the S. aureus cells that are causing this disease. However, a common issue in S. aureus infections is a relapse of disease. Within infected tissue, S. aureus exists as a population of cells, and it adopts a diversity of cell types. In evolutionary biology, the concept of "bet-hedging" has established that even in positive conditions, there are members that arise within a population that would be present as non-beneficial, but if those conditions change, these traits could allow survival. For S. aureus, some of these cells within an infection have a reduced fitness, are not rapidly proliferating or are the cause of an active host response and disease, but these do remain even after the disease seems to have been cleared. This is true for persistence against immune responses but also as a continual presence in spite of antibiotic treatment. We propose that the constant arousal of suboptimal populations at any timepoint is a key strategy for S. aureus long-term infection and survival. Thus, understanding the molecular basis for this feature could be instrumental to combat persistent infections.
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Affiliation(s)
- Matipaishe Mashayamombe
- Department of Vascular Surgery, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
- Basil Hetzel Institute for Translational Research, The Queen Elizabeth Hospital, Adelaide, SA 5000, Australia
| | - Miguel Carda-Diéguez
- Department of Health and Genomics, Center for Advanced Research in Public Health, FISABIO Institute, 46020 Valencia, Spain
| | - Alex Mira
- Department of Health and Genomics, Center for Advanced Research in Public Health, FISABIO Institute, 46020 Valencia, Spain
- School of Health and Welfare, Jönköping University, 551 11 Jönköping, Sweden
| | - Robert Fitridge
- Department of Vascular Surgery, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
- Basil Hetzel Institute for Translational Research, The Queen Elizabeth Hospital, Adelaide, SA 5000, Australia
| | - Peter S. Zilm
- Adelaide Dental School, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Stephen P. Kidd
- Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Research Centre for Infectious Disease, The University of Adelaide, Adelaide, SA 5005, Australia
- Australian Centre for Antimicrobial Resistance Ecology (ACARE), The University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence:
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Dawan J, Ahn J. Bacterial Stress Responses as Potential Targets in Overcoming Antibiotic Resistance. Microorganisms 2022; 10:microorganisms10071385. [PMID: 35889104 PMCID: PMC9322497 DOI: 10.3390/microorganisms10071385] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/03/2022] [Accepted: 07/08/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteria can be adapted to adverse and detrimental conditions that induce general and specific responses to DNA damage as well as acid, heat, cold, starvation, oxidative, envelope, and osmotic stresses. The stress-triggered regulatory systems are involved in bacterial survival processes, such as adaptation, physiological changes, virulence potential, and antibiotic resistance. Antibiotic susceptibility to several antibiotics is reduced due to the activation of stress responses in cellular physiology by the stimulation of resistance mechanisms, the promotion of a resistant lifestyle (biofilm or persistence), and/or the induction of resistance mutations. Hence, the activation of bacterial stress responses poses a serious threat to the efficacy and clinical success of antibiotic therapy. Bacterial stress responses can be potential targets for therapeutic alternatives to antibiotics. An understanding of the regulation of stress response in association with antibiotic resistance provides useful information for the discovery of novel antimicrobial adjuvants and the development of effective therapeutic strategies to control antibiotic resistance in bacteria. Therefore, this review discusses bacterial stress responses linked to antibiotic resistance in Gram-negative bacteria and also provides information on novel therapies targeting bacterial stress responses that have been identified as potential candidates for the effective control of Gram-negative antibiotic-resistant bacteria.
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Affiliation(s)
- Jirapat Dawan
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Korea;
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Korea;
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Gangwon, Korea
- Correspondence: ; Tel.: +82-33-250-6564
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