1
|
Kennelly C, Tran P, Prindle A. Environmental purines decrease Pseudomonas aeruginosa biofilm formation by disrupting c-di-GMP metabolism. Cell Rep 2024; 43:114154. [PMID: 38669142 DOI: 10.1016/j.celrep.2024.114154] [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: 11/06/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Cyclic di-guanosine monophosphate (c-di-GMP) is a bacterial second messenger that governs the lifestyle switch between planktonic and biofilm states. While substantial investigation has focused on the proteins that produce and degrade c-di-GMP, less attention has been paid to the potential for metabolic control of c-di-GMP signaling. Here, we show that micromolar levels of specific environmental purines unexpectedly decrease c-di-GMP and biofilm formation in Pseudomonas aeruginosa. Using a fluorescent genetic reporter, we show that adenosine and inosine decrease c-di-GMP even when competing purines are present. We confirm genetically that purine salvage is required for c-di-GMP decrease. Furthermore, we find that (p)ppGpp prevents xanthosine and guanosine from producing an opposing c-di-GMP increase, reinforcing a salvage hierarchy that favors c-di-GMP decrease even at the expense of growth. We propose that purines can act as a cue for bacteria to shift their lifestyle away from the recalcitrant biofilm state via upstream metabolic control of c-di-GMP signaling.
Collapse
Affiliation(s)
- Corey Kennelly
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Peter Tran
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Arthur Prindle
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.
| |
Collapse
|
2
|
Warsi OM, Upterworth LM, Breidenstein A, Lustig U, Mikkelsen K, Nagy T, Szatmari D, Ingmer H, Andersson DI. Staphylococcus aureus mutants resistant to the feed-additive monensin show increased virulence and altered purine metabolism. mBio 2024; 15:e0315523. [PMID: 38214510 PMCID: PMC10865815 DOI: 10.1128/mbio.03155-23] [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: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024] Open
Abstract
Ionophores are antibacterial compounds that affect bacterial growth by changing intracellular concentrations of the essential cations, sodium and potassium. They are extensively used in animal husbandry to increase productivity and reduce infectious diseases, but our understanding of the potential for and effects of resistance development to ionophores is poorly known. Thus, given their widespread global usage, it is important to determine the potential negative consequences of ionophore use on human and animal health. In this study, we demonstrate that exposure to the ionophore monensin can select for resistant mutants in the human and animal pathogen Staphylococcus aureus, with a majority of the resistant mutants showing increased growth rates in vitro and/or in mice. Whole-genome sequencing and proteomic analysis of the resistant mutants show that the resistance phenotype is associated with de-repression of de novo purine synthesis, which could be achieved through mutations in different transcriptional regulators including mutations in the gene purR, the repressor of the purine de novo synthesis pathway. This study shows that mutants with reduced susceptibility to the ionophore monensin can be readily selected and highlights an unexplored link between ionophore resistance, purine metabolism, and fitness in pathogenic bacteria.IMPORTANCEThis study demonstrates a novel link between ionophore resistance, purine metabolism, and virulence/fitness in the key human and animal pathogen Staphylococcus aureus. The results show that mutants with reduced susceptibility to the commonly used ionophore monensin can be readily selected and that the reduced susceptibility observed is associated with an increased expression of the de novo purine synthesis pathway. This study increases our understanding of the impact of the use of animal feed additives on both human and veterinary medicine.
Collapse
Affiliation(s)
- Omar M. Warsi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lina M. Upterworth
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Annika Breidenstein
- Department of Medical Chemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Ulrika Lustig
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kasper Mikkelsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tamás Nagy
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Dávid Szatmari
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
3
|
Xiong YQ, Li Y, Goncheva MI, Elsayed AM, Zhu F, Li L, Abdelhady W, Flannagan RS, Yeaman MR, Bayer AS, Heinrichs DE. The Purine Biosynthesis Repressor, PurR, Contributes to Vancomycin Susceptibility of Methicillin-resistant Staphylococcus aureus in Experimental Endocarditis. J Infect Dis 2024:jiad577. [PMID: 38297970 DOI: 10.1093/infdis/jiad577] [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: 07/27/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Staphylococcus aureus is the most common cause of life-threatening endovascular infections, including infective endocarditis (IE). These infections, especially when caused by methicillin-resistant strains (MRSA), feature limited therapeutic options and high morbidity and mortality rates. METHODS Herein, we investigated the role of the purine biosynthesis repressor, PurR, in virulence factor expression and vancomycin (VAN) treatment outcomes in experimental IE due to MRSA. RESULTS The PurR-mediated repression of purine biosynthesis was confirmed by enhanced purF expression and production of an intermediate purine metabolite in purR mutant strain. In addition, enhanced expression of the transcriptional regulators, sigB and sarA, and their key downstream virulence genes (eg, fnbA, and hla) was demonstrated in the purR mutant in vitro and within infected cardiac vegetations. Furthermore, purR deficiency enhanced fnbA/fnbB transcription, translating to increased fibronectin adhesion versus the wild type and purR-complemented strains. Notably, the purR mutant was refractory to significant reduction in target tissues MRSA burden following VAN treatment in the IE model. CONCLUSIONS These findings suggest that the purine biosynthetic pathway intersects the coordination of virulence factor expression and in vivo persistence during VAN treatment, and may represent an avenue for novel antimicrobial development targeting MRSA.
Collapse
Affiliation(s)
- Yan Q Xiong
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- Department of Medicine, Division of Infectious Diseases, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Yi Li
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Mariya I Goncheva
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Ahmed M Elsayed
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Fengli Zhu
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Liang Li
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Wessam Abdelhady
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Ronald S Flannagan
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Michael R Yeaman
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- Department of Medicine, Division of Infectious Diseases, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Medicine, Division of Molecular Medicine, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Arnold S Bayer
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- Department of Medicine, Division of Infectious Diseases, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - David E Heinrichs
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| |
Collapse
|
4
|
Tan CAZ, Chong KKL, Yeong DYX, Ng CHM, Ismail MH, Yap ZH, Khetrapal V, Tay VSY, Drautz-Moses DI, Ali Y, Chen SL, Kline KA. Purine and carbohydrate availability drive Enterococcus faecalis fitness during wound and urinary tract infections. mBio 2024; 15:e0238423. [PMID: 38078746 PMCID: PMC10790769 DOI: 10.1128/mbio.02384-23] [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: 09/14/2023] [Accepted: 10/24/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Although E. faecalis is a common wound pathogen, its pathogenic mechanisms during wound infection are unexplored. Here, combining a mouse wound infection model with in vivo transposon and RNA sequencing approaches, we identified the E. faecalis purine biosynthetic pathway and galactose/mannose MptABCD phosphotransferase system as essential for E. faecalis acute replication and persistence during wound infection, respectively. The essentiality of purine biosynthesis and the MptABCD PTS is driven by the consumption of purine metabolites by E. faecalis during acute replication and changing carbohydrate availability during the course of wound infection. Overall, our findings reveal the importance of the wound microenvironment in E. faecalis wound pathogenesis and how these metabolic pathways can be targeted to better control wound infections.
Collapse
Affiliation(s)
- Casandra Ai Zhu Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Kelvin Kian Long Chong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Daryl Yu Xuan Yeong
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Celine Hui Min Ng
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Muhammad Hafiz Ismail
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Zhei Hwee Yap
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Varnica Khetrapal
- Infectious Diseases Translational Research Programme, Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vanessa Shi Yun Tay
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Yusuf Ali
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
- Singapore Eye Research Institute (SERI), Singapore General Hospital, Singapore, Singapore
| | - Swaine L. Chen
- Infectious Diseases Translational Research Programme, Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore, Singapore
| | - Kimberly A. Kline
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| |
Collapse
|
5
|
Kang X, Yang X, He Y, Guo C, Li Y, Ji H, Qin Y, Wu L. Strategies and materials for the prevention and treatment of biofilms. Mater Today Bio 2023; 23:100827. [PMID: 37859998 PMCID: PMC10582481 DOI: 10.1016/j.mtbio.2023.100827] [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: 06/27/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Biofilms are aggregates of organized microbial growth that function as barriers and create a stable internal environment for cell survival. The bacteria in the biofilms exhibit characteristics that are quite different from the planktonic bacteria, such as strong resistance to antibiotics and other bactericides, getting out of host immunity, and developing in harsh environments, which all contribute to the persistent and intractable treatment. Hence, there is an urgent need to develop novel materials and strategies to combat biofilms. However, most of the reviews on anti-biofilms published in recent years are based on specific fields or materials. Microorganisms are ubiquitous, except in the context of medical and health issues; however, biofilms exert detrimental effects on the advancement and progress of various fields. Therefore, this review aims to provide a comprehensive summary of effective strategies and methodologies applicable across all industries. Firstly, the process of biofilms formation was introduced to enhance our comprehension of the "enemy". Secondly, strategies to intervene in the important links of biofilms formation were discussed, taking timely action during the early weak stages of the "enemy". Thirdly, treatment strategies for mature biofilms were summarized to deal with biofilms that break through the defense line. Finally, several substances with antibacterial properties were presented. The review concludes with the standpoint of the author about potential developments of anti-biofilms strategies. This review may help researchers quickly understand the research progress and challenges in the field of anti-biofilms to design more efficient methods and strategies to combat biofilms.
Collapse
Affiliation(s)
- Xiaoxia Kang
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Xiaoxiao Yang
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Yue He
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Conglin Guo
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Yuechen Li
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Haiwei Ji
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Yuling Qin
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| | - Li Wu
- School of Public Health, Nantong Key Laboratory of Public Health and Medical Analysis, Nantong University, Nantong, 226019, China
| |
Collapse
|
6
|
Uddin MJ, Overkleeft HS, Lentz CS. Activity-Based Protein Profiling in Methicillin-Resistant Staphylococcus aureus Reveals the Broad Reactivity of a Carmofur-Derived Probe. Chembiochem 2023; 24:e202300473. [PMID: 37552008 DOI: 10.1002/cbic.202300473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Activity-based protein profiling is a powerful chemoproteomic technique to detect active enzymes and identify targets and off-targets of drugs. Here, we report the use of carmofur- and activity-based probes to identify biologically relevant enzymes in the bacterial pathogen Staphylococcus aureus. Carmofur is an anti-neoplastic prodrug of 5-fluorouracil and also has antimicrobial and anti-biofilm activity. Carmofur probes were originally designed to target human acid ceramidase, a member of the NTN hydrolase family with an active-site cysteine nucleophile. Here, we first profiled the targets of a fluorescent carmofur probe in live S. aureus under biofilm-promoting conditions and in liquid culture, before proceeding to target identification by liquid chromatography/mass spectrometry. Treatment with a carmofur-biotin probe led to enrichment of 20 enzymes from diverse families awaiting further characterization, including the NTN hydrolase-related IMP cyclohydrolase PurH. However, the probe preferentially labeled serine hydrolases, thus displaying a reactivity profile similar to that of carbamates. Our results suggest that the electrophilic N-carbamoyl-5-fluorouracil scaffold could potentially be optimized to achieve selectivity towards diverse enzyme families. The observed promiscuous reactivity profile suggests that the clinical use of carmofur presumably leads to inactivation of a number human and microbial enzymes, which could lead to side effects and/or contribute to therapeutic efficacy.
Collapse
Affiliation(s)
- Md Jalal Uddin
- Department of Medical Biology, UiT- The Arctic University of Norway, 9019, Tromsø, Norway
| | - Hermen S Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Christian S Lentz
- Department of Medical Biology, UiT- The Arctic University of Norway, 9019, Tromsø, Norway
| |
Collapse
|
7
|
Maisat W, Yuki K. Volatile anesthetic isoflurane exposure facilitates Enterococcus biofilm infection. FASEB J 2023; 37:e23186. [PMID: 37665578 PMCID: PMC10495085 DOI: 10.1096/fj.202301128r] [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: 06/06/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
Enterococcus faecalis (E. faecalis) is one of the major pathogenic bacteria responsible for surgical site infections. Biofilm infections are major hospital-acquired infections. Previous studies suggested that ions could regulate biofilm formation in microbes. Volatile anesthetics, frequently administered in surgical setting, target ion channels. Here, we investigated the role of ion channels/transporters and volatile anesthetics in the biofilm formation by E. faecalis MMH594 strain and its ion transporter mutants. We found that a chloride transporter mutant significantly reduced biofilm formation compared to the parental strain. Downregulation of teichoic acid biosynthesis in the chloride transporter mutant impaired biofilm matrix formation and cellular adhesion, leading to mitigated biofilm formation. Among anesthetics, isoflurane exposure enhanced biofilm formation in vitro and in vivo. The upregulation of de novo purine biosynthesis pathway by isoflurane exposure potentially enhanced biofilm formation, an essential process for DNA, RNA, and ATP synthesis. We also demonstrated that isoflurane exposure to E. faecalis increased cyclic-di-AMP and extracellular DNA production, consistent with the increased purine biosynthesis. We further showed that isoflurane enhanced the enzymatic activity of phosphoribosyl pyrophosphate synthetase (PRPP-S). With the hypothesis that isoflurane directly bound to PRPP-S, we predicted isoflurane binding site on it using rigid docking. Our study provides a better understanding of the underlying mechanisms of E. faecalis biofilm formation and highlights the potential impact of an ion transporter and volatile anesthetic on this process. These findings may lead to the development of novel strategies for preventing E. faecalis biofilm formation and improving patient outcomes in clinical settings.
Collapse
Affiliation(s)
- Wiriya Maisat
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children’s Hospital, Boston, MA, USA
- Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Anesthesiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Koichi Yuki
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children’s Hospital, Boston, MA, USA
- Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| |
Collapse
|
8
|
Fujii T, Tochio T, Nishifuji K. Erythritol alters gene transcriptome signatures, cell growth, and biofilm formation in Staphylococcus pseudintermedius. BMC Vet Res 2023; 19:146. [PMID: 37679756 PMCID: PMC10483758 DOI: 10.1186/s12917-023-03711-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/28/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Erythritol was found to inhibit the growth of microorganisms. The present study aimed to demonstrate the growth inhibition of Staphylococcus pseudintermedius by erythritol and to define the changes in gene transcription signatures induced by erythritol. Changes in the gene transcription profiles were analysed by RNA sequencing and quantitative reverse transcription PCR. Gene ontology analysis was performed to assign functional descriptions to the genes. RESULTS Erythritol inhibited S. pseudintermedius growth in a dose-dependent manner. We then performed a transcriptome analysis of S. pseudintermedius with and without 5% (w/w) erythritol exposure to validate the mechanism of growth inhibition. We revealed that erythritol induced up-regulation of three genes (ptsG, ppdK, and ppdkR) that are related to the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). Glucose supplementation restored the up-regulation of the PTS-related genes in response to erythritol. In addition, erythritol down-regulated eleven genes that are located in a single pur-operon and inhibited biofilm formation of S. pseudintermedius. CONCLUSIONS These findings indicated that erythritol antagonistically inhibits PTS-mediated glucose uptake, thereby exerting a growth inhibitory effect on S. pseudintermedius. Moreover, erythritol inhibits the 'de novo' IMP biosynthetic pathway that may contribute to biofilm synthesis in S. pseudintermedius.
Collapse
Affiliation(s)
- Tadashi Fujii
- Research & Development Center, B Food Science Co., Ltd., Aichi, Japan.
- Department of Gastroenterology and Hepatology, Fujita Health University, Aichi, Japan.
| | - Takumi Tochio
- Research & Development Center, B Food Science Co., Ltd., Aichi, Japan
- Department of Gastroenterology and Hepatology, Fujita Health University, Aichi, Japan
| | - Koji Nishifuji
- Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| |
Collapse
|
9
|
Enriquez KT, Plummer WD, Neufer PD, Chazin WJ, Dupont WD, Skaar EP. Temporal modelling of the biofilm lifecycle (TMBL) establishes kinetic analysis of plate-based bacterial biofilm dynamics. J Microbiol Methods 2023; 212:106808. [PMID: 37595876 PMCID: PMC10528067 DOI: 10.1016/j.mimet.2023.106808] [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: 06/30/2023] [Revised: 08/12/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023]
Abstract
Bacterial biofilms are critical to pathogenesis and infection. They are associated with rising rates of antimicrobial resistance. Biofilms are correlated with worse clinical outcomes, making them important to infectious diseases research. There is a gap in knowledge surrounding biofilm kinetics and dynamics which makes biofilm research difficult to translate from bench to bedside. To address this gap, this work employs a well-characterized crystal violet biomass accrual and planktonic cell density assay across a clinically relevant time course and expands statistical analysis to include kinetic information in a protocol termed the TMBL (Temporal Mapping of the Biofilm Lifecycle) assay. TMBL's statistical framework quantitatively compares biofilm communities across time, species, and media conditions in a 96-well format. Measurements from TMBL can reliably be condensed into response features that inform the time-dependent behavior of adherent biomass and planktonic cell populations. Staphylococcus aureus and Pseudomonas aeruginosa biofilms were grown in conditions of metal starvation in nutrient-variable media to demonstrate the rigor and translational potential of this strategy. Significant differences in single-species biofilm formation are seen in metal-deplete conditions as compared to their controls which is consistent with the consensus literature on nutritional immunity that metal availability drives transcriptomic and metabolomic changes in numerous pathogens. Taken together, these results suggest that kinetic analysis of biofilm by TMBL represents a statistically and biologically rigorous approach to studying the biofilm lifecycle as a time-dependent process. In addition to current methods to study the impact of microbe and environmental factors on the biofilm lifecycle, this kinetic assay can inform biological discovery in biofilm formation and maintenance.
Collapse
Affiliation(s)
- Kyle T Enriquez
- Vanderbilt University Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, United States of America; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, United States of America; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - W Dale Plummer
- Department of Biostatistics, Vanderbilt University, Nashville, TN, United States of America
| | - Preston D Neufer
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America; Department of Biochemistry, Vanderbilt University, Nashville, TN, United States of America
| | - Walter J Chazin
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, United States of America; Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America; Department of Biochemistry, Vanderbilt University, Nashville, TN, United States of America
| | - William D Dupont
- Department of Biostatistics, Vanderbilt University, Nashville, TN, United States of America
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, United States of America; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, United States of America.
| |
Collapse
|
10
|
Fu C, Xu Y, Zheng H, Ling X, Zheng C, Tian L, Gu X, Cai J, Yang J, Li Y, Wang P, Liu Y, Lou Y, Zheng M. In vitro antibiofilm and bacteriostatic activity of diacerein against Enterococcus faecalis. AMB Express 2023; 13:85. [PMID: 37573278 PMCID: PMC10423188 DOI: 10.1186/s13568-023-01594-z] [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: 07/29/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023] Open
Abstract
Enterococcus faecalis is one of the main pathogens that causes hospital-acquired infections because it is intrinsically resistant to some antibiotics and often is capable of biofilm formation, which plays a critical role in resisting the external environment. Therefore, attacking biofilms is a potential therapeutic strategy for infections caused by E. faecalis. Current research indicates that diacerein used in the treatment of osteoarthritis showed antimicrobial activity on strains of gram-positive cocci in vitro. In this study, we tested the MICs of diacerein using the broth microdilution method, and successive susceptibility testing verified that E. faecalis is unlikely to develop resistance to diacerein. In addition, we obtained a strain of E. faecalis HE01 with strong biofilm-forming ability from an eye hospital environment and demonstrated that diacerein affected the biofilm development of HE01 in a dose-dependent manner. Then, we explored the mechanism by which diacerein inhibits biofilm formation through qRT-PCR, extracellular protein assays, hydrophobicity assays and transcriptomic analysis. The results showed that biofilm formation was inhibited at the initial adhesion stage by inhibition of the expression of the esp gene, synthesis of bacterial surface proteins and reduction in cell hydrophobicity. In addition, transcriptome analysis showed that diacerein not only inhibited bacterial growth by affecting the oxidative phosphorylation process and substance transport but also inhibited biofilm formation by affecting secondary metabolism, biosynthesis, the ribosome pathway and luxS expression. Thus, our findings provide compelling evidence for the substantial therapeutic potential of diacerein against E. faecalis biofilms.
Collapse
Affiliation(s)
- Chunyan Fu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yuxi Xu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Hao Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xinyi Ling
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chengzhi Zheng
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Leihao Tian
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xiaobin Gu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jiabei Cai
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jing Yang
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yuanyuan Li
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Peiyu Wang
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yuan Liu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Meiqin Zheng
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China.
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China.
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| |
Collapse
|
11
|
Shrestha GS, Vijay AK, Stapleton F, White A, Pickford R, Carnt N. Human tear metabolites associated with nucleoside-signalling pathways in bacterial keratitis. Exp Eye Res 2023; 228:109409. [PMID: 36775205 DOI: 10.1016/j.exer.2023.109409] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/17/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
OBJECTIVE The study aimed to profile and quantify tear metabolites associated with bacterial keratitis using both untargeted and targeted metabolomic platforms. METHODS Untargeted metabolomic analysis using liquid-chromatography-Q Exactive-HF mass-spectrometry explored tear metabolites significantly associated with bacterial keratitis (n = 6) compared to healthy participants (n = 6). Differential statistics and principal component analysis determined meaningful metabolite differences between cases and controls. Purines and nucleosides were further quantified and compared between 15 cases and 15 controls in the targeted metabolomic platform using TSQ quantum access triple quadrupole mass spectrometry. Compound quantification was done by plotting the calibration curves and the difference in the compound levels was evaluated using the Wilcoxon rank-sum test. RESULTS In the untargeted analysis, 49 tear metabolites (27 upregulated and 22 downregulated) were differentially expressed between cases and controls. The untargeted analysis indicated that the purine metabolism pathway was the most affected by bacterial keratitis. Metabolite quantification in the targeted analysis further confirmed the upregulation of xanthine (P = 0.02) and downregulation of adenine (P < 0.0001), adenosine (P < 0.0001) and cytidine (P < 0.0001) in the tears of participants with bacterial keratitis compared to that of healthy participants. CONCLUSIONS Bacterial keratitis significantly changes the tear metabolite profile, including five major compound classes such as indoles, amino acids, nucleosides, carbohydrates, and steroids. This study also indicates that tear fluids can be used to map the metabolic pathways and uncover metabolic markers associated with bacterial keratitis. Conceivably, the inhibition of nucleoside synthesis may contribute to the pathophysiology of bacterial keratitis because nucleosides are required for maintaining cellular energy homeostasis and immune adaptability.
Collapse
Affiliation(s)
| | | | - Fiona Stapleton
- School of Optometry and Vision Science, UNSW Sydney, Australia
| | - Andrew White
- Department of Ophthalmology, Westmead Hospital, University of Sydney, Australia; Westmead Institute for Medical Research, University of Sydney, Australia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, UNSW Sydney, Australia
| | - Nicole Carnt
- School of Optometry and Vision Science, UNSW Sydney, Australia; Westmead Institute for Medical Research, University of Sydney, Australia; Institute of Ophthalmology, University College London, United Kingdom
| |
Collapse
|