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Srithabut S, Chareonsudjai P, Chaianunporn T, Bunma C, Phetcharaburanin J, Suksawat M, Chitcharoen S, Chareonsudjai S. NMR-based metabolomics of Burkholderia pseudomallei biofilms and extracellular polymeric substance cultured in LB and MVBM media. BIOFOULING 2025; 41:498-511. [PMID: 40369969 DOI: 10.1080/08927014.2025.2502936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 04/17/2025] [Accepted: 04/30/2025] [Indexed: 05/16/2025]
Abstract
Burkholderia pseudomallei biofilms are resistant to antibiotics and immune responses, leading to persistent infections. This study aimed to investigate the metabolic profiles of B. pseudomallei in biofilms and the extracellular polymeric substances (EPS) produced during grown in LB or MVBM medium using Nuclear Magnetic Resonance (NMR) spectroscopy to identify key metabolites. The results revealed similar biofilm metabolites in both media. However, betaine was detected in LB, but not in the case of MVBM. Acetate was significantly higher in MVBM compared to that of LB. Pathway analysis revealed that betaine-producing B. pseudomallei biofilm in LB was associated with metabolism of glycine, serine, and threonine, while acetate in MVBM was associated with metabolism of taurine and hypotaurine, phosphonate and phosphinate, and glycolysis/gluconeogenesis. The NMR analysis of EPS disclosed shared metabolites including dimethylsulfide, 1-methyluric acid and oxypurinol. This study provides the first extensive investigation into B. pseudomallei biofilm and EPS metabolites, identifying pathways that offer potential targets for combating B. pseudomallei biofilm-associated infections.
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Affiliation(s)
- Suthantip Srithabut
- Department of Environmental Science, Khon Kaen University, Khon Kaen, Thailand
| | - Pisit Chareonsudjai
- Department of Environmental Science, Khon Kaen University, Khon Kaen, Thailand
| | | | - Chainarong Bunma
- Interdisciplinary Department of Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Microbiology, Khon Kaen University, Khon Kaen, Thailand
- Center of Excellence in Systems Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Jutarop Phetcharaburanin
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University National Phenome Institute, Office of the President, Khon Kaen University, Khon Kaen, Thailand
- Thailand Metabolomics Society, Bangkok, Thailand
| | - Manida Suksawat
- Department of International Technology and Innovation Management, International College, Khon Kaen University, Khon Kaen, Thailand
| | - Suwalak Chitcharoen
- Department of Microbiology, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen, Thailand
| | - Sorujsiri Chareonsudjai
- Department of Microbiology, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen, Thailand
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Monaco A, Caruso M, Bellantuono L, Cazzolla Gatti R, Fania A, Lacalamita A, La Rocca M, Maggipinto T, Pantaleo E, Tangaro S, Amoroso N, Bellotti R. Measuring water pollution effects on antimicrobial resistance through explainable artificial intelligence. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2025; 367:125620. [PMID: 39788180 DOI: 10.1016/j.envpol.2024.125620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 12/29/2024] [Accepted: 12/30/2024] [Indexed: 01/12/2025]
Abstract
Antimicrobial resistance refers to the ability of pathogens to develop resistance to drugs designed to eliminate them, making the infections they cause more difficult to treat and increasing the likelihood of disease diffusion and mortality. As such, antimicrobial resistance is considered as one of the most significant and universal challenges to both health and society, as well as the environment. In our research, we employ the explainable artificial intelligence paradigm to identify the factors that most affect the onset of antimicrobial resistance in diversified territorial contexts, which can vary widely from each other in terms of climatic, economic and social conditions. Specifically, we employ a large set of indicators identified through the One Health framework to predict, at the country level, mortality resulting from antimicrobial resistance related to Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Streptococcus pneumoniae. The analysis reveals the outstanding importance of indicators related to water accessibility and quality in determining mortality due to antimicrobial resistance to the considered pathogens across countries, providing perspective as a potential tool for decision support and monitoring.
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Affiliation(s)
- Alfonso Monaco
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Mario Caruso
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy
| | - Loredana Bellantuono
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy; Università degli Studi di Bari Aldo Moro, Dipartimento di Biomedicina Traslazionale e Neuroscienze (DiBraiN), Bari, 70124, Italy.
| | - Roberto Cazzolla Gatti
- Alma Mater Studiorum University of Bologna, Department of Biological Sciences, Geological and Environmental (BiGeA), Bologna, 40126, Italy
| | - Alessandro Fania
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Antonio Lacalamita
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Marianna La Rocca
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Tommaso Maggipinto
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Ester Pantaleo
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Sabina Tangaro
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy; Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Bari, 70126, Italy
| | - Nicola Amoroso
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy; Università degli Studi di Bari Aldo Moro, Dipartimento di Farmacia - Scienze del Farmaco, Bari, 70125, Italy
| | - Roberto Bellotti
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
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3
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Chambial P, Thakur N, Bhukya PL, Subbaiyan A, Kumar U. Frontiers in superbug management: innovating approaches to combat antimicrobial resistance. Arch Microbiol 2025; 207:60. [PMID: 39953143 DOI: 10.1007/s00203-025-04262-x] [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: 12/26/2024] [Revised: 01/22/2025] [Accepted: 01/31/2025] [Indexed: 02/17/2025]
Abstract
Anti-microbial resistance (AMR) is a global health issue causing significant mortality and economic burden. Pharmaceutical companies' discontinuation of research hinders new agents, while MDR pathogens or "superbugs" worsen the problem. Superbugs pose a threat to common infections and medical procedures, exacerbated by limited antibiotic development and rapid antibiotic resistance. The rising tide of antimicrobial resistance threatens to undermine progress in controlling infectious diseases. This review examines the global proliferation of AMR, its underlying mechanisms, and contributing factors. The study explores various methodologies, emphasizing the significance of precise and timely identification of resistant strains. We discuss recent advancements in CRISPR/Cas9, nanoparticle technology, light-based techniques, and AI-powered antibiogram analysis for combating AMR. Traditional methods often fail to effectively combat multidrug-resistant bacteria, as CRISPR-Cas9 technology offers a more effective approach by cutting specific DNA sequences, precision targeting and genome editing. AI-based smartphone applications for antibiogram analysis in resource-limited settings face challenges like internet connectivity, device compatibility, data quality, energy consumption, and algorithmic limitations. Additionally, light-based antimicrobial techniques are increasingly being used to effectively kill antibiotic-resistant microbial species and treat localized infections. This review provides an in-depth overview of AMR covering epidemiology, evolution, mechanisms, infection prevention, control measures, antibiotic access, stewardship, surveillance, challenges and emerging non-antibiotic therapeutic approaches.
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Affiliation(s)
- Priyanka Chambial
- Department of Biosciences (UIBT), Chandigarh University, NH-05, Ludhiana - Chandigarh State Hwy, Sahibzada Ajit Singh Nagar, Punjab, 140413, India
| | - Neelam Thakur
- Department of Zoology, Sardar Patel University, Vallabh Government College Campus, Paddal, Kartarpur, Mandi, Himachal Pradesh, 175001, India.
| | - Prudhvi Lal Bhukya
- Rodent Experimentation Facility, ICMR-National Animal Facility Resource Facility for Biomedical Research, Genome Valley, Shamirpet, Hyderabad, Telangana, 500101, India
| | - Anbazhagan Subbaiyan
- Rodent Experimentation Facility, ICMR-National Animal Facility Resource Facility for Biomedical Research, Genome Valley, Shamirpet, Hyderabad, Telangana, 500101, India
| | - Umesh Kumar
- Department of Biosciences, IMS Ghaziabad University Courses Campus, NH-09, Adhyatmik Nagar, Ghaziabad, Uttar Pradesh, 201015, India.
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Negahdari B, Sarkoohi P, Ghasemi Nezhad F, Shahbazi B, Ahmadi K. Design of multi-epitope vaccine candidate based on OmpA, CarO and ZnuD proteins against multi-drug resistant Acinetobacter baumannii. Heliyon 2024; 10:e34690. [PMID: 39149030 PMCID: PMC11324976 DOI: 10.1016/j.heliyon.2024.e34690] [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: 09/10/2023] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024] Open
Abstract
Acinetobacter baumannii has been identified as a major cause of nosocomial infections. Acinetobacter infections are often difficult to treat with multidrug resistant phenotypes. One of the most effective ways to combat infectious diseases is through vaccination. In this study, an attempt was made to select the most protective and potent immunostimulatory epitopes based on the epitope-rich domains of the ZnuD, OmpA and CarO proteins of Acinetobacter baumannii to design a vaccine that can protect against this infection. After predicting the epitope of B- and T-cells, seven antigenic regions of three proteins CarO, ZnuD and OmpA, were selected. These regions were bound by a GGGS linker. The binding affinity and molecular interactions of the vaccine with the immune receptors TLR2 and TLR4 were studied using molecular docking analysis. This vaccine design was subjected to in silico immune simulations using C-ImmSim. The designed vaccine was highly antigenic, non-allergenic and stable. TLR2 and TLR4 were selected to analyze the ability of the modeled chimeric protein to interact with immune system receptors. The results showed strong interaction between the designed protein vaccine with TLR2 (-18.8 kcal mol-1) and TLR4 (-15.1 kcal mol-1). To verify the stability of the interactions and the structure of the designed protein, molecular dynamics (MD) simulations were performed for 200 ns. Various analyses using MD showed that the protein structure is stable alone and in interaction with TLR2 and TLR4. The ability of the vaccine candidate protein to stimulate the immune system to produce the necessary cytokines and antibodies against Acinetobacter baumannii was also demonstrated by the ability of the protein designed using the C-ImmSim web server to induce an immune response. Therefore, the designed protein vaccine may be a suitable candidate for in vivo as well as in vitro studies against Acinetobacter baumannii infections.
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Affiliation(s)
- Batul Negahdari
- Student Research Committee, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Parisa Sarkoohi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Forozan Ghasemi Nezhad
- Student Research Committee, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Behzad Shahbazi
- School of Pharmacy, Semnan University of Medical Sciences, Semnan, Iran
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Owojori GO, Lateef SA, Ana GREE. Effectiveness of wastewater treatment plant at the removal of nutrients, pathogenic bacteria, and antibiotic-resistant bacteria in wastewater from hospital source. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:10785-10801. [PMID: 38212560 DOI: 10.1007/s11356-024-31829-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/29/2023] [Indexed: 01/13/2024]
Abstract
This study is aimed at assessing the effectiveness of hospital's wastewater treatment plant (WWTP) in removing nutrients, pathogenic bacteria, and addressing antibiotic resistance using a case study of a tertiary hospital in Ibadan, Nigeria. During the dry and wet seasons in the month of July and December, respectively, samples were collected, and analyzed using standard guidelines to examine significant physicochemical parameters of the WTTP; to evaluate the removal efficiency of biological oxygen demand (BOD) and chemical oxygen demand (COD), and to examine the prevalence of pathogenic and antibiotic-resistant bacteria. The results of this study showed that during the dry season, certain parameters exceeded acceptable limits, including temperature, total suspended solids (TSS), total dissolved solids (TDS), phosphate, and nitrate. Although there were reductions in BOD (1555 mg/L to 482 mg/L) and COD levels (3160 mg/L to 972 mg/L), they remained above acceptable limits by World Health Organization. In the wet season, the level of COD (20 mg/L) in the effluent was within acceptable limit, while the BOD (160 mg/L) was above the acceptable limit. The WWTP effectively removed nutrients and reduced the microbial load, as evident from the absence of fecal coliforms in the effluent in both seasons. In respect to BOD removal efficiency, the level of purification of wastewater by the WWTP was 69% during the dry season, while the removal efficiency of COD was 83.54% which showed the efficiency of the WWTP at the removal of COD. However, antibiotic resistance was still present. The study concludes that while the WWTP effectively addressed nutrients and microbial load, additional measures such as tertiary treatment methods like chlorination and UV radiation are necessary to tackle antibiotic resistance. This is crucial to prevent the release of antibiotic-resistant bacteria into the environment, safeguarding human health, animals, plants, and overall environmental well-being.
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Affiliation(s)
- Grace O Owojori
- Department of Environmental Health Sciences, Faculty of Public Health, College of Medicine, University of Ibadan, Ibadan, Nigeria.
| | - Suraju A Lateef
- Department of Environmental Health Sciences, Faculty of Public Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Godson R E E Ana
- Department of Environmental Health Sciences, Faculty of Public Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
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Bunma C, Noinarin P, Phetcharaburanin J, Chareonsudjai S. Burkholderia pseudomallei biofilm resists Acanthamoeba sp. grazing and produces 8-O-4'-diferulic acid, a superoxide scavenging metabolite after passage through the amoeba. Sci Rep 2023; 13:16578. [PMID: 37789212 PMCID: PMC10547685 DOI: 10.1038/s41598-023-43824-1] [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: 06/22/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023] Open
Abstract
Burkholderia pseudomallei, an etiological agent of melioidosis is an environmental bacterium that can survive as an intracellular pathogen. The biofilm produced by B. pseudomallei is crucial for cellular pathogenesis of melioidosis. The purpose of this investigation is to explore the role of biofilm in survival of B. pseudomallei during encounters with Acanthamoeba sp. using B. pseudomallei H777 (a biofilm wild type), M10 (a biofilm defect mutant) and C17 (a biofilm-complemented strain). The results demonstrated similar adhesion to amoebae by both the biofilm wild type and biofilm mutant strains. There was higher initial internalisation, but the difference diminished after longer encounter with the amoeba. Interestingly, confocal laser scanning microscopy demonstrated that pre-formed biofilm of B. pseudomallei H777 and C17 were markedly more persistent in the face of Acanthamoeba sp. grazing than that of M10. Metabolomic analysis revealed a significant increased level of 8-O-4'-diferulic acid, a superoxide scavenger metabolite, in B. pseudomallei H777 serially passaged in Acanthamoeba sp. The interaction between B. pseudomallei with a free-living amoeba may indicate the evolutionary pathway that enables the bacterium to withstand superoxide radicals in intracellular environments. This study supports the hypothesis that B. pseudomallei biofilm persists under grazing by amoebae and suggests a strategy of metabolite production that turns this bacterium from saprophyte to intracellular pathogen.
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Affiliation(s)
- Chainarong Bunma
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Parumon Noinarin
- Department of Occupational Health and Safety, Faculty of Public Health, Nakhon Ratchasima Rajabhat University, Nakhon Ratchasima, Thailand
| | - Jutarop Phetcharaburanin
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen University Phenome Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Sorujsiri Chareonsudjai
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen, Thailand.
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Abdollahi S, Raoufi Z. A novel vaccine candidate against A. baumannii based on a new OmpW family protein (OmpW2); structural characterization, antigenicity and epitope investigation, and in-vivo analysis. Microb Pathog 2023; 183:106317. [PMID: 37611777 DOI: 10.1016/j.micpath.2023.106317] [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: 04/28/2023] [Revised: 06/06/2023] [Accepted: 08/20/2023] [Indexed: 08/25/2023]
Abstract
A. baumannii is an MDR pathogen whose SARS-CoV-2 has recently increased its mortality rate in hospitalized patients. So, the virulence factors investigation and design of a vaccine against this bacterium seem to be critical. In this regard, the OmpW2 protein was structurally characterized by this study, and its B-T cell epitopes were mapped by bioinformatic tools. In-vivo analyses were employed to verify the immunogenicity of this protein and its selected epitopes. The results indicated that OmpW2 is a conserved virulent antigen, not toxic for the host, and not similar to the human or mouse proteome. A putative interaction between OmpW2 and a Fe-S-cluster redox enzyme was detected. Based on the results, OmpW2 belongs to the OmpW superfamily and eight beta sheets have been predicted in its tight beta-barrel structure. Several exposed epitopes were detected in the OmpW2 sequence and structure, and a sub-unit potential vaccine was generated based on the epitopes. The ELISA results indicated that after the second booster vaccination of BALB/c mice with the whole OmpW2 protein or its sub-unit fragment, the IgG titer significantly raised (p < 0.05). The mortality rate and the bacterial burden in the lung, liver, kidney, and spleen in both passive and active immunized mice were significantly decreased (p ≤ 0.001). In-vivo experiments confirmed that the OmpW2 whole protein and its sub-unit fragment induce the host immune system and can be applied to design a commercial vaccine or diagnostic kit.
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Affiliation(s)
- Sajad Abdollahi
- Department of Biology, Faculty of Basic Science, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran.
| | - Zeinab Raoufi
- Department of Biology, Faculty of Basic Science, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran
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Das G. Acinetobacter baumannii ophthalmia neonatorum - A very rare presentation. Indian J Ophthalmol 2023; 71:2595-2597. [PMID: 37322687 PMCID: PMC10417955 DOI: 10.4103/ijo.ijo_2240_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Affiliation(s)
- Gunasagar Das
- Muktiseva Damayanti Eye Seva Clinic, Sambalpur, Odisha, India
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Malviya J, Alameri AA, Al-Janabi SS, Fawzi OF, Azzawi AL, Obaid RF, Alsudani AA, Alkhayyat AS, Gupta J, Mustafa YF, Karampoor S, Mirzaei R. Metabolomic profiling of bacterial biofilm: trends, challenges, and an emerging antibiofilm target. World J Microbiol Biotechnol 2023; 39:212. [PMID: 37256458 DOI: 10.1007/s11274-023-03651-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/17/2023] [Indexed: 06/01/2023]
Abstract
Biofilm-related infections substantially contribute to bacterial illnesses, with estimates indicating that at least 80% of such diseases are linked to biofilms. Biofilms exhibit unique metabolic patterns that set them apart from their planktonic counterparts, resulting in significant metabolic reprogramming during biofilm formation. Differential glycolytic enzymes suggest that central metabolic processes are markedly different in biofilms and planktonic cells. The glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is highly expressed in Staphylococcus aureus biofilm progenitors, indicating that changes in glycolysis activity play a role in biofilm development. Notably, an important consideration is a correlation between elevated cyclic di-guanylate monophosphate (c-di-GMP) activity and biofilm formation in various bacteria. C-di-GMP plays a critical role in maintaining the persistence of Pseudomonas aeruginosa biofilms by regulating alginate production, a significant biofilm matrix component. Furthermore, it has been demonstrated that S. aureus biofilm development is initiated by several tricarboxylic acid (TCA) intermediates in a FnbA-dependent manner. Finally, Glucose 6-phosphatase (G6P) boosts the phosphorylation of histidine-containing protein (HPr) by increasing the activity of HPr kinase, enhancing its interaction with CcpA, and resulting in biofilm development through polysaccharide intercellular adhesion (PIA) accumulation and icaADBC transcription. Therefore, studying the metabolic changes associated with biofilm development is crucial for understanding the complex mechanisms involved in biofilm formation and identifying potential targets for intervention. Accordingly, this review aims to provide a comprehensive overview of recent advances in metabolomic profiling of biofilms, including emerging trends, prevailing challenges, and the identification of potential targets for anti-biofilm strategies.
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Affiliation(s)
- Jitendra Malviya
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, India
| | - Ameer A Alameri
- Department of Chemistry, College of Science, University of Babylon, Babylon, Iraq
| | - Saif S Al-Janabi
- Medical Laboratory Techniques Department, Al-Maarif University College, Ramadi, Iraq
| | | | | | - Rasha Fadhel Obaid
- Department of Biomedical Engineering, Al-Mustaqbal University College, Babylon, Iraq
| | - Ali A Alsudani
- College of Science, University of Al-Qadisiyah, Al-Diwaniyah, Iraq
| | - Ameer S Alkhayyat
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Jitendra Gupta
- Institute of Pharmaceutical Research, GLA University, Mathura, 281406, U. P., India
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, 41001, Iraq
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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Mogul R, Miller DR, Ramos B, Lalla SJ. Metabolomic and cultivation insights into the tolerance of the spacecraft-associated Acinetobacter toward Kleenol 30, a cleanroom floor detergent. Front Microbiol 2023; 14:1090740. [PMID: 36950167 PMCID: PMC10025500 DOI: 10.3389/fmicb.2023.1090740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/20/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction Stringent cleaning procedures during spacecraft assembly are critical to maintaining the integrity of life-detection missions. To ensure cleanliness, NASA spacecraft are assembled in cleanroom facilities, where floors are routinely cleansed with Kleenol 30 (K30), an alkaline detergent. Methods Through metabolomic and cultivation approaches, we show that cultures of spacecraft-associated Acinetobacter tolerate up to 1% v/v K30 and are fully inhibited at ≥2%; in comparison, NASA cleanrooms are cleansed with ~0.8-1.6% K30. Results For A. johnsonii 2P08AA (isolated from a cleanroom floor), cultivations with 0.1% v/v K30 yield (1) no changes in cell density at late-log phase, (2) modest decreases in growth rate (~17%), (3) negligible lag phase times, (4) limited changes in the intracellular metabolome, and (5) increases in extracellular sugar acids, monosaccharides, organic acids, and fatty acids. For A. radioresistens 50v1 (isolated from a spacecraft surface), cultivations yield (1) ~50% survivals, (2) no changes in growth rate, (3) ~70% decreases in the lag phase time, (4) differential changes in intracellular amino acids, compatible solutes, nucleotide-related metabolites, dicarboxylic acids, and saturated fatty acids, and (5) substantial yet differential impacts to extracellular sugar acids, monosaccharides, and organic acids. Discussion These combined results suggest that (1) K30 manifests strain-dependent impacts on the intracellular metabolomes, cultivation kinetics, and survivals, (2) K30 influences extracellular trace element acquisition in both strains, and (3) K30 is better tolerated by the floor-associated strain. Hence, this work lends support towards the hypothesis that repeated cleansing during spacecraft assembly serve as selective pressures that promote tolerances towards the cleaning conditions.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
- Blue Marble Institute of Science, Seattle, WA, United States
| | - Daniel R. Miller
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
| | - Brian Ramos
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
| | - Sidharth J. Lalla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
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Hou X, Wang J, Mei Y, Ge L, Qian J, Huang Y, Yang M, Li H, Wang Y, Yan Z, Peng D, Zhang J, Zhao N. Antibiofilm mechanism of dielectric barrier discharge cold plasma against Pichia manshurica. INNOV FOOD SCI EMERG 2023. [DOI: 10.1016/j.ifset.2023.103340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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12
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Sánchez-Lozano I, Muñoz-Cruz LC, Hellio C, Band-Schmidt CJ, Cruz-Narváez Y, Becerra-Martínez E, Hernández-Guerrero CJ. Metabolomic Insights of Biosurfactant Activity from Bacillus niabensis against Planktonic Cells and Biofilm of Pseudomonas stutzeri Involved in Marine Biofouling. Int J Mol Sci 2023; 24:ijms24044249. [PMID: 36835662 PMCID: PMC9965525 DOI: 10.3390/ijms24044249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
In marine environments, biofilm can cause negative impacts, including the biofouling process. In the search for new non-toxic formulations that inhibit biofilm, biosurfactants (BS) produced by the genus Bacillus have demonstrated considerable potential. To elucidate the changes that BS from B. niabensis promote in growth inhibition and biofilm formation, this research performed a nuclear magnetic resonance (NMR) metabolomic profile analysis to compare the metabolic differences between planktonic cells and biofilms of Pseudomonas stutzeri, a pioneer fouling bacteria. The multivariate analysis showed a clear separation between groups with a higher concentration of metabolites in the biofilm than in planktonic cells of P. stutzeri. When planktonic and biofilm stages were treated with BS, some differences were found among them. In planktonic cells, the addition of BS had a minor effect on growth inhibition, but at a metabolic level, NADP+, trehalose, acetone, glucose, and betaine were up-regulated in response to osmotic stress. When the biofilm was treated with the BS, a clear inhibition was observed and metabolites such as glucose, acetic acid, histidine, lactic acid, phenylalanine, uracil, and NADP+ were also up-regulated, while trehalose and histamine were down-regulated in response to the antibacterial effect of the BS.
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Affiliation(s)
- Ilse Sánchez-Lozano
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Luz Clarita Muñoz-Cruz
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Claire Hellio
- CNRS, IRD, Ifremer, LEMAR, Univ. Brest, Institut Universitaire Européen de la Mer, F-29280 Plouzané, France
| | - Christine J. Band-Schmidt
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Yair Cruz-Narváez
- Laboratorio de Posgrado de Operaciones Unitarias, Instituto Politécnico Nacional-ESIQIE-UPALM, Unidad Profesional Adolfo López Mateos, Edificio 7, 1.er Piso, Sección A, Av. Luis Enrique Erro S/N, Zacatenco, Delegación Gustavo A. Madero, Mexico City 07738, Mexico
| | - Elvia Becerra-Martínez
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Unidad Profesional Adolfo López Mateos, Av. Luis Enrique Erro S/N, Zacatenco, Delegación Gustavo A. Madero, Mexico City 07738, Mexico
- Correspondence: (E.B.-M.); (C.J.H.-G.)
| | - Claudia J. Hernández-Guerrero
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
- Correspondence: (E.B.-M.); (C.J.H.-G.)
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13
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Dutt Y, Pandey RP, Dutt M, Gupta A, Vibhuti A, Samuel Raj V, Chang CM, Priyadarshini A. Synthesis and Biological Characterization of Phyto-Fabricated Silver Nanoparticles from Azadirachta indica. J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nanoparticles (NPs) have garnered a lot of interest in sectors like medicine, cosmetics, food, and pharmaceuticals for antibacterial catalytic properties, reduced toxicity, and easy production. Biological synthesis of silver nanoparticle (AgNPs) is considered as green, eco-friendly,
and cost-effective approach; therefore, Azadirachta indica extracts were utilized for a dual role of fabrication and functionalization of AgNPs. Optical and physical characterizations were achieved for confirming the biosynthesized AgNPs. SEM images detected quasi-spherical AgNPs of
44.04 to 66.50 nm. Some of potent phytochemicals like flavonoids and proteins from Azadirachta indica formed a strong coating or capping on the AgNPs without affecting their secondary structure by interacting with Ag+ and NPs for the formation of AgNPs. AgNPs exhibited strong
antibacterial activity (MIC 10 μg/ml) against multidrug-resistant bacteria Enterococcus faecalis; at different concentrations, no IC50 values were recorded for AgNPs as well as Azadirachta indica signifying low cytotoxicity in the exposed concentration range. The DNA
degradation activity of AgNPs through the TUNEL assay revealed no significant increase in the overall FITC mean fluorescence intensity as well as a DNA fragmentation index with 5.45% DNA damage (10 μg/ml AgNPs). Drug uptake of AgNPs was also investigated through a permeability assay
via Caco-2 cell lines at test concentrations where apparent permeability was detected as moderate.
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Affiliation(s)
- Yogesh Dutt
- Department of Microbiology, SRM University, 39, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat, Haryana 131029, India
| | - Ramendra Pati Pandey
- Department of Microbiology, SRM University, 39, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat, Haryana 131029, India
| | - Mamta Dutt
- Mamta Dental Clinic, Opposite Sector 29, Main Badkhal Road, Faridabad, Haryana 121002, India
| | - Archana Gupta
- Department of Biotechnology, SRM University, 39, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat, Haryana 131029, India
| | - Arpana Vibhuti
- Department of Biotechnology, SRM University, 39, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat, Haryana 131029, India
| | - V. Samuel Raj
- Department of Microbiology, SRM University, 39, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat, Haryana 131029, India
| | - Chung-Ming Chang
- Master & Ph.D. Program in Biotechnology Industry, Chang Gung University, No. 259, Wenhua 1st Rd., Guishan Dist. Taoyuan City, 33302, Taiwan (R.O.C.)
| | - Anjali Priyadarshini
- Department of Microbiology, SRM University, 39, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat, Haryana 131029, India
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14
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Dutt Y, Dhiman R, Singh T, Vibhuti A, Gupta A, Pandey RP, Raj VS, Chang CM, Priyadarshini A. The Association between Biofilm Formation and Antimicrobial Resistance with Possible Ingenious Bio-Remedial Approaches. Antibiotics (Basel) 2022; 11:930. [PMID: 35884186 PMCID: PMC9312340 DOI: 10.3390/antibiotics11070930] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/03/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023] Open
Abstract
Biofilm has garnered a lot of interest due to concerns in various sectors such as public health, medicine, and the pharmaceutical industry. Biofilm-producing bacteria show a remarkable drug resistance capability, leading to an increase in morbidity and mortality. This results in enormous economic pressure on the healthcare sector. The development of biofilms is a complex phenomenon governed by multiple factors. Several attempts have been made to unravel the events of biofilm formation; and, such efforts have provided insights into the mechanisms to target for the therapy. Owing to the fact that the biofilm-state makes the bacterial pathogens significantly resistant to antibiotics, targeting pathogens within biofilm is indeed a lucrative prospect. The available drugs can be repurposed to eradicate the pathogen, and as a result, ease the antimicrobial treatment burden. Biofilm formers and their infections have also been found in plants, livestock, and humans. The advent of novel strategies such as bioinformatics tools in treating, as well as preventing, biofilm formation has gained a great deal of attention. Development of newfangled anti-biofilm agents, such as silver nanoparticles, may be accomplished through omics approaches such as transcriptomics, metabolomics, and proteomics. Nanoparticles' anti-biofilm properties could help to reduce antimicrobial resistance (AMR). This approach may also be integrated for a better understanding of biofilm biology, guided by mechanistic understanding, virtual screening, and machine learning in silico techniques for discovering small molecules in order to inhibit key biofilm regulators. This stimulated research is a rapidly growing field for applicable control measures to prevent biofilm formation. Therefore, the current article discusses the current understanding of biofilm formation, antibiotic resistance mechanisms in bacterial biofilm, and the novel therapeutic strategies to combat biofilm-mediated infections.
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Affiliation(s)
- Yogesh Dutt
- Department of Microbiology, SRM University, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat 131029, Haryana, India; (Y.D.); (R.D.); (A.V.); (A.G.); (R.P.P.); (V.S.R.)
| | - Ruby Dhiman
- Department of Microbiology, SRM University, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat 131029, Haryana, India; (Y.D.); (R.D.); (A.V.); (A.G.); (R.P.P.); (V.S.R.)
| | - Tanya Singh
- Department of Botany, TPS College, Patliputra University, Patna 800020, Bihar, India;
| | - Arpana Vibhuti
- Department of Microbiology, SRM University, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat 131029, Haryana, India; (Y.D.); (R.D.); (A.V.); (A.G.); (R.P.P.); (V.S.R.)
| | - Archana Gupta
- Department of Microbiology, SRM University, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat 131029, Haryana, India; (Y.D.); (R.D.); (A.V.); (A.G.); (R.P.P.); (V.S.R.)
| | - Ramendra Pati Pandey
- Department of Microbiology, SRM University, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat 131029, Haryana, India; (Y.D.); (R.D.); (A.V.); (A.G.); (R.P.P.); (V.S.R.)
| | - V. Samuel Raj
- Department of Microbiology, SRM University, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat 131029, Haryana, India; (Y.D.); (R.D.); (A.V.); (A.G.); (R.P.P.); (V.S.R.)
| | - Chung-Ming Chang
- Master & Ph.D. Program in Biotechnology Industry, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan
| | - Anjali Priyadarshini
- Department of Microbiology, SRM University, Rajiv Gandhi Education City, Post Office P.S. Rai, Sonepat 131029, Haryana, India; (Y.D.); (R.D.); (A.V.); (A.G.); (R.P.P.); (V.S.R.)
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15
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Narasimman M, Ory J, Bartra SS, Plano GV, Ramasamy R. Evaluation of Bacteria in a Novel In Vitro Biofilm Model of Penile Prosthesis. J Sex Med 2022; 19:1024-1031. [PMID: 35414488 DOI: 10.1016/j.jsxm.2022.03.602] [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: 12/27/2021] [Revised: 03/05/2022] [Accepted: 03/13/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Delayed infection, thought to be due to gradual biofilm formation, remains a feared complication after inflatable penile prosthesis (IPP) insertion. Understanding and preventing biofilm formation is necessary to prevent infections. AIM To develop an in vitro model and compare growth of biofilm by different bacteria on IPPs and evaluate the anti-infective efficacy of the Coloplast Titan and AMS 700 InhibiZone. METHODS Sterile IPPs (Coloplast) were cut into rings and incubated with S. epidermidis, S. aureus, P. aeruginosa, A. baumannii, or K. pneumoniae cultures in tryptic soy broth (TSB) (4 hour) to ensure adequate bacteria attachment, and then in only TSB (120 hours) to allow for biofilm formation. Rings were fixed with ethanol and biofilm measured by spectrophotometer (OD570) after crystal violet staining. This methodology was repeated for S. epidermidis and P. aeruginosa with Coloplast rings dipped in 10 ml of a 10 mg/ml Rifampin, 1 mg/ml Gentamicin, and deionized water solution and undipped AMS InhibiZone rings. Crystal violet assay (OD570) was repeated after incubation within bacteria (2 hour), and then only TSB (120 hours). OUTCOMES The primary outcome of the study was OD570 readings, indirectly measuring biofilm mass on implant rings. RESULTS S. epidermidis, S. aureus, A. baumannii, P. aeruginosa, and K. pneumoniae all formed significant biofilm. P. aeruginosa showed the strongest predilection to grow biofilm on IPPs. P. aeruginosa also formed significant biofilm on antibiotic-treated Coloplast and AMS rings, while S. epidermidis was inhibited. No significant difference was found in biofilm inhibition between the implants. CLINICAL TRANSLATION Our findings suggest gram-negative bacteria may form biofilm more proficiently and quickly on IPPs than gram-positive organisms. Commonly used antibiotic treatments on IPPs may be effective against S. epidermidis but not against P. aeruginosa biofilm formation. STRENGTHS & LIMITATIONS This is the first study comparing biofilm formation by different bacteria organisms on IPPs and the inhibitive ability of Coloplast and AMS implants against biofilm formation. Clinical data on organisms responsible for infected IPPs is needed to determine the clinical relevance of our findings. CONCLUSION Our novel in vitro model of biofilm formation of IPPs evaluated the effect of a gentamicin/rifampin antibiotic dip on Coloplast Titan implants and the anti-infective capacity of the minocycline/rifampin precoated AMS 700 InhibiZone against S. epidermidis and P. aeruginosa. P. aeruginosa was able to grow on both antibiotic-treated implants, with no significant difference, and should continue to be a specific target of investigation to reduce delayed post-operative IPP infections. Narasimman M, Ory J, Bartra SS, et al. Evaluation of Bacteria in a Novel In Vitro Biofilm Model of Penile Prosthesis. J Sex Med 2022;19:1024-1031.
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Affiliation(s)
- Manish Narasimman
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jesse Ory
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA; Department of Urology, Dalhousie University, Halifax, Canada
| | - Sara Schesser Bartra
- Department of Microbiology & Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Gregory V Plano
- Department of Microbiology & Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Ranjith Ramasamy
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA.
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16
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Fu J, Liu C, Li L, Liu J, Tie Y, Wen X, Zhao Q, Qiao Z, An Z, Zheng J. Adaptive response and tolerance to weak acids in
Saccharomyces cerevisiae boulardii
: a metabolomics approach. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junjie Fu
- College of Biotechnology Engineering Sichuan University of Science and Engineering Yibin 644000 China
| | - Chaolan Liu
- Antibiotics Research and Re‐evalution Key Laboratory of Sichuan Province Sichuan Industrial Institute of Antibiotics Chengdu University Chengdu 610052 China
| | - Li Li
- College of Biotechnology Engineering Sichuan University of Science and Engineering Yibin 644000 China
| | - Jun Liu
- College of Biotechnology Engineering Sichuan University of Science and Engineering Yibin 644000 China
| | - Yu Tie
- College of Biotechnology Engineering Sichuan University of Science and Engineering Yibin 644000 China
- Solid‐State Fermentation Resource Utilisation Key Laboratory of Sichuan Province Yibin 644000 China
| | - Xueping Wen
- College of Biotechnology Engineering Sichuan University of Science and Engineering Yibin 644000 China
| | - Qikai Zhao
- College of Biotechnology Engineering Sichuan University of Science and Engineering Yibin 644000 China
- HengfengHuaBang Biological Science and Technology Co., Ltd. Leshan 614000 China
| | | | - Zheming An
- Wuliangye Yibin Co, Ltd Yibin 644000 China
| | - Jia Zheng
- Wuliangye Yibin Co, Ltd Yibin 644000 China
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17
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Leggett A, Li DW, Sindeldecker D, Staats A, Rigel N, Bruschweiler-Li L, Brüschweiler R, Stoodley P. Cadaverine Is a Switch in the Lysine Degradation Pathway in Pseudomonas aeruginosa Biofilm Identified by Untargeted Metabolomics. Front Cell Infect Microbiol 2022; 12:833269. [PMID: 35237533 PMCID: PMC8884266 DOI: 10.3389/fcimb.2022.833269] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 01/18/2022] [Indexed: 12/16/2022] Open
Abstract
There is a critical need to accurately diagnose, prevent, and treat biofilms in humans. The biofilm forming P. aeruginosa bacteria can cause acute and chronic infections, which are difficult to treat due to their ability to evade host defenses along with an inherent antibiotic-tolerance. Using an untargeted NMR-based metabolomics approach, we identified statistically significant differences in 52 metabolites between P. aeruginosa grown in the planktonic and lawn biofilm states. Among them, the metabolites of the cadaverine branch of the lysine degradation pathway were systematically decreased in biofilm. Exogenous supplementation of cadaverine caused significantly increased planktonic growth, decreased biofilm accumulation by 49% and led to altered biofilm morphology, converting to a pellicle biofilm at the air-liquid interface. Our findings show how metabolic pathway differences directly affect the growth mode in P. aeruginosa and could support interventional strategies to control biofilm formation.
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Affiliation(s)
- Abigail Leggett
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Da-Wei Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, United States
| | - Devin Sindeldecker
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, United States
| | - Amelia Staats
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Nicholas Rigel
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, United States
| | - Rafael Brüschweiler
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, United States
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, United States
- *Correspondence: Rafael Brüschweiler, ; Paul Stoodley,
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Department of Orthopaedics, The Ohio State University, Columbus, OH, United States
- National Biofilm Innovation Centre (NBIC) and National Centre for Advanced Tribology at Southampton (nCATS), Mechanical Engineering, University of Southampton, Southampton, United Kingdom
- *Correspondence: Rafael Brüschweiler, ; Paul Stoodley,
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18
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Tong CY, Derek CJC. A Methodological Review on the Characterization of Microalgal Biofilm and Its Extracellular Polymeric Substances. J Appl Microbiol 2022; 132:3490-3514. [DOI: 10.1111/jam.15455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 12/21/2021] [Accepted: 01/17/2022] [Indexed: 11/28/2022]
Affiliation(s)
- C. Y. Tong
- School of Chemical Engineering, Engineering Campus Universiti Sains Malaysia 14300 Nibong Tebal, Penang Malaysia
| | - C. J. C Derek
- School of Chemical Engineering, Engineering Campus Universiti Sains Malaysia 14300 Nibong Tebal, Penang Malaysia
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19
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Kafshnouchi M, Safari M, Khodavirdipour A, Bahador A, Hashemi SH, Alikhani MS, Saidijam M, Alikhani MY. Molecular Detection of blaOXA-type
Carbapenemase Genes and Antimicrobial Resistance Patterns among Clinical Isolates of Acinetobacter baumannii. Glob Med Genet 2021; 9:118-123. [PMID: 35707776 PMCID: PMC9192170 DOI: 10.1055/s-0041-1740019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/18/2021] [Indexed: 12/02/2022] Open
Abstract
Acinetobacter baumannii
is a bacterium found in most places, especially in clinics and hospitals, and an important agent of nosocomial infections. The presence of class D enzymes such as OXA-type carbapenemases in
A. baumannii
is proven to have a key function in resistance to carbapenem. The aim of the current study is to determine the
blaOXA
-type
carbapenemase genes and antimicrobial resistance among clinically isolated samples of
A. baumannii.
We assessed 100 clinically isolated specimens of
A. baumannii
from patients in intensive care units of educational hospitals of Hamadan, West of Iran. The
A. baumannii
isolates' susceptibility to antibiotics was performed employing disk diffusion method. Multiplex polymerase chain reaction was used to identify the
bla
OXA-24-like
,
bla
OXA-23-like
,
bla
OXA-58-like
, and
bla
OXA-51-like
genes.
The bla
OXA-23-like
,
bla
OXA-24-like,
and
bla
OXA-58-like
genes' prevalence were found to be 84, 58, and 3%, respectively. The highest coexistence of the genes was for
bla
OXA-51/23
(84%) followed by
bla
OXA-51/24-like
(58%). The
bla
OXA-51/23-like
pattern of genes is a sort of dominant gene in resistance in
A. baumannii
from Hamadan hospitals. The highest resistance to piperacillin (83%) and ciprofloxacin (81%) has been observed in positive isolates of
bla
OXA-23-like
. The
A. baumannii
isolates with
bla
OXA-58-like
genes did not show much resistance to antibiotics. Based on the results of the phylogenetic tree analysis, all isolates have shown a high degree of similarity. This study showed the high frequency of
OXA
-type carbapenemase genes among
A. baumannii
isolates from Hamadan hospitals, Iran. Thus, applying an appropriate strategy to limit the spreading of these strains and also performing new treatment regimens are necessary.
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Affiliation(s)
| | - Marzieh Safari
- Department of Microbiology, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Khodavirdipour
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Abbas Bahador
- Department of Microbiology, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Hamid Hashemi
- Department of Infectious Diseases, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Massoud Saidijam
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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20
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Abdollahi S, Raoufi Z, Fakoor MH. Physicochemical and structural characterization, epitope mapping and vaccine potential investigation of a new protein containing Tetratrico Peptide Repeats of Acinetobacter baumannii: An in-silico and in-vivo approach. Mol Immunol 2021; 140:22-34. [PMID: 34649027 DOI: 10.1016/j.molimm.2021.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/13/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022]
Abstract
Acinetobacter baumannii is an opportunistic multidrug-resistant pathogen that causes a significant mortality rate. The proteins containing Tetratrico Peptide Repeats (TPRs) are involved in the pathogenicity and virulence of bacteria and have different roles such as transfer of bacterial virulence factors to host cells, binding to the host cells and inhibition of phagolysosomal maturation. So, in this study, physicochemical properties of a new protein containing TPRs in A. baumannii which was named PcTPRs1 by this study were characterized and its 3D structure was predicted by in-silico tools. The protein B and T cell epitopes were mapped and its vaccine potential was in-silico and in-vivo investigated. Domain analysis indicated that the protein contains the Flp pilus assembly protein TadD domain which has three TPRs. The helix is dominant in the protein structure, and this protein is an outer membrane antigen which, is extremely conserved among A. baumannii strains; thus, has good properties to be applied as a recombinant vaccine. The best-predicted and refined model was applied in ligand-binding sites and conformational epitopes prediction. Based on epitope mapping results, several epitopes were characterized which could stimulate both immune systems. BLAST results showed the introduced epitopes are completely conserved among A. baumannii strains. The in-vivo analysis indicates that a 101 amino acid fragment of the protein which contains the best selected epitope, can produce a good protectivity against A. baumannii as well as the whole TPR protein and thus could be investigated as an effective subunit and potential vaccines.
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Affiliation(s)
- Sajad Abdollahi
- Department of Biology, Faculty of Basic Science, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran.
| | - Zeinab Raoufi
- Department of Biology, Faculty of Basic Science, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran.
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21
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Antibiotic Biosynthesis Pathways from Endophytic Streptomyces SUK 48 through Metabolomics and Genomics Approaches. Antibiotics (Basel) 2021; 10:antibiotics10080969. [PMID: 34439018 PMCID: PMC8388883 DOI: 10.3390/antibiotics10080969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/01/2021] [Accepted: 08/04/2021] [Indexed: 01/04/2023] Open
Abstract
Streptomyces sp. has been known to be a major antibiotic producer since the 1940s. As the number of cases related to resistance pathogens infection increases yearly, discovering the biosynthesis pathways of antibiotic has become important. In this study, we present the streamline of a project report summary; the genome data and metabolome data of newly isolated Streptomyces SUK 48 strain are also analyzed. The antibacterial activity of its crude extract is also determined. To obtain genome data, the genomic DNA of SUK 48 was extracted using a commercial kit (Promega) and sent for sequencing (Pac Biosciences technology platform, Menlo Park, CA, USA). The raw data were assembled and polished using Hierarchical Genome Assembly Process 4.0 (HGAP 4.0). The assembled data were structurally predicted using tRNAscan-SE and rnammer. Then, the data were analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG) database and antiSMASH analysis. Meanwhile, the metabolite profile of SUK 48 was determined using liquid chromatography-mass spectrophotometry (LC-MS) for both negative and positive modes. The results showed that the presence of kanamycin and gentamicin, as well as the other 11 antibiotics. Nevertheless, the biosynthesis pathways of aurantioclavine were also found. The cytotoxicity activity showed IC50 value was at 0.35 ± 1.35 mg/mL on the cell viability of HEK 293. In conclusion, Streptomyces sp. SUK 48 has proven to be a non-toxic antibiotic producer such as auranticlavine and gentamicin.
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Aye SM, Galani I, Han ML, Karaiskos I, Creek DJ, Zhu Y, Lin YW, Velkov T, Giamarellou H, Li J. Lipid A profiling and metabolomics analysis of paired polymyxin-susceptible and -resistant MDR Klebsiella pneumoniae clinical isolates from the same patients before and after colistin treatment. J Antimicrob Chemother 2021; 75:2852-2863. [PMID: 32696049 DOI: 10.1093/jac/dkaa245] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The increased incidence of polymyxin-resistant MDR Klebsiella pneumoniae has become a major global health concern. OBJECTIVES To characterize the lipid A profiles and metabolome differences between paired polymyxin-susceptible and -resistant MDR K. pneumoniae clinical isolates. METHODS Three pairs of K. pneumoniae clinical isolates from the same patients were examined [ATH 7 (polymyxin B MIC 0.25 mg/L) versus ATH 8 (64 mg/L); ATH 15 (0.5 mg/L) versus ATH 16 (32 mg/L); and ATH 17 (0.5 mg/L) versus ATH 18 (64 mg/L)]. Lipid A and metabolomes were analysed using LC-MS and bioinformatic analysis was conducted. RESULTS The predominant species of lipid A in all three paired isolates were hexa-acylated and 4-amino-4-deoxy-l-arabinose-modified lipid A species were detected in the three polymyxin-resistant isolates. Significant metabolic differences were evident between the paired isolates. Compared with their corresponding polymyxin-susceptible isolates, the levels of metabolites in amino sugar metabolism (UDP-N-acetyl-α-d-glucosamine and UDP-N-α-acetyl-d-mannosaminuronate) and central carbon metabolism (e.g. pentose phosphate pathway and tricarboxylic acid cycle) were significantly reduced in all polymyxin-resistant isolates [fold change (FC) > 1.5, P < 0.05]. Similarly, nucleotides, amino acids and key metabolites in glycerophospholipid metabolism, namely sn-glycerol-3-phosphate and sn-glycero-3-phosphoethanolamine, were significantly reduced across all polymyxin-resistant isolates (FC > 1.5, P < 0.05) compared with polymyxin-susceptible isolates. However, higher glycerophospholipid levels were evident in polymyxin-resistant ATH 8 and ATH 16 (FC > 1.5, P < 0.05) compared with their corresponding susceptible isolates. CONCLUSIONS To our knowledge, this study is the first to reveal significant metabolic perturbations associated with polymyxin resistance in K. pneumoniae.
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Affiliation(s)
- Su Mon Aye
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Irene Galani
- Fourth Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Mei-Ling Han
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Ilias Karaiskos
- First Department of Internal Medicine-Infectious Diseases, Hygeia General Hospital, Athens, Greece
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052 Victoria, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Yu-Wei Lin
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Helen Giamarellou
- First Department of Internal Medicine-Infectious Diseases, Hygeia General Hospital, Athens, Greece
| | - Jian Li
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
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An AY, Choi KYG, Baghela AS, Hancock REW. An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents. Front Microbiol 2021; 12:640787. [PMID: 33927701 PMCID: PMC8076610 DOI: 10.3389/fmicb.2021.640787] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/23/2021] [Indexed: 12/29/2022] Open
Abstract
Bacterial biofilms are complex and highly antibiotic-resistant aggregates of microbes that form on surfaces in the environment and body including medical devices. They are key contributors to the growing antibiotic resistance crisis and account for two-thirds of all infections. Thus, there is a critical need to develop anti-biofilm specific therapeutics. Here we discuss mechanisms of biofilm formation, current anti-biofilm agents, and strategies for developing, discovering, and testing new anti-biofilm agents. Biofilm formation involves many factors and is broadly regulated by the stringent response, quorum sensing, and c-di-GMP signaling, processes that have been targeted by anti-biofilm agents. Developing new anti-biofilm agents requires a comprehensive systems-level understanding of these mechanisms, as well as the discovery of new mechanisms. This can be accomplished through omics approaches such as transcriptomics, metabolomics, and proteomics, which can also be integrated to better understand biofilm biology. Guided by mechanistic understanding, in silico techniques such as virtual screening and machine learning can discover small molecules that can inhibit key biofilm regulators. To increase the likelihood that these candidate agents selected from in silico approaches are efficacious in humans, they must be tested in biologically relevant biofilm models. We discuss the benefits and drawbacks of in vitro and in vivo biofilm models and highlight organoids as a new biofilm model. This review offers a comprehensive guide of current and future biological and computational approaches of anti-biofilm therapeutic discovery for investigators to utilize to combat the antibiotic resistance crisis.
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Affiliation(s)
| | | | | | - Robert E. W. Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
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Awadh AA, Le Gresley A, Forster-Wilkins G, Kelly AF, Fielder MD. Determination of metabolic activity in planktonic and biofilm cells of Mycoplasma fermentans and Mycoplasma pneumoniae by nuclear magnetic resonance. Sci Rep 2021; 11:5650. [PMID: 33707544 PMCID: PMC7952918 DOI: 10.1038/s41598-021-84326-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
Mycoplasmas are fastidious microorganisms, typically characterised by their restricted metabolism and minimalist genome. Although there is reported evidence that some mycoplasmas can develop biofilms little is known about any differences in metabolism in these organisms between the growth states. A systematic metabolomics approach may help clarify differences associated between planktonic and biofilm associated mycoplasmas. In the current study, the metabolomics of two different mycoplasmas of clinical importance (Mycoplasma pneumoniae and Mycoplasma fermentans) were examined using a novel approach involving nuclear magnetic resonance spectroscopy and principle component analysis. Characterisation of metabolic changes was facilitated through the generation of high-density metabolite data and diffusion-ordered spectroscopy that provided the size and structural information of the molecules under examination. This enabled the discrimination between biofilms and planktonic states for the metabolomic profiles of both organisms. This work identified clear biofilm/planktonic differences in metabolite composition for both clinical mycoplasmas and the outcomes serve to establish a baseline understanding of the changes in metabolism observed in these pathogens in their different growth states. This may offer insight into how these organisms are capable of exploiting and persisting in different niches and so facilitate their survival in the clinical setting.
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Affiliation(s)
- Ammar A. Awadh
- grid.15538.3a0000 0001 0536 3773School of Life Sciences, Pharmacy and Chemistry, SEC Faculty, Kingston University London, Kingston Upon Thames, UK
| | - Adam Le Gresley
- grid.15538.3a0000 0001 0536 3773School of Life Sciences, Pharmacy and Chemistry, SEC Faculty, Kingston University London, Kingston Upon Thames, UK
| | - Gary Forster-Wilkins
- grid.15538.3a0000 0001 0536 3773School of Life Sciences, Pharmacy and Chemistry, SEC Faculty, Kingston University London, Kingston Upon Thames, UK
| | - Alison F. Kelly
- grid.15538.3a0000 0001 0536 3773School of Life Sciences, Pharmacy and Chemistry, SEC Faculty, Kingston University London, Kingston Upon Thames, UK
| | - Mark D. Fielder
- grid.15538.3a0000 0001 0536 3773School of Life Sciences, Pharmacy and Chemistry, SEC Faculty, Kingston University London, Kingston Upon Thames, UK
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25
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Liu L, Guo S, Chen X, Yang S, Deng X, Tu M, Tao Y, Xiang W, Rao Y. Metabolic profiles of Lactobacillus paraplantarum in biofilm and planktonic states and investigation of its intestinal modulation and immunoregulation in dogs. Food Funct 2021; 12:5317-5332. [PMID: 34015803 DOI: 10.1039/d1fo00905b] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The use of probiotics has recently become a considerably promising research area. The most advanced fourth-generation probiotics involve beneficial bacteria enclosed in biofilms. However, differences in the effects of probiotics in biofilm and those in planktonic states are, as yet, unclear. In this study, it was ascertained that the biofilm mode of Lactobacillus paraplantarum L-ZS9 had a comparatively higher density and stronger resistance. Untargeted metabolomics analysis suggested a significant distinction between planktonic and biofilm cells, with amino acids and carbohydrate metabolism both more active in the biofilm mode. Furthermore, the in vivo experiment showed that the biofilm strain displayed better immunomodulation activity, which could increase the relative abundance of Lactobacillus in the intestinal microbiota of dogs. The relative abundance of intestinal microbiota participating in carbohydrate metabolism was higher in the biofilm probiotic-treated dogs. Correlation analysis between L-ZS9-producing metabolites, dog intestinal microbiome diversity and dog blood immune indexes (sIgA or IgG) revealed the interaction between these three components, which might explain the mechanisms by which biofilm L-ZS9 regulated the intestinal microbiome and immunity activity of the host, through the production of various metabolites. Findings of this study will, thus, enhance understanding of the beneficial effects of biofilm probiotics, as well as provide references for further investigation.
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Affiliation(s)
- Lei Liu
- School of food science and bioengineering, Xihua University, Hongguang Street, Pidu District, Chengdu, 610039, China.
| | - Shuyu Guo
- School of food science and bioengineering, Xihua University, Hongguang Street, Pidu District, Chengdu, 610039, China.
| | - Xing Chen
- School of food science and bioengineering, Xihua University, Hongguang Street, Pidu District, Chengdu, 610039, China.
| | - Shuhui Yang
- School of food science and bioengineering, Xihua University, Hongguang Street, Pidu District, Chengdu, 610039, China.
| | - Xi Deng
- School of food science and bioengineering, Xihua University, Hongguang Street, Pidu District, Chengdu, 610039, China.
| | - Mingxia Tu
- School of food science and bioengineering, Xihua University, Hongguang Street, Pidu District, Chengdu, 610039, China.
| | - Yufei Tao
- School of food science and bioengineering, Xihua University, Hongguang Street, Pidu District, Chengdu, 610039, China.
| | - Wenliang Xiang
- School of food science and bioengineering, Xihua University, Hongguang Street, Pidu District, Chengdu, 610039, China.
| | - Yu Rao
- School of food science and bioengineering, Xihua University, Hongguang Street, Pidu District, Chengdu, 610039, China.
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Seneviratne CJ, Suriyanarayanan T, Widyarman AS, Lee LS, Lau M, Ching J, Delaney C, Ramage G. Multi-omics tools for studying microbial biofilms: current perspectives and future directions. Crit Rev Microbiol 2020; 46:759-778. [PMID: 33030973 DOI: 10.1080/1040841x.2020.1828817] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The advent of omics technologies has greatly improved our understanding of microbial biology, particularly in the last two decades. The field of microbial biofilms is, however, relatively new, consolidated in the 1980s. The morphogenic switching by microbes from planktonic to biofilm phenotype confers numerous survival advantages such as resistance to desiccation, antibiotics, biocides, ultraviolet radiation, and host immune responses, thereby complicating treatment strategies for pathogenic microorganisms. Hence, understanding the mechanisms governing the biofilm phenotype can result in efficient treatment strategies directed specifically against molecular markers mediating this process. The application of omics technologies for studying microbial biofilms is relatively less explored and holds great promise in furthering our understanding of biofilm biology. In this review, we provide an overview of the application of omics tools such as transcriptomics, proteomics, and metabolomics as well as multi-omics approaches for studying microbial biofilms in the current literature. We also highlight how the use of omics tools directed at various stages of the biological information flow, from genes to metabolites, can be integrated via multi-omics platforms to provide a holistic view of biofilm biology. Following this, we propose a future artificial intelligence-based multi-omics platform that can predict the pathways associated with different biofilm phenotypes.
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Affiliation(s)
- Chaminda J Seneviratne
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore.,Duke NUS Medical School, Singapore, Singapore
| | - Tanujaa Suriyanarayanan
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore.,Duke NUS Medical School, Singapore, Singapore
| | - Armelia Sari Widyarman
- Department of Microbiology, Faculty of Dentistry, Trisakti University, Grogol, West Jakarta, Indonesia
| | - Lye Siang Lee
- Duke-NUS Medical School, Metabolomics Lab, Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Matthew Lau
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore
| | - Jianhong Ching
- Duke-NUS Medical School, Metabolomics Lab, Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Christopher Delaney
- School of Medicine, Dentistry & Nursing, Glasgow Dental Hospital & School, University of Glasgow, Glasgow, UK
| | - Gordon Ramage
- School of Medicine, Dentistry & Nursing, Glasgow Dental Hospital & School, University of Glasgow, Glasgow, UK
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Sadiq FA, Yan B, Zhao J, Zhang H, Chen W. Untargeted metabolomics reveals metabolic state of Bifidobacterium bifidum in the biofilm and planktonic states. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2019.108772] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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28
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In Vitro Anti-Biofilm Activity of Curcumin Nanoparticles in Acinetobacter baumannii: A Culture-Based and Molecular Approach. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2019. [DOI: 10.5812/archcid.83263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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29
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Abstract
Acinetobacter baumannii is a typically short, almost round, rod-shaped (coccobacillus) Gram-negative bacterium. It can be an opportunistic pathogen in humans, affecting people with compromised immune systems, and it is becoming increasingly important as a hospital-associated (nosocomial) infection. It has also been isolated from environmental soil and water samples. In this work, unlike conventional medical methods like antibiotics, the influence of atmospheric-pressure cold plasma on this bacterium is evaluated by means of a colony count technique and scanning electron microscopy. The plasma used here refers to streamers axially propagating into a helium channel penetrating the atmospheric air. The plasma is probed with high resolution optical emission spectroscopy and copious reactive species are unveiled under low-temperature conditions. Based on the experimental results, post-treatment (delayed) biochemical effects on Acinetobacter baumannii and morphological modifications appear dominant, leading to complete deactivation of this bacterium.
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30
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Chan KM, Cheng CH, Wu TH, Lee CF, Wu TJ, Chou HS, Lee WC. Impact of donor with evidence of bacterial infections on deceased donor liver transplantation: a retrospective observational cohort study in Taiwan. BMJ Open 2019; 9:e023908. [PMID: 30904845 PMCID: PMC6475220 DOI: 10.1136/bmjopen-2018-023908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/05/2018] [Accepted: 01/25/2019] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE The shortage of available donor organs is an unsolvable concern leading to an expansion in the donor criteria for organ transplantation. Here, we describe our experience and assess the outcomes in recipients who obtained a graft from a donor with bacterial infections in deceased donor liver transplantation (DDLT). METHODS All DDLTs between January 1991 and February 2017 were retrospectively reviewed. Patients were categorised into two groups based on the recipients who obtained a graft from a donor with (group I) or without (group II) evidence of bacterial infections. Outcomes and bacterial infections were compared between the two groups of recipients. RESULTS Overall, a total of 285 DDLTs were performed from 248 donors consisting of 48 split liver grafts and 208 whole liver grafts. Of those, 98 recipients (group I, 34.3%) were transplanted with a graft from 78 donors with positive bacterial cultures. Donor sputum cultures had the highest rate of positive bacterial growth, accounting for 26.6% of donors. Overall survival (OS) was not significantly different between the two groups (p=0.9746). The OS rates at 1 and 3 years were 73.5% and 69.2%, respectively, in the group I recipients versus 68.8% and 62.4% in the group II recipients. Importantly, no hospital mortality was related to donor-derived bacterial infections. CONCLUSION Transmission of bacteria from the donor to the recipient is infrequent in DDLT. Therefore, potential donors with positive bacterial infections should not be excluded for organ transplantation to increase organ availability and ameliorate the organ shortage.
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Affiliation(s)
- Kun-Ming Chan
- Department of General Surgery, Chang Gung Memorial Hospital Linkou Branch, Taoyuan city, Taiwan
| | - Chih-Hsien Cheng
- Department of General Surgery, Chang Gung Memorial Hospital Linkou Branch, Taoyuan city, Taiwan
| | - Tsung-Han Wu
- Department of General Surgery, Chang Gung Memorial Hospital Linkou Branch, Taoyuan city, Taiwan
| | - Chen-Fang Lee
- Department of General Surgery, Chang Gung Memorial Hospital Linkou Branch, Taoyuan city, Taiwan
| | - Ting-Jung Wu
- Department of General Surgery, Chang Gung Memorial Hospital Linkou Branch, Taoyuan city, Taiwan
| | - Hong-Shiue Chou
- Department of General Surgery, Chang Gung Memorial Hospital Linkou Branch, Taoyuan city, Taiwan
| | - Wei-Chen Lee
- Department of General Surgery, Chang Gung Memorial Hospital Linkou Branch, Taoyuan city, Taiwan
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Abstract
The aim of this study was to analyze the metabolome of several Klebsiella pneumoniae strains characterized by different resistance patterns. A total of 59 bacterial strains (27 carbapenemase-negative and 32 carbapenemase-positive) were included and their metabolic features were assessed in basal conditions. Moreover, 8 isolates (4 wild-type and 4 KPC-producers) were randomly selected to evaluate the impact of sub-lethal concentrations of meropenem on bacterial metabolism. The metabolomic analysis was performed by 1H-NMR spectroscopy both on filtered supernatants and cell lysates. A total of 40 and 20 molecules were quantified in the intracellular and the extracellular metabolome, respectively. While in basal conditions only five metabolites showed significant differences between carbapenemase-positive and negative strains, the use of meropenem had a profound impact on the whole bacterial metabolism. In the intracellular compartment, a reduction of different overflow metabolites and organic acids (e.g. formate, acetate, isobutyrate) was noticed, whereas, in the extracellular metabolome, the levels of several organic acids (e.g. succinate, acetate, formate, lactate) and amino acids (aspartate, threonine, lysine, alanine) were modified by meropenem stimulation. Interestingly, carbapenemase-positive and negative strains reacted differently to meropenem in terms of number and type of perturbed metabolites. In wild-type strains, meropenem had great impact on the metabolic pathways related to methane metabolism and alanine, aspartate and glutamate metabolism, whereas in KPC-producers the effect was predominant on pyruvate metabolism. The knowledge about the bacterial metabolic profiles could help to set up innovative diagnostic methods and new antimicrobial strategies to fight the global crisis against carbapenemase-positive K. pneumoniae.
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32
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Eze EC, Chenia HY, El Zowalaty ME. Acinetobacter baumannii biofilms: effects of physicochemical factors, virulence, antibiotic resistance determinants, gene regulation, and future antimicrobial treatments. Infect Drug Resist 2018; 11:2277-2299. [PMID: 30532562 PMCID: PMC6245380 DOI: 10.2147/idr.s169894] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Acinetobacter baumannii is a leading cause of nosocomial infections due to its increased antibiotic resistance and virulence. The ability of A. baumannii to form biofilms contributes to its survival in adverse environmental conditions including hospital environments and medical devices. A. baumannii has undoubtedly propelled the interest of biomedical researchers due to its broad range of associated infections especially in hospital intensive care units. The interplay among microbial physicochemistry, alterations in the phenotype and genotypic determinants, and the impact of existing ecological niche and the chemistry of antimicrobial agents has led to enhanced biofilm formation resulting in limited access of drugs to their specific targets. Understanding the triggers to biofilm formation is a step towards limiting and containing biofilm-associated infections and development of biofilm-specific countermeasures. The present review therefore focused on explaining the impact of environmental factors, antimicrobial resistance, gene alteration and regulation, and the prevailing microbial ecology in A. baumannii biofilm formation and gives insights into prospective anti-infective treatments.
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Affiliation(s)
- Emmanuel C Eze
- Virology and Microbiology Research Group, School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa,
| | - Hafizah Y Chenia
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mohamed E El Zowalaty
- Virology and Microbiology Research Group, School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa,
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Shirmohammadlou N, Zeighami H, Haghi F, Kashefieh M. Resistance pattern and distribution of carbapenemase and antiseptic resistance genes among multidrug-resistant Acinetobacter baumannii isolated from intensive care unit patients. J Med Microbiol 2018; 67:1467-1473. [DOI: 10.1099/jmm.0.000826] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Neda Shirmohammadlou
- 1Department of Microbiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Habib Zeighami
- 1Department of Microbiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Fakhri Haghi
- 1Department of Microbiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mehdi Kashefieh
- 2Social Security Organization, Aalinasab Hospital, Tabriz, Iran
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Wang Y, Li L, Han Y, Liu J, Yang K. Intestinal bacteria in bioaerosols and factors affecting their survival in two oxidation ditch process municipal wastewater treatment plants located in different regions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 154:162-170. [PMID: 29471278 DOI: 10.1016/j.ecoenv.2018.02.041] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 05/04/2023]
Abstract
Samples from two oxidation ditch process municipal wastewater treatment plants (MWTPs) (HJK and GXQ) in two regions of China were analysed for bacteria, particles, total organic carbon, and water-soluble ions in bioaerosols. Diversity and potential pathogen populations were evaluated by high-throughput sequencing. Bioaerosol sources, factors affecting intestinal bacterial survival, and the relationship between bioaerosols and water were analysed by Source tracker and partial least squares-discriminant, principal component, and canonical correspondence analyses. Culturable bacteria concentrations were 110-846 and 27-579 CFU/m3 at HJK and GXQ, respectively. Intestinal bacteria constituted 6-33% of bacteria. Biochemical reaction tank, sludge dewatering house (SDH), and fine screen samples showed the greatest contribution to bioaerosol contamination. Enterobacter aerogenes was the main intestinal bacteria (> 99.5%) in HJK and detected at each sampling site. Enterobacter aerogenes (98.67% in SDH), Aeromonas sp. (76.3% in biochemical reaction tank), and Acinetobacter baumannii (99.89% in fine screens) were the main intestinal bacteria in GXQ. Total suspended particulate masses in SDH were 229.46 and 141.6 μg/m3 in HJK and GXQ, respectively. Percentages of insoluble compounds in total suspended particulates decreased as height increased. The main soluble ions in bioaerosols were Ca2+, Na+, Cl-, and SO42-, which ranged from 3.8 to 27.55 μg/m3 in the MWTPs. Water was a main source of intestinal bacteria in bioaerosols from the MWTPs. Bioaerosols in HJK but not in GXQ were closely related. Relative humidity and some ions positively influenced intestinal bacteria in bioaerosols, while wind speed and solar illumination had a negative influence.
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Affiliation(s)
- Yanjie Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Lin Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Yunping Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Junxin Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Kaixiong Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
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Favre L, Ortalo-Magné A, Pichereaux C, Gargaros A, Burlet-Schiltz O, Cotelle V, Culioli G. Metabolome and proteome changes between biofilm and planktonic phenotypes of the marine bacterium Pseudoalteromonas lipolytica TC8. BIOFOULING 2018; 34:132-148. [PMID: 29319346 DOI: 10.1080/08927014.2017.1413551] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/29/2017] [Indexed: 06/07/2023]
Abstract
A number of bacteria adopt various lifestyles such as planktonic free-living or sessile biofilm stages. This enables their survival and development in a wide range of contrasting environments. With the aim of highlighting specific metabolic shifts between these phenotypes and to improve the overall understanding of marine bacterial adhesion, a dual metabolomics/proteomics approach was applied to planktonic and biofilm cultures of the marine bacterium Pseudoalteromonas lipolytica TC8. The liquid chromatography mass spectrometry (LC-MS) based metabolomics study indicated that membrane lipid composition was highly affected by the culture mode: phosphatidylethanolamine (PEs) derivatives were over-produced in sessile cultures while ornithine lipids (OLs) were more specifically synthesized in planktonic samples. In parallel, differences between proteomes revealed that peptidases, oxidases, transcription factors, membrane proteins and the enzymes involved in histidine biosynthesis were over-expressed in biofilms while proteins involved in heme production, nutrient assimilation, cell division and arginine/ornithine biosynthesis were specifically up-regulated in free-living cells.
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Affiliation(s)
- Laurie Favre
- a MAPIEM EA 4323 , Université de Toulon , Toulon , France
| | | | - Carole Pichereaux
- b Fédération de Recherche FR3450 , CNRS , Toulouse , France
- c Institut de Pharmacologie et de Biologie Structurale, IPBS , Université de Toulouse, CNRS, UPS , Toulouse , France
| | - Audrey Gargaros
- c Institut de Pharmacologie et de Biologie Structurale, IPBS , Université de Toulouse, CNRS, UPS , Toulouse , France
| | - Odile Burlet-Schiltz
- c Institut de Pharmacologie et de Biologie Structurale, IPBS , Université de Toulouse, CNRS, UPS , Toulouse , France
| | - Valérie Cotelle
- d Laboratoire de Recherche en Sciences Végétales , Université de Toulouse, CNRS, UPS , Castanet-Tolosan , France
| | - Gérald Culioli
- a MAPIEM EA 4323 , Université de Toulon , Toulon , France
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Metabolomic analysis of low and high biofilm-forming Helicobacter pylori strains. Sci Rep 2018; 8:1409. [PMID: 29362474 PMCID: PMC5780479 DOI: 10.1038/s41598-018-19697-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/08/2018] [Indexed: 12/16/2022] Open
Abstract
The biofilm-forming-capability of Helicobacter pylori has been suggested to be among factors influencing treatment outcome. However, H. pylori exhibit strain-to-strain differences in biofilm-forming-capability. Metabolomics enables the inference of spatial and temporal changes of metabolic activities during biofilm formation. Our study seeks to examine the differences in metabolome of low and high biofilm-formers using the metabolomic approach. Eight H. pylori clinical strains with different biofilm-forming-capability were chosen for metabolomic analysis. Bacterial metabolites were extracted using Bligh and Dyer method and analyzed by Liquid Chromatography/Quadrupole Time-of-Flight mass spectrometry. The data was processed and analyzed using the MassHunter Qualitative Analysis and the Mass Profiler Professional programs. Based on global metabolomic profiles, low and high biofilm-formers presented as two distinctly different groups. Interestingly, low-biofilm-formers produced more metabolites than high-biofilm-formers. Further analysis was performed to identify metabolites that differed significantly (p-value < 0.005) between low and high biofilm-formers. These metabolites include major categories of lipids and metabolites involve in prostaglandin and folate metabolism. Our findings suggest that biofilm formation in H. pylori is complex and probably driven by the bacterium’ endogenous metabolism. Understanding the underlying metabolic differences between low and high biofilm-formers may enhance our current understanding of pathogenesis, extragastric survival and transmission of H. pylori infections.
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Bacterial Substrate Transformation Tracked by Stable-Isotope-Guided NMR Metabolomics: Application in a Natural Aquatic Microbial Community. Metabolites 2017; 7:metabo7040052. [PMID: 29048351 PMCID: PMC5746732 DOI: 10.3390/metabo7040052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/08/2017] [Accepted: 10/16/2017] [Indexed: 12/25/2022] Open
Abstract
The transformation of organic substrates by heterotrophic bacteria in aquatic environments constitutes one of the key processes in global material cycles. The development of procedures that would enable us to track the wide range of organic compounds transformed by aquatic bacteria would greatly improve our understanding of material cycles. In this study, we examined the applicability of nuclear magnetic resonance spectroscopy coupled with stable-isotope labeling to the investigation of metabolite transformation in a natural aquatic bacterial community. The addition of a model substrate (13C6–glucose) to a coastal seawater sample and subsequent incubation resulted in the detection of >200 peaks and the assignment of 22 metabolites from various chemical classes, including amino acids, dipeptides, organic acids, nucleosides, nucleobases, and amino alcohols, which had been identified as transformed from the 13C6–glucose. Additional experiments revealed large variability in metabolite transformation and the key compounds, showing the bacterial accumulation of glutamate over the incubation period, and that of 3-hydroxybutyrate with increasing concentrations of 13C6–glucose added. These results suggest the potential ability of our approach to track substrate transformation in aquatic bacterial communities. Further applications of this procedure may provide substantial insights into the metabolite dynamics in aquatic environments.
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Zhang C, Wang Z, Zhang D, Zhou J, Lu C, Su X, Ding D. Proteomics and 1H NMR-based metabolomics analysis of pathogenic Vibrio vulnificus aquacultures isolated from sewage drains. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:23704-23713. [PMID: 28864971 DOI: 10.1007/s11356-017-0007-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Vibrio bacteria live in both marine and freshwater habitats and are associated with aquatic animals. Vibrio vulnificus is a pathogenic bacterium that infects people and livestock. It is usually found in offshore waters or within fish and shellfish. This study presents a comparative proteomic analysis of the outer membrane protein (OMP) changes in V. vulnificus proteins after stimulation with sewage from sewage drains. Using two-dimensional electrophoresis followed by MALDI-TOF MS/MS, 32 protein spots with significant differences in abundance were identified and characterized. These identified proteins were found to be involved in various functional categories, including catalysis, transport, membrane proteins progresses, receptor activity, energy metabolism, cytokine activity, and protein metabolism. The mRNA expression levels of 12 differential proteins were further assessed by qRT-PCR. Seven genes including carboxypeptidase, hemoglobin receptor, succinate dehydrogenase iron-sulfur subunit, ATP synthase subunit alpha, thioredoxin, succinyl-CoA synthetase subunit, and alanine dehydrogenase were downregulated upon stimulation, whereas the protein expression levels HupA receptor, type I secretion outer membrane protein, glutamine synthetase, superoxide dismutase, OmpU, and VuuA were upregulated. 1H NMR spectra showed 18 dysregulated metabolites from V. vulnificus after the sewage stimulation and the pathogenicity was enhanced after that.
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Affiliation(s)
- Chundan Zhang
- School of Marine Science, Ningbo University, Ningbo, China
| | - Zhonghua Wang
- School of Marine Science, Ningbo University, Ningbo, China
| | - Dijun Zhang
- School of Marine Science, Ningbo University, Ningbo, China
| | - Jun Zhou
- School of Marine Science, Ningbo University, Ningbo, China
| | - Chenyang Lu
- School of Marine Science, Ningbo University, Ningbo, China
| | - Xiurong Su
- School of Marine Science, Ningbo University, Ningbo, China.
| | - Dewen Ding
- School of Marine Science, Ningbo University, Ningbo, China.
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Alkasaby NM, El Sayed Zaki M. Molecular Study of Acinetobacter baumannii Isolates for Metallo- β-Lactamases and Extended-Spectrum- β-Lactamases Genes in Intensive Care Unit, Mansoura University Hospital, Egypt. Int J Microbiol 2017; 2017:3925868. [PMID: 28567057 PMCID: PMC5439075 DOI: 10.1155/2017/3925868] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 11/17/2022] Open
Abstract
Acinetobacter baumannii (A. baumannii) has been known as a causative pathogen of hospital acquired infections. The aim of this study is to examine the presence of A. baumannii among clinical isolates from intensive care unit (ICU) in Mansoura University Hospital (MUH), its antibiotic resistance pattern, and prevalence of antibiotic resistance genes metallo-β-lactamases (MBLs) and extended-spectrum-β-lactamases (ESBLs) among A. baumannii isolates. A. baumannii was identified by colony morphology, API 20E, and confirmed by detecting the bla OXA-51-like carbapenemase gene by PCR. Phenotypic expression of MBLs resistance was demonstrated by Combined Disk Test (CDT) in 273 isolates (97.5%) and of ESBLs was demonstrated by double disc synergy method (DDST) in 6 isolates (2.1%). MBLs genes were positive in 266 isolates (95%) and ESBLs genes were positive in 8 isolates (2.9%). The most frequent genes of MBLs studied genes were IMP (95.7%) followed by SIM and GIM (47.1% and 42.9%; resp.). For ESBL genes, the most frequent gene was TEM (2.9%). From this study, we conclude that multidrug resistant (MDR) A. baumannii with MBLs activity was the most common isolate. Careful monitoring for the presence of MDR A. baumannii among hospitalized patients is recommended to avoid wide dissemination of antibiotic resistance.
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Affiliation(s)
- Nashwa M. Alkasaby
- Medical Microbiology and Immunology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Maysaa El Sayed Zaki
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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40
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Favre L, Ortalo-Magné A, Greff S, Pérez T, Thomas OP, Martin JC, Culioli G. Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters. J Proteome Res 2017; 16:1962-1975. [PMID: 28362105 DOI: 10.1021/acs.jproteome.6b01027] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Most marine bacteria can form biofilms, and they are the main components of biofilms observed on marine surfaces. Biofilms constitute a widespread life strategy, as growing in such structures offers many important biological benefits. The molecular compounds expressed in biofilms and, more generally, the metabolomes of marine bacteria remain poorly studied. In this context, a nontargeted LC-MS metabolomics approach of marine biofilm-forming bacterial strains was developed. Four marine bacteria, Persicivirga (Nonlabens) mediterranea TC4 and TC7, Pseudoalteromonas lipolytica TC8, and Shewanella sp. TC11, were used as model organisms. The main objective was to search for some strain-specific bacterial metabolites and to determine how culture parameters (culture medium, growth phase, and mode of culture) may affect the cellular metabolism of each strain and thus the global interstrain metabolic discrimination. LC-MS profiling and statistical partial least-squares discriminant analyses showed that the four strains could be differentiated at the species level whatever the medium, the growth phase, or the mode of culture (planktonic vs biofilm). A MS/MS molecular network was subsequently built and allowed the identification of putative bacterial biomarkers. TC8 was discriminated by a series of ornithine lipids, while the P. mediterranea strains produced hydroxylated ornithine and glycine lipids. Among the P. mediterranea strains, TC7 extracts were distinguished by the occurrence of diamine derivatives, such as putrescine amides.
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Affiliation(s)
- Laurie Favre
- Université de Toulon , MAPIEM, EA 4323, La Garde Cedex 83130, France
| | | | - Stéphane Greff
- CNRS, Aix Marseille Univ , IRD, Avignon Univ. Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Station marine d'Endoume, Marseille 13007, France
| | - Thierry Pérez
- CNRS, Aix Marseille Univ , IRD, Avignon Univ. Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Station marine d'Endoume, Marseille 13007, France
| | - Olivier P Thomas
- CNRS, Aix Marseille Univ , IRD, Avignon Univ. Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Station marine d'Endoume, Marseille 13007, France.,National University of Ireland Galway , School of Chemistry, Marine Biodiscovery, Galway, Ireland
| | | | - Gérald Culioli
- Université de Toulon , MAPIEM, EA 4323, La Garde Cedex 83130, France
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Liao Y, Williams TJ, Ye J, Charlesworth J, Burns BP, Poljak A, Raftery MJ, Cavicchioli R. Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi. Sci Rep 2016; 6:37454. [PMID: 27874045 PMCID: PMC5118699 DOI: 10.1038/srep37454] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/26/2016] [Indexed: 12/21/2022] Open
Abstract
Biofilms enhance rates of gene exchange, access to specific nutrients, and cell survivability. Haloarchaea in Deep Lake, Antarctica, are characterized by high rates of intergenera gene exchange, metabolic specialization that promotes niche adaptation, and are exposed to high levels of UV-irradiation in summer. Halorubrum lacusprofundi from Deep Lake has previously been reported to form biofilms. Here we defined growth conditions that promoted the formation of biofilms and used microscopy and enzymatic digestion of extracellular material to characterize biofilm structures. Extracellular DNA was found to be critical to biofilms, with cell surface proteins and quorum sensing also implicated in biofilm formation. Quantitative proteomics was used to define pathways and cellular processes involved in forming biofilms; these included enhanced purine synthesis and specific cell surface proteins involved in DNA metabolism; post-translational modification of cell surface proteins; specific pathways of carbon metabolism involving acetyl-CoA; and specific responses to oxidative stress. The study provides a new level of understanding about the molecular mechanisms involved in biofilm formation of this important member of the Deep Lake community.
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Affiliation(s)
- Y Liao
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - T J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J Ye
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia.,Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J Charlesworth
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - B P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - A Poljak
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - M J Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - R Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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Mamani S, Moinier D, Denis Y, Soulère L, Queneau Y, Talla E, Bonnefoy V, Guiliani N. Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analog. Front Microbiol 2016; 7:1365. [PMID: 27683573 PMCID: PMC5021923 DOI: 10.3389/fmicb.2016.01365] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/17/2016] [Indexed: 12/13/2022] Open
Abstract
While a functional quorum sensing system has been identified in the acidophilic chemolithoautotrophic Acidithiobacillus ferrooxidans ATCC 23270(T) and shown to modulate cell adhesion to solid substrates, nothing is known about the genes it regulates. To address the question of how quorum sensing controls biofilm formation in A. ferrooxidans (T), the transcriptome of this organism in conditions in which quorum sensing response is stimulated by a synthetic superagonist AHL (N-acyl homoserine lactones) analog has been studied. First, the effect on biofilm formation of a synthetic AHL tetrazolic analog, tetrazole 9c, known for its agonistic QS activity, was assessed by fluorescence and electron microscopy. A fast adherence of A. ferrooxidans (T) cells on sulfur coupons was observed. Then, tetrazole 9c was used in DNA microarray experiments that allowed the identification of genes regulated by quorum sensing signaling, and more particularly, those involved in early biofilm formation. Interestingly, afeI gene, encoding the AHL synthase, but not the A. ferrooxidans quorum sensing transcriptional regulator AfeR encoding gene, was shown to be regulated by quorum sensing. Data indicated that quorum sensing network represents at least 4.5% (141 genes) of the ATCC 23270(T) genome of which 42.5% (60 genes) are related to biofilm formation. Finally, AfeR was shown to bind specifically to the regulatory region of the afeI gene at the level of the palindromic sequence predicted to be the AfeR binding site. Our results give new insights on the response of A. ferrooxidans to quorum sensing and on biofilm biogenesis.
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Affiliation(s)
- Sigde Mamani
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche ScientifiqueMarseille, France; Laboratorio de Comunicación Bacteriana, Departamento de Biología, Facultad de Ciencias, Universitad de ChileSantiago, Chile
| | - Danielle Moinier
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Yann Denis
- Plateforme Transcriptome, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Laurent Soulère
- Université Lyon, Institut National des Sciences Appliquées de Lyon, UMR 5246, Centre National de la Recherche Scientifique, Université Lyon 1, École Supérieure de Chimie Physique Electronique de Lyon, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires Villeurbanne, France
| | - Yves Queneau
- Université Lyon, Institut National des Sciences Appliquées de Lyon, UMR 5246, Centre National de la Recherche Scientifique, Université Lyon 1, École Supérieure de Chimie Physique Electronique de Lyon, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires Villeurbanne, France
| | - Emmanuel Talla
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Violaine Bonnefoy
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Nicolas Guiliani
- Laboratorio de Comunicación Bacteriana, Departamento de Biología, Facultad de Ciencias, Universitad de Chile Santiago, Chile
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43
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Bashir M, Ahmed M, Weinmaier T, Ciobanu D, Ivanova N, Pieber TR, Vaishampayan PA. Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens. Front Microbiol 2016; 7:1321. [PMID: 27667984 PMCID: PMC5017214 DOI: 10.3389/fmicb.2016.01321] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 08/10/2016] [Indexed: 01/09/2023] Open
Abstract
Strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. Therefore, spacecraft are assembled in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. We wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. Three geographically distinct cleanrooms were sampled during the assembly of three NASA spacecraft: The Lockheed Martin Aeronautics' Multiple Testing Facility during DAWN, the Kennedy Space Center's Payload Hazardous Servicing Facility (KSC-PHSF) during Phoenix, and the Jet Propulsion Laboratory's Spacecraft Assembly Facility during Mars Science Laboratory. Sample sets were collected from the KSC-PHSF cleanroom at three time points: before arrival of the Phoenix spacecraft, during the assembly and testing of the Phoenix spacecraft, and after removal of the spacecraft from the KSC-PHSF facility. All samples were subjected to metagenomic shotgun sequencing on an Illumina HiSeq 2500 platform. Strict decontamination procedures had a greater impact on microbial communities than sampling location Samples collected during spacecraft assembly were dominated by Acinetobacter spp. We found pathogens and potential virulence factors, which determine pathogenicity in all the samples tested during this study. Though the relative abundance of pathogens was lowest during the Phoenix assembly, potential virulence factors were higher during assembly compared to before and after assembly, indicating a survival advantage. Decreased phylogenetic and pathogenic diversity indicates that decontamination and preventative measures were effective against the majority of microorganisms and well implemented, however, pathogen abundance still increased over time. Four potential pathogens, Acinetobacter baumannii, Acinetobacter lwoffii, Escherichia coli and Legionella pneumophila, and their corresponding virulence factors were present in all cleanroom samples. This is the first functional metagenomics study describing presence of pathogens and their corresponding virulence factors in cleanroom environments. The results of this study should be considered for microbial monitoring of enclosed environments such as schools, homes, hospitals and more isolated habitation such the International Space Station and future manned missions to Mars.
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Affiliation(s)
- Mina Bashir
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Division of Endocrinology and Diabetology, Medical University of GrazGraz, Austria
| | - Mahjabeen Ahmed
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Department of Biological Sciences, California State Polytechnic UniversityPomona, CA, USA
| | - Thomas Weinmaier
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | - Doina Ciobanu
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Natalia Ivanova
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Thomas R Pieber
- Division of Endocrinology and Diabetology, Medical University of Graz Graz, Austria
| | - Parag A Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology Pasadena, CA, USA
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Mahamad Maifiah MH, Cheah SE, Johnson MD, Han ML, Boyce JD, Thamlikitkul V, Forrest A, Kaye KS, Hertzog P, Purcell AW, Song J, Velkov T, Creek DJ, Li J. Global metabolic analyses identify key differences in metabolite levels between polymyxin-susceptible and polymyxin-resistant Acinetobacter baumannii. Sci Rep 2016; 6:22287. [PMID: 26924392 PMCID: PMC4770286 DOI: 10.1038/srep22287] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 02/11/2016] [Indexed: 02/07/2023] Open
Abstract
Multidrug-resistant Acinetobacter baumannii presents a global medical crisis and polymyxins are used as the last-line therapy. This study aimed to identify metabolic differences between polymyxin-susceptible and polymyxin-resistant A. baumannii using untargeted metabolomics. The metabolome of each A. baumannii strain was measured using liquid chromatography-mass spectrometry. Multivariate and univariate statistics and pathway analyses were employed to elucidate metabolic differences between the polymyxin-susceptible and -resistant A. baumannii strains. Significant differences were identified between the metabolic profiles of the polymyxin-susceptible and -resistant A. baumannii strains. The lipopolysaccharide (LPS) deficient, polymyxin-resistant 19606R showed perturbation in specific amino acid and carbohydrate metabolites, particularly pentose phosphate pathway (PPP) and tricarboxylic acid (TCA) cycle intermediates. Levels of nucleotides were lower in the LPS-deficient 19606R. Furthermore, 19606R exhibited a shift in its glycerophospholipid profile towards increased abundance of short-chain lipids compared to the parent polymyxin-susceptible ATCC 19606. In contrast, in a pair of clinical isolates 03-149.1 (polymyxin-susceptible) and 03-149.2 (polymyxin-resistant, due to modification of lipid A), minor metabolic differences were identified. Notably, peptidoglycan biosynthesis metabolites were significantly depleted in both of the aforementioned polymyxin-resistant strains. This is the first comparative untargeted metabolomics study to show substantial differences in the metabolic profiles of the polymyxin-susceptible and -resistant A. baumannii.
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Affiliation(s)
- Mohd Hafidz Mahamad Maifiah
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Soon-Ee Cheah
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Matthew D. Johnson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Mei-Ling Han
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - John D. Boyce
- Department of Microbiology, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Visanu Thamlikitkul
- Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Alan Forrest
- UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7569, USA
| | - Keith S. Kaye
- Detroit Medical Centre and Wayne State University, University Health Centre, Detroit, MI, 48201, USA
| | - Paul Hertzog
- Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Tony Velkov
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Jian Li
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
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45
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Papa R, Selan L, Parrilli E, Tilotta M, Sannino F, Feller G, Tutino ML, Artini M. Anti-Biofilm Activities from Marine Cold Adapted Bacteria Against Staphylococci and Pseudomonas aeruginosa. Front Microbiol 2015; 6:1333. [PMID: 26696962 PMCID: PMC4677098 DOI: 10.3389/fmicb.2015.01333] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/13/2015] [Indexed: 01/18/2023] Open
Abstract
Microbial biofilms have great negative impacts on the world’s economy and pose serious problems to industry, public health and medicine. The interest in the development of new approaches for the prevention and treatment of bacterial adhesion and biofilm formation has increased. Since, bacterial pathogens living in biofilm induce persistent chronic infections due to the resistance to antibiotics and host immune system. A viable approach should target adhesive properties without affecting bacterial vitality in order to avoid the appearance of resistant mutants. Many bacteria secrete anti-biofilm molecules that function in regulating biofilm architecture or mediating the release of cells from it during the dispersal stage of biofilm life cycle. Cold-adapted marine bacteria represent an untapped reservoir of biodiversity able to synthesize a broad range of bioactive compounds, including anti-biofilm molecules. The anti-biofilm activity of cell-free supernatants derived from sessile and planktonic cultures of cold-adapted bacteria belonging to Pseudoalteromonas, Psychrobacter, and Psychromonas species were tested against Staphylococcus aureus, Staphylococcus epidermidis, and Pseudomonas aeruginosa strains. Reported results demonstrate that we have selected supernatants, from cold-adapted marine bacteria, containing non-biocidal agents able to destabilize biofilm matrix of all tested pathogens without killing cells. A preliminary physico-chemical characterization of supernatants was also performed, and these analyses highlighted the presence of molecules of different nature that act by inhibiting biofilm formation. Some of them are also able to impair the initial attachment of the bacterial cells to the surface, thus likely containing molecules acting as anti-biofilm surfactant molecules. The described ability of cold-adapted bacteria to produce effective anti-biofilm molecules paves the way to further characterization of the most promising molecules and to test their use in combination with conventional antibiotics.
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Affiliation(s)
- Rosanna Papa
- Department of Public Health and Infectious Diseases, Sapienza University Rome, Italy
| | - Laura Selan
- Department of Public Health and Infectious Diseases, Sapienza University Rome, Italy
| | | | - Marco Tilotta
- Department of Public Health and Infectious Diseases, Sapienza University Rome, Italy
| | - Filomena Sannino
- Department of Chemical Sciences, University of Naples Federico II Naples, Italy
| | - Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, University of Liège Liège, Belgium
| | - Maria L Tutino
- Department of Chemical Sciences, University of Naples Federico II Naples, Italy
| | - Marco Artini
- Department of Public Health and Infectious Diseases, Sapienza University Rome, Italy
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Abstract
Worldwide, infectious diseases are one of the leading causes of death among children. At least 65% of all infections are caused by the biofilm mode of bacterial growth. Bacteria colonise surfaces and grow as multicellular biofilm communities surrounded by a polymeric matrix as a common survival strategy. These sessile communities endow bacteria with high tolerance to antimicrobial agents and hence cause persistent and chronic bacterial infections, such as dental caries, periodontitis, otitis media, cystic fibrosis and pneumonia. The highly complex nature and the rapid adaptability of the biofilm population impede our understanding of the process of biofilm formation, but an important role for oxygen-binding proteins herein is clear. Much research on this bacterial lifestyle is already performed, from genome/proteome analysis to in vivo antibiotic susceptibility testing, but without significant progress in biofilm treatment or eradication. This review will present the multiple challenges of biofilm research and discuss possibilities to cross these barriers in future experimental studies.
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Affiliation(s)
- Joke Donné
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sylvia Dewilde
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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Wong WZ, H'ng PS, Chin KL, Sajap AS, Tan GH, Paridah MT, Othman S, Chai EW, Go WZ. Preferential Use of Carbon Sources in Culturable Aerobic Mesophilic Bacteria of Coptotermes curvignathus's (Isoptera: Rhinotermitidae) Gut and Its Foraging Area. ENVIRONMENTAL ENTOMOLOGY 2015; 44:1367-1374. [PMID: 26314017 DOI: 10.1093/ee/nvv115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 06/29/2015] [Indexed: 06/04/2023]
Abstract
The lower termite, Coptotermes curvignathus, is one of the most prominent plantation pests that feed upon, digest, and receive nourishment from exclusive lignocellulose diets. The objective of this study was to examine the utilization of sole carbon sources by isolated culturable aerobic bacteria among communities from the gut and foraging pathway of C. curvignathus. We study the bacteria occurrence from the gut of C. curvignathus and its surrounding feeding area by comparing the obtained phenotypic fingerprint with Biolog's extensive species library. A total of 24 bacteria have been identified mainly from the family Enterobacteriaceae from the identification of Biolog Gen III. Overall, the bacteria species in the termite gut differ from those of foraging pathway within a location, except Acintobacter baumannii, which was the only bacteria species found in both habitats. Although termites from a different study area do not have the same species of bacteria in the gut, they do have a bacterial community with similar role in degrading certain carbon sources. Sugars were preferential in termite gut isolates, while nitrogen carbon sources were preferential in foraging pathway isolates. The preferential use of specific carbon sources by these two bacterial communities reflects the role of bacteria for regulation of carbon metabolism in the termite gut and foraging pathway.
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Affiliation(s)
- W Z Wong
- Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - P S H'ng
- Institute of Tropical Forestry and Forest Product, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - K L Chin
- Institute of Tropical Forestry and Forest Product, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Ahmad Said Sajap
- Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - G H Tan
- Faculty of Agricultural, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - M T Paridah
- Institute of Tropical Forestry and Forest Product, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Soni Othman
- Crop Improvement and Protection Unit (UPPT), Rubber Research Institute, Malaysian Rubber Board, 47000 Sg. Buloh, Selangor, Malaysia
| | - E W Chai
- Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - W Z Go
- Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Food metabolomics: from farm to human. Curr Opin Biotechnol 2015; 37:16-23. [PMID: 26426959 DOI: 10.1016/j.copbio.2015.09.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/15/2015] [Accepted: 09/11/2015] [Indexed: 01/18/2023]
Abstract
Metabolomics, one of the latest components in the suite of systems biology, has been used to understand the metabolism and physiology of living systems, including microorganisms, plants, animals and humans. Food metabolomics can be defined as the application of metabolomics in food systems, including food resources, food processing and diet for humans. The study of food metabolomics has increased gradually in the recent years, because food systems are directly related to nutrition and human health. This review describes the recent trends and applications of metabolomics to food systems, from farm to human, including food resource production, industrial food processing and food intake by humans.
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Wong HS, Maker GL, Trengove RD, O'Handley RM. Gas chromatography-mass spectrometry-based metabolite profiling of Salmonella enterica serovar Typhimurium differentiates between biofilm and planktonic phenotypes. Appl Environ Microbiol 2015; 81:2660-6. [PMID: 25636852 PMCID: PMC4375307 DOI: 10.1128/aem.03658-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/27/2015] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to utilize gas chromatography coupled with mass spectrometry (GC-MS) to compare and identify patterns of biochemical change between Salmonella cells grown in planktonic and biofilm phases and Salmonella biofilms of different ages. Our results showed a clear separation between planktonic and biofilm modes of growth. The majority of metabolites contributing to variance between planktonic and biofilm supernatants were identified as amino acids, including alanine, glutamic acid, glycine, and ornithine. Metabolites contributing to variance in intracellular profiles were identified as succinic acid, putrescine, pyroglutamic acid, and N-acetylglutamic acid. Principal-component analysis revealed no significant differences between the various ages of intracellular profiles, which would otherwise allow differentiation of biofilm cells on the basis of age. A shifting pattern across the score plot was illustrated when analyzing extracellular metabolites sampled from different days of biofilm growth, and amino acids were again identified as the metabolites contributing most to variance. An understanding of biofilm-specific metabolic responses to perturbations, especially antibiotics, can lead to the identification of novel drug targets and potential therapies for combating biofilm-associated diseases. We concluded that under the conditions of this study, GC-MS can be successfully applied as a high-throughput technique for "bottom-up" metabolomic biofilm research.
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Affiliation(s)
- Hui San Wong
- The University of Adelaide, School of Animal and Veterinary Science, Adelaide, South Australia, Australia Murdoch University, School of Veterinary and Life Sciences, Perth, Western Australia, Australia
| | - Garth L Maker
- Murdoch University, School of Veterinary and Life Sciences, Perth, Western Australia, Australia Murdoch University, Metabolomics Australia, Perth, Western Australia, Australia
| | - Robert D Trengove
- Murdoch University, Metabolomics Australia, Perth, Western Australia, Australia
| | - Ryan M O'Handley
- The University of Adelaide, School of Animal and Veterinary Science, Adelaide, South Australia, Australia
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Prevalence of ESBL and MBL encoding genes in Acinetobacter baumannii strains isolated from patients of intensive care units (ICU). Saudi J Biol Sci 2015; 22:424-9. [PMID: 26150748 PMCID: PMC4486466 DOI: 10.1016/j.sjbs.2015.01.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/30/2014] [Accepted: 01/10/2015] [Indexed: 11/24/2022] Open
Abstract
The aim of this study was to investigate the prevalence of ESBL and MBL encoding genes among A. baumannii isolates. In this cross sectional study, 100 A. baumannii strains were isolated from ICU wards of 3 educational hospitals of Hamadan City, Iran in 2011. Phenotypic identification of the production of ESBLs and MBLs has been carried out by using E-test and DDST methods, respectively. PCR technique was used for amplification of the ESBL and MBL encoding genes, namely: CTX-M, SHV, TEM, OXA-51, VIM-Family, IMP-Family, SPM-1, SIM-1, and GIM-1. Eighty seven (87%), 95 (95%), 98 (98%) and 95 (95%) out of 100 A. baumannii isolates were resistant to imipenem, meropenem, ceftazidime and cefotaxime, respectively. Also, 99% and 7% of the isolates were MBLs and ESBLs produced phenotypically. Thirty (30%), 20 (20%) and 58 (58%) out of 100 A. baumannii isolates have been confirmed to harbor the blaVIM-family, TEM and SHV genes, respectively. Our results show no significant relationship between the detected gens with production of MBLs and ESBLs in spite of high prevalence of MBL encoding and drug resistant A. baumannii. Probably some other genes rather than what we studied are involved in phenotypic production of MBLs and ESBLs and subsequent drug resistance in Hamadan area, Iran.
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