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Bolsan AC, Sampaio GV, Rodrigues HC, Silva De Souza S, Edwiges T, Celant De Prá M, Gabiatti NC. Phage formulations and delivery strategies: Unleashing the potential against antibiotic-resistant bacteria. Microbiol Res 2024; 282:127662. [PMID: 38447457 DOI: 10.1016/j.micres.2024.127662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/14/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024]
Abstract
Bacterial control promoted by bacteriophages (phages) is an attractive tool in the face of the antibiotic crisis triggered by the exacerbated use of these drugs. Despite the growing interest in using these viruses, some gaps still need answers, such as the protection and delivery of phages. Some limitation points involve the degradation of phage proteins by enzymes or inactivation in low-pH environments. In this review, a literature search using keywords related to the field of virus delivery formulations was done to understand the current scenario of using delivery techniques and phage formulations. A total of 2096 raw results were obtained, which resulted in 140 publications after refinement. These studies were analyzed for main application techniques and areas, keywords, and countries. Of the total, 57% of the publications occurred in the last five years, and the encapsulation technique was the most used among the articles analyzed. As excipient agents, lactose, trehalose, mannitol, PEG, and Leucine stand out. The development of phage formulations, protection approaches, their delivery routes, and the knowledge about the best application strategy enables the use of these organisms in several sectors. It can act as a powerful tool against antibiotic-resistant bacteria.
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Affiliation(s)
- Alice Chiapetti Bolsan
- Programa de Pós Graduação em Sustentabilidade Ambiental Urbana (PPGSAU) - Universidade Tecnológica Federal do Paraná, Curitiba, PR 81280-340, Brazil
| | - Gabrielli Vaz Sampaio
- Laboratório de Genética, Instituto Butantan - Universidade de São Paulo, São Paulo, SP 05508-900, Brazil
| | - Heloisa Campeão Rodrigues
- Programa de Pós Graduação em Biotecnologia (PPGBIOTEC) - Universidade Tecnológica Federal do Paraná, Dois Vizinhos, PR 85660-000, Brazil
| | - Samara Silva De Souza
- Programa de Pós Graduação em Biotecnologia (PPGBIOTEC) - Universidade Tecnológica Federal do Paraná, Dois Vizinhos, PR 85660-000, Brazil
| | - Thiago Edwiges
- Programa de Pós Graduação em Sustentabilidade Ambiental Urbana (PPGSAU) - Universidade Tecnológica Federal do Paraná, Curitiba, PR 81280-340, Brazil
| | - Marina Celant De Prá
- Programa de Pós Graduação em Biotecnologia (PPGBIOTEC) - Universidade Tecnológica Federal do Paraná, Dois Vizinhos, PR 85660-000, Brazil
| | - Naiana Cristine Gabiatti
- Programa de Pós Graduação em Biotecnologia (PPGBIOTEC) - Universidade Tecnológica Federal do Paraná, Dois Vizinhos, PR 85660-000, Brazil.
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Wu LY, Wijesekara Y, Piedade GJ, Pappas N, Brussaard CPD, Dutilh BE. Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes. Genome Biol 2024; 25:97. [PMID: 38622738 PMCID: PMC11020464 DOI: 10.1186/s13059-024-03236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance. RESULTS We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered. CONCLUSIONS Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.
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Affiliation(s)
- Ling-Yi Wu
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Yasas Wijesekara
- Institute of Bioinformatics, University Medicine Greifswald, Felix Hausdorff Str. 8, 17475, Greifswald, Germany
| | - Gonçalo J Piedade
- Department Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, PO Box 59, Texel, 1790 AB, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Nikolaos Pappas
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Corina P D Brussaard
- Department Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, PO Box 59, Texel, 1790 AB, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany.
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Qamar H, Owais M, Hussain T. Nano-microbial based technology employing polyvalent phage conjugate: A next generation weapon for antimicrobial resistance lurking behind wastewater. ENVIRONMENTAL RESEARCH 2022; 215:114079. [PMID: 36030912 DOI: 10.1016/j.envres.2022.114079] [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: 03/16/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Worldwide, due to a dearth of innovative interventions, new forms of antimicrobial resistance (AMR) are being discovered every day in clinical and environmental settings. Therefore, it is necessary to remove these contaminants directly or indirectly from the environment. Nanomicrobial-based technology employing nanomaterials with microbes is a new paradigm that finds a place in the antimicrobial crisis. Microbial entities such as phages can be used to treat antimicrobial resistance, but phage resistance is challenging and limits its applicability. Similarly, nanotechnology will not be able to selectively remove resistant strains from the environment individually. Therefore, we employ nanomicrobial-based technology that aims to fill these gaps. In the present study, polyvalent phages were isolated from wastewater with an easy-to-use modified multi-host sequential approach, characterized and conjugated with magnetite (Fe3O4) nanoparticles with the modified formulation to form nanomicrobial conjugates (NMCs). These NMCs were subjected to characterization and in vitro antibacterial studies. The results indicated a significant polyvalency of phages in the order of Caudovirales. Transmission electron microscopy (TEM) analysis of Fe3O4 nanoparticles formed by the co-precipitation method showed a particle size of 30 ± 5 nm and the selected area electron diffraction (SAED) pattern indicates a single-phase crystalline structure. To form NMCs, isolated phages (105 PFU/mL) were immobilized onto Fe3O4 nanoparticles. Further, surface modification of Fe3O4 nanoparticles enables the covalent association of phages. Biosurfactant-functionalized Fe3O4 nanoparticles (FNMCs) were found to have higher phage loading capacity, with a significant value of p < 0.0127 and a zeta potential of -22.2 mV. TEM studies and in vitro biofilm assay showed that NMCs exhibit promising antibacterial activity against various resistant bacterial strains. Pilot studies showed that NMCs can selectively eliminate up to 98.3% of AMR in wastewater. Thus, these findings indicate a synergistic effect of both phage and nanomaterial and this technology is expected to be a new lead in wastewater management.
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Affiliation(s)
- Hina Qamar
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India; Department of Botany, Aligarh Muslim University, Aligarh, India.
| | - Mohd Owais
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Touseef Hussain
- Department of Botany, Aligarh Muslim University, Aligarh, India
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Characterization and complete genome analysis of a novel Escherichia phage, vB_EcoM-RPN242. Arch Virol 2022; 167:1675-1679. [DOI: 10.1007/s00705-022-05479-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/04/2022] [Indexed: 01/10/2023]
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Complete genome analysis of the novel Alcaligenes faecalis phage vB_AfaP_QDWS595. Arch Virol 2022; 167:931-934. [PMID: 35118527 DOI: 10.1007/s00705-022-05373-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/16/2022] [Indexed: 11/02/2022]
Abstract
A novel lytic phage named vB_AfaP_QDWS595 infecting Alcaligenes faecalis was isolated and characterized in this study. The genome of phage vB_AfaP_QDWS595 was sequenced and analyzed, and the result revealed that the phage contained 70,466 bp of double-stranded DNA with 41.12% GC content. There were 74 putative genes encoding proteins as well as 11 tRNAs predicted in the phage genome. Phenotype and phylogeny analysis indicated that this phage might be a new member of the family Schitoviridae.
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Ramos-Vivas J, Elexpuru-Zabaleta M, Samano ML, Barrera AP, Forbes-Hernández TY, Giampieri F, Battino M. Phages and Enzybiotics in Food Biopreservation. Molecules 2021; 26:molecules26175138. [PMID: 34500572 PMCID: PMC8433972 DOI: 10.3390/molecules26175138] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 12/27/2022] Open
Abstract
Presently, biopreservation through protective bacterial cultures and their antimicrobial products or using antibacterial compounds derived from plants are proposed as feasible strategies to maintain the long shelf-life of products. Another emerging category of food biopreservatives are bacteriophages or their antibacterial enzymes called "phage lysins" or "enzybiotics", which can be used directly as antibacterial agents due to their ability to act on the membranes of bacteria and destroy them. Bacteriophages are an alternative to antimicrobials in the fight against bacteria, mainly because they have a practically unique host range that gives them great specificity. In addition to their potential ability to specifically control strains of pathogenic bacteria, their use does not generate a negative environmental impact as in the case of antibiotics. Both phages and their enzymes can favor a reduction in antibiotic use, which is desirable given the alarming increase in resistance to antibiotics used not only in human medicine but also in veterinary medicine, agriculture, and in general all processes of manufacturing, preservation, and distribution of food. We present here an overview of the scientific background of phages and enzybiotics in the food industry, as well as food applications of these biopreservatives.
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Affiliation(s)
- José Ramos-Vivas
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | - María Elexpuru-Zabaleta
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
| | - María Luisa Samano
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | - Alina Pascual Barrera
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | | | - Francesca Giampieri
- Department of Clinical Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: (F.G.); (M.B.); Tel.: +339-071-220-4136 (F.G.); +339-071-220-4646 (M.B.)
| | - Maurizio Battino
- Department of Clinical Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Correspondence: (F.G.); (M.B.); Tel.: +339-071-220-4136 (F.G.); +339-071-220-4646 (M.B.)
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