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Bisen M, Kharga K, Mehta S, Jabi N, Kumar L. Bacteriophages in nature: recent advances in research tools and diverse environmental and biotechnological applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22199-22242. [PMID: 38411907 DOI: 10.1007/s11356-024-32535-3] [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: 11/16/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Bacteriophages infect and replicate within bacteria and play a key role in the environment, particularly in microbial ecosystems and bacterial population dynamics. The increasing recognition of their significance stems from their wide array of environmental and biotechnological uses, which encompass the mounting issue of antimicrobial resistance (AMR). Beyond their therapeutic potential in combating antibiotic-resistant infections, bacteriophages also find vast applications such as water quality monitoring, bioremediation, and nutrient cycling within environmental sciences. Researchers are actively involved in isolating and characterizing bacteriophages from different natural sources to explore their applications. Gaining insights into key aspects such as the life cycle of bacteriophages, their host range, immune interactions, and physical stability is vital to enhance their application potential. The establishment of diverse phage libraries has become indispensable to facilitate their wide-ranging uses. Consequently, numerous protocols, ranging from traditional to cutting-edge techniques, have been developed for the isolation, detection, purification, and characterization of bacteriophages from diverse environmental sources. This review offers an exploration of tools, delves into the methods of isolation, characterization, and the extensive environmental applications of bacteriophages, particularly in areas like water quality assessment, the food sector, therapeutic interventions, and the phage therapy in various infections and diseases.
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Affiliation(s)
- Monish Bisen
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Kusum Kharga
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Sakshi Mehta
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Nashra Jabi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Lokender Kumar
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India.
- Cancer Biology Laboratory, Raj Khosla Centre for Cancer Research, Shoolini University, Himachal Pradesh, Solan, 173229, India.
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Petrosino A, Saporetti R, Starinieri F, Sarti E, Ulfo L, Boselli L, Cantelli A, Morini A, Zadran SK, Zuccheri G, Pasquini Z, Di Giosia M, Prodi L, Pompa PP, Costantini PE, Calvaresi M, Danielli A. A modular phage vector platform for targeted photodynamic therapy of Gram-negative bacterial pathogens. iScience 2023; 26:108032. [PMID: 37822492 PMCID: PMC10563061 DOI: 10.1016/j.isci.2023.108032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/04/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023] Open
Abstract
Growing antibiotic resistance has encouraged the revival of phage-inspired antimicrobial approaches. On the other hand, photodynamic therapy (PDT) is considered a very promising research domain for the protection against infectious diseases. Yet, very few efforts have been made to combine the advantages of both approaches in a modular, retargetable platform. Here, we foster the M13 bacteriophage as a multifunctional scaffold, enabling the selective photodynamic killing of bacteria. We took advantage of the well-defined molecular biology of M13 to functionalize its capsid with hundreds of photo-activable Rose Bengal sensitizers and contemporarily target this light-triggerable nanobot to specific bacterial species by phage display of peptide targeting moieties fused to the minor coat protein pIII of the phage. Upon light irradiation of the specimen, the targeted killing of diverse Gram(-) pathogens occurred at subnanomolar concentrations of the phage vector. Our findings contribute to the development of antimicrobials based on targeted and triggerable phage-based nanobiotherapeutics.
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Affiliation(s)
- Annapaola Petrosino
- Dipartimento di Farmacia e Biotecnologie (FaBiT) – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 3, 40126 Bologna, Italy
| | - Roberto Saporetti
- Dipartimento di Chimica “Giacomo Ciamician” – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
| | - Francesco Starinieri
- Dipartimento di Farmacia e Biotecnologie (FaBiT) – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 3, 40126 Bologna, Italy
| | - Edoardo Sarti
- Dipartimento di Farmacia e Biotecnologie (FaBiT) – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 3, 40126 Bologna, Italy
| | - Luca Ulfo
- Dipartimento di Farmacia e Biotecnologie (FaBiT) – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 3, 40126 Bologna, Italy
| | - Luca Boselli
- Nanobiointeractions and Nanodiagnostics Laboratory, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163 Genova, Italy
| | - Andrea Cantelli
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" Unit of Bologna, Italy
- IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Andrea Morini
- Dipartimento di Farmacia e Biotecnologie (FaBiT) – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 3, 40126 Bologna, Italy
| | - Suleman Khan Zadran
- Dipartimento di Farmacia e Biotecnologie (FaBiT) – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 3, 40126 Bologna, Italy
| | - Giampaolo Zuccheri
- Dipartimento di Farmacia e Biotecnologie (FaBiT) – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 3, 40126 Bologna, Italy
- CIRI SDV – Centro Interdipartimentale Scienze della Vita - Alma Mater Studiorum - Università di Bologna, Via Tolara di Sopra, 41/E - 40064 Ozzano dell'Emilia (BO), Italy
| | - Zeno Pasquini
- Infectious Diseases Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy
| | - Matteo Di Giosia
- Dipartimento di Chimica “Giacomo Ciamician” – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
| | - Luca Prodi
- Dipartimento di Chimica “Giacomo Ciamician” – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
- CIRI SDV – Centro Interdipartimentale Scienze della Vita - Alma Mater Studiorum - Università di Bologna, Via Tolara di Sopra, 41/E - 40064 Ozzano dell'Emilia (BO), Italy
| | - Pier Paolo Pompa
- Nanobiointeractions and Nanodiagnostics Laboratory, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163 Genova, Italy
| | - Paolo Emidio Costantini
- Dipartimento di Farmacia e Biotecnologie (FaBiT) – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 3, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “Giacomo Ciamician” – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
- CIRI SDV – Centro Interdipartimentale Scienze della Vita - Alma Mater Studiorum - Università di Bologna, Via Tolara di Sopra, 41/E - 40064 Ozzano dell'Emilia (BO), Italy
| | - Alberto Danielli
- Dipartimento di Farmacia e Biotecnologie (FaBiT) – Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 3, 40126 Bologna, Italy
- CIRI SDV – Centro Interdipartimentale Scienze della Vita - Alma Mater Studiorum - Università di Bologna, Via Tolara di Sopra, 41/E - 40064 Ozzano dell'Emilia (BO), Italy
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Nang SC, Lin YW, Petrovic Fabijan A, Chang RYK, Rao GG, Iredell J, Chan HK, Li J. Pharmacokinetics/pharmacodynamics of phage therapy: a major hurdle to clinical translation. Clin Microbiol Infect 2023:S1198-743X(23)00046-0. [PMID: 36736661 DOI: 10.1016/j.cmi.2023.01.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
BACKGROUND The increasing emergence of antimicrobial resistance worldwide has led to renewed interest in phage therapy. Unlike antibiotics, the lack of pharmacokinetics/pharmacodynamics (PK/PD) information represents a major challenge for phage therapy. As therapeutic phages are biological entities with the ability to self-replicate in the presence of susceptible bacteria, their PK/PD is far more complicated than that of antibiotics. OBJECTIVES This narrative review examines the current literature on phage pharmacology and highlights major pharmacological challenges for phage therapy. SOURCES Included articles were identified by searching PubMed and Google Scholar till June 2022. The search terms were 'bacteriophage', 'antimicrobial', 'pharmacokinetics' and 'pharmacodynamics'. Additional relevant references were obtained from articles retrieved from the primary search. CONTENT In this review, phage PK is first discussed, focusing on absorption, distribution, metabolism, and elimination. Key factors affecting phage antimicrobial activities are reviewed, including multiplicity of infection, passive and active phage therapy, and the involvement of the human immune system. Importantly, we emphasize the impact of phage self-replication on the PK/PD and the fundamental phage characteristics that are required for PK/PD modelling and clinical translation. IMPLICATIONS Recent progress in phage pharmacology has shown that we are in a far better position now to treat infections with phage therapy than a century ago. However, phage therapy is still in its infancy when compared to antibiotics due to the scarce pharmacological knowledge (e.g. PK/PD). Optimization of phage PK/PD is key for translation of phage therapy in patients.
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Affiliation(s)
- Sue C Nang
- Biomedicine Discovery Institute, Infection Program, Department of Microbiology, Monash University, Victoria, Australia
| | - Yu-Wei Lin
- Biomedicine Discovery Institute, Infection Program, Department of Microbiology, Monash University, Victoria, Australia
| | - Aleksandra Petrovic Fabijan
- Westmead Hospital, Western Sydney Local Health District, Westmead, New South Wales, Australia; Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia; School of Medicine, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia
| | - Rachel Y K Chang
- Advanced Drug Delivery Group, Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia; AcuraBio Pty Ltd, Darra, Queensland, Australia
| | - Gauri G Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, North Carolina, USA
| | - Jonathan Iredell
- Westmead Hospital, Western Sydney Local Health District, Westmead, New South Wales, Australia; Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia; School of Medicine, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia
| | - Hak-Kim Chan
- Advanced Drug Delivery Group, Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Infection Program, Department of Microbiology, Monash University, Victoria, Australia.
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Wang P, Chen S, Liao C, Jia Y, Li J, Shang K, Chen J, Cao P, Li W, Li Y, Yu Z, Ding K. Probiotic Properties of Chicken-Derived Highly Adherent Lactic Acid Bacteria and Inhibition of Enteropathogenic Bacteria in Caco-2 Cells. Microorganisms 2022; 10:microorganisms10122515. [PMID: 36557770 PMCID: PMC9788042 DOI: 10.3390/microorganisms10122515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Lactic acid bacteria (LAB) as probiotic candidates have various beneficial functions, such as regulating gut microbiota, inhibiting intestinal pathogens, and improving gut immunity. The colonization of the intestine is a prerequisite for probiotic function. Therefore, it is necessary to screen the highly adherent LAB. In this study, the cell surface properties, such as hydrophobicity, auto-aggregation, co-aggregation, and adhesion abilities of the six chicken-derived LAB to Caco-2 cells were investigated. All six strains showed different hydrophobicity (21.18-95.27%), auto-aggregation (13.61-30.17%), co-aggregation with Escherichia coli ATCC 25922 (10.23-36.23%), and Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311 (11.71-39.35%), and adhesion to Caco-2 cells (8.57-26.37%). Pediococcus pentosaceus 2-5 and Lactobacillus reuteri L-3 were identified as the strains with strong adhesion abilities (26.37% and 21.57%, respectively). Moreover, these strains could survive in a gastric acid environment at pH 2, 3, and 4 for 3 h and in a bile salt environment at 0.1%, 0.2%, and 0.3% (w/v) concentration for 6 h. Furthermore, the cell-free supernatant of P. pentosaceus 2-5 and L. reuteri L-3 inhibited the growth of enteropathogenic bacteria and the strains inhibited the adhesion of these pathogens to Caco-2 cells. In this study, these results suggested that P. pentosaceus 2-5 and L. reuteri L-3, isolated from chicken intestines might be good probiotic candidates to be used as feed additives or delivery vehicles of biologically active substances.
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Affiliation(s)
- Pudi Wang
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Luoyang 471003, China
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
| | - Songbiao Chen
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Luoyang 471003, China
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
| | - Chengshui Liao
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Luoyang 471003, China
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
| | - Yanyan Jia
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Luoyang 471003, China
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
| | - Jing Li
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Luoyang 471003, China
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
| | - Ke Shang
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Luoyang 471003, China
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
| | - Jian Chen
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Luoyang 471003, China
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
| | - Pinghua Cao
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
| | - Wang Li
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
| | - Yuanxiao Li
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
| | - Zuhua Yu
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Luoyang 471003, China
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
- Correspondence: (Z.Y.); (K.D.)
| | - Ke Ding
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Luoyang 471003, China
- Laboratory of Functional Microbiology and Animal Health, Henan University of Science and Technology, Luoyang 471003, China
- Correspondence: (Z.Y.); (K.D.)
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Zhang X, Zhuang J, Huang L, Zhang X. Palmitic Amide Triggers Virus Life Cycle via Enhancing Host Energy Metabolism. Front Microbiol 2022; 13:924533. [PMID: 35756035 PMCID: PMC9224243 DOI: 10.3389/fmicb.2022.924533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/11/2022] [Indexed: 11/18/2022] Open
Abstract
Viruses contribute to the mortality of organisms, consequentially altering biological species composition of an ecosystem and having a threat on human health. As the most famous model for the initiation of virus infection, the Hershey-Chase experiment has revealed that on infection, the bacteriophage genomic DNA is injected into its host bacterium, while the viral capsid is left on the outer membrane of host cell. However, little is known about the injection of any other materials into the cytoplasm of host cells along with genomic DNA to trigger the virus life cycle. In this study, the results showed that palmitic amide packaged in the virions of GVE2, a bacteriophage infecting deep-sea hydrothermal vent thermophile Geobacillus sp. E263, promoted virus infection. Palmitic amide was interacted with acetate kinase to increase its enzymatic activity, thus enhancing the acetate-mediated energy metabolism. Furthermore, palmitic amide promoted tricarboxylic acid cycle (TCA cycle) to support virus infection. These data indicated that palmitic amide, packaged in the virions, might serve as a second messenger at the initiation step of virus infection by enhancing the host energy metabolism. Therefore our study revealed a novel mechanism for the initiation of the virus life cycle.
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Affiliation(s)
- Xinyi Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou, China
| | - Jianjian Zhuang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou, China
| | - Liquan Huang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou, China
| | - Xiaobo Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou, China
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Moorthy GS, Greenberg RG, Hornik CD, Cassino C, Ghahramani P, Kumar KR, Fowler VG, Cohen-Wolkowiez M. Safety and Pharmacokinetics of Exebacase in an Infant With Disseminated Staphylococcus aureus Infection. Clin Infect Dis 2021; 75:338-341. [PMID: 34894129 PMCID: PMC9410717 DOI: 10.1093/cid/ciab1015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 12/13/2022] Open
Abstract
Exebacase, an antistaphylococcal lysin produced from a bacteriophage-encoded gene, is a promising adjunctive therapy for severe methicillin-resistant Staphylococcus aureus infections. We describe the first infant to receive exebacase, dosing, and pharmacokinetics. Exebacase may be safe and efficacious in children; however, further clinical trials are needed to optimize dosing.
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Affiliation(s)
| | - Rachel G Greenberg
- Duke University Medical Center, Durham, North Carolina, USA,Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Chi D Hornik
- Duke University Medical Center, Durham, North Carolina, USA,Duke Clinical Research Institute, Durham, North Carolina, USA
| | | | | | - Karan R Kumar
- Duke University Medical Center, Durham, North Carolina, USA,Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Vance G Fowler
- Duke University Medical Center, Durham, North Carolina, USA,Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Michael Cohen-Wolkowiez
- Correspondence: M. Cohen-Wolkowiez, Duke Clinical Research Institute, 300 W Morgan St, Box 3850, Durham, NC 27701 ()
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Abstract
Control of pathogenic bacteria by deliberate application of predatory phages has potential as a powerful therapy against antibiotic-resistant bacteria. The key advantages of phage biocontrol over antibacterial chemotherapy are: (1) an ability to self-propagate inside host bacteria, (2) targeted predation of specific species or strains of bacteria, (3) adaptive molecular machinery to overcome resistance in target bacteria. However, realizing the potential of phage biocontrol is dependent on harnessing or adapting these responses, as many phage species switch between lytic infection cycles (resulting in lysis) and lysogenic infection cycles (resulting in genomic integration) that increase the likelihood of survival of the phage in response to external stress or host depletion. Similarly, host range will need to be optimized to make phage therapy medically viable whilst avoiding the potential for deleteriously disturbing the commensal microbiota. Phage training is a new approach to produce efficient phages by capitalizing on the evolved response of wild-type phages to bacterial resistance. Here we will review recent studies reporting successful trials of training different strains of phages to switch into lytic replication mode, overcome bacterial resistance, and increase their host range. This review will also highlight the current knowledge of phage training and future implications in phage applications and phage therapy and summarize the recent pipeline of the magistral preparation to produce a customized phage for clinical trials and medical applications.
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