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Gomez JB, Waters CM. A Vibrio cholerae Type IV restriction system targets glucosylated 5-hydroxymethylcytosine to protect against phage infection. J Bacteriol 2024:e0014324. [PMID: 39230524 DOI: 10.1128/jb.00143-24] [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: 04/05/2024] [Accepted: 08/03/2024] [Indexed: 09/05/2024] Open
Abstract
A major challenge faced by Vibrio cholerae is constant predation by bacteriophage (phage) in aquatic reservoirs and during infection of human hosts. To overcome phage predation, V. cholerae has acquired and/or evolved a myriad of phage defense systems. Although several novel defense systems have been discovered, we hypothesized that more were encoded in V. cholerae given the low diversity of phages that have been isolated, which infect this species. Using a V. cholerae genomic library, we identified a Type IV restriction system consisting of two genes within a 16-kB region of the Vibrio pathogenicity island-2, which we name TgvA and TgvB (Type I-embedded gmrSD-like system of VPI-2). We show that both TgvA and TgvB are required for defense against T2, T4, and T6 by targeting glucosylated 5-hydroxymethylcytosine (5hmC). T2 or T4 phages that lose the glucose modifications are resistant to TgvAB defense but exhibit a significant evolutionary tradeoff, becoming susceptible to other Type IV restriction systems that target unglucosylated 5hmC. We also show that the Type I restriction-modification system that embeds the tgvAB genes protects against phage T3, secΦ18, secΦ27, and λ, suggesting that this region is a phage defense island. Our study uncovers a novel Type IV restriction system in V. cholerae, increasing our understanding of the evolution and ecology of V. cholerae, while highlighting the evolutionary interplay between restriction systems and phage genome modification.IMPORTANCEBacteria are constantly being predated by bacteriophage (phage). To counteract this predation, bacteria have evolved a myriad of defense systems. Some of these systems specifically digest infecting phage by recognizing unique base modifications present on the phage DNA. In this study, we discover a Type IV restriction system encoded in V. cholerae, which we name TgvAB, and demonstrate it recognizes and restricts phage that have 5-hydroxymethylcytosine glucosylated DNA. Moreover, the evolution of resistance to TgvAB render phage susceptible to other Type IV restriction systems, demonstrating a significant evolutionary tradeoff. These results enhance our understanding of the evolution of V. cholerae and more broadly how bacteria evade phage predation.
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Affiliation(s)
- Jasper B Gomez
- Department of Microbiology, Genetics, & Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Christopher M Waters
- Department of Microbiology, Genetics, & Immunology, Michigan State University, East Lansing, Michigan, USA
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2
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Huang D, Xia R, Chen C, Liao J, Chen L, Wang D, Alvarez PJJ, Yu P. Adaptive strategies and ecological roles of phages in habitats under physicochemical stress. Trends Microbiol 2024; 32:902-916. [PMID: 38433027 DOI: 10.1016/j.tim.2024.02.002] [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: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rong Xia
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chengyi Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Linxing Chen
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Dongsheng Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314100, China.
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3
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Ikpe F, Williams T, Orok E, Ikpe A. Antimicrobial resistance: use of phage therapy in the management of resistant infections. Mol Biol Rep 2024; 51:925. [PMID: 39167154 DOI: 10.1007/s11033-024-09870-2] [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: 12/15/2023] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
The emergence and increase in antimicrobial resistance (AMR) is now widely recognized as a major public health challenge. Traditional antimicrobial drugs are becoming increasingly ineffective, while the development of new antibiotics is waning. As a result, alternative treatments for infections are garnering increased interest. Among these alternatives, bacteriophages, also known as phages, are gaining renewed attention and are reported to offer a promising solution to alleviate the burden of bacterial infections. This review discusses the current successes of phage therapy (PT) against multidrug-resistant organisms (MDROs), such as Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter spp. The review also compares the efficacy of PT with that of chemical antibiotics, reporting on its benefits and limitations, while highlighting its impact on the human gut microbiome and immune system. Despite its potential, phage therapy is reported to face challenges such as the narrow antibacterial range, the complexity of developing phage cocktails, and the need for precise dosing and duration protocols. Nevertheless, continued research, improved regulatory frameworks, and increased public awareness are essential to realize its full potential and integration into standard medical practice, paving the way for innovative treatments that can effectively manage infections in an era of rising antimicrobial resistance.
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Affiliation(s)
- Favour Ikpe
- Department of Pharmaceutical Microbiology and Biotechnology, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Tonfamoworio Williams
- Department of Pharmaceutical Microbiology and Biotechnology, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Edidiong Orok
- Department of Clinical Pharmacy and Public Health, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria.
| | - Augustine Ikpe
- Department of Sciences, Champion Group of Schools, Okene, Kogi State, Nigeria
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4
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Costa P, Pereira C, Romalde JL, Almeida A. A game of resistance: War between bacteria and phages and how phage cocktails can be the solution. Virology 2024; 599:110209. [PMID: 39186863 DOI: 10.1016/j.virol.2024.110209] [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: 05/29/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024]
Abstract
While phages hold promise as an antibiotic alternative, they encounter significant challenges in combating bacterial infections, primarily due to the emergence of phage-resistant bacteria. Bacterial defence mechanisms like superinfection exclusion, CRISPR, and restriction-modification systems can hinder phage effectiveness. Innovative strategies, such as combining different phages into cocktails, have been explored to address these challenges. This review delves into these defence mechanisms and their impact at each stage of the infection cycle, their challenges, and the strategies phages have developed to counteract them. Additionally, we examine the role of phage cocktails in the evolving landscape of antibacterial treatments and discuss recent studies that highlight the effectiveness of diverse phage cocktails in targeting essential bacterial receptors and combating resistant strains.
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Affiliation(s)
- Pedro Costa
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Carla Pereira
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CRETUS & CIBUS - Faculty of Biology, University of Santiago de Compostela, CP 15782 Santiago de Compostela, Spain.
| | - Adelaide Almeida
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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5
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Guo M, Zhang Y, Wu L, Xiong Y, Xia L, Cheng Y, Ma J, Wang H, Sun J, Wang Z, Yan Y. Development and mouse model evaluation of a new phage cocktail intended as an alternative to antibiotics for treatment of Staphylococcus aureus-induced bovine mastitis. J Dairy Sci 2024; 107:5974-5987. [PMID: 38522833 DOI: 10.3168/jds.2024-24540] [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: 12/13/2023] [Accepted: 02/19/2024] [Indexed: 03/26/2024]
Abstract
Bovine mastitis is a prevalent infectious disease in dairy herds worldwide, resulting in substantial economic losses. Staphylococcus aureus is a major cause of mastitis in animals, and its antibiotic resistance poses challenges for treatment. Recently, renewed interest has focused on the development of alternative methods to antibiotic therapy, including bacteriophages (phages), for controlling bacterial infections. In this study, 2 lytic phages, vB_SauM_JDYN (JDYN) and vB_SauM_JDF86 (JDF86), were isolated from the cattle sewage effluent samples collected from dairy farms in Shanghai. The 2 phages have a broad bactericidal spectrum against Staphylococcus of various origins. Genomic and morphological analyses revealed that the 2 phages belonged to the Myoviridae family. Moreover, JDYN and JDF86 remained stable under a wide temperature and pH range and were almost unaffected in chloroform. In this study, we prepared a phage cocktail (PHC-1) which consisted of a 1:1:1 ratio of JDYN, JDF86, and SLPW (a previously characterized phage). We found that PHC-1 showed the strongest bacteriolytic effect and the lowest frequency of emergence of bacteriophage insensitive mutants compared with monophages. Bovine mammary epithelial cells and lactating mice mastitis models were used to evaluate the effectiveness of PHC-1 in vitro and in vivo, respectively. The results demonstrated that PHC-1 treatment significantly reduced bacterial load, alleviated inflammatory response, and improved mastitis pathology. Altogether, these results suggest that PHC-1 has the potential to treat S. aureus-induced bovine mastitis and that phage cocktails can combat antibiotic-resistant S. aureus infections.
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Affiliation(s)
- Mengting Guo
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 201100, China
| | - Yumin Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 201100, China
| | - Lifei Wu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 201100, China
| | - Yangjing Xiong
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 201100, China
| | - Lu Xia
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 201100, China
| | - Yuqiang Cheng
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 201100, China
| | - Jingjiao Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 201100, China
| | - Hengan Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 201100, China
| | - Jianhe Sun
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 201100, China
| | - Zhaofei Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 201100, China.
| | - Yaxian Yan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 201100, China.
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Wan X, Mahillon J, Yuan Z, Zhang G, Geng P, Hu X. Characterization of vB_SalS_PSa2, a T5-like Demerecviridae bacteriophage, and its potential use in food matrices. Virology 2024; 596:110101. [PMID: 38754335 DOI: 10.1016/j.virol.2024.110101] [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: 01/22/2024] [Revised: 04/17/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024]
Abstract
This study characterizes a newly isolated Demerecviridae phage, named vB_SalS_PSa2, belonging to the phage T5 group. The main variations between vB_SalS_PSa2 and T5 concern structural proteins related to morphology and host recognition. vB_SalS_PSa2 is infective to 19 out of the 25 tested Salmonella enterica (including the rare "Sendai" and "Equine" serotypes) and Escherichia coli isolates, most of them being multidrug resistant. vB_SalS_PSa2 displayed good thermal stability (4-60 °C) and broad pH stability (4.0-12.0). It also exhibited antibacterial activity against S. enterica sv. Paratyphi A Enb50 at 4 °C in milk during the whole tested period (5 d), and for 3-6 h at both 25 and 37 °C. Furthermore, vB_SalS_PSa2 was able to inhibit biofilm formation and to show degradation activity on mature biofilms of E. coli K12 and S. enterica sv. Paratyphi Enb50 in both LB and milk. Altogether, these results indicate that phage vB_SalS_PSa2 is a valuable candidate for controlling foodborne S. enterica and E. coli pathogens.
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Affiliation(s)
- Xiaofu Wan
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, B-1348, Belgium
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430070, China
| | - Gan Zhang
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Peiling Geng
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Xiaomin Hu
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China.
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7
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Parker DR, Nugen SR. Bacteriophage-Based Bioanalysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:393-410. [PMID: 39018352 DOI: 10.1146/annurev-anchem-071323-084224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
Bacteriophages, which are viral predators of bacteria, have evolved to efficiently recognize, bind, infect, and lyse their host, resulting in the release of tens to hundreds of propagated viruses. These abilities have attracted biosensor developers who have developed new methods to detect bacteria. Recently, several comprehensive reviews have covered many of the advances made regarding the performance of phage-based biosensors. Therefore, in this review, we first describe the landscape of phage-based biosensors and then cover advances in other aspects of phage biology and engineering that can be used to make high-impact contributions to biosensor development. Many of these advances are in fields adjacent to analytical chemistry such as synthetic biology, machine learning, and genetic engineering and will allow those looking to develop phage-based biosensors to start taking alternative approaches, such as a bottom-up design and synthesis of custom phages with the singular task of detecting their host.
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Affiliation(s)
- David R Parker
- Department of Food Science, Cornell University, Ithaca, New York, USA;
| | - Sam R Nugen
- Department of Food Science, Cornell University, Ithaca, New York, USA;
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Barrio-Pujante A, Bleriot I, Blasco L, Fernández-Garcia L, Pacios O, Ortiz-Cartagena C, Cuenca FF, Oteo-Iglesias J, Tomás M. Regulation of anti-phage defense mechanisms by using cinnamaldehyde as a quorum sensing inhibitor. Front Microbiol 2024; 15:1416628. [PMID: 38989015 PMCID: PMC11233531 DOI: 10.3389/fmicb.2024.1416628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024] Open
Abstract
Background Multidrug-resistant bacteria and the shortage of new antibiotics constitute a serious health problem. This problem has led to increased interest in the use of bacteriophages, which have great potential as antimicrobial agents but also carry the risk of inducing resistance. The objective of the present study was to minimize the development of phage resistance in Klebsiella pneumoniae strains by inhibiting quorum sensing (QS) and thus demonstrate the role of QS in regulating defense mechanisms. Results Cinnamaldehyde (CAD) was added to K. pneumoniae cultures to inhibit QS and thus demonstrate the role of the signaling system in regulating the anti-phage defense mechanism. The QS inhibitory activity of CAD in K. pneumoniae was confirmed by a reduction in the quantitative expression of the lsrB gene (AI-2 pathway) and by proteomic analysis. The infection assays showed that the phage was able to infect a previously resistant K. pneumoniae strain in the cultures to which CAD was added. The results were confirmed using proteomic analysis. Thus, anti-phage defense-related proteins from different systems, such as cyclic oligonucleotide-based bacterial anti-phage signaling systems (CBASS), restriction-modification (R-M) systems, clustered regularly interspaced short palindromic repeat-Cas (CRISPR-Cas) system, and bacteriophage control infection (BCI), were present in the cultures with phage but not in the cultures with phage and CAD. When the QS and anti-phage defense systems were inhibited by the combined treatment, proteins related to phage infection and proliferation, such as the tail fiber protein, the cell division protein DamX, and the outer membrane channel protein TolC, were detected. Conclusion Inhibition of QS reduces phage resistance in K. pneumoniae, resulting in the infection of a previously resistant strain by phage, with a significant increase in phage proliferation and a significant reduction in bacterial growth. QS inhibitors could be considered for therapeutic application by including them in phage cocktails or in phage-antibiotic combinations to enhance synergistic effects and reduce the emergence of antimicrobial resistance.
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Affiliation(s)
- Antonio Barrio-Pujante
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Inés Bleriot
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Lucía Blasco
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Laura Fernández-Garcia
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Olga Pacios
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Concha Ortiz-Cartagena
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Felipe Fernández Cuenca
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena, Instituto de Biomedicina de Sevilla (Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla), Sevilla, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- MEPRAM, Proyecto de Medicina de Precisión Contra las Resistencias Antimicrobianas, Madrid, Spain
| | - Jesús Oteo-Iglesias
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- MEPRAM, Proyecto de Medicina de Precisión Contra las Resistencias Antimicrobianas, Madrid, Spain
- Laboratorio de Referencia e Investigación de Resistencias a Antibióticos e Infecciones Sanitarias, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María Tomás
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
- MEPRAM, Proyecto de Medicina de Precisión Contra las Resistencias Antimicrobianas, Madrid, Spain
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Chin KW, Khoo SC, Paul RPM, Luang-In V, Lam SD, Ma NL. Potential of Synbiotics and Probiotics as Chemopreventive Agent. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10299-z. [PMID: 38896220 DOI: 10.1007/s12602-024-10299-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2024] [Indexed: 06/21/2024]
Abstract
Cancer remains a global problem, with millions of new cases diagnosed yearly and countless lives lost. The financial burden of cancer therapy, along with worries about the long-term safety of existing medicines, necessitates the investigation of alternative approaches to cancer prevention. Probiotics generate chemopreventive compounds such as bacteriocins, short-chain fatty acids (SCFA), and extracellular polymeric substances (EPS), which have demonstrated the ability to impede cancer cell proliferation, induce apoptosis, and bolster the expression of pro-apoptotic genes. On the other hand, prebiotics, classified as non-digestible food ingredients, promote the proliferation of probiotics within the colon, thereby ensuring sustained functionality of the gut microbiota. Consequently, the synergistic effect of combining prebiotics with probiotics, known as the synbiotic effect, in dietary interventions holds promise for potentially mitigating cancer risk and augmenting preventive measures. The utilization of gut microbiota in cancer treatment has shown promise in alleviating adverse health effects. This review explored the potential and the role of probiotics and synbiotics in enhancing health and contributing to cancer prevention efforts. In this review, the applications of functional probiotics and synbiotics, the mechanisms of action of probiotics in cancer, and the relationship of probiotics with various drugs were discussed, shedding light on the potential of probiotics and synbiotics to alleviate the burdens of cancer treatment.
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Affiliation(s)
- Kah Wei Chin
- Bioses Research Interest Group (BIOSES), Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, 21030, Terengganu, Malaysia
| | - Shing Ching Khoo
- Bioses Research Interest Group (BIOSES), Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, 21030, Terengganu, Malaysia
| | - Richard Paul Merisha Paul
- Bioses Research Interest Group (BIOSES), Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, 21030, Terengganu, Malaysia
| | - Vijitra Luang-In
- Natural Antioxidant Innovation Research Unit, Department of Biotechnology, Faculty of Technology, Mahasarakham University, Khamriang, 44150, Kantarawichai, Maha Sarakham, Thailand
| | - Su Datt Lam
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Nyuk Ling Ma
- Bioses Research Interest Group (BIOSES), Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, 21030, Terengganu, Malaysia.
- Department of Sustainable Engineering, Institute of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India.
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10
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Xu Q, Tang L, Liu W, Xu N, Hu Y, Zhang Y, Chen S. Phage protein Gp11 blocks Staphylococcus aureus cell division by inhibiting peptidoglycan biosynthesis. mBio 2024; 15:e0067924. [PMID: 38752726 PMCID: PMC11237401 DOI: 10.1128/mbio.00679-24] [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: 03/08/2024] [Accepted: 04/10/2024] [Indexed: 06/13/2024] Open
Abstract
Phages and bacteria have a long history of co-evolution. However, these dynamics of phage-host interactions are still largely unknown; identification of phage inhibitors that remodel host metabolism will provide valuable information for target development for antimicrobials. Here, we perform a comprehensive screen for early-gene products of ΦNM1 that inhibit cell growth in Staphylococcus aureus. A small membrane protein, Gp11, with inhibitory effects on S. aureus cell division was identified. A bacterial two-hybrid library containing 345 essential S. aureus genes was constructed to screen for targets of Gp11, and Gp11 was found to interact with MurG and DivIC. Defects in cell growth and division caused by Gp11 were dependent on MurG and DivIC, which was further confirmed using CRISPRi hypersensitivity assay. Gp11 interacts with MurG, the protein essential for cell wall formation, by inhibiting the production of lipid II to regulate peptidoglycan (PG) biosynthesis on the cell membrane. Gp11 also interacts with cell division protein DivIC, an essential part of the division machinery necessary for septal cell wall assembly, to disrupt the recruitment of division protein FtsW. Mutations in Gp11 result in loss of its ability to cause growth defects, whereas infection with phage in which the gp11 gene has been deleted showed a significant increase in lipid II production in S. aureus. Together, our findings reveal that a phage early-gene product interacts with essential host proteins to disrupt PG biosynthesis and block S. aureus cell division, suggesting a potential pathway for the development of therapeutic approaches to treat pathogenic bacterial infections. IMPORTANCE Understanding the interplay between phages and their hosts is important for the development of novel therapies against pathogenic bacteria. Although phages have been used to control methicillin-resistant Staphylococcus aureus infections, our knowledge related to the processes in the early stages of phage infection is still limited. Owing to the fact that most of the phage early proteins have been classified as hypothetical proteins with uncertain functions, we screened phage early-gene products that inhibit cell growth in S. aureus, and one protein, Gp11, selectively targets essential host genes to block the synthesis of the peptidoglycan component lipid II, ultimately leading to cell growth arrest in S. aureus. Our study provides a novel insight into the strategy by which Gp11 blocks essential host cellular metabolism to influence phage-host interaction. Importantly, dissecting the interactions between phages and host cells will contribute to the development of new and effective therapies to treat bacterial infections.
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Affiliation(s)
- Qi Xu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Tang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weilin Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Neng Xu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yong Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Shiyun Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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11
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Azam AH, Sato K, Miyanaga K, Nakamura T, Ojima S, Kondo K, Tamura A, Yamashita W, Tanji Y, Kiga K. Selective bacteriophages reduce the emergence of resistant bacteria in bacteriophage-antibiotic combination therapy. Microbiol Spectr 2024; 12:e0042723. [PMID: 38695573 PMCID: PMC11237537 DOI: 10.1128/spectrum.00427-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/09/2024] [Indexed: 06/06/2024] Open
Abstract
Escherichia coli O157:H7 is a globally important foodborne pathogen with implications for food safety. Antibiotic treatment for O157 may potentially contribute to the exacerbation of hemolytic uremic syndrome, and the increasing prevalence of antibiotic-resistant strains necessitates the development of new treatment strategies. In this study, the bactericidal effects and resistance development of antibiotic and bacteriophage monotherapy were compared with those of combination therapy against O157. Experiments involving continuous exposure of O157 to phages and antibiotics, along with genetic deletion studies, revealed that the deletion of glpT and uhpT significantly increased resistance to fosfomycin. Furthermore, we found that OmpC functions as a receptor for the PP01 phage, which infects O157, and FhuA functions as a receptor for the newly isolated SP15 phage, targeting O157. In the glpT and uhpT deletion mutants, additional deletion in ompC, the receptor for the PP01 phage, increased resistance to fosfomycin. These findings suggest that specific phages may contribute to antibiotic resistance by selecting the emergence of gene mutations responsible for both phage and antibiotic resistance. While combination therapy with phages and antibiotics holds promise for the treatment of bacterial infections, careful consideration of phage selection is necessary.IMPORTANCEThe combination treatment of fosfomycin and bacteriophages against Escherichia coli O157 demonstrated superior bactericidal efficacy compared to monotherapy, effectively suppressing the emergence of resistance. However, mutations selected by phage PP01 led to enhanced resistance not only to the phage but also to fosfomycin. These findings underscore the importance of exercising caution in selecting phages for combination therapy, as resistance selected by specific phages may increase the risk of developing antibiotic resistance.
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Affiliation(s)
- Aa Haeruman Azam
- Therapeutic Drugs and Vaccine Development Research Center, National Institute of Infectious Diseases, Toyama-ku, Shinjuku, Tokyo, Japan
| | - Koji Sato
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsutacho, Yokohama, Japan
| | - Kazuhiko Miyanaga
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsutacho, Yokohama, Japan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsukeshi, Tochigi, Japan
| | - Tomohiro Nakamura
- Therapeutic Drugs and Vaccine Development Research Center, National Institute of Infectious Diseases, Toyama-ku, Shinjuku, Tokyo, Japan
| | - Shinjiro Ojima
- Therapeutic Drugs and Vaccine Development Research Center, National Institute of Infectious Diseases, Toyama-ku, Shinjuku, Tokyo, Japan
| | - Kohei Kondo
- Therapeutic Drugs and Vaccine Development Research Center, National Institute of Infectious Diseases, Toyama-ku, Shinjuku, Tokyo, Japan
| | - Azumi Tamura
- Therapeutic Drugs and Vaccine Development Research Center, National Institute of Infectious Diseases, Toyama-ku, Shinjuku, Tokyo, Japan
| | - Wakana Yamashita
- Therapeutic Drugs and Vaccine Development Research Center, National Institute of Infectious Diseases, Toyama-ku, Shinjuku, Tokyo, Japan
| | - Yasunori Tanji
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsutacho, Yokohama, Japan
| | - Kotaro Kiga
- Therapeutic Drugs and Vaccine Development Research Center, National Institute of Infectious Diseases, Toyama-ku, Shinjuku, Tokyo, Japan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsukeshi, Tochigi, Japan
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12
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Zeng Y, Shen M, Liu S, Zhou X. Characterization and resistance mechanism of phage-resistant strains of Salmonella enteritidis. Poult Sci 2024; 103:103756. [PMID: 38652948 PMCID: PMC11063523 DOI: 10.1016/j.psj.2024.103756] [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: 02/07/2024] [Revised: 03/25/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024] Open
Abstract
In the face of the increasingly severe problem of antibiotic resistance, phage therapy is regarded as a highly potential alternative. Compared with traditional antimicrobial agents, a key research area of phage therapy is the study of phage-resistant mutant bacteria. To effectively monitor and prevent this resistance, it is crucial to conduct in-depth exploration of the mechanism behind phage resistance. In this study, a strain of Salmonella enteritidis (sm140) and the corresponding phage (Psm140) were isolated from chicken liver and sewage, respectively. Using the double-layer plate method, successfully screened out phage-resistant mutant strains. Whole-genome resequencing of 3 resistant strains found that the wbaP gene of all 3 strains had mutations at a specific position (1,118), with the base changing from G to A. This mutation causes the gene-encoded glycine to be replaced by aspartic acid. Subsequent studies found that the frequency of this gene mutation is extremely high, reaching 84%, and all mutations occur at the same position. To further explore the relationship between the wbaP gene and phage resistance, knockout strains and complement strains of the wbaP gene were constructed. The experimental results confirmed the association between the wbaP gene and phage resistance. At the same time, biological characteristics and virulence were evaluated for wild strains, resistant strains, knockout strains, and complement strains. It was found that mutations or deletions of the wbaP gene lead to a decrease in bacterial environmental adaptability and virulence. Through systematic research on the mechanism and biological characteristics of phage resistance, this study provides important references and guidance for the development of new phage therapies, promoting progress in the field of antimicrobial treatment. At the same time, the emergence of phage resistance due to wbaP gene mutations is reported for the first time in salmonella, providing a new perspective and ideas for further studying phage resistance mechanisms.
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Affiliation(s)
- Yukun Zeng
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Mangmang Shen
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Shenglong Liu
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Xin Zhou
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
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13
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Li P, Guo G, Zheng X, Xu S, Zhou Y, Qin X, Hu Z, Yu Y, Tan Z, Ma J, Chen L, Zhang W. Therapeutic efficacy of a K5-specific phage and depolymerase against Klebsiella pneumoniae in a mouse model of infection. Vet Res 2024; 55:59. [PMID: 38715095 PMCID: PMC11077817 DOI: 10.1186/s13567-024-01311-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/14/2024] [Indexed: 05/12/2024] Open
Abstract
Klebsiella pneumoniae has become one of the most intractable gram-negative pathogens infecting humans and animals due to its severe antibiotic resistance. Bacteriophages and protein products derived from them are receiving increasing amounts of attention as potential alternatives to antibiotics. In this study, we isolated and investigated the characteristics of a new lytic phage, P1011, which lyses K5 K. pneumoniae specifically among 26 serotypes. The K5-specific capsular polysaccharide-degrading depolymerase dep1011 was identified and expressed. By establishing murine infection models using bovine strain B16 (capable of supporting phage proliferation) and human strain KP181 (incapable of sustaining phage expansion), we explored the safety and efficacy of phage and dep1011 treatments against K5 K. pneumoniae. Phage P1011 resulted in a 60% survival rate of the mice challenged with K. pneumoniae supporting phage multiplication, concurrently lowering the bacterial burden in their blood, liver, and lungs. Unexpectedly, even when confronted with bacteria impervious to phage multiplication, phage therapy markedly decreased the number of viable organisms. The protective efficacy of the depolymerase was significantly better than that of the phage. The depolymerase achieved 100% survival in both treatment groups regardless of phage propagation compatibility. These findings indicated that P1011 and dep1011 might be used as potential antibacterial agents to control K5 K. pneumoniae infection.
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Affiliation(s)
- Pei Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China
- The Sanya Institute of Nanjing Agricultural University, Yabulun Industrial Park, Yazhou Bay Science and Technology City, Sanya, 572024, China
| | - Genglin Guo
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Xiangkuan Zheng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China
- The Sanya Institute of Nanjing Agricultural University, Yabulun Industrial Park, Yazhou Bay Science and Technology City, Sanya, 572024, China
| | - Sixiang Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China
- The Sanya Institute of Nanjing Agricultural University, Yabulun Industrial Park, Yazhou Bay Science and Technology City, Sanya, 572024, China
| | - Yu Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China
- The Sanya Institute of Nanjing Agricultural University, Yabulun Industrial Park, Yazhou Bay Science and Technology City, Sanya, 572024, China
| | - Xiayan Qin
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China
| | - Zimeng Hu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China
- The Sanya Institute of Nanjing Agricultural University, Yabulun Industrial Park, Yazhou Bay Science and Technology City, Sanya, 572024, China
| | - Yanfei Yu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Zhongming Tan
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210014, China
| | - Jiale Ma
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China
| | - Long Chen
- Department of Clinical Laboratory, Zhangjiagang Hospital Affiliated to Soochow University, Zhangjiagang, 215600, China.
| | - Wei Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China.
- The Sanya Institute of Nanjing Agricultural University, Yabulun Industrial Park, Yazhou Bay Science and Technology City, Sanya, 572024, China.
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14
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Li Y, Zhou W, Gao Y, Li X, Yuan L, Zhu G, Gu X, Yang Z. Nanozyme colourimetry based on temperate bacteriophage for rapid and sensitive detection of Staphylococcus aureus in food matrices. Int J Food Microbiol 2024; 416:110657. [PMID: 38452659 DOI: 10.1016/j.ijfoodmicro.2024.110657] [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: 10/31/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024]
Abstract
Although bacteriophage-based biosensors are promising tools for rapid, convenient, and sensitive detection of Staphylococcus aureus in food products, the effect of biosensors using temperate phages as biorecognition elements to detect viable S. aureus isolates remains unclear. In this study, three temperate S. aureus phages were isolated and their biological features (one-step growth, host range, pH stability, temperature stability, and adsorption rate) were evaluated as the biological element. The selected phage SapYZUs8 was immobilized on the nanozyme Cu-MOF via electrostatic interactions to generate SapYZUs8@Cu-MOF, and its detection performance in real food (skim milk and pork) was then evaluated. Compared with phages SapYZUm7 and SapYZUs16, phage SapYZUs8 exhibited a broader host range, greater pH stability (3-12), and a better absorption rate (92 %, 8 min) suitable for S. aureus detection, which is likely the result of the DNA replication (DNA helicase) and phage tail protein genes in the SapYZUs8 genome. Therefore, phage SapYZUs8 was fixed on Cu-MOF to generate SapYZUs8@Cu-MOF, which exhibited good sensitivity and specificity for rapid colourimetric detection of viable S. aureus. The method took <0.5 h, and the detection limit was 1.09 × 102 CFU/mL. In addition, SapYZUs8@Cu-MOF was successfully employed for the colourimetric detection of S. aureus in food samples without interference from different food additives, NaCl concentrations, or pH values. With these benefits, it allows rapid visual assessment of S. aureus levels.
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Affiliation(s)
- Yajie Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Wenyuan Zhou
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Yajun Gao
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Xuan Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Lei Yuan
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xuewen Gu
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhenquan Yang
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China
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15
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Antoine C, Laforêt F, Fall A, Blasdel B, Delcenserie V, Thiry D. K1 capsule-dependent phage-driven evolution in Escherichia coli leading to phage resistance and biofilm production. J Appl Microbiol 2024; 135:lxae109. [PMID: 38688866 DOI: 10.1093/jambio/lxae109] [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: 11/13/2023] [Revised: 03/27/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
AIMS Understanding bacterial phage resistance mechanisms has implications for developing phage-based therapies. This study aimed to explore the development of phage resistance in Escherichia coli K1 isolates' to K1-ULINTec4, a K1-dependent bacteriophage. METHODS AND RESULTS Resistant colonies were isolated from two different strains (APEC 45 and C5), both previously exposed to K1-ULINTec4. Genome analysis and several parameters were assessed, including growth capacity, phage adsorption, phenotypic impact at capsular level, biofilm production, and virulence in the in vivo Galleria mellonella larvae model. One out of the six resistant isolates exhibited a significantly slower growth rate, suggesting the presence of a resistance mechanism altering its fitness. Comparative genomic analysis revealed insertion sequences in the region 2 of the kps gene cluster involved in the capsule biosynthesis. In addition, an immunoassay targeting the K1 capsule showed a very low positive reaction compared to the control. Nevertheless, microscopic images of resistant strains revealed the presence of capsules with a clustered organization of bacterial cells and biofilm assessment showed an increased biofilm production compared to the sensitive strains. In the G. mellonella model, larvae infected with phage-resistant isolates showed better survival rates than larvae infected with phage-sensitive strains. CONCLUSIONS A phage resistance mechanism was identified at the genomic level and had a negative impact on the K1 capsule production. The resistant isolates showed an increased biofilm production and a decreased virulence in vivo.
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Affiliation(s)
- Céline Antoine
- Department of Infectious and Parasitic Diseases, Veterinary bacteriology, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium
- Food Science Department, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium
| | - Fanny Laforêt
- Department of Infectious and Parasitic Diseases, Veterinary bacteriology, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium
- Food Science Department, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium
| | | | - Bob Blasdel
- Vésale Bioscience, Vésale Pharmaceutica, 5310 Noville-sur-Mehaigne, Belgium
| | - Véronique Delcenserie
- Food Science Department, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium
| | - Damien Thiry
- Department of Infectious and Parasitic Diseases, Veterinary bacteriology, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium
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16
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Xu Y, Yang T, Miao Y, Zhang Q, Yang M, Mao C. Injectable Phage-Loaded Microparticles Effectively Release Phages to Kill Methicillin-Resistant Staphylococcus aureus. ACS APPLIED MATERIALS & INTERFACES 2024; 16:17232-17241. [PMID: 38554078 PMCID: PMC11009905 DOI: 10.1021/acsami.3c19443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 01/30/2024] [Indexed: 04/01/2024]
Abstract
The increasing prevalence of bacterial multidrug antibiotic resistance has led to a serious threat to public health, emphasizing the urgent need for alternative antibacterial therapeutics. Lytic phages, a class of viruses that selectively infect and kill bacteria, offer promising potential as alternatives to antibiotics. However, injectable carriers with a desired release profile remain to be developed to deliver them to infection sites. To address this challenge, phage-loaded microparticles (Phage-MPs) have been developed to deliver phages to the infection site and release phages for an optimal therapeutic effect. The Phage-MPs are synthesized by allowing phages to be electrostatically attached onto the porous polyethylenimine-modified silk fibroin microparticles (SF-MPs). The high specific surface area of SF-MPs allows them to efficiently load phages, reaching about 1.25 × 1010 pfu per mg of microparticles. The Phage-MPs could release phages in a controlled manner to achieve potent antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). Unlike the diffuse biodistribution of free phages post-intraperitoneal injection, Phage-MPs could continuously release phages to effectively boost the local phage concentration at the bacterial infection site after they are intraperitoneally injected into an abdominal MRSA-infected mouse model. In a mouse abdominal MRSA infection model, Phage-MPs significantly reduce the bacterial load in major organs, achieving an efficient therapeutic effect. Furthermore, Phage-MPs demonstrate outstanding biocompatibility both in vitro and in vivo. Overall, our research lays the foundation for a new generation of phage-based therapies to combat antibiotic-resistant bacterial infections.
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Affiliation(s)
- Yajing Xu
- School
of Materials Science and Engineering, Zhejiang
University, Hangzhou 310058, Zhejiang, China
| | - Tao Yang
- School
of Materials Science and Engineering, Zhejiang
University, Hangzhou 310058, Zhejiang, China
| | - Yao Miao
- School
of Materials Science and Engineering, Zhejiang
University, Hangzhou 310058, Zhejiang, China
| | - Qinglei Zhang
- Institute
of Applied Bioresource Research, College of Animal Science, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, Zhejiang, China
| | - Mingying Yang
- Institute
of Applied Bioresource Research, College of Animal Science, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, Zhejiang, China
| | - Chuanbin Mao
- Department
of Biomedical Engineering, The Chinese University
of Hong Kong, Shatin 999077, Hong Kong SAR, China
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17
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Gomez JB, Waters CM. A Vibrio cholerae Type IV restriction system targets glucosylated 5-hydroxyl methyl cytosine to protect against phage infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588314. [PMID: 38617239 PMCID: PMC11014532 DOI: 10.1101/2024.04.05.588314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A major challenge faced by Vibrio cholerae is constant predation by bacteriophage (phage) in aquatic reservoirs and during infection of human hosts. To overcome phage predation, V. cholerae has evolved a myriad of phage defense systems. Although several novel defense systems have been discovered, we hypothesized more were encoded in V. cholerae given the relative paucity of phage that have been isolated which infect this species. Using a V. cholerae genomic library, we identified a Type IV restriction system consisting of two genes within a 16kB region of the Vibrio pathogenicity island-2 that we name TgvA and TgvB (Type I-embedded gmrSD-like system of VPI-2). We show that both TgvA and TgvB are required for defense against T2, T4, and T6 by targeting glucosylated 5-hydroxymethylcytosine (5hmC). T2 or T4 phages that lose the glucose modification are resistant to TgvAB defense but exhibit a significant evolutionary tradeoff becoming susceptible to other Type IV restriction systems that target unglucosylated 5hmC. We show that additional phage defense genes are encoded in VPI-2 that protect against other phage like T3, secΦ18, secΦ27 and λ. Our study uncovers a novel Type IV restriction system in V. cholerae, increasing our understanding of the evolution and ecology of V. cholerae while highlighting the evolutionary interplay between restriction systems and phage genome modification.
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Affiliation(s)
- Jasper B Gomez
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Christopher M Waters
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
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18
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Roughgarden J. Lytic/Lysogenic Transition as a Life-History Switch. Virus Evol 2024; 10:veae028. [PMID: 38756985 PMCID: PMC11097211 DOI: 10.1093/ve/veae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 05/18/2024] Open
Abstract
The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.
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Affiliation(s)
- Joan Roughgarden
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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19
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Acton L, Pye HV, Thilliez G, Kolenda R, Matthews M, Turner AK, Yasir M, Holden E, Al-Khanaq H, Webber M, Adriaenssens EM, Kingsley RA. Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica. J Virol 2024; 98:e0147623. [PMID: 38376991 PMCID: PMC10949491 DOI: 10.1128/jvi.01476-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing, and agriculture. In this study, we isolated 12 bacteriophages termed SPLA phage which infect the foodborne pathogen Salmonella enterica. To determine phage host range, a diverse collection of Enterobacteriaceae and Salmonella enterica was used and genes involved in infection by six SPLA phages were identified using Salmonella Typhimurium strain ST4/74. Candidate host receptors included lipopolysaccharide (LPS), cellulose, and BtuB. Lipopolysaccharide was identified as a susceptibility factor for phage SPLA1a and mutations in LPS biosynthesis genes spontaneously emerged during culture with S. Typhimurium. Conversely, LPS was a resistance factor for phage SPLA5b which suggested that emergence of LPS mutations in culture with SPLA1a represented collateral sensitivity to SPLA5b. We show that bacteria-phage co-culture with SPLA1a and SPLA5b was more successful in limiting the emergence of phage resistance compared to single phage co-culture. Identification of host susceptibility and resistance genes and understanding infection dynamics are critical steps in the rationale design of phage cocktails against specific bacterial pathogens.IMPORTANCEAs antibiotic resistance continues to emerge in bacterial pathogens, bacterial viruses (phage) represent a potential alternative or adjunct to antibiotics. One challenge for their implementation is the predisposition of bacteria to rapidly acquire resistance to phages. We describe a functional genomics approach to identify mechanisms of susceptibility and resistance for newly isolated phages that infect and lyse Salmonella enterica and use this information to identify phage combinations that exploit collateral sensitivity, thus increasing efficacy. Collateral sensitivity is a phenomenon where resistance to one class of antibiotics increases sensitivity to a second class of antibiotics. We report a functional genomics approach to rationally design a phage combination with a collateral sensitivity dynamic which resulted in increased efficacy. Considering such evolutionary trade-offs has the potential to manipulate the outcome of phage therapy in favor of resolving infection without selecting for escape mutants and is applicable to other virus-host interactions.
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Affiliation(s)
- Luke Acton
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | - Hannah V. Pye
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | - Gaëtan Thilliez
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Rafał Kolenda
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Michaela Matthews
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - A. Keith Turner
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Muhammad Yasir
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Emma Holden
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Haider Al-Khanaq
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Mark Webber
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | | | - Robert A. Kingsley
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
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20
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Al-Adham ISI, Jaber N, Ali Agha ASA, Al-Remawi M, Al-Akayleh F, Al-Muhtaseb N, Collier PJ. Sporadic regional re-emergent cholera: a 19th century problem in the 21st century. J Appl Microbiol 2024; 135:lxae055. [PMID: 38449342 DOI: 10.1093/jambio/lxae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 02/24/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Cholera, caused by Vibrio cholerae, is a severe diarrheal disease that necessitates prompt diagnosis and effective treatment. This review comprehensively examines various diagnostic methods, from traditional microscopy and culture to advanced nucleic acid testing like polymerase spiral reaction and rapid diagnostic tests, highlighting their advantages and limitations. Additionally, we explore evolving treatment strategies, with a focus on the challenges posed by antibiotic resistance due to the activation of the SOS response pathway in V. cholerae. We discuss promising alternative treatments, including low-pressure plasma sterilization, bacteriophages, and selenium nanoparticles. The paper emphasizes the importance of multidisciplinary approaches combining novel diagnostics and treatments in managing and preventing cholera, a persistent global health challenge. The current re-emergent 7th pandemic of cholera commenced in 1961 and shows no signs of abeyance. This is probably due to the changing genetic profile of V. cholerae concerning bacterial pathogenic toxins. Given this factor, we argue that the disease is effectively re-emergent, particularly in Eastern Mediterranean countries such as Lebanon, Syria, etc. This review considers the history of the current pandemic, the genetics of the causal agent, and current treatment regimes. In conclusion, cholera remains a significant global health challenge that requires prompt diagnosis and effective treatment. Understanding the history, genetics, and current treatments is crucial in effectively addressing this persistent and re-emergent disease.
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Affiliation(s)
- Ibrahim S I Al-Adham
- Faculty of Pharmacy and Medical Sciences, University of Petra, Amman 961343, Jordan
| | - Nisrein Jaber
- Faculty of Pharmacy, Al Zaytoonah University of Jordan, Amman 11733, Jordan
| | - Ahmed S A Ali Agha
- Faculty of Pharmacy and Medical Sciences, University of Petra, Amman 961343, Jordan
| | - Mayyas Al-Remawi
- Faculty of Pharmacy and Medical Sciences, University of Petra, Amman 961343, Jordan
| | - Faisal Al-Akayleh
- Faculty of Pharmacy and Medical Sciences, University of Petra, Amman 961343, Jordan
| | - Najah Al-Muhtaseb
- Faculty of Pharmacy and Medical Sciences, University of Petra, Amman 961343, Jordan
| | - Phillip J Collier
- Faculty of Pharmacy and Medical Sciences, University of Petra, Amman 961343, Jordan
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21
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Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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22
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Olovo CV, Wiredu Ocansey DK, Ji Y, Huang X, Xu M. Bacterial membrane vesicles in the pathogenesis and treatment of inflammatory bowel disease. Gut Microbes 2024; 16:2341670. [PMID: 38666762 PMCID: PMC11057571 DOI: 10.1080/19490976.2024.2341670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/08/2024] [Indexed: 05/01/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic and debilitating condition of relapsing and remitting inflammation in the gastrointestinal tract. Conventional therapeutic approaches for IBD have shown limited efficacy and detrimental side effects, leading to the quest for novel and effective treatment options for the disease. Bacterial membrane vesicles (MVs) are nanosized lipid particles secreted by lysis or blebbing processes from both Gram-negative and Gram-positive bacteria. These vesicles, known to carry bioactive components, are facsimiles of the parent bacterium and have been implicated in the onset and progression, as well as in the amelioration of IBD. This review discusses the overview of MVs and their impact in the pathogenesis, diagnosis, and treatment of IBD. We further discuss the technical challenges facing this research area and possible research questions addressing these challenges. We summarize recent advances in the diverse relationship between IBD and MVs, and the application of this knowledge as a viable and potent therapeutic strategy for IBD.
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Affiliation(s)
- Chinasa Valerie Olovo
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
- Department of Medical Laboratory Science, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Ying Ji
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xinxiang Huang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Digestive Diseases, Jiangsu University, Zhenjiang, Jiangsu, China
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23
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das Neves Costa LCP, Siqueira JAM, Teixeira DM, da Piedade GJL, Júnior ECS, Ferreira JL, da Silva LD, Gabbay YB. Circulation of adenovirus and other viruses in urban drainage channels: an environmental surveillance in Belém, Amazon region, Brazil. Braz J Microbiol 2023; 54:2939-2949. [PMID: 37747624 PMCID: PMC10689653 DOI: 10.1007/s42770-023-01125-9] [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: 06/15/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Urban channels in amazon cities are very polluted, with garbage and sewage disposal in these aquatic environments, favoring the high dissemination of waterborne viruses such as human adenovirus (HAdV). The aim of this study was to perform the detection and molecular characterization of adenovirus in urban channels and in a wastewater treatment plant located in a metropolitan city in the Amazon. Additionally, metagenomic analyses were performed to assess viral diversity. Samples were concentrated by organic flocculation, analyzed by quantitative real time PCR (qPCR) and sequenced (Sanger e next generation sequencing). Cell culture was performed to verify the viability of HAdV particles. A total of 104 samples were collected, being the HAdV positivity of 76% (79/104). Among the positive samples, 29.1% (23/79) were characterized as HAdV-F40 (87%, 20/23), HAdV-F41 (8.7%, 2/23), and HAdV-B (4.3%, 1/23). Average precipitation rates ranged from 163 to 614 mm, while the pH ranged from 6.9 to 7.6. Eight positive samples were inoculated into A549 cells and in 4 of these, was observed changes in the structure of the cell monolayer, alteration in the structure of the cell monolayer was observed, but without amplification when analyzed by PCR. The metagenomic data demonstrated the presence of 14 viral families, being the most abundant: Myoviridae (41% of available reads), Siphoviridae (24.5%), Podoviridae (14.1%), and Autographiviridae (6.9%) with more than 85% of the total number of identified reads. This study reinforcing that continuous surveillance may contribute to monitoring viral diversity in aquatic environments and provide early warning of potential outbreaks.
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Affiliation(s)
| | - Jones Anderson Monteiro Siqueira
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - Dielle Monteiro Teixeira
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - Guilherme Junior Leite da Piedade
- Postgraduate Program in Virology, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - Edivaldo Costa Sousa Júnior
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - James Lima Ferreira
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - Luciana Damascena da Silva
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
| | - Yvone Benchimol Gabbay
- Virology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, PA, Brazil
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24
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Fujiki J, Schnabl B. Phage therapy: Targeting intestinal bacterial microbiota for the treatment of liver diseases. JHEP Rep 2023; 5:100909. [PMID: 37965159 PMCID: PMC10641246 DOI: 10.1016/j.jhepr.2023.100909] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/16/2023] Open
Abstract
Phage therapy has been overshadowed by antibiotics for decades. However, it is being revisited as a powerful approach against antimicrobial-resistant bacteria. As bacterial microbiota have been mechanistically linked to gastrointestinal and liver diseases, precise editing of the gut microbiota via the selective bactericidal action of phages has prompted renewed interest in phage therapy. In this review, we summarise the basic virological properties of phages and the latest findings on the composition of the intestinal phageome and the changes associated with liver diseases. We also review preclinical and clinical studies assessing phage therapy for the treatment of gastrointestinal and liver diseases, as well as future prospects and challenges.
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Affiliation(s)
- Jumpei Fujiki
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
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25
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Biomaterial therapeutic strategies for treatment of bacterial lung infections. Biofilm 2023; 5:100111. [PMID: 36909663 PMCID: PMC9999167 DOI: 10.1016/j.bioflm.2023.100111] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Bacterial infections of the lung frequently occur as a secondary infection to many respiratory viral infections and conditions, including influenza, COVID-19, chronic obstructive pulmonary disease (COPD), and cystic fibrosis (CF). Currently, clinical standard treats bacterial infections of the lung with antibiotic drugs. However, the use of broad-spectrum antibiotics can disrupt host microbiomes, lead to patient discomfort, and current clinical settings face the constantly increasing threat of drug-resistant bacteria. Biofilms further obstruct effective treatment due to their protective matrix layer, which shields bacteria from both the host immune system and antimicrobial drugs and subsequently promotes drug resistance. Alternative antimicrobial agents, including bacteriophages and antimicrobial peptides, have been utilized to treat drug-resistant bacteria. However, these antimicrobial agents have significant limitations pertaining to their ability to arrive at infection sites without compromised function and ability to persist over an extended period to fully treat infections. Enhanced delivery strategies present great promise in addressing these issues by using micro/nanoparticle carriers that shield antimicrobial agents in transit and result in sustained release, enhancing subsequent therapeutic effect and can even be modulated to be multi-functional to further improve recovery following bacterial infection.
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26
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Meng R, Zeng M, Ji Y, Huang X, Xu M. The potential role of gut microbiota outer membrane vesicles in colorectal cancer. Front Microbiol 2023; 14:1270158. [PMID: 38029123 PMCID: PMC10661380 DOI: 10.3389/fmicb.2023.1270158] [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: 07/31/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Colorectal cancer (CRC) is a common malignant digestive tract tumor in colorectal regions. Considerable evidence now shows that the gut microbiota have essential roles in CRC occurrence and development. Most Gram-negative bacteria release outer membrane vesicles (OMVs) via outer membrane blistering, which contain specific cargoes which interact with host cells via intercellular communications, host immune regulation, and gut microbiota homeostasis. Studies have also shown that OMVs selectively cluster near tumor cells, thus cancer treatment strategies based on OMVs have attracted considerable research attention. However, little is known about the possible impact of gut microbiota OMVs in CRC pathophysiology. Therefore, in this review, we summarize the research progress on molecular composition and function of OMV, and review the microbial dysbiosis in CRC. We then focus on the potential role of gut microbiota OMVs in CRC. Finally, we examine the clinical potential of OMVs in CRC treatment, and their main advantages and challenges in tumor therapy.
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Affiliation(s)
- Ran Meng
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Minmin Zeng
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ying Ji
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xinxiang Huang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Digestive Diseases, Jiangsu University, Zhenjiang, Jiangsu, China
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27
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Grigson SR, Giles SK, Edwards RA, Papudeshi B. Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy. Clin Infect Dis 2023; 77:S352-S359. [PMID: 37932119 PMCID: PMC10627814 DOI: 10.1093/cid/ciad539] [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] [Indexed: 11/08/2023] Open
Abstract
Bacteriophages, or phages, are viruses that infect bacteria shaping microbial communities and ecosystems. They have gained attention as potential agents against antibiotic resistance. In phage therapy, lytic phages are preferred for their bacteria killing ability, while temperate phages, which can transfer antibiotic resistance or toxin genes, are avoided. Selection relies on plaque morphology and genome sequencing. This review outlines annotating genomes, identifying critical genomic features, and assigning functional labels to protein-coding sequences. These annotations prevent the transfer of unwanted genes, such as antimicrobial resistance or toxin genes, during phage therapy. Additionally, it covers International Committee on Taxonomy of Viruses (ICTV)-an established phage nomenclature system for simplified classification and communication. Accurate phage genome annotation and nomenclature provide insights into phage-host interactions, replication strategies, and evolution, accelerating our understanding of the diversity and evolution of phages and facilitating the development of phage-based therapies.
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Affiliation(s)
- Susanna R Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Sarah K Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
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28
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Smith KR, Bumunang EW, Schlechte J, Waldner M, Anany H, Walker M, MacLean K, Stanford K, Fairbrother JM, Alexander TW, McAllister TA, Abdul-Careem MF, Niu YD. The Isolation and Characterization of Bacteriophages Infecting Avian Pathogenic Escherichia coli O1, O2 and O78 Strains. Viruses 2023; 15:2095. [PMID: 37896873 PMCID: PMC10612097 DOI: 10.3390/v15102095] [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: 09/04/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Avian pathogenic Escherichia coli (APEC), such as O1, O2 and O78, are important serogroups relating to chicken health, being responsible for colibacillosis. In this study, we isolated and characterized bacteriophages (phages) from hen feces and human sewage in Alberta with the potential for controlling colibacillosis in laying hens. The lytic profile, host range, pH tolerance and morphology of seven APEC-infecting phages (ASO1A, ASO1B, ASO2A, ASO78A, ASO2B, AVIO78A and ASO78B) were assessed using a microplate phage virulence assay and transmission electron microscopy (TEM). The potential safety of phages at the genome level was predicted using AMRFinderPlus and the Virulence Factor Database. Finally, phage genera and genetic relatedness with other known phages from the NCBI GenBank database were inferred using the virus intergenomic distance calculator and single gene-based phylogenetic trees. The seven APEC-infecting phages preferentially lysed APEC strains in this study, with ECL21443 (O2) being the most susceptible to phages (n = 5). ASO78A had the broadest host range, lysing all tested strains (n = 5) except ECL20885 (O1). Phages were viable at a pH of 2.5 or 3.5-9.0 after 4 h of incubation. Based on TEM, phages were classed as myovirus, siphovirus and podovirus. No genes associated with virulence, antimicrobial resistance or lysogeny were detected in phage genomes. Comparative genomic analysis placed six of the seven phages in five genera: Felixounavirus (ASO1A and ASO1B), Phapecoctavirus (ASO2A), Tequatrovirus (ASO78A), Kayfunavirus (ASO2B) and Sashavirus (AVIO78A). Based on the nucleotide intergenomic similarity (<70%), phage ASO78B was not assigned a genus in the siphovirus and could represent a new genus in class Caudoviricetes. The tail fiber protein phylogeny revealed variations within APEC-infecting phages and closely related phages. Diverse APEC-infecting phages harbored in the environment demonstrate the potential to control colibacillosis in poultry.
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Affiliation(s)
- Kat R. Smith
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (K.R.S.); (J.S.); (M.W.); (K.M.); (M.F.A.-C.)
| | - Emmanuel W. Bumunang
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada; (E.W.B.); (T.W.A.); (T.A.M.)
| | - Jared Schlechte
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (K.R.S.); (J.S.); (M.W.); (K.M.); (M.F.A.-C.)
| | - Matthew Waldner
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (K.R.S.); (J.S.); (M.W.); (K.M.); (M.F.A.-C.)
| | - Hany Anany
- Agriculture and Agri-Food Canada, Guelph Research and Development Centre, Guelph, ON N1G 5C9, Canada;
| | - Matthew Walker
- Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
| | - Kellie MacLean
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (K.R.S.); (J.S.); (M.W.); (K.M.); (M.F.A.-C.)
| | - Kim Stanford
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 1M4, Canada;
| | - John M. Fairbrother
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | - Trevor W. Alexander
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada; (E.W.B.); (T.W.A.); (T.A.M.)
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada; (E.W.B.); (T.W.A.); (T.A.M.)
| | - Mohamed Faizal Abdul-Careem
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (K.R.S.); (J.S.); (M.W.); (K.M.); (M.F.A.-C.)
| | - Yan D. Niu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (K.R.S.); (J.S.); (M.W.); (K.M.); (M.F.A.-C.)
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Skliros D, Droubogiannis S, Kalloniati C, Katharios P, Flemetakis E. Perturbation of Quorum Sensing after the Acquisition of Bacteriophage Resistance Could Contribute to Novel Traits in Vibrio alginolyticus. Microorganisms 2023; 11:2273. [PMID: 37764117 PMCID: PMC10535087 DOI: 10.3390/microorganisms11092273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Bacteria employ a wide range of molecular mechanisms to confer resistance to bacteriophages, and these mechanisms are continuously being discovered and characterized. However, there are instances where certain bacterial species, despite lacking these known mechanisms, can still develop bacteriophage resistance through intricate metabolic adaptation strategies, potentially involving mutations in transcriptional regulators or phage receptors. Vibrio species have been particularly useful for studying the orchestrated metabolic responses of Gram-negative marine bacteria in various challenges. In a previous study, we demonstrated that Vibrio alginolyticus downregulates the expression of specific receptors and transporters in its membrane, which may enable the bacterium to evade infection by lytic bacteriophages. In our current study, our objective was to explore how the development of bacteriophage resistance in Vibrio species disrupts the quorum-sensing cascade, subsequently affecting bacterial physiology and metabolic capacity. Using a real-time quantitative PCR (rt-QPCR) platform, we examined the expression pattern of quorum-sensing genes, auto-inducer biosynthesis genes, and cell density regulatory proteins in phage-resistant strains. Our results revealed that bacteriophage-resistant bacteria downregulate the expression of quorum-sensing regulatory proteins, such as LuxM, LuxN, and LuxP. This downregulation attenuates the normal perception of quorum-sensing peptides and subsequently diminishes the expression of cell density regulatory proteins, including LuxU, aphA, and LuxR. These findings align with the diverse phenotypic traits observed in the phage-resistant strains, such as altered biofilm formation, reduced planktonic growth, and reduced virulence. Moreover, the transcriptional depletion of aphA, the master regulator associated with low cell density, was linked to the downregulation of genes related to virulence. This phenomenon appears to be phage-specific, suggesting a finely tuned metabolic adaptation driven by phage-host interaction. These findings contribute to our understanding of the role of Vibrio species in microbial marine ecology and highlight the complex interplay between phage resistance, quorum sensing, and bacterial physiology.
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Affiliation(s)
- Dimitrios Skliros
- Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece; (D.S.); (C.K.)
| | - Stavros Droubogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece; (S.D.); (P.K.)
| | - Chrysanthi Kalloniati
- Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece; (D.S.); (C.K.)
- Department of Marine Sciences, University of the Aegean, 81100 Mytilene, Greece
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece; (S.D.); (P.K.)
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece; (D.S.); (C.K.)
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30
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Duan X, Jiang L, Guo M, Li C. Isolation, characterization and application of a lytic phage vB_VspM_VS1 against Vibrio splendidus biofilm. PLoS One 2023; 18:e0289895. [PMID: 37656737 PMCID: PMC10473537 DOI: 10.1371/journal.pone.0289895] [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: 04/04/2023] [Accepted: 07/27/2023] [Indexed: 09/03/2023] Open
Abstract
Vibrio splendidus is a common pathogen in the ocean that infects Apostichopus japonicus, Atlantic salmon and Crassostrea gigas, leading to a variety of diseases. In this study, a virulent phage vB_VspM_VS1, which infects V. splendidus, was isolated from aquaculture ponds in Dalian, China, and it belongs to the family Straboviridae in the order Caudoviricetes. vB_VspM_VS1 had an adsorption rate of 96% in 15 min, a latent period of 65 min, and a burst size of 140 ± 6 PFU/cell. The complete genome of phage vB_VspM_VS1 consists of a linear double-stranded DNA that is 248,270 bp in length with an average G + C content of 42.5% and 389 putative protein-coding genes; 116 genes have known functions. There are 4 tail fiber genes in the positive and negative strands of the phage vB_VspM_VS1 genome. The protein domain of the phage vB_VspM_VS1 tail fibers was obtained from the Protein Data Bank and the SMART (http://smart.embl.de) database. Bacterial challenge tests revealed that the growth of V. splendidus HS0 was apparently inhibited (OD600 < 0.01) in 12 h at an MOI of 10. In against biofilms, we also showed that the OD570 value of the vB_VspM_VS1-treated group (MOI = 1) decreased significantly to 0.04 ± 0.01 compared with that of the control group (0.48 ± 0.08) at 24 h. This study characterizes the genome of the phage vB_VspM_VS1 that infects the pathogenic bacterium V. splendidus of A. japonicus.
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Affiliation(s)
- Xuemei Duan
- State Key Laboratory for Quality and Safety of Agroproducts, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Liming Jiang
- State Key Laboratory for Quality and Safety of Agroproducts, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
- School of Medicine, Ningbo University, Ningbo, China
| | - Ming Guo
- State Key Laboratory for Quality and Safety of Agroproducts, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Chenghua Li
- State Key Laboratory for Quality and Safety of Agroproducts, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
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Dong Y, Huang Y, Fan H, Song L, An X, Xu S, Li M, Tong Y. Characterization, complete genome sequencing, and CRISPR/Cas9 system-based decontamination of a novel Escherichia coli phage TR1 from fermentation substrates. Front Microbiol 2023; 14:1230775. [PMID: 37637117 PMCID: PMC10450929 DOI: 10.3389/fmicb.2023.1230775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Phage contamination has become a major concern for industrial bacteria, such as Escherichia coli BL21(DE3), used in fermentation processes. Herein, we report a CRISPR/Cas9 defense system-based strategy to precisely prey and degrade phage DNA to decontaminate target phages. First, we isolated a novel phage from fermentation substrates with BL21(DE3) as the host, named TR1. It showed a typical podovirus morphology with a head diameter of 51.46 ± 2.04 nm and a tail length of 9.31 ± 2.77 nm. The burst size of phage TR1 was 151 PFU/cell, suggesting its strong fecundity in the fermentation system. Additionally, whole-genome sequencing revealed that phage TR1 has a DNA genome of 44,099 bp in length with a 43.8% GC content, encoding a total of 68 open reading frames. Comparative genomics and phylogenetic analysis designated this phage to be a new species of the genus Christensenvirus. To counteract phage TR1, we employed the CRISPR/Cas9 system-based strategy and constructed two phage-resistant E. coli strains, BL21-C and BL21-T, based on conserved genes. Both EOP assays and growth curves indicated strong phage resistance of the recombinant strains, without affecting cell growth. Therefore, this study aimed to provide a resilient strategy to respond to ever-changing phages and ongoing phage-host arm race in industrial fermentation environments by the personalized design of spacers in the recombinant CRISPR/Cas system-containing plasmid. More importantly, our research sparks the use of phage defense mechanism to prevent phage contamination in extensive biotechnological applications.
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Affiliation(s)
- Yuqi Dong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yunfei Huang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shan Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Qinhuangdao Bohai Biological Research Institute, Beijing University of Chemical Technology, Qinhuangdao, Hebei, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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You H, Wang M, Wang S, Xu J, Hu S, Li T, Yu Z, Tang D, Gan N. Ultrasensitive and Specific Phage@DNAzyme Probe-Triggered Fluorescent Click Chemistry for On-Site Detection of Foodborne Pathogens Using a Smartphone. Anal Chem 2023. [PMID: 37471313 DOI: 10.1021/acs.analchem.3c00603] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Rapid, specific, and on-site detection of virulent foodborne pathogenic strains plays a key role in controlling food safety. In this work, an ultrasensitive and specific Phage@DNAzyme signal probe was designed to detect foodborne pathogens. The proposed sensing probe was composed of the selected phage and functionalized DNAzyme, which realized the specific recognition of target foodborne pathogens at the strain level and the efficient catalysis of copper(II) based azide-alkyne cycloaddition (CuAAC) click reaction with fluorescent signal, respectively. As a proof of concept, the virulent Escherichia coli O157:H7 (E. coli O157:H7) as the representative analyte was first enriched and purified from the complex food samples by a 4-mercaptophenylboronic acid-modified gold slide. Following, the Phage@DNAzyme probes were specifically combined with the captured E. coli O157: H7 and catalyzed the click reaction between 3-azido-7-hydroxycoumarin and 3-butyn-1-ol with the assistance of Cu(II) to generate a visual fluorescent signal. Finally, the corresponding fluorescent signals were measured by a smartphone to quantify the target concentrations. Under optimized conditions, the bioassay exhibited a wide linear range from 102 to 108 CFU/mL and the detection limit was 50 CFU/mL (S/N = 3). It was further extended to the detection of another foodborne pathogen Salmonella typhimurium with satisfying sensing performances. This work gives a new path for developing rapid, specific, and on-site detection methods for trace levels of pathogenic strains in foods.
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Affiliation(s)
- Hang You
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Ming Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Shuai Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Jie Xu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Shuhao Hu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Tianhua Li
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Zhenzhong Yu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Dianping Tang
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Ning Gan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
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Sokolova D, Smolarska A, Bartnik P, Rabalski L, Kosinski M, Narajczyk M, Krzyżanowska DM, Rajewska M, Mruk I, Czaplewska P, Jafra S, Czajkowski R. Spontaneous mutations in hlyD and tuf genes result in resistance of Dickeya solani IPO 2222 to phage ϕD5 but cause decreased bacterial fitness and virulence in planta. Sci Rep 2023; 13:7534. [PMID: 37160956 PMCID: PMC10169776 DOI: 10.1038/s41598-023-34803-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/07/2023] [Indexed: 05/11/2023] Open
Abstract
Lytic bacteriophages able to infect and kill Dickeya spp. can be readily isolated from virtually all Dickeya spp. containing environments, yet little is known about the selective pressure those viruses exert on their hosts. Two spontaneous D. solani IPO 2222 mutants (0.8% of all obtained mutants), DsR34 and DsR207, resistant to infection caused by lytic phage vB_Dsol_D5 (ΦD5) were identified in this study that expressed a reduced ability to macerate potato tuber tissues compared to the wild-type, phage-susceptible D. solani IPO 2222 strain. Genome sequencing revealed that genes encoding: secretion protein HlyD (in mutant DsR34) and elongation factor Tu (EF-Tu) (in mutant DsR207) were altered in these strains. These mutations impacted the DsR34 and DsR207 proteomes. Features essential for the ecological success of these mutants in a plant environment, including their ability to use various carbon and nitrogen sources, production of plant cell wall degrading enzymes, ability to form biofilms, siderophore production, swimming and swarming motility and virulence in planta were assessed. Compared to the wild-type strain, D. solani IPO 2222, mutants DsR34 and DsR207 had a reduced ability to macerate chicory leaves and to colonize and cause symptoms in growing potato plants.
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Affiliation(s)
- Daryna Sokolova
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, 148 Academika Zabolotnoho St., Kyiv, 03143, Ukraine
| | - Anna Smolarska
- Department of Cancer Biology, Institute of Biology, Warsaw, University of Life Sciences (SGGW), J. Ciszewskiego 8, 02-786, Warsaw, Poland
| | - Przemysław Bartnik
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland
| | - Lukasz Rabalski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland
| | - Maciej Kosinski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland
| | - Magdalena Narajczyk
- Laboratory of Electron Microscopy, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Dorota M Krzyżanowska
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland
| | - Magdalena Rajewska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama, 58, 80-307, Gdansk, Poland
| | - Inez Mruk
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307, Gdansk, Poland
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307, Gdansk, Poland
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama, 58, 80-307, Gdansk, Poland
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland.
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Huang D, Yuan MM, Chen J, Zheng X, Wong D, Alvarez PJJ, Yu P. The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes. ISME COMMUNICATIONS 2023; 3:46. [PMID: 37142716 PMCID: PMC10160068 DOI: 10.1038/s43705-023-00249-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Prokaryotic antiviral systems are important mediators for prokaryote-phage interactions, which have significant implications for the survival of prokaryotic community. However, the prokaryotic antiviral systems under environmental stress are poorly understood, limiting the understanding of microbial adaptability. Here, we systematically investigated the profile of the prokaryotic antiviral systems at the community level and prokaryote-phage interactions in the drinking water microbiome. Chlorine disinfectant was revealed as the main ecological driver for the difference in prokaryotic antiviral systems and prokaryote-phage interactions. Specifically, the prokaryotic antiviral systems in the microbiome exhibited a higher abundance, broader antiviral spectrum, and lower metabolic burden under disinfectant stress. Moreover, significant positive correlations were observed between phage lysogenicity and enrichment of antiviral systems (e.g., Type IIG and IV restriction-modification (RM) systems, and Type II CRISPR-Cas system) in the presence of disinfection, indicating these antiviral systems might be more compatible with lysogenic phages and prophages. Accordingly, there was a stronger prokaryote-phage symbiosis in disinfected microbiome, and the symbiotic phages carried more auxiliary metabolic genes (AMGs) related to prokaryotic adaptability as well as antiviral systems, which might further enhance prokaryote survival in drinking water distribution systems. Overall, this study demonstrates that the prokaryotic antiviral systems had a close association with their symbiotic phages, which provides novel insights into prokaryote-phage interactions and microbial environmental adaptation.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Xiaoxuan Zheng
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Dongsheng Wong
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
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Aman Mohammadi M, Maximiano MR, Hosseini SM, Franco OL. CRISPR-Cas engineering in food science and sustainable agriculture: recent advancements and applications. Bioprocess Biosyst Eng 2023; 46:483-497. [PMID: 36707422 DOI: 10.1007/s00449-022-02842-5] [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: 08/20/2022] [Accepted: 12/14/2022] [Indexed: 01/29/2023]
Abstract
The developments in the food supply chain to support the growing population of the world is one of today's most pressing issues, and to achieve this goal improvements should be performed in both crops and microbes. For this purpose, novel approaches such as genome editing (GE) methods have upgraded the biological sciences for genome manipulation and, among such methods, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are the main exciting innovations since the Green Revolution. CRISPR/Cas systems can be a potent tool for the food industry, improvement of agricultural crops and even for protecting food-grade bacteria from foreign genetic invasive elements. This review introduces the history and mechanism of the CRISPR-Cas system as a genome editing tool and its applications in the vaccination of starter cultures, production of antimicrobials and bioactive compounds, and genome editing of microorganisms.
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Affiliation(s)
- Masoud Aman Mohammadi
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences, Food Science and Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mariana Rocha Maximiano
- S-Inova Biotech, Graduate Program in Biotechnology, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Graduate Program in Genomic Science and Biotechnology, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Seyede Marzieh Hosseini
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences, Food Science and Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Octavio Luiz Franco
- S-Inova Biotech, Graduate Program in Biotechnology, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Graduate Program in Genomic Science and Biotechnology, Universidade Católica de Brasília, Brasília, DF, Brazil
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Aytar Çelik P, Erdogan-Gover K, Barut D, Enuh BM, Amasya G, Sengel-Türk CT, Derkus B, Çabuk A. Bacterial Membrane Vesicles as Smart Drug Delivery and Carrier Systems: A New Nanosystems Tool for Current Anticancer and Antimicrobial Therapy. Pharmaceutics 2023; 15:pharmaceutics15041052. [PMID: 37111538 PMCID: PMC10142793 DOI: 10.3390/pharmaceutics15041052] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Bacterial membrane vesicles (BMVs) are known to be critical communication tools in several pathophysiological processes between bacteria and host cells. Given this situation, BMVs for transporting and delivering exogenous therapeutic cargoes have been inspiring as promising platforms for developing smart drug delivery systems (SDDSs). In the first section of this review paper, starting with an introduction to pharmaceutical technology and nanotechnology, we delve into the design and classification of SDDSs. We discuss the characteristics of BMVs including their size, shape, charge, effective production and purification techniques, and the different methods used for cargo loading and drug encapsulation. We also shed light on the drug release mechanism, the design of BMVs as smart carriers, and recent remarkable findings on the potential of BMVs for anticancer and antimicrobial therapy. Furthermore, this review covers the safety of BMVs and the challenges that need to be overcome for clinical use. Finally, we discuss the recent advancements and prospects for BMVs as SDDSs and highlight their potential in revolutionizing the fields of nanomedicine and drug delivery. In conclusion, this review paper aims to provide a comprehensive overview of the state-of-the-art field of BMVs as SDDSs, encompassing their design, composition, fabrication, purification, and characterization, as well as the various strategies used for targeted delivery. Considering this information, the aim of this review is to provide researchers in the field with a comprehensive understanding of the current state of BMVs as SDDSs, enabling them to identify critical gaps and formulate new hypotheses to accelerate the progress of the field.
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Affiliation(s)
- Pınar Aytar Çelik
- Environmental Protection and Control Program, Eskisehir Osmangazi University, Eskisehir 26110, Turkey
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, Eskisehir 26040, Turkey
| | - Kubra Erdogan-Gover
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, Eskisehir 26040, Turkey
| | - Dilan Barut
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, Eskisehir 26040, Turkey
| | - Blaise Manga Enuh
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, Eskisehir 26040, Turkey
| | - Gülin Amasya
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Ankara University, Ankara 06100, Turkey
| | - Ceyda Tuba Sengel-Türk
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Ankara University, Ankara 06100, Turkey
| | - Burak Derkus
- Department of Chemistry, Faculty of Science, Ankara University, Ankara 06560, Turkey
| | - Ahmet Çabuk
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, Eskisehir 26040, Turkey
- Department of Biology, Faculty of Science, Eskisehir Osmangazi University, Eskisehir 26040, Turkey
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Kim H, Seo J. A Novel Strategy to Identify Endolysins with Lytic Activity against Methicillin-Resistant Staphylococcus aureus. Int J Mol Sci 2023; 24:ijms24065772. [PMID: 36982851 PMCID: PMC10059956 DOI: 10.3390/ijms24065772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in the dairy industry has become a fundamental concern. Endolysins are bacteriophage-derived peptidoglycan hydrolases that induce the rapid lysis of host bacteria. Herein, we evaluated the lytic activity of endolysin candidates against S. aureus and MRSA. To identify endolysins, we used a bioinformatical strategy with the following steps: (1) retrieval of genetic information, (2) annotation, (3) selection of MRSA, (4) selection of endolysin candidates, and (5) evaluation of protein solubility. We then characterized the endolysin candidates under various conditions. Approximately 67% of S. aureus was detected as MRSA, and 114 putative endolysins were found. These 114 putative endolysins were divided into three groups based on their combinations of conserved domains. Considering protein solubility, we selected putative endolysins 117 and 177. Putative endolysin 117 was the only successfully overexpressed endolysin, and it was renamed LyJH1892. LyJH1892 showed potent lytic activity against both methicillin-susceptible S. aureus and MRSA and showed broad lytic activity against coagulase-negative staphylococci. In conclusion, this study demonstrates a rapid strategy for the development of endolysin against MRSA. This strategy could also be used to combat other antibiotic-resistant bacteria.
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Aloke C, Achilonu I. Coping with the ESKAPE pathogens: Evolving strategies, challenges and future prospects. Microb Pathog 2023; 175:105963. [PMID: 36584930 DOI: 10.1016/j.micpath.2022.105963] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022]
Abstract
Globally, the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are the major cause of nosocomial infections. These pathogens are multidrug resistant, and their negative impacts have brought serious health challenges and economic burden on many countries worldwide. Thus, this narrative review exploits different emerging alternative therapeutic strategies including combination antibiotics, antimicrobial peptides ((AMPs), bacteriophage and photodynamic therapies used in the treatment of the ESKAPE pathogens, their merits, limitations, and future prospects. Our findings indicate that ESKAPE pathogens exhibit resistance to drug using different mechanisms including drug inactivation by irreversible enzyme cleavage, drug-binding site alteration, diminution in permeability of drug or drug efflux increment to reduce accumulation of drug as well as biofilms production. However, the scientific community has shown significant interest in using these novel strategies with numerous benefits although they have some limitations including but not limited to instability and toxicity of the therapeutic agents, or the host developing immune response against the therapeutic agents. Thus, comprehension of resistance mechanisms of these pathogens is necessary to further develop or modify these approaches in order to overcome these health challenges including the barriers of bacterial resistance.
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Affiliation(s)
- Chinyere Aloke
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg, 2050, South Africa; Department of Medical Biochemistry, Alex Ekwueme Federal University Ndufu-Alike, Ebonyi State, Nigeria.
| | - Ikechukwu Achilonu
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg, 2050, South Africa
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Sun L, You J, Li D, Zhang Z, Qin X, Pang W, Li P, Han Q, Li Y, Huang Z, Zhang X, Gong M, Yang H. Variants of a putative baseplate wedge protein extend the host range of Pseudomonas phage K8. MICROBIOME 2023; 11:18. [PMID: 36721246 PMCID: PMC9887876 DOI: 10.1186/s40168-022-01459-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/31/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Narrow host range is a major limitation for phage applications, but phages can evolve expanded host range through adaptations in the receptor-binding proteins. RESULTS Here, we report that Pseudomonas phage K8 can evolve broader host range and higher killing efficiency at the cost of virion stability. Phage K8 host range mutant K8-T239A carries a mutant version of the putative baseplate wedge protein GP075, termed GP075m. While phage K8 adsorbs to hosts via the O-specific antigen of bacterial LPS, phage K8-T239A uses GP075m to also bind the bacterial core oligosaccharide, enabling infection of bacterial strains resistant to K8 infection due to modified O-specific antigens. This mutation in GP075 also alters inter-protein interactions among phage proteins, and reduces the stability of phage particles to environmental stressors like heat, acidity, and alkalinity. We find that a variety of mutations in gp075 are widespread in K8 populations, and that the gp075-like genes are widely distributed among the domains of life. CONCLUSION Our data show that a typical life history tradeoff occurs between the stability and the host range in the evolution of phage K8. Reservoirs of viral gene variants may be widely present in phage communities, allowing phages to rapidly adapt to any emerging environmental stressors. Video Abstract.
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Affiliation(s)
- Li Sun
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jiajia You
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Donghang Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhiqiang Zhang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xuying Qin
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Wenjing Pang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Peize Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Qingzhu Han
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yueying Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhiwei Huang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xixi Zhang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | | | - Hongjiang Yang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
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A Glimpse at the Anti-Phage Defenses Landscape in the Foodborne Pathogen Salmonella enterica subsp. enterica serovar Typhimurium. Viruses 2023; 15:v15020333. [PMID: 36851545 PMCID: PMC9958689 DOI: 10.3390/v15020333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Bacteriophages, which specifically infect and kill bacteria, are currently used as additives to control pathogens such as Salmonella in human food (PhageGuard S®) or animal feed (SalmoFREE®, Bafasal®). Indeed, salmonellosis is among the most important zoonotic foodborne illnesses. The presence of anti-phage defenses protecting bacteria against phage infection could impair phage applications aiming at reducing the burden of foodborne pathogens such as Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) to the food industry. In this study, the landscape of S. Typhimurium anti-phage defenses was bioinformatically investigated in publicly available genomes using the webserver PADLOC. The primary anti-phage systems identified in S. Typhimurium use nucleic acid degradation and abortive infection mechanisms. Reference systems were identified on an integrative and conjugative element, a transposon, a putative integrative and mobilizable element, and prophages. Additionally, the mobile genetic elements (MGEs) containing a subset of anti-phage systems were found in the Salmonella enterica species. Lastly, the MGEs alone were also identified in the Enterobacteriaceae family. The presented diversity assessment of the anti-phage defenses and investigation of their dissemination through MGEs in S. Typhimurium constitute a first step towards the design of preventive measures against the spread of phage resistance that may hinder phage applications.
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Jo SJ, Kim SG, Lee YM, Giri SS, Kang JW, Lee SB, Jung WJ, Hwang MH, Park J, Cheng C, Roh E, Park SC. Evaluation of the Antimicrobial Potential and Characterization of Novel T7-Like Erwinia Bacteriophages. BIOLOGY 2023; 12:biology12020180. [PMID: 36829459 PMCID: PMC9953017 DOI: 10.3390/biology12020180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/15/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
The recent outbreak of blight in pome fruit plants has been a major concern as there are two indistinguishable Erwinia species, Erwinia amylovora and E. pyrifoliae, which cause blight in South Korea. Although there is a strict management protocol consisting of antibiotic-based prevention, the area and the number of cases of outbreaks have increased. In this study, we isolated four bacteriophages, pEp_SNUABM_03, 04, 11, and 12, that infect both E. amylovora and E. pyrifoliae and evaluated their potential as antimicrobial agents for administration against Erwinia-originated blight in South Korea. Morphological analysis revealed that all phages had podovirus-like capsids. The phage cocktail showed a broad spectrum of infectivity, infecting 98.91% of E. amylovora and 100% of E. pyrifoliae strains. The antibacterial effect was observed after long-term cocktail treatment against E. amylovora, whereas it was observed for both short- and long-term treatments against E. pyrifoliae. Genomic analysis verified that the phages did not encode harmful genes such as antibiotic resistance or virulence genes. All phages were stable under general orchard conditions. Collectively, we provided basic data on the potential of phages as biocontrol agents that target both E. amylovora and E. pyrifoliae.
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Affiliation(s)
- Su Jin Jo
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Young Min Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeong Woo Kang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Won Joon Jung
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Mae Hyun Hwang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaehong Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Chi Cheng
- Laboratory of Aquatic Nutrition and Ecology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
- Correspondence: ; Tel.: +82-2-880-1282; Fax: +82-2-873-1213
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Biological properties of Staphylococcus virus ΦSA012 for phage therapy. Sci Rep 2022; 12:21297. [PMID: 36494564 PMCID: PMC9734660 DOI: 10.1038/s41598-022-25352-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Staphylococcus virus ΦSA012 has a wide host range and efficient lytic activity. Here, we assessed the biological stability of ΦSA012 against temperature, freeze-thawing, and pH to clinically apply the phage. In addition, inoculation of ΦSA012 through i.p. and i.v. injections into mice revealed that phages were reached the limit of detection in serum and accumulated notably spleens without inflammation at 48 h post-inoculation. Furthermore, inoculation of ΦSA012 through s.c. injections in mice significantly induced IgG, which possesses neutralizing activity against ΦSA012 and other Staphylococcus viruses, ΦSA039 and ΦMR003, but not Pseudomonas viruses ΦS12-3 and ΦR18 or Escherichia viruses T1, T4, and T7 in vitro. Immunoelectron microscopic analysis showed that purified anti-phage IgG recognizes the long-tail fiber of staphylococcus viruses. Although S. aureus inoculation resulted in a 25% survival rate in a mouse i.p. model, ΦSA012 inoculation (i.p.) improved the survival rate to 75%; however, the survival rate of ΦSA012-immunized mice decreased to less than non-immunized mice with phage i.v. injection at a MOI of 100. These results indicated that ΦSA012 possesses promise for use against staphylococcal infections but we should carefully address the appropriate dose and periods of phage administration. Our findings facilitate understandings of staphylococcus viruses for phage therapy.
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Kim SG, Lee SB, Jo SJ, Cho K, Park JK, Kwon J, Giri SS, Kim SW, Kang JW, Jung WJ, Lee YM, Roh E, Park SC. Phage Cocktail in Combination with Kasugamycin as a Potential Treatment for Fire Blight Caused by Erwinia amylovora. Antibiotics (Basel) 2022; 11:1566. [PMID: 36358221 PMCID: PMC9686651 DOI: 10.3390/antibiotics11111566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 08/27/2023] Open
Abstract
Recently, there has been an increasing number of blight disease reports associated with Erwinia amylovora and Erwinia pyrifoliae in South Korea. Current management protocols that have been conducted with antibiotics have faced resistance problems and the outbreak has not decreased. Because of this concern, the present study aimed to provide an alternative method to control the invasive fire blight outbreak in the nation using bacteriophages (phages) in combination with an antibiotic agent (kasugamycin). Among 54 phage isolates, we selected five phages, pEa_SNUABM_27, 31, 32, 47, and 48, based on their bacteriolytic efficacy. Although only phage pEa_SNUABM_27 showed host specificity for E. amylovora, all five phages presented complementary lytic potential that improved the host infectivity coverage of each phage All the phages in the cocktail solution could lyse phage-resistant strains. These strains had a decreased tolerance to the antibiotic kasugamycin, and a synergistic effect of phages and antibiotics was demonstrated both in vitro and on immature wound-infected apples. It is noteworthy that the antibacterial effect of the phage cocktail or phage cocktail-sub-minimal inhibitory concentration (MIC) of kasugamycin was significantly higher than the kasugamycin at the MIC. The selected phages were experimentally stable under environmental factors such as thermal or pH stress. Genomic analysis revealed these are novel Erwinia-infecting phages, and did not encode antibiotic-, virulence-, or lysogenic phage-related genes. In conclusion, we suggest the potential of the phage cocktail and kasugamycin combination as an effective strategy that would minimize the use of antibiotics, which are being excessively used in order to control fire blight pathogens.
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Affiliation(s)
- Sang-Guen Kim
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Sung-Bin Lee
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Su-Jin Jo
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Kevin Cho
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Jung-Kum Park
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Sang-Wha Kim
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Jeong-Woo Kang
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Won-Joon Jung
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Young-Min Lee
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea
| | - Se-Chang Park
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
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Tang X, Fan C, Zeng G, Zhong L, Li C, Ren X, Song B, Liu X. Phage-host interactions: The neglected part of biological wastewater treatment. WATER RESEARCH 2022; 226:119183. [PMID: 36244146 DOI: 10.1016/j.watres.2022.119183] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/29/2022] [Accepted: 09/29/2022] [Indexed: 05/25/2023]
Abstract
In wastewater treatment plants (WWTPs), the stable operation of biological wastewater treatment is strongly dependent on the stability of associated microbiota. Bacteriophages (phages), viruses that specifically infect bacteria and archaea, are highly abundant and diverse in WWTPs. Although phages do not have known metabolic functions for themselves, they can shape functional microbiota via various phage-host interactions to impact biological wastewater treatment. However, the developments of phage-host interaction in WWTPs and their impact on biological wastewater treatment are overlooked. Here, we review the current knowledge regarding the phage-host interactions in biological wastewater treatment, mainly focusing on the characteristics of different phage populations, the phage-driven changes in functional microbiota, and the potential driving factors of phage-host interactions. We also discuss the efforts required further to understand and manipulate the phage-host interactions in biological wastewater treatment. Overall, this review advocates more attention to the phage dynamics in WWTPs.
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Affiliation(s)
- Xiang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Chao Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China; Nova Skantek (Hunan) Environ Energy Co., Ltd., Changsha 410100, P.R. China
| | - Xiaoya Ren
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Xigui Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
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Hibstu Z, Belew H, Akelew Y, Mengist HM. Phage Therapy: A Different Approach to Fight Bacterial Infections. Biologics 2022; 16:173-186. [PMID: 36225325 PMCID: PMC9550173 DOI: 10.2147/btt.s381237] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022]
Abstract
Phage therapy is one of the alternatives to treat infections caused by both antibiotic-sensitive and antibiotic-resistant bacteria, with no or low toxicity to patients. It was started a century ago, although rapidly growing bacterial antimicrobial resistance, resulting in high levels of morbidity, mortality, and financial cost, has initiated the revival of phage therapy. It involves the use of live lytic, bioengineered, phage-encoded biological products, in combination with chemical antibiotics to treat bacterial infections. Importantly, phages will be removed from the body within seven days of clearing an infection. They target specific bacterial strains and cause minimal disruption to the microbial balance in humans. Phages for medication must be screened for the absence of resistant genes, virulent genes, cytotoxicity, and their interaction with the host tissue and organs. Since they are immunogenic, applying a high phage titer for therapy exposes them and activates the host immune system. To date, no serious side effects have been reported with human phage therapy. In this review, we describe phage–phagocyte interaction, bacterial resistance to phages, how phages conquer bacterial resistance, the role of genetic engineering and other technologies in phage therapy, and the therapeutic application of modified phages and phage-encoded products. We also highlight the comparison of antibiotics and lytic phage therapy, the pros and cons of phage therapy, determinants of human phage therapy trials, phage quality and safety requirements, phage storage and handling, and current challenges in phage therapy.
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Affiliation(s)
- Zigale Hibstu
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia,Correspondence: Zigale Hibstu, Email
| | - Habtamu Belew
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Yibeltal Akelew
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Hylemariam Mihiretie Mengist
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
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Song Y, He S, Jopkiewicz A, Setroikromo R, van Merkerk R, Quax WJ. Development and application of CRISPR-based genetic tools in Bacillus species and Bacillus phages. J Appl Microbiol 2022; 133:2280-2298. [PMID: 35797344 PMCID: PMC9796756 DOI: 10.1111/jam.15704] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 01/07/2023]
Abstract
Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been developed into a precise and efficient genome editing tool. Since its discovery as an adaptive immune system in prokaryotes, it has been applied in many different research fields including biotechnology and medical sciences. The high demand for rapid, highly efficient and versatile genetic tools to thrive in bacteria-based cell factories accelerates this process. This review mainly focuses on significant advancements of the CRISPR system in Bacillus subtilis, including the achievements in gene editing, and on problems still remaining. Next, we comprehensively summarize this genetic tool's up-to-date development and utilization in other Bacillus species, including B. licheniformis, B. methanolicus, B. anthracis, B. cereus, B. smithii and B. thuringiensis. Furthermore, we describe the current application of CRISPR tools in phages to increase Bacillus hosts' resistance to virulent phages and phage genetic modification. Finally, we suggest potential strategies to further improve this advanced technique and provide insights into future directions of CRISPR technologies for rendering Bacillus species cell factories more effective and more powerful.
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Affiliation(s)
- Yafeng Song
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern ChinaInstitute of Microbiology, Guangdong Acadamy of SciencesGuangzhouChina
| | - Siqi He
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Anita Jopkiewicz
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Wim J. Quax
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
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Bacteriophage-antibiotic combination therapy against extensively drug-resistant Pseudomonas aeruginosa infection to allow liver transplantation in a toddler. Nat Commun 2022; 13:5725. [PMID: 36175406 PMCID: PMC9523064 DOI: 10.1038/s41467-022-33294-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/13/2022] [Indexed: 12/12/2022] Open
Abstract
Post-operative bacterial infections are a leading cause of mortality and morbidity after ongoing liver transplantation. Bacteria causing these infections in the hospital setting can exhibit high degrees of resistance to multiple types of antibiotics, which leads to major therapeutic hurdles. Alternate ways of treating these antibiotic-resistant infections are thus urgently needed. Phage therapy is one of them and consists in using selected bacteriophage viruses - viruses who specifically prey on bacteria, naturally found in various environmental samples - as bactericidal agents in replacement or in combination with antibiotics. The use of phage therapy raises various research questions to further characterize what determines therapeutic success or failure. In this work, we report the story of a toddler who suffered from extensively drug-resistant Pseudomonas aeruginosa sepsis after liver transplantation. He was treated by a bacteriophage-antibiotic intravenous combination therapy for 86 days. This salvage therapy was well tolerated, without antibody-mediated phage neutralization. It was associated with objective clinical and microbiological improvement, eventually allowing for liver retransplantation and complete resolution of all infections. Clear in vitro phage-antibiotic synergies were observed. The occurrence of bacterial phage resistance did not result in therapeutic failure, possibly due to phage-induced virulence tradeoffs, which we investigated in different experimental models.
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Uddin Mahamud AGMS, Nahar S, Ashrafudoulla M, Park SH, Ha SD. Insights into antibiofilm mechanisms of phytochemicals: Prospects in the food industry. Crit Rev Food Sci Nutr 2022; 64:1736-1763. [PMID: 36066482 DOI: 10.1080/10408398.2022.2119201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The recalcitrance of microbial aggregation or biofilm in the food industry underpins the emerging antimicrobial resistance among foodborne pathogens, exacerbating the phenomena of food spoilage, processing and safety management failure, and the prevalence of foodborne illnesses. The challenges of growing tolerance to current chemical and disinfectant-based antibiofilm strategies have driven the urgency in finding a less vulnerable to bacterial resistance, effective alternative antibiofilm agent. To address these issues, various novel strategies are suggested in current days to combat bacterial biofilm. Among the innovative approaches, phytochemicals have already demonstrated their excellent performance in preventing biofilm formation and bactericidal actions against resident bacteria within biofilms. However, the diverse group of phytochemicals and their different modes of action become a barrier to applying them against specific pathogenic biofilm-formers. This phenomenon mandates the need to elucidate the multi-mechanistic actions of phytochemicals to design an effective novel antibiofilm strategy. Therefore, this review critically illustrates the structure - activity relationship, functional sites of actions, and target molecules of diverse phytochemicals regarding multiple major antibiofilm mechanisms and reversal mechanisms of antimicrobial resistance. The implementation of the in-depth knowledge will hopefully aid future studies for developing phytochemical-based next-generation antimicrobials.
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Affiliation(s)
- A G M Sofi Uddin Mahamud
- School of Food Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Shamsun Nahar
- School of Food Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Md Ashrafudoulla
- School of Food Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Si Hong Park
- Department of Food Science and Technology, Oregon State University, Corvallis, OR, USA
| | - Sang-Do Ha
- School of Food Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
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Chitayat Levi L, Rippin I, Ben Tulila M, Galron R, Tuller T. Modulating Gene Expression within a Microbiome Based on Computational Models. BIOLOGY 2022; 11:biology11091301. [PMID: 36138780 PMCID: PMC9495703 DOI: 10.3390/biology11091301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/20/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Development of computational biology methodologies has provided comprehensive understanding of the complexity of microbiomes, and the extensive ways in which they influence their environment. This has awakened a new research goal, aiming to not only understand the mechanisms in which microbiomes function, but to actively modulate and engineer them for various purposes. However, current microbiome engineering techniques are usually manually tailored for a specific system and neglect the different interactions between the new genetic information and the bacterial population, turning a blind eye to processes such as horizontal gene transfer, mutations, and other genetic alterations. In this work, we developed a generic computational method to automatically tune the expression of heterologous genes within a microbiome according to given preferences, to allow the functionality of the engineering process to propagate in longer periods of time. This goal was achieved by treating each part of the gene individually and considering long term fitness effects on the environment, providing computational and experimental evidence for this approach. Abstract Recent research in the field of bioinformatics and molecular biology has revealed the immense complexity and uniqueness of microbiomes, while also showcasing the impact of the symbiosis between a microbiome and its host or environment. A core property influencing this process is horizontal gene transfer between members of the bacterial community used to maintain genetic variation. The essential effect of this mechanism is the exposure of genetic information to a wide array of members of the community, creating an additional “layer” of information in the microbiome named the “plasmidome”. From an engineering perspective, introduction of genetic information to an environment must be facilitated into chosen species which will be able to carry out the desired effect instead of competing and inhibiting it. Moreover, this process of information transfer imposes concerns for the biosafety of genetic engineering of microbiomes as exposure of genetic information into unwanted hosts can have unprecedented ecological impacts. Current technologies are usually experimentally developed for a specific host/environment, and only deal with the transformation process itself at best, ignoring the impact of horizontal gene transfer and gene-microbiome interactions that occur over larger periods of time in uncontrolled environments. The goal of this research was to design new microbiome-specific versions of engineered genetic information, providing an additional layer of compatibility to existing engineering techniques. The engineering framework is entirely computational and is agnostic to the selected microbiome or gene by reducing the problem into the following set up: microbiome species can be defined as wanted or unwanted hosts of the modification. Then, every element related to gene expression (e.g., promoters, coding regions, etc.) and regulation is individually examined and engineered by novel algorithms to provide the defined expression preferences. Additionally, the synergistic effect of the combination of engineered gene blocks facilitates robustness to random mutations that might occur over time. This method has been validated using both computational and experimental tools, stemming from the research done in the iGEM 2021 competition, by the TAU group.
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Affiliation(s)
- Liyam Chitayat Levi
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv 997801, Israel
| | - Ido Rippin
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 997801, Israel
| | - Moran Ben Tulila
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv 997801, Israel
| | - Rotem Galron
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv 997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv 997801, Israel
- The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 997801, Israel
- Correspondence:
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Isaev A, Andriianov A, Znobishcheva E, Zorin E, Morozova N, Severinov K. Editing of Phage Genomes—Recombineering-assisted SpCas9 Modification of Model Coliphages T7, T5, and T3. Mol Biol 2022. [DOI: 10.1134/s0026893322060073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Bacteriophages—viruses that infect bacterial cells—are the most abundant biological entities on Earth. The use of phages in fundamental research and industry requires tools for precise manipulation of their genomes. Yet, compared to bacterial genome engineering, modification of phage genomes is challenging because of the lack of selective markers and thus requires laborious screenings of recombinant/mutated phage variants. The development of the CRISPR-Cas technologies allowed to solve this issue by the implementation of negative selection that eliminates the parental phage genomes. In this manuscript, we summarize current methods of phage genome engineering and their coupling with CRISPR-Cas technologies. We also provide examples of our successful application of these methods for introduction of specific insertions, deletions, and point mutations in the genomes of model Escherichia coli lytic phages T7, T5, and T3.
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