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Braunstein R, Hubanic G, Yerushalmy O, Oren-Alkalay S, Rimon A, Coppenhagen-Glazer S, Niv O, Marom H, Barsheshet A, Hazan R. Successful phage-antibiotic therapy of P. aeruginosa implant-associated infection in a Siamese cat. Vet Q 2024; 44:1-9. [PMID: 38726795 PMCID: PMC11089911 DOI: 10.1080/01652176.2024.2350661] [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: 09/09/2023] [Accepted: 04/27/2024] [Indexed: 05/15/2024] Open
Abstract
Antibiotic-resistant pathogens are a growing global issue, leading to untreatable infectious diseases in both humans and animals. Personalized bacteriophage (phage) therapy, the use of specific anti-bacterial viruses, is currently a leading approach to combat antibiotic-resistant infections. The implementation of phage therapy has primarily been focused on humans, almost neglecting the impact of such infections on the health and welfare of companion animals. Pets also have the potential to spread resistant infections to their owners or the veterinary staff through zoonotic transmission. Here, we showcase personalized phage-antibiotic treatment of a cat with a multidrug-resistant Pseudomonas aeruginosa implant-associated infection post-arthrodesis surgery. The treatment encompassed a tailored combination of an anti-P. aeruginosa phage and ceftazidime, precisely matched to the pathogen. The phage was topically applied to the surgical wound while the antibiotic was administered intramuscularly. After two treatment courses spanning 7 and 3 weeks, the surgical wound, which had previously remained open for five months, fully closed. To the best of our knowledge, this is the first case of personalized phage therapy application in felines, which provides further evidence of the effectiveness of this approach. The successful outcome paves the way for personalized phage-antibiotic treatments against persistent infections therapy in veterinary practice.
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Affiliation(s)
- Ron Braunstein
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
| | - Goran Hubanic
- Vet-Holim, Animal Medical Center, Kiryat-Anavim, Israel
| | - Ortal Yerushalmy
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
| | - Sivan Oren-Alkalay
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
| | - Amit Rimon
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
- Tzameret, The Military Track of Medicine, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Shunit Coppenhagen-Glazer
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
| | - Ofir Niv
- Vet-Holim, Animal Medical Center, Kiryat-Anavim, Israel
| | - Hilik Marom
- Vet-Holim, Animal Medical Center, Kiryat-Anavim, Israel
| | | | - Ronen Hazan
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Israel
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2
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Lyytinen OL, Dapuliga C, Wallinger D, Patpatia S, Audu BJ, Kiljunen SJ. Three novel Enterobacter cloacae bacteriophages for therapeutic use from Ghanaian natural waters. Arch Virol 2024; 169:156. [PMID: 38967872 PMCID: PMC11226500 DOI: 10.1007/s00705-024-06081-9] [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: 11/24/2023] [Accepted: 05/15/2024] [Indexed: 07/06/2024]
Abstract
Infections caused by multidrug-resistant (MDR) bacteria are a growing global concern. Enterobacter cloacae complex (ECC) species are particularly adept at developing antibiotic resistance. Phage therapy is proposed as an alternative treatment for pathogens that no longer respond to antibiotics. Unfortunately, ECC phages are understudied when compared to phages of many other bacterial species. In this Ghanaian-Finnish study, we isolated two ECC strains from ready-to-eat food samples and three novel phages from natural waters against these strains. We sequenced the genomic DNA of the novel Enterobacter phages, fGh-Ecl01, fGh-Ecl02, and fGh-Ecl04, and assessed their therapeutic potential. All of the phages were found to be lytic, easy to propagate, and lacking any toxic, integrase, or antibiotic resistance genes and were thus considered suitable for therapy purposes. They all were found to be related to T4-type viruses: fGh-Ecl01 and fGh-Ecl04 to karamviruses and fGh-Ecl02 to agtreviruses. Testing of Finnish clinical ECC strains showed promising susceptibility to these novel phages. As many as 61.1% of the strains were susceptible to fGh-Ecl01 and fGh-Ecl04, and 7.4% were susceptible to fGh-Ecl02. Finally, we investigated the susceptibility of the newly isolated ECC strains to three antibiotics - meropenem, ciprofloxacin, and cefepime - in combination with the novel phages. The use of phages and antibiotics together had synergistic effects. When using an antibiotic-phage combination, even low concentrations of antibiotics fully inhibited the growth of bacteria.
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Affiliation(s)
- O L Lyytinen
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - C Dapuliga
- Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - D Wallinger
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - S Patpatia
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - B J Audu
- National Veterinary Research Institute, Vom, Nigeria
| | - S J Kiljunen
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
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3
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Kovacs CJ, Antonacci A, Graham A, Jessup F, Rankin W, Brasko B, Maguire F, Washington MA, Kua SC, Burpo FJ, Barnhill JC. Comparing Methods to Genetically Engineer Bacteriophage and Increase Host Range. Mil Med 2024; 189:e1488-e1496. [PMID: 38780999 DOI: 10.1093/milmed/usae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/15/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
INTRODUCTION Antibacterial resistance is an emerging problem in military medicine. Disruptions to the health care systems in war-torn countries that result from ongoing conflict can potentially exacerbate this problem and increase the risk to U.S. forces in the deployed environment. Therefore, novel therapies are needed to mitigate the impact of these potentially devastating infections on military operations. Bacteriophages are viruses that infect and kill bacteria. They can be delivered as therapeutic agents and offer a promising alternative to traditional antibiotic chemotherapy. There are several potential benefits to their use, including high specificity and comparative ease of use in the field setting. However, the process of engineering phages for military medical applications can be a laborious and time-consuming endeavor. This review examines available techniques and compares their efficacy. MATERIALS AND METHODS This review evaluates the scientific literature on the development and application of four methods of bacteriophage genome engineering and their consideration in the context of military applications. Preffered Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed for a systematic review of available literature that met criteria for analysis and inclusion. The research completed for this review article originated from the United States Military Academy's library "Scout" search engine, which compiles results from 254 available databases (including PubMed, Google Scholar, and SciFinder). Particular attention was focused on identifying useful mechanistic insight into the nature of the engineering technique, the ease of use, and the applicability of the technique to countering the problem of antimicrobial resistance in the military setting. RESULTS A total of 52 studies were identified that met inclusion criteria following PRISMA guidelines. The bioengineering techniques analyzed included homologous recombination (12 articles), in vivo recombineering (9 articles), bacteriophage recombineering of electroporated DNA (7 articles), and the CRISPR-Cas system (10 articles). Rates of success and fidelity varied across each platform, and comparative benefits and drawbacks are considered. CONCLUSIONS Each of the phage engineering techniques addressed herein varies in amount of effort and overall success rate. CRISPR-Cas-facilitated modification of phage genomes presents a highly efficient method that does not require a lengthy purification and screening process. It therefore appears to be the method best suited for military medical applications.
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Affiliation(s)
- Christopher J Kovacs
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Alessia Antonacci
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Abigail Graham
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Faye Jessup
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - William Rankin
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Brianna Brasko
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Fiona Maguire
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Michael A Washington
- Department of Clinical Investigation, Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA 30905, USA
| | - Siang C Kua
- Department of Clinical Investigation, Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA 30905, USA
| | - F John Burpo
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Jason C Barnhill
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
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Li L, Fan R, Chen Y, Zhang Q, Zhao X, Hu M, Lv Q, Luo Y, Xu X, Cai Y, Liu Y. Characterization, genome analysis, and therapeutic evaluation of a novel Salmonella phage vB_SalS_JNS02: a candidate bacteriophage for phage therapy. Poult Sci 2024; 103:103845. [PMID: 38788486 PMCID: PMC11144812 DOI: 10.1016/j.psj.2024.103845] [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: 02/19/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Phage therapy is gaining momentum as an alternative to antibiotics in the treatment of salmonellosis caused by Salmonella. In this study, a novel Salmonella phage, vB_SalS_JNS02, was isolated successfully from poultry farms in Shandong, China. The biological characteristics of vB_SalS_JNS02 were analysed, which revealed a short latent period of approximately 10 min and a burst size of 110 PFU/cell. Moreover, vB_SalS_JNS02 exhibited remarkable stability across a wide pH range (pH 3-12) and temperatures ranging from 30 to 80°C. Genome sequencing analysis provided valuable insights into the genetic composition of vB_SalS_JNS02, which consists of a double-stranded DNA genome that spans 42,450 base pairs and has a G + C content of 49.4%. Of significant importance, the genomic sequence of vB_SalS_JNS02 did not contain any genes related to lysogenicity, virulence, or antibiotic resistance. The phage's efficacy was evaluated in a larval challenge study. Treatment with the phage resulted in increased survival of Galleria mellonella larvae (100, 70, and 85%) (MOI 0.1) in the prophylactic treatment, co-infection treatment, and remedial treatment experiments, respectively. Another in vivo experiment investigated the potential application of the phage in broiler chickens and revealed that a single oral dose of vB_SalS_JNS02 (108 PFU/mL, 100 µL/chick) administered 3 h after S. enteritidis oral administration provided effective protection. The introduction of bacteriophage not only enhances the production of secretory immunoglobulin A (sIgA), but also induces alterations in the composition of the gut microbial community. Phage therapy increases the relative abundance of beneficial bacteria, which helps to maintain intestinal barrier homeostasis. However, it is unable to fully restore the disrupted intestinal microbiome caused by S. enteritidis infection. Importantly, no significant adverse effects were observed in the animal subjects following oral administration of the phage, and our findings highlight vB_SalS_JNS02 is a hopeful candidate as a promising tool to target Salmonella infections in poultry.
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Affiliation(s)
- Lulu Li
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, 250100, China
| | - Ruining Fan
- College of Animal Science and Technology, Shandong Agricultural University, Taian, 272018, China
| | - Yibao Chen
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, 250100, China
| | - Qing Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, 250100, China
| | - Xiaonan Zhao
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, 250100, China
| | - Ming Hu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, 250100, China
| | - Qianghua Lv
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, 250100, China
| | - Yanbo Luo
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, 250100, China
| | - Xiaohui Xu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, 250100, China
| | - Yumei Cai
- College of Animal Science and Technology, Shandong Agricultural University, Taian, 272018, China
| | - Yuqing Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, 250100, China; Shandong vamph animal health products Co., LTD, Jinan, 250100.
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5
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González-Gómez JP, Rodríguez-Arellano SN, Gomez-Gil B, Vergara-Jiménez MDJ, Chaidez C. Genomic and biological characterization of bacteriophages against Enterobacter cloacae, a high-priority pathogen. Virology 2024; 595:110100. [PMID: 38714025 DOI: 10.1016/j.virol.2024.110100] [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: 11/08/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
Enterobacter cloacae is a clinically significant pathogen due to its multi-resistance to antibiotics, presenting a challenge in the treatment of infections. As concerns over antibiotic resistance escalate, novel therapeutic approaches have been explored. Bacteriophages, characterized by their remarkable specificity and ability to self-replicate within target bacteria, are emerging as a promising alternative therapy. In this study, we isolated and partially characterized nine lytic bacteriophages targeting E. cloacae, with two selected for comprehensive genomic analysis based on their host range and bacteriolytic activity. All identified phages exhibited a narrow host range, demonstrated stability within a temperature range of 30-60 °C, displayed pH tolerance from 3 to 10, and showed an excellent bacteriolytic capacity for up to 18 h. Notably, the fully characterized phage genomes revealed an absence of lysogenic, virulence, or antibiotic-resistance genes, positioning them as promising candidates for therapeutic intervention against E. cloacae-related diseases. Nonetheless, translating this knowledge into practical therapeutic applications mandates a deeper understanding of bacteriophage interactions within complex biological environments.
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Affiliation(s)
- Jean Pierre González-Gómez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico
| | | | - Bruno Gomez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Unidad Mazatlán en Acuicultura y Manejo Ambiental, AP 711, Mazatlan, Sinaloa, Mexico
| | | | - Cristobal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico.
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6
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Ulrich L, Steiner LX, Giez C, Lachnit T. Optimizing bacteriophage treatment of resistant Pseudomonas. mSphere 2024:e0070723. [PMID: 38934592 DOI: 10.1128/msphere.00707-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/15/2024] [Indexed: 06/28/2024] Open
Abstract
Phage therapy is increasing in relevance as an alternative treatment to combat antibiotic resistant bacteria. Phage cocktails are the state-of-the-art method of administering phages in clinical settings, preferred over monophage treatment because of their ability to eliminate multiple bacterial strains and reduce resistance formation. In our study, we compare monophage applications and phage cocktails to our chosen method of phage sequential treatments. To do so, we isolated four novel bacteriophages capable of infecting Pseudomonas alcaligenes T3, a close relative of P. aeruginosa, and characterized them using sequencing and transmission electron microscopy. While investigating monophage treatments, we observed that different phage concentrations had a strong impact on the timing and amount of resistance formation. When using phage cocktails, we observed that P. alcaligenes were capable of forming resistance in the same timespan it took them to become resistant to single phages. We isolated mutants resistant to each single phage as well as mutants exposed to phage cocktails, resulting in bacteria resistant to all four phages at once. Sequencing these mutants showed that different treatments yielded unique single nucleotide polymorphism mutation patterns. In order to combat resistance formation, we added phages one by one in intervals of 24 h, thus managing to delay resistance development and keeping bacterial growth significantly lower compared to phage cocktails.IMPORTANCEWHO declared antimicrobial resistance a top threat to global health; while antibiotics have stood at the forefront in the fight against bacterial infection, the increasing number of multidrug-resistant bacteria highlights a need to branch out in order to address the threat of antimicrobial resistance. Bacteriophages, viruses solely infecting bacteria, could present a solution due to their abundance, versatility, and adaptability. For this study, we isolated new phages infecting a fast-mutating Pseudomonas alcaligenes strain capable of forming resistance within 30 h. By using a sequential treatment approach of adding one phage after another, we were able to curb bacterial growth significantly more compared to state-of-the-art phage cocktails.
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Affiliation(s)
- Laura Ulrich
- Zoological Institute, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Leon X Steiner
- RD3 Marine Ecology, RU Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Christoph Giez
- Zoological Institute, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Tim Lachnit
- Zoological Institute, Christian-Albrechts Universität zu Kiel, Kiel, Germany
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7
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Ruan C, Ramoneda J, Kan A, Rudge TJ, Wang G, Johnson DR. Phage predation accelerates the spread of plasmid-encoded antibiotic resistance. Nat Commun 2024; 15:5397. [PMID: 38926498 PMCID: PMC11208555 DOI: 10.1038/s41467-024-49840-7] [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: 02/19/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024] Open
Abstract
Phage predation is generally assumed to reduce microbial proliferation while not contributing to the spread of antibiotic resistance. However, this assumption does not consider the effect of phage predation on the spatial organization of different microbial populations. Here, we show that phage predation can increase the spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth by reshaping spatial organization. Using two strains of the bacterium Escherichia coli, we demonstrate that phage predation slows the spatial segregation of the strains during growth. This increases the number of cell-cell contacts and the extent of conjugation-mediated plasmid transfer between them. The underlying mechanism is that phage predation shifts the location of fastest growth from the biomass periphery to the interior where cells are densely packed and aligned closer to parallel with each other. This creates straighter interfaces between the strains that are less likely to merge together during growth, consequently slowing the spatial segregation of the strains and enhancing plasmid transfer between them. Our results have implications for the design and application of phage therapy and reveal a mechanism for how microbial functions that are deleterious to human and environmental health can proliferate in the absence of positive selection.
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Affiliation(s)
- Chujin Ruan
- College of Land Science and Technology, China Agricultural University, Beijing, China
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Josep Ramoneda
- Spanish Research Council (CSIC), Center for Advanced Studies of Blanes (CEAB), Blanes, Spain
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
| | - Anton Kan
- Department of Materials, Swiss Federal Institute of Technology (ETH), Zürich, Switzerland
| | - Timothy J Rudge
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Gang Wang
- College of Land Science and Technology, China Agricultural University, Beijing, China.
- National Black Soil & Agriculture Research, China Agricultural University, Beijing, China.
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
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8
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Grodner B, Shi H, Farchione O, Vill AC, Ntekas I, Diebold PJ, Wu DT, Chen CY, Kim DM, Zipfel WR, Brito IL, De Vlaminck I. Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes. Nat Microbiol 2024:10.1038/s41564-024-01735-5. [PMID: 38918467 DOI: 10.1038/s41564-024-01735-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 05/17/2024] [Indexed: 06/27/2024]
Abstract
The exchange of mobile genetic elements (MGEs) facilitates the spread of functional traits including antimicrobial resistance within bacterial communities. Tools to spatially map MGEs and identify their bacterial hosts in complex microbial communities are currently lacking, limiting our understanding of this process. Here we combined single-molecule DNA fluorescence in situ hybridization (FISH) with multiplexed ribosomal RNA-FISH to enable simultaneous visualization of both MGEs and bacterial taxa. We spatially mapped bacteriophage and antimicrobial resistance (AMR) plasmids and identified their host taxa in human oral biofilms. This revealed distinct clusters of AMR plasmids and prophage, coinciding with densely packed regions of host bacteria. Our data suggest spatial heterogeneity in bacterial taxa results in heterogeneous MGE distribution within the community, with MGE clusters resulting from horizontal gene transfer hotspots or expansion of MGE-carrying strains. Our approach can help advance the study of AMR and phage ecology in biofilms.
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Affiliation(s)
- Benjamin Grodner
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Hao Shi
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Kanvas Biosciences, Inc, Monmouth Junction, NJ, USA
| | - Owen Farchione
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Albert C Vill
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ioannis Ntekas
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Peter J Diebold
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - David T Wu
- Division of Periodontology, Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Chia-Yu Chen
- Division of Periodontology, Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - David M Kim
- Division of Periodontology, Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Warren R Zipfel
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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9
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Anjum MS, Khaliq S, Ashraf N, Anwar MA, Akhtar K. Bioactive Streptomycetes: A Powerful Tool to Synthesize Diverse Nanoparticles With Multifarious Properties. J Basic Microbiol 2024:e2400129. [PMID: 38922954 DOI: 10.1002/jobm.202400129] [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: 03/05/2024] [Revised: 05/16/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Nanobiotechnology has gained significant attention due to its capacity to generate substantial benefits through the integration of microbial biotechnology and nanotechnology. Among microbial organisms, Actinomycetes, particularly the prominent genus Streptomycetes, have garnered attention for their prolific production of antibiotics. Streptomycetes have emerged as pivotal contributors to the discovery of a substantial number of antibiotics and play a dominant role in combating infectious diseases on a global scale. Despite the noteworthy progress achieved through the development and utilization of antibiotics to combat infectious pathogens, the prevalence of infectious diseases remains a prominent cause of mortality worldwide, particularly among the elderly and children. The emergence of antibiotic resistance among pathogens has diminished the efficacy of antibiotics in recent decades. Nevertheless, Streptomycetes continue to demonstrate their potential by producing bioactive metabolites for the synthesis of nanoparticles. Streptomycetes are instrumental in producing nanoparticles with diverse bioactive characteristics, including antiviral, antibacterial, antifungal, antioxidant, and antitumor properties. Biologically synthesized nanoparticles have exhibited a meaningful reduction in the impact of antibiotic resistance, providing resources for the development of new and effective drugs. This review succinctly outlines the significant applications of Streptomycetes as a crucial element in nanoparticle synthesis, showcasing their potential for diverse and enhanced beneficial applications.
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Affiliation(s)
- Muhammad Sultan Anjum
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Neelma Ashraf
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
- Institute of Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, Albert-Ludwig University of Freiburg, Freiburg im Breisgau, Germany
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
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10
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Asgharzadeh Kangachar S, Logel DY, Trofimova E, Zhu HX, Zaugg J, Schembri MA, Weynberg KD, Jaschke PR. Discovery and characterisation of new phage targeting uropathogenic Escherichia coli. Virology 2024; 597:110148. [PMID: 38941748 DOI: 10.1016/j.virol.2024.110148] [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: 01/31/2024] [Revised: 06/02/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
Antimicrobial resistance is an escalating threat with few new therapeutic options in the pipeline. Urinary tract infections (UTIs) are one of the most prevalent bacterial infections globally and are prone to becoming recurrent and antibiotic resistant. We discovered and characterized six novel Autographiviridae and Guernseyvirinae bacterial viruses (phage) against uropathogenic Escherichia coli (UPEC), a leading cause of UTIs. The phage genomes were between 39,471 bp - 45,233 bp, with 45.0%-51.0% GC%, and 57-84 predicted coding sequences per genome. We show that tail fiber domain structure, predicted host capsule type, and host antiphage repertoire correlate with phage host range. In vitro characterisation of phage cocktails showed synergistic improvement against a mixed UPEC strain population and when sequentially dosed. Together, these phage are a new set extending available treatments for UTI from UPEC, and phage vM_EcoM_SHAK9454 represents a promising candidate for further improvement through engineering.
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Affiliation(s)
- Shahla Asgharzadeh Kangachar
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Dominic Y Logel
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Ellina Trofimova
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Hannah X Zhu
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Julian Zaugg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), University of Queensland, Brisbane, Queensland, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Karen D Weynberg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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11
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Al-Anany AM, Fatima R, Nair G, Mayol JT, Hynes AP. Temperate phage-antibiotic synergy across antibiotic classes reveals new mechanism for preventing lysogeny. mBio 2024; 15:e0050424. [PMID: 38757974 DOI: 10.1128/mbio.00504-24] [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: 02/21/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
A recent demonstration of synergy between a temperate phage and the antibiotic ciprofloxacin suggested a scalable approach to exploiting temperate phages in therapy, termed temperate phage-antibiotic synergy, which specifically interacted with the lysis-lysogeny decision. To determine whether this would hold true across antibiotics, we challenged Escherichia coli with the phage HK97 and a set of 13 antibiotics spanning seven classes. As expected, given the conserved induction pathway, we observed synergy with classes of drugs known to induce an SOS response: a sulfa drug, other quinolones, and mitomycin C. While some β-lactams exhibited synergy, this appeared to be traditional phage-antibiotic synergy, with no effect on the lysis-lysogeny decision. Curiously, we observed a potent synergy with antibiotics not known to induce the SOS response: protein synthesis inhibitors gentamicin, kanamycin, tetracycline, and azithromycin. The synergy results in an eightfold reduction in the effective minimum inhibitory concentration of gentamicin, complete eradication of the bacteria, and, when administered at sub-optimal doses, drastically decreases the frequency of lysogens emerging from the combined challenge. However, lysogens exhibit no increased sensitivity to the antibiotic; synergy was maintained in the absence of RecA; and the antibiotic reduced the initial frequency of lysogeny rather than selecting against formed lysogens. Our results confirm that SOS-inducing antibiotics broadly result in temperate-phage-specific synergy, but that other antibiotics can interact with temperate phages specifically and result in synergy. This is the first report of a means of chemically blocking entry into lysogeny, providing a new means for manipulating the key lysis-lysogeny decision.IMPORTANCEThe lysis-lysogeny decision is made by most bacterial viruses (bacteriophages, phages), determining whether to kill their host or go dormant within it. With over half of the bacteria containing phages waiting to wake, this is one of the most important behaviors in all of biology. These phages are also considered unusable for therapy because of this behavior. In this paper, we show that many antibiotics bias this behavior to "wake" the dormant phages, forcing them to kill their host, but some also prevent dormancy in the first place. These will be important tools to study this critical decision point and may enable the therapeutic use of these phages.
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Affiliation(s)
- Amany M Al-Anany
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rabia Fatima
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gayatri Nair
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jordan T Mayol
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Alexander P Hynes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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12
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Vukovic D, Gostimirovic S, Cvetanovic J, Gavric D, Aleksic Sabo V, Todorovic D, Medic D, Knezevic P. Antibacterial Potential of Non-Tailed Icosahedral Phages Alone and in Combination with Antibiotics. Curr Microbiol 2024; 81:215. [PMID: 38849666 DOI: 10.1007/s00284-024-03705-w] [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: 01/29/2024] [Accepted: 04/13/2024] [Indexed: 06/09/2024]
Abstract
Non-tailed icosahedral phages belonging to families Fiersviridae (phages MS2 and Qbeta), Tectiviridae (PRD1) and Microviridae (phiX174) have not been considered in detail so far as potential antibacterial agents. The aim of the study was to examine various aspects of the applicability of these phages as antibacterial agents. Antibacterial potential of four phages was investigated via bacterial growth and biofilm formation inhibition, lytic spectra determination, and phage safety examination. The phage phiX174 was combined with different classes of antibiotics to evaluate potential synergistic interactions. In addition, the incidence of phiX174-insensitive mutants was analyzed. The results showed that only phiX174 out of four phages tested against their corresponding hosts inhibited bacterial growth for > 90% at different multiplicity of infection and that only this phage considerably prevented biofilm formation. Although all phages show the absence of potentially undesirable genes, they also have extremely narrow lytic spectra. The synergism was determined between phage phiX174 and ceftazidime, ceftriaxone, ciprofloxacin, macrolides, and chloramphenicol. It was shown that the simultaneous application of agents is more effective than successive treatment, where one agent is applied first. The analysis of the appearance of phiX174 bacteriophage-insensitive mutants showed that mutations occur with a frequency of 10-3. The examined non-tailed phages have a limited potential for use as antibacterial agents, primarily due to a very narrow lytic spectrum and the high frequency of resistant mutants appearance, but Microviridae can be considered in the future as biocontrol agents against susceptible strains of E. coli in combinations with conventional antimicrobial agents.
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Affiliation(s)
- Darija Vukovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Sonja Gostimirovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Jelena Cvetanovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Damir Gavric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Verica Aleksic Sabo
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | | | - Deana Medic
- Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | - Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia.
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13
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Zborowsky S, Seurat J, Balacheff Q, Ecomard S, Nguyen Ngoc Minh C, Titécat M, Evrard E, Rodriguez-Gonzalez RA, Marchi J, Weitz JS, Debarbieux L. Macrophage-induced reduction of bacteriophage density limits the efficacy of in vivo pulmonary phage therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575879. [PMID: 38293203 PMCID: PMC10827109 DOI: 10.1101/2024.01.16.575879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The rise of antimicrobial resistance has led to renewed interest in evaluating phage therapy. In murine models highly effective treatment of acute pneumonia caused by Pseudomonas aeruginosa relies on the synergistic antibacterial activity of bacteriophages with neutrophils. Here, we show that depletion of alveolar macrophages (AM) shortens the survival of mice without boosting the P. aeruginosa load in the lungs. Unexpectedly, upon bacteriophage treatment, pulmonary levels of P. aeruginosa were significantly lower in AM-depleted than in immunocompetent mice. To explore potential mechanisms underlying the benefit of AM-depletion in treated mice, we developed a mathematical model of phage, bacteria, and innate immune system dynamics. Simulations from the model fitted to data suggest that AM reduce bacteriophage density in the lungs. We experimentally confirmed that the in vivo decay of bacteriophage is faster in immunocompetent compared to AM-depleted animals. These findings demonstrate the involvement of feedback between bacteriophage, bacteria, and the immune system in shaping the outcomes of phage therapy in clinical settings.
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Affiliation(s)
- Sophia Zborowsky
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
- These authors contributed equally
| | - Jérémy Seurat
- Institut de Biologie, Ecole Normale Supérieure, Paris 75005, France
- School of Biological Sciences, Georgia Institute of Technology, Atlanta GA 30332, USA
- These authors contributed equally
| | - Quentin Balacheff
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
- CHU Felix Guyon, Service des maladies respiratoires, La Réunion, France
| | - Solène Ecomard
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
- DGA, Paris 75015, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Chau Nguyen Ngoc Minh
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Marie Titécat
- Université de Lille, INSERM, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, Lille 59000, France
| | - Emma Evrard
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
| | - Rogelio A. Rodriguez-Gonzalez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta GA 30332, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta GA 30332, USA
| | - Jacopo Marchi
- Department of Biology, University of Maryland, College Park MD 20742, USA
| | - Joshua S. Weitz
- Institut de Biologie, Ecole Normale Supérieure, Paris 75005, France
- School of Biological Sciences, Georgia Institute of Technology, Atlanta GA 30332, USA
- Department of Biology, University of Maryland, College Park MD 20742, USA
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, Bacteriophage Bacterium Host, Paris 75015, France
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14
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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 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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15
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Ednacot EMQ, Nabhani A, Dinh DM, Morehouse BR. Pharmacological potential of cyclic nucleotide signaling in immunity. Pharmacol Ther 2024; 258:108653. [PMID: 38679204 DOI: 10.1016/j.pharmthera.2024.108653] [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: 01/07/2024] [Revised: 03/16/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
Abstract
Cyclic nucleotides are important signaling molecules that play many critical physiological roles including controlling cell fate and development, regulation of metabolic processes, and responding to changes in the environment. Cyclic nucleotides are also pivotal regulators in immune signaling, orchestrating intricate processes that maintain homeostasis and defend against pathogenic threats. This review provides a comprehensive examination of the pharmacological potential of cyclic nucleotide signaling pathways within the realm of immunity. Beginning with an overview of the fundamental roles of cAMP and cGMP as ubiquitous second messengers, this review delves into the complexities of their involvement in immune responses. Special attention is given to the challenges associated with modulating these signaling pathways for therapeutic purposes, emphasizing the necessity for achieving cell-type specificity to avert unintended consequences. A major focus of the review is on the recent paradigm-shifting discoveries regarding specialized cyclic nucleotide signals in the innate immune system, notably the cGAS-STING pathway. The significance of cyclic dinucleotides, exemplified by 2'3'-cGAMP, in controlling immune responses against pathogens and cancer, is explored. The evolutionarily conserved nature of cyclic dinucleotides as antiviral agents, spanning across diverse organisms, underscores their potential as targets for innovative immunotherapies. Findings from the last several years have revealed a striking diversity of novel bacterial cyclic nucleotide second messengers which are involved in antiviral responses. Knowledge of the existence and precise identity of these molecules coupled with accurate descriptions of their associated immune defense pathways will be essential to the future development of novel antibacterial therapeutic strategies. The insights presented herein may help researchers navigate the evolving landscape of immunopharmacology as it pertains to cyclic nucleotides and point toward new avenues or lines of thinking about development of therapeutics against the pathways they regulate.
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Affiliation(s)
- Eirene Marie Q Ednacot
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Ali Nabhani
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - David M Dinh
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Benjamin R Morehouse
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92697, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92697, USA.
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16
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Liu S, Xu H, Cao R, Yang Z, Li X. Isolation, Identification, and Biological Characterization of Phage vB_KpnM_KpVB3 Targeting Carbapenem-Resistant Klebsiella pneumoniae ST11. J Glob Antimicrob Resist 2024; 37:179-184. [PMID: 38561142 DOI: 10.1016/j.jgar.2024.03.007] [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: 11/19/2023] [Revised: 02/28/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVES This study aimed to isolate a phage capable of lysing carbapenem-resistant Klebsiella pneumoniae (CRKP) and to analyse its biological characteristics and whole-genome sequence. METHODS The phage was isolated and purified from the sewage. Transmission electron microscopy (TEM) was employed to observe the bacteriophage's morphology. Phenotypic characterization of the bacteriophages was determined. The genomic information was analysed. Evolutionary relationships were established through comparative genomics, proteomics, and phylogenetic analysis. RESULTS The isolation of a virulent phage, named Klebsiella phage vB_KpnM_KpVB3, was notable for forming 6-7 mm transparent circular zones, each surrounded by a distinct halo. The phage had a head diameter of ca. 30 nm and a tail length of ca. 20 nm, being identified as a member of the Myoviridae family and the Caudovirales order. The optimal multiplicity of infection (MOI) was 0.00001, with an incubation period of 20 minutes and a lysis period of 60 minutes, and the number of released phages after lysis was 133±35 PFU/cell. The phage was relatively stable at temperatures ranging from 10°C to 40°C and at pH values ranging from 3 to 11. Its lytic efficiency against CRKP was 30.30%. It has been shown to be able to destroy the biofilm of host bacteria. The bacteriophage genome consists of double-stranded DNA (dsDNA) with a total length of 48,394 base pairs, a GC content of 48.99%, and 78 open reading frames (ORFs). CONCLUSION The study resulted in the isolation vB_KpnM_KpVB3, a phage demonstrating potential therapeutic efficacy against infections caused by CRKP.
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Affiliation(s)
- Shihui Liu
- Department of Clinical Laboratory, The First affiliated Hospital of Wannan Medical College Yijishan Hospital, Wuhu, China
| | - Hao Xu
- Department of Clinical Laboratory, The First affiliated Hospital of Wannan Medical College Yijishan Hospital, Wuhu, China
| | - Ruonan Cao
- Department of Clinical Laboratory, The First affiliated Hospital of Wannan Medical College Yijishan Hospital, Wuhu, China
| | - Zhenghai Yang
- Department of Clinical Laboratory, The First affiliated Hospital of Wannan Medical College Yijishan Hospital, Wuhu, China.
| | - Xiaoning Li
- Department of Clinical Laboratory, The First affiliated Hospital of Wannan Medical College Yijishan Hospital, Wuhu, China.
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17
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Kovacs CJ, Rapp EM, McKenzie SM, Mazur MZ, Mchale RP, Brasko B, Min MY, Burpo FJ, Barnhill JC. Disruption of Biofilm by Bacteriophages in Clinically Relevant Settings. Mil Med 2024; 189:e1294-e1302. [PMID: 37847552 DOI: 10.1093/milmed/usad385] [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: 05/15/2023] [Revised: 07/29/2023] [Accepted: 09/19/2023] [Indexed: 10/18/2023] Open
Abstract
INTRODUCTION Antibiotic-resistant bacteria are a growing threat to civilian and military health today. Although infections were once easily treatable by antibiotics and wound cleaning, the frequent mutation of bacteria has created strains impermeable to antibiotics and physical attack. Bacteria further their pathogenicity because of their ability to form biofilms on wounds, medical devices, and implant surfaces. Methods for treating biofilms in clinical settings are limited, and when formed by antibiotic-resistant bacteria, can generate chronic infections that are recalcitrant to available therapies. Bacteriophages are natural viral predators of bacteria, and their ability to rapidly destroy their host has led to increased attention in potential phage therapy applications. MATERIALS AND METHODS The present article sought to address a knowledge gap in the available literature pertaining to the usage of bacteriophage in clinically relevant settings and the resolution of infections particular to military concerns. PRISMA guidelines were followed for a systematic review of available literature that met the criteria for analysis and inclusion. The research completed for this review article originated from the U.S. Military Academy's library "Scout" search engine, which complies results from 254 available databases (including PubMed, Google Scholar, and SciFinder). The search criteria included original studies that employed bacteriophage use against biofilms, as well as successful phage therapy strategies for combating chronic bacterial infections. We specifically explored the use of bacteriophage against antibiotic- and treatment-resistant bacteria. RESULTS A total of 80 studies were identified that met the inclusion criteria following PRISMA guidelines. The application of bacteriophage has been demonstrated to robustly disrupt biofilm growth in wounds and on implant surfaces. When traditional therapies have failed to disrupt biofilms and chronic infections, a combination of these treatments with phage has proven to be effective, often leading to complete wound healing without reinfection. CONCLUSIONS This review article examines the available literature where bacteriophages have been utilized to treat biofilms in clinically relevant settings. Specific attention is paid to biofilms on implant medical devices, biofilms formed on wounds, and clinical outcomes, where phage treatment has been efficacious. In addition to the clinical benefit of phage therapies, the military relevance and treatment of combat-related infections is also examined. Phages offer the ability to expand available treatment options in austere environments with relatively low cost and effort, allowing the impacted warfighter to return to duty quicker and healthier.
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Affiliation(s)
- Christopher J Kovacs
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Erika M Rapp
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Sophia M McKenzie
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Michael Z Mazur
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Riley P Mchale
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Briana Brasko
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Michael Y Min
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - F John Burpo
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Jason C Barnhill
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
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18
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Wang B, Du L, Dong B, Kou E, Wang L, Zhu Y. Current Knowledge and Perspectives of Phage Therapy for Combating Refractory Wound Infections. Int J Mol Sci 2024; 25:5465. [PMID: 38791502 PMCID: PMC11122179 DOI: 10.3390/ijms25105465] [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: 03/22/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Wound infection is one of the most important factors affecting wound healing, so its effective control is critical to promote the process of wound healing. However, with the increasing prevalence of multi-drug-resistant (MDR) bacterial strains, the prevention and treatment of wound infections are now more challenging, imposing heavy medical and financial burdens on patients. Furthermore, the diminishing effectiveness of conventional antimicrobials and the declining research on new antibiotics necessitate the urgent exploration of alternative treatments for wound infections. Recently, phage therapy has been revitalized as a promising strategy to address the challenges posed by bacterial infections in the era of antibiotic resistance. The use of phage therapy in treating infectious diseases has demonstrated positive results. This review provides an overview of the mechanisms, characteristics, and delivery methods of phage therapy for combating pathogenic bacteria. Then, we focus on the clinical application of various phage therapies in managing refractory wound infections, such as diabetic foot infections, as well as traumatic, surgical, and burn wound infections. Additionally, an analysis of the potential obstacles and challenges of phage therapy in clinical practice is presented, along with corresponding strategies for addressing these issues. This review serves to enhance our understanding of phage therapy and provides innovative avenues for addressing refractory infections in wound healing.
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Affiliation(s)
- Bo Wang
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
| | - Lin Du
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
| | - Baiping Dong
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
| | - Erwen Kou
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
| | - Liangzhe Wang
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
| | - Yuanjie Zhu
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai 200052, China
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19
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Lossouarn J, Beurrier E, Bouteau A, Moncaut E, Sir Silmane M, Portalier H, Zouari A, Cattoir V, Serror P, Petit MA. The virtue of training: extending phage host spectra against vancomycin-resistant Enterococcus faecium strains using the Appelmans method. Antimicrob Agents Chemother 2024; 68:e0143923. [PMID: 38591854 PMCID: PMC11210271 DOI: 10.1128/aac.01439-23] [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: 11/02/2023] [Accepted: 03/14/2024] [Indexed: 04/10/2024] Open
Abstract
Phage therapy has (re)emerged as a serious possibility for combating multidrug-resistant bacterial infections, including those caused by vancomycin-resistant Enterococcus faecium strains. These opportunistic pathogens belong to a specific clonal complex 17, against which relatively few phages have been screened. We isolated a collection of 21 virulent phages growing on these vancomycin-resistant isolates. Each of these phages harbored a typical narrow plaquing host range, lysing at most 5 strains and covering together 10 strains of our panel of 14 clinical isolates. To enlarge the host spectrum of our phages, the Appelmans protocol was used. We mixed four out of our most complementary phages in a cocktail that we iteratively grew on eight naive strains from our panel, of which six were initially refractory to at least three of the combined phages. Fifteen successive passages permitted to significantly improve the lytic activity of the cocktail, from which phages with extended host ranges within the E. faecium species could be isolated. A single evolved phage able to kill up to 10 of the 14 initial E. faecium strains was obtained, and it barely infected nearby species. All evolved phages had acquired point mutations or a recombination event in the tail fiber genetic region, suggesting these genes might have driven phage evolution by contributing to their extended host spectra.
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Affiliation(s)
- Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Elsa Beurrier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Astrid Bouteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Elisabeth Moncaut
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Maria Sir Silmane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Heïdi Portalier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Asma Zouari
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière et CNR de la Résistance aux Antibiotiques (laboratoire associé "Entérocoques"), Rennes, France
| | - Vincent Cattoir
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière et CNR de la Résistance aux Antibiotiques (laboratoire associé "Entérocoques"), Rennes, France
- Université de Rennes, INSERM, UMR_S1230 BRM, Rennes, France
| | - Pascale Serror
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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20
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Zhen J, Liu R, Man C, Xu S, Zhang W, Zou L, Liu W, Ni HB, Zou M, He T, Wang R, Zhang XX, Zhang C. Bacteriophage LHE83 targeting OmpA as a receptor exhibited synergism with spectinomycin against Escherichia coli. Poult Sci 2024; 103:103643. [PMID: 38537406 PMCID: PMC10987938 DOI: 10.1016/j.psj.2024.103643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/07/2024] Open
Abstract
Understanding the characteristics of bacteriophages is crucial for the optimization of phage therapy. In this study, the biological and genomic characteristics of coliphage LHE83 were determined and its synergistic effects with different types of antibiotics against E. coli E82 were investigated. Phage LHE83 displayed a contractile tail morphology and had a titer of 3.02 × 109 pfu/mL at an optimal MOI of 0.01. Meanwhile, phage LHE83 exhibited good physical and chemical factors tolerance. The 1-step growth analysis revealed a latent period of approx. 10 min with a burst size of 87 pfu/infected cell. Phage LHE83 belongs to the genus Dhakavirus. Its genome consists of 170,464 bp with a 40% GC content, and a total of 268 Open Reading Frames (ORF) were predicted with no detected virulent or resistant genes. ORF 213 was predicted to encode the receptor binding protein (RBP) and confirmed by the antibody-blocking assay. Furthermore, a phage-resistant strain E. coli E82R was generated by co-culturing phage LHE83 with E. coli E82. Genomic analysis revealed that OmpA served as the receptor for phage LHE83, which was further confirmed by phage adsorption assay using E. coli BL21ΔOmpA, E. coli BL21ΔOmpA: OmpA and E. coli BL21:OmpA strains. Additionally, a synergistic effect was observed between phage LHE83 and spectinomycin against the drug-resistant strain E. coli E82. These results provide a theoretical basis for understanding the interactions between phages, antibiotics, and host bacteria, which can assist in the clinical application of phages and antibiotics against drug-resistant bacteria.
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Affiliation(s)
- Jianyu Zhen
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Rui Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Cheng Man
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Shijie Xu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenxiu Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ling Zou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Hong-Bo Ni
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ming Zou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Tao He
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ran Wang
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiao-Xuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China.
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21
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Fang Q, Yin X, He Y, Feng Y, Zhang L, Luo H, Yin G, McNally A, Zong Z. Safety and efficacy of phage application in bacterial decolonisation: a systematic review. THE LANCET. MICROBE 2024; 5:e489-e499. [PMID: 38452780 DOI: 10.1016/s2666-5247(24)00002-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/24/2023] [Accepted: 01/04/2024] [Indexed: 03/09/2024]
Abstract
Colonisation by bacterial pathogens typically precedes invasive infection and seeds transmission. Thus, effective decolonisation strategies are urgently needed. The literature reports attempts to use phages for decolonisation. To assess the in-vivo efficacy and safety of phages for bacterial decolonisation, we performed a systematic review by identifying relevant studies to assess the in-vivo efficacy and safety of phages for bacterial decolonisation. We searched PubMed, Embase (Ovid), MEDLINE (Ovid), Web of Science, and the Cochrane Library to identify relevant articles published between Jan 1, 1990, and May 12, 2023, without language restrictions. We included studies that assessed the efficacy of phage for bacterial decolonisation in humans or vertebrate animal models. This systematic review is registered with PROSPERO, CRD42023457637. We identified 6694 articles, of which 56 (51 animal studies and five clinical reports) met the predetermined selection criteria and were included in the final analysis. The gastrointestinal tract (n=49, 88%) was the most studied bacterial colonisation site, and other sites were central venous catheters, lung, nose, skin, and urinary tract. Of the 56 included studies, the bacterial load at the colonisation site was reported to decrease significantly in 45 (80%) studies, but only five described eradication of the target bacteria. 15 studies reported the safety of phages for decolonisation. No obvious adverse events were reported in both the short-term and long-term observation period. Given the increasing life-threatening risks posed by bacteria that are difficult to treat, phages could be an alternative option for bacterial decolonisation, although further optimisation is required before their application to meet clinical needs.
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Affiliation(s)
- Qingqing Fang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Department of General Practice, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Xin Yin
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Yanling He
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Yan Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Linwan Zhang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Department of Clinical Research Management, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Huan Luo
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Geng Yin
- Department of General Practice, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.
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22
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Porcari S, Fusco W, Spivak I, Fiorani M, Gasbarrini A, Elinav E, Cammarota G, Ianiro G. Fine-tuning the gut ecosystem: the current landscape and outlook of artificial microbiome therapeutics. Lancet Gastroenterol Hepatol 2024; 9:460-475. [PMID: 38604200 DOI: 10.1016/s2468-1253(23)00357-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 04/13/2024]
Abstract
The gut microbiome is acknowledged as a key determinant of human health, and technological progress in the past two decades has enabled the deciphering of its composition and functions and its role in human disorders. Therefore, manipulation of the gut microbiome has emerged as a promising therapeutic option for communicable and non-communicable disorders. Full exploitation of current therapeutic microbiome modulators (including probiotics, prebiotics, and faecal microbiota transplantation) is hindered by several factors, including poor precision, regulatory and safety issues, and the impossibility of providing reproducible and targeted treatments. Artificial microbiota therapeutics (which include a wide range of products, such as microbiota consortia, bacteriophages, bacterial metabolites, and engineered probiotics) have appeared as an evolution of current microbiota modulators, as they promise safe and reproducible effects, with variable levels of precision via different pathways. We describe the landscape of artificial microbiome therapeutics, from those already on the market to those still in the pipeline, and outline the major challenges for positioning these therapeutics in clinical practice.
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Affiliation(s)
- Serena Porcari
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - William Fusco
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Igor Spivak
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Medical Clinic III, University Hospital Aachen, Aachen, Germany
| | - Marcello Fiorani
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Antonio Gasbarrini
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Microbiome and Cancer Division, DKFZ, Heidelberg, Germany
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.
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23
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Liu Y, Lin Y, Zhu W. Systemic Effects of a Phage Cocktail on Healthy Weaned Piglets. BIOLOGY 2024; 13:271. [PMID: 38666883 PMCID: PMC11048100 DOI: 10.3390/biology13040271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024]
Abstract
Numerous studies have demonstrated that bacteriophages (phages) can effectively treat intestinal bacterial infections. However, research on the impact of phages on overall body health once they enter the intestine is limited. This study utilized weaned piglets as subjects to evaluate the systemic effects of an orally administered phage cocktail on their health. Twelve 21-day-old weaned piglets were divided into control (CON) and phage gavage (Phages) groups. The phage cocktail consisted of five lytic phages, targeting Salmonella enterica serovar Choleraesuis (S. choleraesuis), Enteropathogenic Escherichia coli (EPEC), and Shiga tox-in-producing Escherichia coli (STEC). The phages group received 10 mL of phage cocktail orally for 20 consecutive days. The results show that the phage gavage did not affect the piglets' growth performance, serum biochemical indices, or most organ indices, except for the pancreas. However, the impact on the intestine was complex. Firstly, although the pancreatic index decreased, it did not affect the secretion of digestive enzymes in the intestine. Secondly, phages increased the pH of jejunum chyme and relative weight of the ileum, and enhanced intestinal barrier function without affecting the morphology of the intestine. Thirdly, phages did not proliferate in the intestine, but altered the intestinal microbiota structure and increased concentrations of microbial metabolites isobutyric acid and isovaleric acid in the colonic chyme. In addition, phages impacted the immune status, significantly increasing serum IgA, IgG, and IgM, as well as serum and intestinal mucosal IFN-γ, IL-1β, IL-17, and TGF-β, and decreasing IL-4 and IL-10. They also activated toll-like receptors TLR-4 and TLR-9. Apart from an increase in basophil numbers, the counts of other immune cells in the blood did not change. This study indicates that the impact of phages on body health is complex, especially regarding immune status, warranting further attention. Short-term phage gavage did not have significant negative effects on health but could enhance intestinal barrier function.
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Affiliation(s)
- Yankun Liu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (W.Z.)
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Lin
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (W.Z.)
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
- National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (W.Z.)
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
- National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing 210095, China
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24
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Turchi B, Campobasso C, Nardinocchi A, Wagemans J, Torracca B, Lood C, Di Giuseppe G, Nieri P, Bertelloni F, Turini L, Ruffo V, Lavigne R, Di Luca M. Isolation and characterization of novel Staphylococcus aureus bacteriophage Hesat from dairy origin. Appl Microbiol Biotechnol 2024; 108:299. [PMID: 38619619 PMCID: PMC11018700 DOI: 10.1007/s00253-024-13129-y] [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: 09/05/2023] [Revised: 03/05/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024]
Abstract
A novel temperate phage, named Hesat, was isolated by the incubation of a dairy strain of Staphylococcus aureus belonging to spa-type t127 with either bovine or ovine milk. Hesat represents a new species of temperate phage within the Phietavirus genus of the Azeredovirinae subfamily. Its genome has a length of 43,129 bp and a GC content of 35.11% and contains 75 predicted ORFs, some of which linked to virulence. This includes (i) a pathogenicity island (SaPln2), homologous to the type II toxin-antitoxin system PemK/MazF family toxin; (ii) a DUF3113 protein (gp30) that is putatively involved in the derepression of the global repressor Stl; and (iii) a cluster coding for a PVL. Genomic analysis of the host strain indicates Hesat is a resident prophage. Interestingly, its induction was obtained by exposing the bacterium to milk, while the conventional mitomycin C-based approach failed. The host range of phage Hesat appears to be broad, as it was able to lyse 24 out of 30 tested S. aureus isolates. Furthermore, when tested at high titer (108 PFU/ml), Hesat phage was also able to lyse a Staphylococcus muscae isolate, a coagulase-negative staphylococcal strain. KEY POINTS: • A new phage species was isolated from a Staphylococcus aureus bovine strain. • Pathogenicity island and PVL genes are encoded within phage genome. • The phage is active against most of S. aureus strains from both animal and human origins.
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Affiliation(s)
- Barbara Turchi
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Claudia Campobasso
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Arianna Nardinocchi
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Jeroen Wagemans
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Beatrice Torracca
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
- Department of Microbial and Molecular Systems, Centre for Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium
| | | | - Paola Nieri
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano 6, 56126, Pisa, Italy
| | - Fabrizio Bertelloni
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Luca Turini
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Valeria Ruffo
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Mariagrazia Di Luca
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy.
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25
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Berkson JD, Wate CE, Allen GB, Schubert AM, Dunbar KE, Coryell MP, Sava RL, Gao Y, Hastie JL, Smith EM, Kenneally CR, Zimmermann SK, Carlson PE. Phage-specific immunity impairs efficacy of bacteriophage targeting Vancomycin Resistant Enterococcus in a murine model. Nat Commun 2024; 15:2993. [PMID: 38582763 PMCID: PMC10998888 DOI: 10.1038/s41467-024-47192-w] [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: 01/12/2023] [Accepted: 03/22/2024] [Indexed: 04/08/2024] Open
Abstract
Bacteriophage therapy is a promising approach to address antimicrobial infections though questions remain regarding the impact of the immune response on clinical effectiveness. Here, we develop a mouse model to assess phage treatment using a cocktail of five phages from the Myoviridae and Siphoviridae families that target Vancomycin-Resistant Enterococcus gut colonization. Phage treatment significantly reduces fecal bacterial loads of Vancomycin-Resistant Enterococcus. We also characterize immune responses elicited following administration of the phage cocktail. While minimal innate responses are observed after phage administration, two rounds of treatment induces phage-specific neutralizing antibodies and accelerate phage clearance from tissues. Interestingly, the myophages in our cocktail induce a more robust neutralizing antibody response than the siphophages. This anti-phage immunity reduces the effectiveness of the phage cocktail in our murine model. Collectively, this study shows phage-specific immune responses may be an important consideration in the development of phage cocktails for therapeutic use.
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Affiliation(s)
- Julia D Berkson
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Claire E Wate
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Garrison B Allen
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Alyxandria M Schubert
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Kristin E Dunbar
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Michael P Coryell
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Rosa L Sava
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Yamei Gao
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Viral Products, Laboratory of Pediatric and Respiratory Viral Diseases, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Jessica L Hastie
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Emily M Smith
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Charlotte R Kenneally
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Sally K Zimmermann
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Paul E Carlson
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA.
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26
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Yang D, Xiang Y, Song F, Li H, Ji X. Phage therapy: A renewed approach against oral diseases caused by Enterococcus faecalis infections. Microb Pathog 2024; 189:106574. [PMID: 38354990 DOI: 10.1016/j.micpath.2024.106574] [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: 09/27/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 02/16/2024]
Abstract
Antibiotics play an important role in the treatment of infectious diseases. Long-term overuse or misuse of antibiotics, however, has triggered the global crisis of antibiotic resistance, bringing challenges to treating clinical infection. Bacteriophages (phages) are the viruses infecting bacterial cells. Due to high host specificity, high bactericidal activity, and good biosafety, phages have been used as natural alternative antibacterial agents to fight against multiple drug-resistant bacteria. Enterococcus faecalis is the main species detected in secondary persistent infection caused by failure of root canal therapy. Due to strong tolerance and the formation of biofilm, E. faecalis can survive the changes in pH, temperature, and osmotic pressure in the mouth and thus is one of the main causes of periapical lesions. This paper summarizes the advantages of phage therapy, its applications in treating oral diseases caused by E. faecalis infections, and the challenges it faces. It offers a new perspective on phage therapy in oral diseases.
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Affiliation(s)
- Dan Yang
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yingying Xiang
- Department of Stomatology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650031, China
| | - Fei Song
- Department of Minimally Invasive Intervention, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
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Manohar P, Loh B, Turner D, Tamizhselvi R, Mathankumar M, Elangovan N, Nachimuthu R, Leptihn S. In vitro and in vivo evaluation of the biofilm-degrading Pseudomonas phage Motto, as a candidate for phage therapy. Front Microbiol 2024; 15:1344962. [PMID: 38559352 PMCID: PMC10978715 DOI: 10.3389/fmicb.2024.1344962] [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: 11/27/2023] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
Infections caused by Pseudomonas aeruginosa are becoming increasingly difficult to treat due to the emergence of strains that have acquired multidrug resistance. Therefore, phage therapy has gained attention as an alternative to the treatment of pseudomonal infections. Phages are not only bactericidal but occasionally show activity against biofilm as well. In this study, we describe the Pseudomonas phage Motto, a T1-like phage that can clear P. aeruginosa infections in an animal model and also exhibits biofilm-degrading properties. The phage has a substantial anti-biofilm activity against strong biofilm-producing isolates (n = 10), with at least a twofold reduction within 24 h. To demonstrate the safety of using phage Motto, cytotoxicity studies were conducted with human cell lines (HEK 293 and RAW 264.7 macrophages). Using a previously established in vivo model, we demonstrated the efficacy of Motto in Caenorhabditis elegans, with a 90% survival rate when treated with the phage at a multiplicity of infection of 10.
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Affiliation(s)
- Prasanth Manohar
- School of Bioscience and Technology, Vellore Institute of Technology (VIT), Vellore, India
| | - Belinda Loh
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Ramasamy Tamizhselvi
- School of Bioscience and Technology, Vellore Institute of Technology (VIT), Vellore, India
| | - Marimuthu Mathankumar
- School of Bioscience and Technology, Vellore Institute of Technology (VIT), Vellore, India
| | - Namasivayam Elangovan
- Department of Biotechnology, School of Bioscience, Periyar University, Salem, Tamil Nadu, India
| | - Ramesh Nachimuthu
- School of Bioscience and Technology, Vellore Institute of Technology (VIT), Vellore, India
| | - Sebastian Leptihn
- Department of Biochemistry, Health and Medical University, Erfurt, Germany
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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28
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Song M, Tang Q, Ding Y, Tan P, Zhang Y, Wang T, Zhou C, Xu S, Lyu M, Bai Y, Ma X. Staphylococcus aureus and biofilms: transmission, threats, and promising strategies in animal husbandry. J Anim Sci Biotechnol 2024; 15:44. [PMID: 38475886 DOI: 10.1186/s40104-024-01007-6] [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: 11/04/2023] [Accepted: 02/03/2024] [Indexed: 03/14/2024] Open
Abstract
Staphylococcus aureus (S. aureus) is a common pathogenic bacterium in animal husbandry that can cause diseases such as mastitis, skin infections, arthritis, and other ailments. The formation of biofilms threatens and exacerbates S. aureus infection by allowing the bacteria to adhere to pathological areas and livestock product surfaces, thus triggering animal health crises and safety issues with livestock products. To solve this problem, in this review, we provide a brief overview of the harm caused by S. aureus and its biofilms on livestock and animal byproducts (meat and dairy products). We also describe the ways in which S. aureus spreads in animals and the threats it poses to the livestock industry. The processes and molecular mechanisms involved in biofilm formation are then explained. Finally, we discuss strategies for the removal and eradication of S. aureus and biofilms in animal husbandry, including the use of antimicrobial peptides, plant extracts, nanoparticles, phages, and antibodies. These strategies to reduce the spread of S. aureus in animal husbandry help maintain livestock health and improve productivity to ensure the ecologically sustainable development of animal husbandry and the safety of livestock products.
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Affiliation(s)
- Mengda Song
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Innovative Utilization of Local Cattle and Sheep Germplasm Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Qi Tang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yakun Ding
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Peng Tan
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yucheng Zhang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Tao Wang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Chenlong Zhou
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shenrui Xu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mengwei Lyu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yueyu Bai
- Key Laboratory of Innovative Utilization of Local Cattle and Sheep Germplasm Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Xi Ma
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Migueletti MR, García Rey J, Micheloni J, Lomanto C, Martelli E, Sánchez G, Colombo JM, Vallecillo LM, Lamagni F, Giusti T, Acosta F, Villagrán F, Gvozdenovich M, Pricco Frakich A, Pianesi T, Tulin G, Mascali FC, Petitti TD, Torres Manno MA, Fusari CM, Buttigliero L, Giordana MF, Gramajo H, Diacovich L, Espariz M, Mussi MA. Complete genome sequence of the Microbacterium foliorum bacteriophage Garey24. Microbiol Resour Announc 2024; 13:e0121523. [PMID: 38315107 DOI: 10.1128/mra.01215-23] [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: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
In this work, we report the discovery and characterization of Garey24, a bacteriophage that forms medium-size plaques with halo rings isolated from a soil sample in Funes, Argentina. Its 41,522 bp circularly permuted genome contains 63 putative protein-coding genes. Based on gene content similarity, Garey24 was assigned to subcluster EA1.
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Affiliation(s)
- Matías R Migueletti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julieta García Rey
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Josefina Micheloni
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Camila Lomanto
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Elisa Martelli
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gastón Sánchez
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julián M Colombo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luciano M Vallecillo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Francisco Lamagni
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás Giusti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Fabrina Acosta
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Franco Villagrán
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Martín Gvozdenovich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Abril Pricco Frakich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tulio Pianesi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gonzalo Tulin
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Florencia C Mascali
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás D Petitti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariano A Torres Manno
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Corina M Fusari
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | | | - Hugo Gramajo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lautaro Diacovich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Martín Espariz
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María Alejandra Mussi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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Shanmugasundaram S, Nayak N, Puzhankara L, Kedlaya MN, Rajagopal A, Karmakar S. Bacteriophages: the dawn of a new era in periodontal microbiology? Crit Rev Microbiol 2024; 50:212-223. [PMID: 36883683 DOI: 10.1080/1040841x.2023.2182667] [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: 10/31/2022] [Revised: 01/02/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
The oral microbiome, populated by a diverse range of species, plays a critical role in the initiation and progression of periodontal disease. The most dominant yet little-discussed players in the microbiome, the bacteriophages, influence the health and disease of the host in various ways. They, not only contribute to periodontal health by preventing the colonization of pathogens and disrupting biofilms but also play a role in periodontal disease by upregulating the virulence of periodontal pathogens through the transfer of antibiotic resistance and virulence factors. Since bacteriophages selectively infect only bacterial cells, they have an enormous scope to be used as a therapeutic strategy; recently, phage therapy has been successfully used to treat antibiotic-resistant systemic infections. Their ability to disrupt biofilms widens the scope against periodontal pathogens and dental plaque biofilms in periodontitis. Future research focussing on the oral phageome and phage therapy's effectiveness and safety could pave way for new avenues in periodontal therapy. This review explores our current understanding of bacteriophages, their interactions in the oral microbiome, and their therapeutic potential in periodontal disease.
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Affiliation(s)
- Shashikiran Shanmugasundaram
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Namratha Nayak
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lakshmi Puzhankara
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Madhurya N Kedlaya
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anjale Rajagopal
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shaswata Karmakar
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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31
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Kang D, Bagchi D, Chen IA. Pharmacokinetics and Biodistribution of Phages and their Current Applications in Antimicrobial Therapy. ADVANCED THERAPEUTICS 2024; 7:2300355. [PMID: 38933919 PMCID: PMC11198966 DOI: 10.1002/adtp.202300355] [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: 09/29/2023] [Indexed: 06/28/2024]
Abstract
Antimicrobial resistance remains a critical global health concern, necessitating the investigation of alternative therapeutic approaches. With the diminished efficacy of conventional small molecule drugs due to the emergence of highly resilient bacterial strains, there is growing interest in the potential for alternative therapeutic modalities. As naturally occurring viruses of bacteria, bacteriophage (or phage) are being re-envisioned as a platform to engineer properties that can be tailored to target specific bacterial strains and employ diverse antibacterial mechanisms. However, limited understanding of key pharmacological properties of phage is a major challenge to translating its use from preclinical to clinical settings. Here, we review modern advancements in phage-based antimicrobial therapy and discuss the in vivo pharmacokinetics and biodistribution of phage, addressing critical challenges in their application that must be overcome for successful clinical implementation.
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Affiliation(s)
- Dayeon Kang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 90024 USA
| | - Damayanti Bagchi
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 90024 USA
| | - Irene A. Chen
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 90024 USA
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32
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Zajacova A, Scaramozzino MU, Bellini A, Purwar P, Ricciardi S, Migliore M, Meloni F, Esendagli D. ERS International Congress 2023: highlights from the Thoracic Surgery and Lung Transplantation Assembly. ERJ Open Res 2024; 10:00854-2023. [PMID: 38590936 PMCID: PMC11000272 DOI: 10.1183/23120541.00854-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 04/10/2024] Open
Abstract
Five sessions presented at the European Respiratory Society Congress 2023 were selected by Assembly 8, consisting of thoracic surgeons and lung transplant professionals. Highlights covering management of adult spontaneous pneumothorax, malignant pleural effusion, infectious and immune-mediated complications after lung transplantation, as well as the pro and con debate on age limit in lung transplantation and results of the ScanCLAD study were summarised by early career members, supervised by the assembly faculty.
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Affiliation(s)
- Andrea Zajacova
- Prague Lung Transplant Program, Department of Pneumology, Second Faculty of Medicine, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Marco Umberto Scaramozzino
- Pulmonology “La Madonnina” Reggio Calabria, Reggio Calabria, Italy
- Villa aurora Hospital Reggio Calabria, Reggio Calabria, Italy
| | - Alice Bellini
- Division of Thoracic Surgery, Department of Medical and Surgical Sciences (DIMEC) of the Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Giovanni Battista Morgagni-Luigi Pierantoni Hospital, Forlì, Italy
| | | | - Sara Ricciardi
- Unit of Thoracic Surgery, San Camillo Forlanini Hospital, Rome, Italy
- Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Marcello Migliore
- Program of Minimally Invasive Thoracic Surgery and New Technologies, Policlinic Hospital, Department of Surgery and Medical Specialties, University of Catania, Catania, Italy
- Thoracic Surgery and Lung Transplantation, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Federica Meloni
- Transplant Center, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Dorina Esendagli
- Baskent University, Faculty of Medicine, Chest Diseases Department, Ankara, Turkey
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Hassannia M, Naderifar M, Salamy S, Akbarizadeh MR, Mohebi S, Moghadam MT. Engineered phage enzymes against drug-resistant pathogens: a review on advances and applications. Bioprocess Biosyst Eng 2024; 47:301-312. [PMID: 37962644 DOI: 10.1007/s00449-023-02938-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023]
Abstract
In recent decades, the expansion of multi and extensively drug-resistant (MDR and XDR) bacteria has reached an alarming rate, causing serious health concerns. Infections caused by drug-resistant bacteria have been associated with morbidity and mortality, making tackling bacterial resistance an urgent and unmet challenge that needs to be addressed properly. Endolysins are phage-encoded enzymes that can specifically degrade the bacterial cell wall and lead to bacterial death. There is remarkable evidence that corroborates the unique ability of endolysins to rapidly digest the peptidoglycan particular bonds externally without the assistance of phage. Thus, their modulation in therapeutic approaches has opened new options for therapeutic applications in the fight against bacterial infections in the human and veterinary sectors, as well as within the agricultural and biotechnology areas. The use of genetically engineered phage enzymes (EPE) promises to generate endolysin variants with unique properties for prophylactic and therapeutic applications. These approaches have gained momentum to accelerate basic as well as translational phage research and the potential development of therapeutics in the near future. This review will focus on the novel knowledge into EPE and demonstrate that EPE has far better performance than natural endolysins and phages in dealing with antibiotic-resistant infections. Therefore, it provides essential information for clinical trials involving EPE.
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Affiliation(s)
- Mohadeseh Hassannia
- Department of Genetic, Faculty of Science, Islamic Azad University, Tehran, Iran
| | - Mahin Naderifar
- School of Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Shakiba Salamy
- Department of Microbiology, Faculty of Pharmacy, Islamic Azad University, Tehran, Iran
| | | | - Samane Mohebi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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34
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Feng L, Chen H, Qian C, Zhao Y, Wang W, Liu Y, Xu M, Cao J, Zhou T, Wu Q. Resistance, mechanism, and fitness cost of specific bacteriophages for Pseudomonas aeruginosa. mSphere 2024; 9:e0055323. [PMID: 38299825 PMCID: PMC10900902 DOI: 10.1128/msphere.00553-23] [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: 09/27/2023] [Accepted: 12/20/2023] [Indexed: 02/02/2024] Open
Abstract
The bacteriophage is an effective adjunct to existing antibiotic therapy; however, in the course of bacteriophage therapy, host bacteria will develop resistance to bacteriophages, thus affecting the efficacy. Therefore, it is important to describe how bacteria evade bacteriophage attack and the consequences of the biological changes that accompany the development of bacteriophage resistance before the bacteriophage is applied. The specific bacteriophage vB3530 of Pseudomonas aeruginosa (P. aeruginosa) has stable biological characteristics, short incubation period, strong in vitro cleavage ability, and absence of virulence or resistance genes. Ten bacteriophage-resistant strains (TL3780-R) were induced using the secondary infection approach, and the plaque assay showed that vB3530 was less sensitive to TL3780-R. Identification of bacteriophage adsorption receptors showed that the bacterial surface polysaccharide was probably the adsorption receptor of vB3530. In contrast to the TL3780 parental strain, TL3780-R is characterized by the absence of long lipopolysaccharide chains, which may be caused by base insertion of wzy or deletion of galU. It is also intriguing to observe that, in comparison to the parent strain, the bacteriophage-resistant strains TL3780-R mostly exhibited a large cost of fitness (growth rate, biofilm formation, motility, and ability to produce enhanced pyocyanin). In addition, TL3780-R9 showed increased susceptibility to aminoglycosides and chlorhexidine, which may be connected to the loss and down-regulation of mexX expression. Consequently, these findings fully depicted the resistance mechanism of P. aeruginosa to vB3530 and the fitness cost of bacteriophage resistance, laying a foundation for further application of bacteriophage therapy.IMPORTANCEThe bacteriophage is an effective adjunct to existing antibiotic therapy; However, bacteria also develop defensive mechanisms against bacteriophage attack. Thus, there is an urgent need to deeply understand the resistance mechanism of bacteria to bacteriophages and the fitness cost of bacteriophage resistance so as to lay the foundation for subsequent application of the phage. In this study, a specific bacteriophage vB3530 of P. aeruginosa had stable biological characteristics, short incubation period, strong in vitro cleavage ability, and absence of virulence or resistance genes. In addition, we found that P. aeruginosa may lead to phage resistance due to the deletion of galU and the base insertion of wzy, involved in the synthesis of lipopolysaccharides. Simultaneously, we showed the association with the biological state of the bacteria after bacteria acquire bacteriophage resistance, which is extremely relevant to guide the future application of therapeutic bacteriophages.
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Affiliation(s)
- Luozhu Feng
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Department of Clinical Laboratory, the First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China
| | - Huanchang Chen
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Changrui Qian
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yining Zhao
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Weixiang Wang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yan Liu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Mengxin Xu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jianming Cao
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Tieli Zhou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qing Wu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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35
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Kirk D, Costeira R, Visconti A, Khan Mirzaei M, Deng L, Valdes AM, Menni C. Bacteriophages, gut bacteria, and microbial pathways interplay in cardiometabolic health. Cell Rep 2024; 43:113728. [PMID: 38300802 DOI: 10.1016/j.celrep.2024.113728] [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: 10/20/2023] [Revised: 12/18/2023] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
Cardiometabolic diseases are leading causes of mortality in Western countries. Well-established risk factors include host genetics, lifestyle, diet, and the gut microbiome. Moreover, gut bacterial communities and their activities can be altered by bacteriophages (also known simply as phages), bacteria-infecting viruses, making these biological entities key regulators of human cardiometabolic health. The manipulation of bacterial populations by phages enables the possibility of using phages in the treatment of cardiometabolic diseases through phage therapy and fecal viral transplants. First, however, a deeper understanding of the role of the phageome in cardiometabolic diseases is required. In this review, we first introduce the phageome as a component of the gut microbiome and discuss fecal viral transplants and phage therapy in relation to cardiometabolic diseases. We then summarize the current state of phageome research in cardiometabolic diseases and propose how the phageome might indirectly influence cardiometabolic health through gut bacteria and their metabolites.
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Affiliation(s)
- Daniel Kirk
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas Hospital, Westminster Bridge Road, London SE1 7EH, UK
| | - Ricardo Costeira
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas Hospital, Westminster Bridge Road, London SE1 7EH, UK
| | - Alessia Visconti
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas Hospital, Westminster Bridge Road, London SE1 7EH, UK; Center for Biostatistics, Epidemiology, and Public Health, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, 85764 Neuherberg, Germany; School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, 85764 Neuherberg, Germany; School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Ana M Valdes
- Academic Rheumatology, Clinical Sciences Building, Nottingham City Hospital, University of Nottingham, Nottingham, UK
| | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas Hospital, Westminster Bridge Road, London SE1 7EH, UK.
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36
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Brás A, Braz M, Martinho I, Duarte J, Pereira C, Almeida A. Effect of Bacteriophages against Biofilms of Escherichia coli on Food Processing Surfaces. Microorganisms 2024; 12:366. [PMID: 38399770 PMCID: PMC10892694 DOI: 10.3390/microorganisms12020366] [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: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The bacterial adhesion to food processing surfaces is a threat to human health, as these surfaces can serve as reservoirs of pathogenic bacteria. Escherichia coli is an easily biofilm-forming bacterium involved in surface contamination that can lead to the cross-contamination of food. Despite the application of disinfection protocols, contamination through food processing surfaces continues to occur. Hence, new, effective, and sustainable alternative approaches are needed. Bacteriophages (or simply phages), viruses that only infect bacteria, have proven to be effective in reducing biofilms. Here, phage phT4A was applied to prevent and reduce E. coli biofilm on plastic and stainless steel surfaces at 25 °C. The biofilm formation capacity of phage-resistant and sensitive bacteria, after treatment, was also evaluated. The inactivation effectiveness of phage phT4A was surface-dependent, showing higher inactivation on plastic surfaces. Maximum reductions in E. coli biofilm of 5.5 and 4.0 log colony-forming units (CFU)/cm2 after 6 h of incubation on plastic and stainless steel, respectively, were observed. In the prevention assays, phage prevented biofilm formation in 3.2 log CFU/cm2 after 12 h. Although the emergence of phage-resistant bacteria has been observed during phage treatment, phage-resistant bacteria had a lower biofilm formation capacity compared to phage-sensitive bacteria. Overall, the results suggest that phages may have applicability as surface disinfectants against pathogenic bacteria, but further studies are needed to validate these findings using phT4A under different environmental conditions and on different materials.
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Affiliation(s)
| | | | | | | | - Carla Pereira
- Department of Biology, CESAM, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal; (A.B.); (M.B.); (I.M.); (J.D.)
| | - Adelaide Almeida
- Department of Biology, CESAM, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal; (A.B.); (M.B.); (I.M.); (J.D.)
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Zhang J, Lu T, Song Y, Rocha UND, Liu J, Nikolausz M, Wei Y, Richnow HH. Viral Communities Contribute More to the Lysis of Antibiotic-Resistant Bacteria than the Transduction of Antibiotic Resistance Genes in Anaerobic Digestion Revealed by Metagenomics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2346-2359. [PMID: 38267392 PMCID: PMC10851435 DOI: 10.1021/acs.est.3c07664] [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: 09/16/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Ecological role of the viral community on the fate of antibiotic resistance genes (ARGs) (reduction vs proliferation) remains unclear in anaerobic digestion (AD). Metagenomics revealed a dominance of Siphoviridae and Podoviridae among 13,895 identified viral operational taxonomic units (vOTUs) within AD, and only 21 of the vOTUs carried ARGs, which only accounted for 0.57 ± 0.43% of AD antibiotic resistome. Conversely, ARGs locating on plasmids and integrative and conjugative elements accounted for above 61.0%, indicating a substantial potential for conjugation in driving horizontal gene transfer of ARGs within AD. Virus-host prediction based on CRISPR spacer, tRNA, and homology matches indicated that most viruses (80.2%) could not infect across genera. Among 480 high-quality metagenome assembly genomes, 95 carried ARGs and were considered as putative antibiotic-resistant bacteria (pARB). Furthermore, lytic phages of 66 pARBs were identified and devoid of ARGs, and virus/host abundance ratios with an average value of 71.7 indicated extensive viral activity and lysis. The infectivity of lytic phage was also elucidated through laboratory experiments concerning changes of the phage-to-host ratio, pH, and temperature. Although metagenomic evidence for dissemination of ARGs by phage transduction was found, the higher proportion of lytic phages infecting pARBs suggested that the viral community played a greater role in reducing ARB numbers than spreading ARGs in AD.
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Affiliation(s)
- Junya Zhang
- State
Key Joint Laboratory of Environmental Simulation and Pollution Control,
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Department
of Isotope Biogeochemistry, Helmholtz Centre
for Environmental Research–UFZ, Leipzig 04318, Germany
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Tiedong Lu
- Agricultural
Resource and Environment Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laborarory of
Arable Lnad Conservation, Nanning 530007, Guangxi, China
| | - Yunpeng Song
- State
Key Joint Laboratory of Environmental Simulation and Pollution Control,
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Ulisses Nunes da Rocha
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research–UFZ, Leipzig 04318, Germany
| | - Jibao Liu
- State
Key Joint Laboratory of Environmental Simulation and Pollution Control,
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Marcell Nikolausz
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research–UFZ, Leipzig 04318, Germany
| | - Yuansong Wei
- State
Key Joint Laboratory of Environmental Simulation and Pollution Control,
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Hans Hermann Richnow
- Department
of Isotope Biogeochemistry, Helmholtz Centre
for Environmental Research–UFZ, Leipzig 04318, Germany
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Di Napoli M, Castagliuolo G, Pio S, Di Nardo I, Russo T, Antonini D, Notomista E, Varcamonti M, Zanfardino A. Study of the Antimicrobial Activity of the Human Peptide SQQ30 against Pathogenic Bacteria. Antibiotics (Basel) 2024; 13:145. [PMID: 38391531 PMCID: PMC10886087 DOI: 10.3390/antibiotics13020145] [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: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Given the continuous increase in antibiotic resistance, research has been driven towards the isolation of new antimicrobial molecules. Short, charged, and very hydrophobic antimicrobial peptides have a direct action against biological membranes, which are less prone to developing resistance. Using a bioinformatic tool, we chose the SQQ30 peptide, isolated from the human SOGA1 protein. The antimicrobial activity of this peptide against various Gram-negative and Gram-positive bacterial strains and against a fungal strain was studied. A mechanism of action directed against biological membranes was outlined. When administered in combination with the antibiotic ciprofloxacin and with the TRS21 (buforin II), another antimicrobial peptide, SQQ30 can be used with a lower MIC, showing additivity and synergism, respectively. Particularly interesting is the ability of SQQ30 to bind LPS in Gram-negative strains, preventing the eukaryotic cell from releasing inflammatory mediators. Our study indicates SQQ30 as a novel and promising antimicrobial agent.
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Affiliation(s)
- Michela Di Napoli
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Giusy Castagliuolo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Sara Pio
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Ilaria Di Nardo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Teresa Russo
- IPCB-Institute for Polymers, Composites and Biomaterials, National Research Council of Italy, 80125 Naples, Italy
| | - Dario Antonini
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Mario Varcamonti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Anna Zanfardino
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
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Hahn J, Ding S, Im J, Harimoto T, Leong KW, Danino T. Bacterial therapies at the interface of synthetic biology and nanomedicine. NATURE REVIEWS BIOENGINEERING 2024; 2:120-135. [PMID: 38962719 PMCID: PMC11218715 DOI: 10.1038/s44222-023-00119-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 07/05/2024]
Abstract
Bacteria are emerging as living drugs to treat a broad range of disease indications. However, the inherent advantages of these replicating and immunostimulatory therapies also carry the potential for toxicity. Advances in synthetic biology and the integration of nanomedicine can address this challenge through the engineering of controllable systems that regulate spatial and temporal activation for improved safety and efficacy. Here, we review recent progress in nanobiotechnology-driven engineering of bacteria-based therapies, highlighting limitations and opportunities that will facilitate clinical translation.
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Affiliation(s)
- Jaeseung Hahn
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Suwan Ding
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jongwon Im
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Tetsuhiro Harimoto
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
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Qi G, Liu X, Shi L, Zhuang J, Liu B. Targeted Depletion of Individual Pathogen by Bacteria-Templated Polymer. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307940. [PMID: 37921569 DOI: 10.1002/adma.202307940] [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: 08/07/2023] [Revised: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Selective and targeted removal of individual species or strains of bacteria from complex communities can be desirable over traditional and broadly acting antibiotics in several conditions. However, strategies that can detect and ablate bacteria with high specificity are emerging in recent years. Herein, a platform is reported that uses bacteria as a template to synthesize polymers containing guanidinium groups for self-selective depletion of specific pathogenic bacteria without disturbing microbial communities. Different from conventional antibiotics, repeated treatment of bacteria with the templated polymers does not evolve drug resistance mutants after 20 days of serial passaging. Especially, high in vivo therapeutic effectiveness of the templated polymers is achieved in E. coli- and P. aeruginosa-induced microbial peritonitis. The templated polymers have shown high selectivity in in vivo antimicrobial activity, which has excellent potential as systemic antimicrobials against bacterial infections.
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Affiliation(s)
- Guobin Qi
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Xianglong Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou, 350207, China
| | - Leilei Shi
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
| | - Jiahao Zhuang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou, 350207, China
- Institute for Functional Intelligent Materials, National University of Singapore, Blk S9, Level 9, 4 Science Drive 2, Singapore, 117544, Singapore
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Narayanan KB, Bhaskar R, Choi SM, Han SS. Development of carrageenan-immobilized lytic coliphage vB_Eco2571-YU1 hydrogel for topical delivery of bacteriophages in wound dressing applications. Int J Biol Macromol 2024; 259:129349. [PMID: 38219934 DOI: 10.1016/j.ijbiomac.2024.129349] [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: 08/08/2023] [Revised: 12/31/2023] [Accepted: 01/07/2024] [Indexed: 01/16/2024]
Abstract
Bacteriophages are employed as cost-effective and efficient antibacterial agents to counter the emergence of antibiotic-resistant bacteria and other host bacteria in phage therapy. The increasing incidence of skin wounds is a significant concern in clinical practice, especially considering the limitations of antibiotic therapy. Furthermore, the lack of an effective delivery system that preserves the stability of bacteriophages hampers their clinical implementation. In recent years, there has been a growing amount of research on bacteriophage applications in veterinary and biomedical sciences. In our study, lytic coliphage vB_Eco2571-YU1 was isolated against pathogenic Escherichia coli host bacteria, and hydrogel wound dressing materials were fabricated with marine polysaccharide carrageenan (carr-vB_Eco2571-YU1) for their antibacterial activity. Transmission electron microscopy (TEM) morphology identified it as a Myoviridae coliphage with an icosahedral head length and width of approximately 60 and 56.8 nm, respectively, and a tail length of 119.7 nm. The one-step growth curve of coliphage revealed a latent period of 10 min, a rise period of 15 min, and a burst size of 120 virions per cell. The bacteriolytic activity of unimmobilized coliphages was observed within 2 h; however, strain-specific phage resistance was acquired after 9 h. In contrast, carr-vB_Eco2571-YU1 showed a sharp decline in the growth of bacteria in the log phase after 2 h and did not allow for the acquisition of phage resistance by the E. coli strain. The stability of coliphage under different pH, temperature, osmolarity, detergents, and organic solvents was evaluated. We also studied the long-term storage of carr-vB_Eco2571-YU1 hydrogels at 4 °C and found that the titer value decreased during a time-dependent period of 28 days. These hydrogels were also found to be hemocompatible using a hemolysis assay. The addition of plasticizer (0.6 % (w/v)) to the carrageenan (2 % (w/v)) to prepare carr-vB_Eco2571-YU1 hydrogels showed a decrease in compressive strength with enhanced elasticity. This phage therapy using polymeric immobilization of bacteriophages is a promising next-generation wound dressing biomaterial alternative to conventional wound and skin care management.
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Affiliation(s)
- Kannan Badri Narayanan
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea.
| | - Rakesh Bhaskar
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea
| | - Soon Mo Choi
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea
| | - Sung Soo Han
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea.
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Liu H, Yu Y, Dong A, Elsabahy M, Yang Y, Gao H. Emerging strategies for combating Fusobacterium nucleatum in colorectal cancer treatment: Systematic review, improvements and future challenges. EXPLORATION (BEIJING, CHINA) 2024; 4:20230092. [PMID: 38854496 PMCID: PMC10867388 DOI: 10.1002/exp.20230092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/16/2023] [Indexed: 06/11/2024]
Abstract
Colorectal cancer (CRC) is generally characterized by a high prevalence of Fusobacterium nucleatum (F. nucleatum), a spindle-shaped, Gram-negative anaerobe pathogen derived from the oral cavity. This tumor-resident microorganism has been closely correlated with the occurrence, progression, chemoresistance and immunosuppressive microenvironment of CRC. Furthermore, F. nucleatum can specifically colonize CRC tissues through adhesion on its surface, forming biofilms that are highly resistant to commonly used antibiotics. Accordingly, it is crucial to develop efficacious non-antibiotic approaches to eradicate F. nucleatum and its biofilms for CRC treatment. In recent years, various antimicrobial strategies, such as natural extracts, inorganic chemicals, organic chemicals, polymers, inorganic-organic hybrid materials, bacteriophages, probiotics, and vaccines, have been proposed to combat F. nucleatum and F. nucleatum biofilms. This review summarizes the latest advancements in anti-F. nucleatum research, elucidates the antimicrobial mechanisms employed by these systems, and discusses the benefits and drawbacks of each antimicrobial technology. Additionally, this review also provides an outlook on the antimicrobial specificity, potential clinical implications, challenges, and future improvements of these antimicrobial strategies in the treatment of CRC.
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Affiliation(s)
- Hongyu Liu
- State Key Laboratory of Separation Membranes and Membrane ProcessesSchool of Materials Science and EngineeringTiangong UniversityTianjinP. R. China
| | - Yunjian Yu
- State Key Laboratory of Separation Membranes and Membrane ProcessesSchool of Materials Science and EngineeringTiangong UniversityTianjinP. R. China
| | - Alideertu Dong
- College of Chemistry and Chemical EngineeringInner Mongolia UniversityHohhotP. R. China
| | - Mahmoud Elsabahy
- Department of PharmaceuticsFaculty of PharmacyAssiut UniversityAssiutEgypt
| | - Ying‐Wei Yang
- International Joint Research Laboratory of Nano‐Micro Architecture ChemistryCollege of ChemistryJilin UniversityChangchunP. R. China
| | - Hui Gao
- State Key Laboratory of Separation Membranes and Membrane ProcessesSchool of Materials Science and EngineeringTiangong UniversityTianjinP. R. China
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Li XT, Peng SY, Feng SM, Bao TY, Li SZ, Li SY. Recent Progress in Phage-Based Nanoplatforms for Tumor Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307111. [PMID: 37806755 DOI: 10.1002/smll.202307111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/18/2023] [Indexed: 10/10/2023]
Abstract
Nanodrug delivery systems have demonstrated a great potential for tumor therapy with the development of nanotechnology. Nonetheless, traditional drug delivery systems are faced with issues such as complex synthetic procedures, low reproducibility, nonspecific distribution, impenetrability of biological barrier, systemic toxicity, etc. In recent years, phage-based nanoplatforms have attracted increasing attention in tumor treatment for their regular structure, fantastic carrying property, high transduction efficiency and biosafety. Notably, therapeutic or targeting peptides can be expressed on the surface of the phages through phage display technology, enabling the phage vectors to possess multifunctions. As a result, the drug delivery efficiency on tumor will be vastly improved, thereby enhancing the therapeutic efficacy while reducing the side effects on normal tissues. Moreover, phages can overcome the hindrance of biofilm barrier to elicit antitumor effects, which exhibit great advantages compared with traditional synthetic drug delivery systems. Herein, this review not only summarizes the structure and biology of the phages, but also presents their potential as prominent nanoplatforms against tumor in different pathways to inspire the development of effective nanomedicine.
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Affiliation(s)
- Xiao-Tong Li
- Department of Anesthesiology, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, P. R. China
| | - Shu-Yi Peng
- Department of Anesthesiology, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, P. R. China
| | - Shao-Mei Feng
- Department of Anesthesiology, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, P. R. China
| | - Ting-Yu Bao
- Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Sheng-Zhang Li
- Department of Clinical Medicine, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Shi-Ying Li
- Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, P. R. China
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44
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Liu K, Wang C, Zhou X, Guo X, Yang Y, Liu W, Zhao R, Song H. Bacteriophage therapy for drug-resistant Staphylococcus aureus infections. Front Cell Infect Microbiol 2024; 14:1336821. [PMID: 38357445 PMCID: PMC10864608 DOI: 10.3389/fcimb.2024.1336821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Drug-resistant Staphylococcus aureus stands as a prominent pathogen in nosocomial and community-acquired infections, capable of inciting various infections at different sites in patients. This includes Staphylococcus aureus bacteremia (SaB), which exhibits a severe infection frequently associated with significant mortality rate of approximately 25%. In the absence of better alternative therapies, antibiotics is still the main approach for treating infections. However, excessive use of antibiotics has, in turn, led to an increase in antimicrobial resistance. Hence, it is imperative that new strategies are developed to control drug-resistant S. aureus infections. Bacteriophages are viruses with the ability to infect bacteria. Bacteriophages, were used to treat bacterial infections before the advent of antibiotics, but were subsequently replaced by antibiotics due to limited theoretical understanding and inefficient preparation processes at the time. Recently, phages have attracted the attention of many researchers again because of the serious problem of antibiotic resistance. This article provides a comprehensive overview of phage biology, animal models, diverse clinical case treatments, and clinical trials in the context of drug-resistant S. aureus phage therapy. It also assesses the strengths and limitations of phage therapy and outlines the future prospects and research directions. This review is expected to offer valuable insights for researchers engaged in phage-based treatments for drug-resistant S. aureus infections.
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Affiliation(s)
- Kaixin Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chao Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xudong Zhou
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- College of Public Health, China Medical University, Shenyang, China
| | - Xudong Guo
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yi Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Wanying Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Rongtao Zhao
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- College of Public Health, Zhengzhou University, Zhengzhou, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- College of Public Health, China Medical University, Shenyang, China
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Dzuvor CKO. Toward Clinical Applications: Transforming Nonantibiotic Antibacterials into Effective Next-Generation Supramolecular Therapeutics. ACS NANO 2024; 18:2564-2577. [PMID: 38227832 DOI: 10.1021/acsnano.3c11045] [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: 01/18/2024]
Abstract
Antibiotic resistance is a major driver of morbidity and mortality worldwide, necessitating alternatives. Due to their mechanism of action, bacteriophages, endolysins, and antimicrobial peptides (coined herein as nonantibiotic antibacterials, NAA) have risen to tackle this problem and led to paradigms in treating antibiotic-resistant bacterial infections. However, their clinical applications remain challenging and have been seriously hampered by cytotoxicity, instability, weak bioactivity, low on-target bioavailability, high pro-inflammatory responses, shorter half-life, and circulatory properties. Hence, to transit preclinical phases and beyond, it has become imperative to radically engineer these alternatives into innovative and revolutionary therapeutics to overcome recalcitrant infections. This perspective highlights the promise of these agents, their limitations, promising designs, nanotechnology, and delivery approaches that can be harnessed to transform these agents. Finally, I provide an outlook on the remaining challenges that need to be tackled for their widespread clinical administration.
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Affiliation(s)
- Christian K O Dzuvor
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
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Liu GY, Yu D, Fan MM, Zhang X, Jin ZY, Tang C, Liu XF. Antimicrobial resistance crisis: could artificial intelligence be the solution? Mil Med Res 2024; 11:7. [PMID: 38254241 PMCID: PMC10804841 DOI: 10.1186/s40779-024-00510-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Antimicrobial resistance is a global public health threat, and the World Health Organization (WHO) has announced a priority list of the most threatening pathogens against which novel antibiotics need to be developed. The discovery and introduction of novel antibiotics are time-consuming and expensive. According to WHO's report of antibacterial agents in clinical development, only 18 novel antibiotics have been approved since 2014. Therefore, novel antibiotics are critically needed. Artificial intelligence (AI) has been rapidly applied to drug development since its recent technical breakthrough and has dramatically improved the efficiency of the discovery of novel antibiotics. Here, we first summarized recently marketed novel antibiotics, and antibiotic candidates in clinical development. In addition, we systematically reviewed the involvement of AI in antibacterial drug development and utilization, including small molecules, antimicrobial peptides, phage therapy, essential oils, as well as resistance mechanism prediction, and antibiotic stewardship.
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Affiliation(s)
- Guang-Yu Liu
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Key Laboratory of Inflammation and Immunoregulation of Hangzhou, Hangzhou Normal University, Hangzhou, 311121, China
| | - Dan Yu
- National Key Discipline of Pediatrics Key Laboratory of Major Diseases in Children Ministry of Education, Laboratory of Dermatology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Mei-Mei Fan
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Key Laboratory of Inflammation and Immunoregulation of Hangzhou, Hangzhou Normal University, Hangzhou, 311121, China
| | - Xu Zhang
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ze-Yu Jin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christoph Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
| | - Xiao-Fen Liu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of the People's Republic of China, National Clinical Research Centre for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
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Varming AK, Huang Z, Hamad GM, Rasmussen KK, Ingmer H, Kilstrup M, Lo Leggio L. CI:Mor interactions in the lysogeny switches of Lactococcus lactis TP901-1 and Staphylococcus aureus φ13 bacteriophages. MICROBIOME RESEARCH REPORTS 2024; 3:15. [PMID: 38841409 PMCID: PMC11149083 DOI: 10.20517/mrr.2023.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 06/07/2024]
Abstract
Aim: To structurally characterize in detail the interactions between the phage repressor (CI) and the antirepressor (Mor) in the lysis-lysogeny switches of two Gram-positive bacteriophages, the lactococcal TP901-1 and staphylococcal φ13. Methods: We use crystallographic structure determination, computational structural modeling, and analysis, as well as biochemical methods, to elucidate similarities and differences in the CI:Mor interactions for the two genetic switches. Results: By comparing a newly determined and other available crystal structures for the N-terminal domain of CI (CI-NTD), we show that the CI interface involved in Mor binding undergoes structural changes upon binding in TP901-1. Most importantly, we show experimentally for the first time the direct interaction between CI and Mor for φ13, and model computationally the interaction interface. The computational modeling supports similar side chain rearrangements in TP901-1 and φ13. Conclusion: This study ascertains experimentally that, like in the TP901-1 lysogeny switch, staphylococcal φ13 CI and Mor interact with each other. The structural basis of the interaction of φ13 CI and Mor was computationally modeled and is similar to the interaction demonstrated experimentally between TP901-1 CI-NTD and Mor, likely involving similar rearrangement of residue side chains during the formation of the complex. The study identifies one CI residue, Glu69, which unusually interacts primarily through its aliphatic chain with an aromatic residue on Mor after changing its conformation compared to the un-complexed structure. This and other residues at the interface are suggested for investigation in future studies.
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Affiliation(s)
- Anders K. Varming
- Department of Chemistry, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Zhiyu Huang
- Department of Chemistry, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Ghofran M. Hamad
- Department of Chemistry, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Kim K. Rasmussen
- Department of Chemistry, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg DK-1870, Denmark
| | - Mogens Kilstrup
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen DK-2100, Denmark
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García-Cruz JC, Rebollar-Juarez X, Limones-Martinez A, Santos-Lopez CS, Toya S, Maeda T, Ceapă CD, Blasco L, Tomás M, Díaz-Velásquez CE, Vaca-Paniagua F, Díaz-Guerrero M, Cazares D, Cazares A, Hernández-Durán M, López-Jácome LE, Franco-Cendejas R, Husain FM, Khan A, Arshad M, Morales-Espinosa R, Fernández-Presas AM, Cadet F, Wood TK, García-Contreras R. Resistance against two lytic phage variants attenuates virulence and antibiotic resistance in Pseudomonas aeruginosa. Front Cell Infect Microbiol 2024; 13:1280265. [PMID: 38298921 PMCID: PMC10828002 DOI: 10.3389/fcimb.2023.1280265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 12/22/2023] [Indexed: 02/02/2024] Open
Abstract
Background Bacteriophage therapy is becoming part of mainstream Western medicine since antibiotics of clinical use tend to fail. It involves applying lytic bacteriophages that self-replicate and induce cell lysis, thus killing their hosts. Nevertheless, bacterial killing promotes the selection of resistant clones which sometimes may exhibit a decrease in bacterial virulence or antibiotic resistance. Methods In this work, we studied the Pseudomonas aeruginosa lytic phage φDCL-PA6 and its variant φDCL-PA6α. Additionally, we characterized and evaluated the production of virulence factors and the virulence in a Galleria mellonella model of resistant mutants against each phage for PA14 and two clinical strains. Results Phage φDCL-PA6α differs from the original by only two amino acids: one in the baseplate wedge subunit and another in the tail fiber protein. According to genomic data and cross-resistance experiments, these changes may promote the change of the phage receptor from the O-antigen to the core lipopolysaccharide. Interestingly, the host range of the two phages differs as determined against the Pseudomonas aeruginosa reference strains PA14 and PAO1 and against nine multidrug-resistant isolates from ventilator associated pneumonia. Conclusions We show as well that phage resistance impacts virulence factor production. Specifically, phage resistance led to decreased biofilm formation, swarming, and type III secretion; therefore, the virulence towards Galleria mellonella was dramatically attenuated. Furthermore, antibiotic resistance decreased for one clinical strain. Our study highlights important potential advantages of phage therapy's evolutionary impact that may be exploited to generate robust therapy schemes.
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Affiliation(s)
- Juan Carlos García-Cruz
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Xareni Rebollar-Juarez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Aldo Limones-Martinez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Cristian Sadalis Santos-Lopez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Universidad Univer Milenium, Toluca de Lerdo, Mexico
| | - Shotaro Toya
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Corina Diana Ceapă
- Microbiology Laboratory, Chemistry Institute, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Lucia Blasco
- Microbiología Traslacional y Multidisciplinar (MicroTM), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
- Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - María Tomás
- Microbiología Traslacional y Multidisciplinar (MicroTM), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
- Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Clara Estela Díaz-Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores (FES) Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Estado de México, Mexico
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores (FES) Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Estado de México, Mexico
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México, Mexico
| | - Miguel Díaz-Guerrero
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Daniel Cazares
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Adrián Cazares
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Melisa Hernández-Durán
- Laboratorio de Microbiología Clínica, División de Infectología, Instituto Nacional de Rehabilitación, Luis Guillermo Ibarra Ibarra, Mexico, Mexico
| | - Luis Esaú López-Jácome
- Laboratorio de Microbiología Clínica, División de Infectología, Instituto Nacional de Rehabilitación, Luis Guillermo Ibarra Ibarra, Mexico, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Rafael Franco-Cendejas
- Subdirección de Investigación Biomédica, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Mexico, Mexico
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Altaf Khan
- Department of Pharmacology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Arshad
- Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Ana María Fernández-Presas
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Frederic Cadet
- PEACCEL, Artificial Intelligence Department, AI for Biologics, Paris, France
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, United States
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
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Stamm J, Merkle JA, Abernathy A, Ackerman E, Brown J, Harris A, Hoffman K, Hoskins A, Jahn A, Jones N, Kitch A, Mathavan N, Rose N, Taylor J. Complete genome sequences of Streptomyces griseus phages Spelly and Phredrick. Microbiol Resour Announc 2024; 13:e0104923. [PMID: 38112473 PMCID: PMC10793280 DOI: 10.1128/mra.01049-23] [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: 11/07/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023] Open
Abstract
We present the complete genome sequences of two viruses with siphovirus morphology, isolated from soils collected in Southwestern Indiana using the host Streptomyces griseus. Spelly is a BE2 cluster phage with a 131,347-bp genome. Phredrick is a BK1 cluster phage with a 128,873-bp genome.
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Affiliation(s)
- Joyce Stamm
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Julie A. Merkle
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Ava Abernathy
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Elizabeth Ackerman
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - John Brown
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Abbey Harris
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Kayli Hoffman
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Ashleigh Hoskins
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Abbie Jahn
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Nathan Jones
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Ashley Kitch
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Nandini Mathavan
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Nat Rose
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Joey Taylor
- Department of Biology, University of Evansville, Evansville, Indiana, USA
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50
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Samson R, Dharne M, Khairnar K. Bacteriophages: Status quo and emerging trends toward one health approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168461. [PMID: 37967634 DOI: 10.1016/j.scitotenv.2023.168461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the "One Health" framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft-matter research. Herein, we present a comprehensive review, coupling the substantial aspects of phages with their applicability status and emerging opportunities in several interdependent areas under one health concept. Consolidating the recent state-of-the-art studies that integrate human, animal, plant, and environment health, the following points have been highlighted: (i) The biomedical and pharmacological advantages of phages and their antimicrobial derivatives with particular emphasis on in-vivo and clinical studies. (ii) The remarkable potential of phages to be altered, improved, and applied for drug delivery, biosensors, biomedical imaging, tissue engineering, energy, and catalysis. (iii) Resurgence of phages in biocontrol of plant, food, and animal-borne pathogens. (iv) Commercialization of phage-based products, current challenges, and perspectives.
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Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Krishna Khairnar
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
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