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Ferriol-González C, Concha-Eloko R, Bernabéu-Gimeno M, Fernández-Cuenca F, Cañada-García JE, García-Cobos S, Sanjuán R, Domingo-Calap P. Targeted phage hunting to specific Klebsiella pneumoniae clinical isolates is an efficient antibiotic resistance and infection control strategy. Microbiol Spectr 2024; 12:e0025424. [PMID: 39194291 PMCID: PMC11448410 DOI: 10.1128/spectrum.00254-24] [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: 01/30/2024] [Accepted: 08/06/2024] [Indexed: 08/29/2024] Open
Abstract
Klebsiella pneumoniae is one of the most threatening multi-drug-resistant pathogens today, with phage therapy being a promising alternative for personalized treatments. However, the intrinsic capsule diversity in Klebsiella spp. poses a substantial barrier to the phage host range, complicating the development of broad-spectrum phage-based treatments. Here, we have isolated and genomically characterized phages capable of infecting each of the acquired 77 reference serotypes of Klebsiella spp., including capsular types widespread among high-risk K. pneumoniae clones causing nosocomial infections. We demonstrated the possibility of isolating phages for all capsular types in the collection, revealing high capsular specificity among taxonomically related phages, in contrast to a few phages that exhibited broad-spectrum infection capabilities. To decipher the determinants of the specificity of these phages, we focused on their receptor-binding proteins, with particular attention to depolymerases. We also explored the possibility of designing a broad-spectrum phage cocktail based on phages isolated in reference capsular-type strains and determining the ability to lyse relevant clinical isolates. A combination of 12 phages capable of infecting 55% of the reference Klebsiella spp. serotypes was tested on a panel of carbapenem-resistant K. pneumoniae clinical isolates. Thirty-one percent of isolates were susceptible to the phage cocktail. However, our results suggest that in a highly variable encapsulated bacterial host, phage hunting must be directed to the specific Klebsiella isolates. This work is a step forward in the understanding of the complexity of phage-host interactions and highlights the importance of implementing precise and phage-specific strategies to treat K. pneumoniae infections worldwide.IMPORTANCEThe emergence of resistant bacteria is a serious global health problem. In the absence of effective treatments, phages are a personalized and effective therapeutic alternative. However, little is still known about phage-host interactions, which are key to implementing effective strategies. Here, we focus on the study of Klebsiella pneumoniae, a highly pathogenic encapsulated bacterium. The complexity and variability of the capsule, where in most cases phage receptors are found, make it difficult for phage-based treatments. Here, we isolated a large collection of Klebsiella phages against all the reference strains and in a cohort of clinical isolates. Our results suggest that clinical isolates represent a challenge, especially high-risk clones. Thus, we propose targeted phage hunting as an effective strategy to implement phage-derived therapies. Our results are a step forward for new phage-based strategies to control K. pneumoniae infections, highlighting the importance of understanding phage-host interactions to design personalized treatments against Klebsiella spp.
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Affiliation(s)
- Celia Ferriol-González
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Robby Concha-Eloko
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Mireia Bernabéu-Gimeno
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Felipe Fernández-Cuenca
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen Macarena-CSIC-Universidad de Sevilla, Sevilla, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier E Cañada-García
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia García-Cobos
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Sanjuán
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
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Singh J, Lynch S, Iredell J, Selvadurai H. Safety and tolerability of bronchoscopic and nebulised administration of bacteriophage. Virus Res 2024; 348:199442. [PMID: 39074617 PMCID: PMC11341935 DOI: 10.1016/j.virusres.2024.199442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/09/2024] [Accepted: 07/25/2024] [Indexed: 07/31/2024]
Abstract
INTRODUCTION Pseudomonas aeruginosa is an organism well known for causing significant morbidity and mortality in people living with chronic lung conditions such as cystic fibrosis. We describe the safety, tolerability, and potential efficacy of bronchoscopic and nebulised bacteriophage administration, offering insights into a potential breakthrough for the treatment of chronic infections particularly in children and adolescents. METHOD A 12-year-old female (F12) and a 17-year-old male (M17), both diagnosed with cystic fibrosis and chronic P. aeruginosa lung infection, underwent bacteriophage treatment (BT). The administration involved bronchoscopic instillation and subsequent nebulisation. This was performed concurrently with intravenous antibiotics and regular physiotherapy delivered in an in-patient setting for 14 days. Microbiological, clinical, and lung function assessments were conducted to assess this treatment modality. RESULTS No adverse events (fever, localised reaction, wheeze or bronchospasm) occurred during BT. F12 demonstrated a 4% increase, while M17 showed a 5% improvement in FEV1% from their best FEV1% over the past three years following BT. A 12% (F12) and an 8% (M17) improvement from baseline FEV1% was observed. For F12 P. aeruginosa was not isolated from her sputum despite 12 previous hospitalisations for intravenous antibiotics. CONCLUSION Bronchoscopic and nebulised routes of bacteriophage administration were well-tolerated in these two adolescents. This early report underscores the potential of this treatment modality and encourages clinicians and researchers to actively explore this innovative approach.
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Affiliation(s)
- Jagdev Singh
- Department of Respiratory Medicine, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia.
| | - Stephanie Lynch
- Westmead Institute of Medical Research, Sydney, NSW, Australia
| | - Jonathan Iredell
- Westmead Institute of Medical Research, Sydney, NSW, Australia; Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Hiran Selvadurai
- Department of Respiratory Medicine, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
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Natarajan SP, Teh SH, Lin LC, Lin NT. In Vitro and In Vivo Assessments of Newly Isolated N4-like Bacteriophage against ST45 K62 Capsular-Type Carbapenem-Resistant Klebsiella pneumoniae: vB_kpnP_KPYAP-1. Int J Mol Sci 2024; 25:9595. [PMID: 39273543 PMCID: PMC11395603 DOI: 10.3390/ijms25179595] [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: 07/22/2024] [Revised: 08/26/2024] [Accepted: 08/31/2024] [Indexed: 09/15/2024] Open
Abstract
The rise of carbapenem-resistant Klebsiella pneumoniae (CRKP) presents a significant global challenge in clinical and healthcare settings, severely limiting treatment options. This study aimed to utilize a bacteriophage as an alternative therapy against carbapenem-resistant K. pneumoniae. A novel lytic N4-like Klebsiella phage, vB_kpnP_KPYAP-1 (KPYAP-1), was isolated from sewage. It demonstrated efficacy against the K62 serotype polysaccharide capsule of blaOXA-48-producing K. pneumoniae. KPYAP-1 forms small, clear plaques, has a latent period of 20 min, and reaches a growth plateau at 35 min, with a burst size of 473 plaque-forming units (PFUs) per infected cell. Phylogenetic analysis places KPYAP-1 in the Schitoviridae family, Enquatrovirinae subfamily, and Kaypoctavirus genus. KPYAP-1 employs an N4-like direct terminal repeat mechanism for genome packaging and encodes a large virion-encapsulated RNA polymerase. It lacks integrase or repressor genes, antibiotic resistance genes, bacterial virulence factors, and toxins, ensuring its safety for therapeutic use. Comparative genome analysis revealed that the KPYAP-1 genome is most similar to the KP8 genome, yet differs in tail fiber protein, indicating variations in host recognition. In a zebrafish infection model, KPYAP-1 significantly improved the survival rate of infected fish by 92% at a multiplicity of infection (MOI) of 10, demonstrating its potential for in vivo treatment. These results highlight KPYAP-1 as a promising candidate for developing phage-based therapies targeting carbapenemase-producing K. pneumoniae.
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Affiliation(s)
- Shanmuga Priya Natarajan
- Master Program in Biomedical Sciences, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan
| | - Soon-Hian Teh
- Division of Infectious Diseases, Department of Internal Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan
| | - Ling-Chun Lin
- Master Program in Biomedical Sciences, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan
| | - Nien-Tsung Lin
- Master Program in Biomedical Sciences, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan
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4
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Vitiello A, Rezza G, Silenzi A, Salzano A, Alise M, Boccellino MR, Ponzo A, Zovi A, Sabbatucci M. Therapeutic Strategies to Combat Increasing Rates of Multidrug Resistant Pathogens. Pharm Res 2024; 41:1557-1571. [PMID: 39107513 DOI: 10.1007/s11095-024-03756-5] [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: 03/24/2024] [Accepted: 07/29/2024] [Indexed: 08/30/2024]
Abstract
The emergence of antimicrobic-resistant infectious pathogens and the consequent rising in the incidence and prevalence of demises caused by or associated to infections which are not sensitive to drug treatments is one of today's major global health challenges. Antimicrobial resistance (AMR) can bring to therapeutic failure, infection's persistence and risk of serious illness, in particular in vulnerable populations such as the elderly, patients with neoplastic diseases or the immunocompromised. It is assessed that AMR will induce until 10 million deaths per year by 2050, becoming the leading cause of disease-related deaths. The World Health Organisation (WHO) and the United Nations General Assembly urgently call for new measures to combat the phenomenon. Research and development of new antimicrobial agents has decreased due to market failure. However, promising results are coming from new alternative therapeutic strategies such as monoclonal antibodies, microbiome modulators, nanomaterial-based therapeutics, vaccines, and phages. This narrative review aimed to analyse the benefits and weaknesses of alternative therapeutic strategies to antibiotics which treat multidrug-resistant bacterial infections.
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Affiliation(s)
- Antonio Vitiello
- Directorate-General for Health Prevention, Ministry of Health, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Giovanni Rezza
- Directorate-General for Health Prevention, Ministry of Health, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Andrea Silenzi
- Directorate-General for Health Prevention, Ministry of Health, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Antonio Salzano
- Directorate-General for Health Prevention, Ministry of Health, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Mosè Alise
- Directorate General of Animal Health and Veterinary Medicines, Ministry of Health, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | | | - Annarita Ponzo
- Department of Biology L. Spallanzani, University of Pavia, Pavia, Italy
| | - Andrea Zovi
- Directorate General for Hygiene, Food Safety and Nutrition, Ministry of Health, Viale Giorgio Ribotta 5, 00144, Rome, Italy.
| | - Michela Sabbatucci
- Department Infectious Diseases, Italian National Institute of Health, Viale Regina Elena 299, 00161, Rome, Italy
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5
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Xu K, Zhang Q, Zhu D, Jiang Z. Hydrogels in Gene Delivery Techniques for Regenerative Medicine and Tissue Engineering. Macromol Biosci 2024; 24:e2300577. [PMID: 38265144 DOI: 10.1002/mabi.202300577] [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: 12/16/2023] [Revised: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Hydrogels are 3D networks swollen with water. They are biocompatible, strong, and moldable and are emerging as a promising biomedical material for regenerative medicine and tissue engineering to deliver therapeutic genes. The excellent natural extracellular matrix simulation properties of hydrogels enable them to be co-cultured with cells or enhance the expression of viral or non-viral vectors. Its biocompatibility, high strength, and degradation performance also make the action process of carriers in tissues more ideal, making it an ideal biomedical material. It has been shown that hydrogel-based gene delivery technologies have the potential to play therapy-relevant roles in organs such as bone, cartilage, nerve, skin, reproductive organs, and liver in animal experiments and preclinical trials. This paper reviews recent articles on hydrogels in gene delivery and explains the manufacture, applications, developmental timeline, limitations, and future directions of hydrogel-based gene delivery techniques.
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Affiliation(s)
- Kexing Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Qinmeng Zhang
- Zhejiang University School of Medicine, Hangzhou, China
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Danji Zhu
- Zhejiang University School of Medicine, Hangzhou, China
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Zhiwei Jiang
- Zhejiang University School of Medicine, Hangzhou, China
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
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6
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Wang X, Tang Y, Yue X, Wang S, Yang K, Xu Y, Shen Q, Friman VP, Wei Z. The role of rhizosphere phages in soil health. FEMS Microbiol Ecol 2024; 100:fiae052. [PMID: 38678007 PMCID: PMC11065364 DOI: 10.1093/femsec/fiae052] [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: 12/31/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yike Tang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiufeng Yue
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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7
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Podlacha M, Gaffke L, Grabowski Ł, Mantej J, Grabski M, Pierzchalska M, Pierzynowska K, Węgrzyn G, Węgrzyn A. Bacteriophage DNA induces an interrupted immune response during phage therapy in a chicken model. Nat Commun 2024; 15:2274. [PMID: 38480702 PMCID: PMC10937645 DOI: 10.1038/s41467-024-46555-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 03/01/2024] [Indexed: 03/17/2024] Open
Abstract
One of the hopes for overcoming the antibiotic resistance crisis is the use of bacteriophages to combat bacterial infections, the so-called phage therapy. This therapeutic approach is generally believed to be safe for humans and animals as phages should infect only prokaryotic cells. Nevertheless, recent studies suggested that bacteriophages might be recognized by eukaryotic cells, inducing specific cellular responses. Here we show that in chickens infected with Salmonella enterica and treated with a phage cocktail, bacteriophages are initially recognized by animal cells as viruses, however, the cGAS-STING pathway (one of two major pathways of the innate antiviral response) is blocked at the stage of the IRF3 transcription factor phosphorylation. This inhibition is due to the inability of RNA polymerase III to recognize phage DNA and to produce dsRNA molecules which are necessary to stimulate a large protein complex indispensable for IRF3 phosphorylation, indicating the mechanism of the antiviral response impairment.
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Affiliation(s)
- Magdalena Podlacha
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Łukasz Grabowski
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Jagoda Mantej
- Univentum Labs, Bażyńskiego 4, 80-309, Gdansk, Poland
| | - Michał Grabski
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Małgorzata Pierzchalska
- Department of Biotechnology and General Technology of Foods, Faculty of Food Technology, University of Agriculture, Balicka 122, 30-149, Cracow, Poland
| | - Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Alicja Węgrzyn
- Phage Therapy Center, University Center for Applied and Interdisciplinary Research, University of Gdansk, Kładki 24, 80-822, Gdansk, Poland.
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8
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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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9
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Kim K, Jang H, Kim E, Kim H, Sung GY. Recent advances in understanding the role of the skin microbiome in the treatment of atopic dermatitis. Exp Dermatol 2023; 32:2048-2061. [PMID: 37767872 DOI: 10.1111/exd.14940] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/31/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023]
Abstract
The skin is the largest organ in the human body, and histologically consists of the epidermis, dermis and subcutaneous tissue. Humans maintain a cooperative symbiotic relationship with their skin microbiota, a complex community of bacteria, fungi and viruses that live on the surface of the skin, and which act as a barrier to protect the body from the inside and outside. The skin is a 'habitat' and vast 'ecosystem' inhabited by countless microbes; as such, relationships have been forged through millions of years of coevolution. It is not surprising then that microbes are key participants in shaping and maintaining essential physiological processes. In addition to maintaining barrier function, the unique symbiotic microbiota that colonizes the skin increases the immune response and provides protection against pathogenic microbes. This review examines our current understanding of skin microbes in shaping and enhancing the skin barrier, as well as skin microbiome-host interactions and their roles in skin diseases, such as atopic dermatitis (AD). We also report on the current status of AD therapeutic drugs that target the skin microbiome, related research on current therapeutic strategies, and the limitations and future considerations of skin microbiome research. In particular, as a future strategy, we discuss the need for a skin-on-a-chip-based microphysiological system research model amenable to biomimetic in vitro studies and human skin equivalent models, including skin appendages.
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Affiliation(s)
- Kyunghee Kim
- Interdisciplinary Program of Nano-Medical Device Engineering, Hallym University, Chuncheon, Korea
- Integrative Materials Research Institute, Hallym University, Chuncheon, Korea
| | - Hyeji Jang
- Interdisciplinary Program of Nano-Medical Device Engineering, Hallym University, Chuncheon, Korea
- Integrative Materials Research Institute, Hallym University, Chuncheon, Korea
| | - Eunyul Kim
- Interdisciplinary Program of Nano-Medical Device Engineering, Hallym University, Chuncheon, Korea
- Integrative Materials Research Institute, Hallym University, Chuncheon, Korea
| | - Hyeju Kim
- Interdisciplinary Program of Nano-Medical Device Engineering, Hallym University, Chuncheon, Korea
- Integrative Materials Research Institute, Hallym University, Chuncheon, Korea
| | - Gun Yong Sung
- Interdisciplinary Program of Nano-Medical Device Engineering, Hallym University, Chuncheon, Korea
- Integrative Materials Research Institute, Hallym University, Chuncheon, Korea
- Major in Materials Science and Engineering, Hallym University, Chuncheon, Korea
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10
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Emencheta SC, Olovo CV, Eze OC, Kalu CF, Berebon DP, Onuigbo EB, Vila MMDC, Balcão VM, Attama AA. The Role of Bacteriophages in the Gut Microbiota: Implications for Human Health. Pharmaceutics 2023; 15:2416. [PMID: 37896176 PMCID: PMC10609668 DOI: 10.3390/pharmaceutics15102416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/18/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteriophages (phages) are nano-sized viruses characterized by their inherent ability to live off bacteria. They utilize diverse mechanisms to absorb and gain entry into the bacterial cell wall via the release of viral genetic material, which uses the replication mechanisms of the host bacteria to produce and release daughter progeny virions that attack the surrounding host cells. They possess specific characteristics, including specificity for particular or closely related bacterial species. They have many applications, including as potential alternatives to antibiotics against multi-resistant bacterial pathogens and as control agents in bacteria-contaminated environments. They are ubiquitously abundant in nature and have diverse biota, including in the gut. Gut microbiota describes the community and interactions of microorganisms within the intestine. As with bacteria, parasitic bacteriophages constantly interact with the host bacterial cells within the gut system and have obvious implications for human health. However, it is imperative to understand these interactions as they open up possible applicable techniques to control gut-implicated bacterial diseases. Thus, this review aims to explore the interactions of bacteriophages with bacterial communities in the gut and their current and potential impacts on human health.
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Affiliation(s)
- Stephen C. Emencheta
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
| | - Chinasa V. Olovo
- Department of Microbiology, University of Nigeria, Nsukka 410001, Nigeria;
| | - Osita C. Eze
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Chisom F. Kalu
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Dinebari P. Berebon
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Ebele B. Onuigbo
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Marta M. D. C. Vila
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
| | - Victor M. Balcão
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
| | - Anthony A. Attama
- Department of Pharmaceutics, University of Nigeria, Nsukka 410001, Nigeria
- Institute for Drug-Herbal Medicine-Excipient Research and Development, University of Nigeria, Nsukka 410001, Nigeria
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Singh J, Fitzgerald DA, Jaffe A, Hunt S, Barr JJ, Iredell J, Selvadurai H. Single-arm, open-labelled, safety and tolerability of intrabronchial and nebulised bacteriophage treatment in children with cystic fibrosis and Pseudomonas aeruginosa. BMJ Open Respir Res 2023; 10:e001360. [PMID: 37160359 PMCID: PMC10173968 DOI: 10.1136/bmjresp-2022-001360] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 04/21/2023] [Indexed: 05/11/2023] Open
Abstract
INTRODUCTION Cystic fibrosis (CF) is a multisystem condition that is complicated by recurrent pulmonary infections requiring aggressive antibiotic treatment. This predisposes the patient to complications such as sensorineural hearing loss, renal impairment, hypersensitivity and the development of antibiotic resistance. Pseudomonas aeruginosa is one of the more common organisms which cause recurrent infections and result in greater morbidity and mortality in people living with CF. Bacteriophages have been identified as a potential alternative or adjunct to antibiotics. We hypothesise that bacteriophage therapy is a safe and well-tolerated treatment in children with CF infected with P. aeruginosa infection in their airways. METHODS This single-arm, open-labelled, non-randomised trial will run for a maximum period of 36 months with up to 10 participants. Adolescents (≥12 years and <18 years of age) who continue to shed P.aeruginosa (within 3 months of enrolment) despite undergoing eradication therapy previously, will be considered for this trial. Non-genetically modified bacteriophages that have demonstrated obligate lytic activity against each of the study participants' P. aeruginosa strains will be selected and prepared according to a combination of established protocols (isolation, purification, sterility testing and packaging) to achieve close to good manufacturing practice recommendations. The selected bacteriophage will be administered endo-bronchially first under direct vision, followed by two times a day nebulisation for 7 days in addition to standard CF treatment (intravenous antibiotics, physiotherapy to be completed as inpatient for 10-14 days). Safety and tolerability will be defined as the absence of (1) fever above 38.5°C occurring within 1 hour of the administration of the nebulised bacteriophage, (2) a 10% decline in spirometry (forced expiratory volume in 1 s %) measured preadministration and postadministration of the first dose of nebulised bacteriophage. Clinical reviews including repeat sputum cultures and spirometry will be performed at 3, 6, 9 and 12 months following bacteriophage treatment. ETHICS AND DISSEMINATION Our clinical trial is conducted in accordance with (1) good clinical practice, (2) Australian legislation, (3) National Health and Medical Research Council guidelines for the ethical conduct of research. TRIAL REGISTRATION NUMBER Australia and New Zealand Clinical Trial Registry (ACTRN12622000767707).
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Affiliation(s)
- Jagdev Singh
- Department of Respiratory Medicine, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Dominic A Fitzgerald
- Department of Respiratory Medicine, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Adam Jaffe
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sharon Hunt
- Department of Respiratory Medicine, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | | | - Jonathan Iredell
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Department of Infectious Diseases, Westmead Hospital, Westmead, New South Wales, Australia
| | - Hiran Selvadurai
- Department of Respiratory Medicine, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
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Shafigh Kheljan F, Sheikhzadeh Hesari F, Aminifazl MS, Skurnik M, Goladze S, Zarrini G. Design of Phage-Cocktail-Containing Hydrogel for the Treatment of Pseudomonas aeruginosa-Infected Wounds. Viruses 2023; 15:803. [PMID: 36992511 PMCID: PMC10051971 DOI: 10.3390/v15030803] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/12/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Recently, the treatment of infected wounds has become a global problem due to increased antibiotic resistance in bacteria. The Gram-negative opportunistic pathogen Pseudomonas aeruginosa is often present in chronic skin infections, and it has become a threat to public health as it is increasingly multidrug resistant. Due to this, new measures to enable treatment of infections are necessary. Treatment of bacterial infections with bacteriophages, known as phage therapy, has been in use for a century, and has potential with its antimicrobial effect. The main purpose of this study was to create a phage-containing wound dressing with the ability to prevent bacterial infection and rapid wound healing without side effects. Several phages against P. aeruginosa were isolated from wastewater, and two polyvalent phages were used to prepare a phage cocktail. The phage cocktail was loaded in a hydrogel composed of polymers of sodium alginate (SA) and carboxymethyl cellulose (CMC). To compare the antimicrobial effects, hydrogels containing phages, ciprofloxacin, or phages plus ciprofloxacin were produced, and hydrogels without either. The antimicrobial effect of these hydrogels was investigated in vitro and in vivo using an experimental mouse wound infection model. The wound-healing process in different mouse groups showed that phage-containing hydrogels and antibiotic-containing hydrogels have almost the same antimicrobial effect. However, in terms of wound healing and pathological process, the phage-containing hydrogels performed better than the antibiotic alone. The best performance was achieved with the phage-antibiotic hydrogel, indicating a synergistic effect between the phage cocktail and the antibiotic. In conclusion, phage-containing hydrogels eliminate efficiently P. aeruginosa in wounds and may be a proper option for treating infectious wounds.
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Affiliation(s)
- Fatemeh Shafigh Kheljan
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran; (F.S.K.); (F.S.H.)
| | - Farzam Sheikhzadeh Hesari
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran; (F.S.K.); (F.S.H.)
| | - Mohammad Sadegh Aminifazl
- Department of Applied Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 5166616471, Iran;
| | - Mikael Skurnik
- Human Microbiome Research Program, Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, 00014 HUS Helsinki, Finland; (M.S.); (S.G.)
| | - Sophia Goladze
- Human Microbiome Research Program, Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, 00014 HUS Helsinki, Finland; (M.S.); (S.G.)
| | - Gholamreza Zarrini
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran; (F.S.K.); (F.S.H.)
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Mohammadi M, Saffari M, Siadat SD, Hejazi SH, Shayestehpour M, Motallebi M, Eidi M. Isolation, characterization, therapeutic potency, and genomic analysis of a novel bacteriophage vB_KshKPC-M against carbapenemase-producing Klebsiella pneumoniae strains (CRKP) isolated from Ventilator-associated pneumoniae (VAP) infection of COVID-19 patients. Ann Clin Microbiol Antimicrob 2023; 22:18. [PMID: 36829156 PMCID: PMC9955523 DOI: 10.1186/s12941-023-00567-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/15/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a significant clinical problem, given the lack of therapeutic options. The CRKP strains have emerged as an essential worldwide healthcare issue during the last 10 years. Global expansion of the CRKP has made it a significant public health hazard. We must consider to novel therapeutic techniques. Bacteriophages are potent restorative cases against infections with multiple drug-resistant bacteria. The Phages offer promising prospects for the treatment of CRKP infections. OBJECTIVE In this study, a novel K. pneumoniae phage vB_KshKPC-M was isolated, characterized, and sequenced, which was able to infect and lyse Carbapenem-resistant K. pneumoniae host specifically. METHODS One hundred clinical isolates of K. pneumoniae were collected from patients with COVID-19 associated with ventilator-associated acute pneumonia hospitalized at Shahid Beheshti Hospital, Kashan, Iran, from 2020 to 2021. Initially, all samples were cultured, and bacterial isolates identified by conventional biochemical tests, and then the ureD gene was used by PCR to confirm the isolates. The Antibiotic susceptibility test in the disc diffusion method and Minimum inhibitory concentrations for Colistin was done and interpreted according to guidelines. Phenotypic and molecular methods determined the Carbapenem resistance of isolates. The blaKPC, blaNDM, and blaOXA-23 genes were amplified for this detection. Biofilm determination of CRKP isolates was performed using a quantitative microtiter plate (MTP) method. The phage was isolated from wastewater during the summer season at a specific position from Beheshti Hospital (Kashan, Iran). The sample was processed and purified against the bacterial host, a CRKP strain isolated from a patient suffering from COVID-19 pneumoniae and resistance to Colistin with high potency for biofilm production. This isolate is called Kp100. The separated phages were diluted and titration by the double overlay agar plaque assay. The separate Phage is concentrated with 10% PEG and stored at -80 °C until use. The phage host range was identified by the spot test method. The purified phage morphology was determined using a transmission electron microscope. The phage stability tests (pH and temperature) were analyzed. The effect of cationic ions on phage adsorption was evaluated. The optimal titer of bacteriophage was determined to reduce the concentration of the CRKP strain. One-step growth assays were performed to identify the purified phage burst's latent cycle and size. The SDS-PAGE was used for phage proteins analysis. Phage DNA was extracted by chloroform technique, and the whole genome of lytic phage was sequenced using Illumina HiSeq technology (Illumina, San Diego, CA). For quality assurance and preprocessing, such as trimming, Geneious Prime 2021.2.2 and Spades 3.9.0. The whole genome sequence of the lytic phage is linked to the GenBank database accession number. RASTtk-v1.073 was used to predict and annotate the ORFs. Prediction of ORF was performed using PHASTER software. ResFinder is used to assess the presence of antimicrobial resistance and virulence genes in the genome. The tRNAs can-SE v2.0.6 is used to determine the presence of tRNA in the genome. Linear genome comparisons of phages and visualization of coding regions were performed using Easyfig 2.2.3 and Mauve 2.4.0. Phage lifestyles were predicted using the program PHACTS. Phylogenetic analysis and amino acid sequences of phage core proteins, such as the major capsid protein. Phylogenies were reconstructed using the Neighbor-Joining method with 1000 bootstrap repeat. HHpred software was used to predict depolymerase. In this study, GraphPad Prism version 9.1 was used for the statistical analysis. Student's t-test was used to compare the sets and the control sets, and the significance level was set at P ≤ 0.05. RESULTS Phage vB_KshKPC-M is assigned to the Siphoviridae, order Caudovirales. It was identified as a linear double-stranded DNA phage of 54,378 bp with 50.08% G + C content, had a relatively broad host range (97.7%), a short latency of 20 min, and a high burst size of 260 PFU/cell, and was maintained stable at different pH (3-11) and temperature (45-65 °C). The vB_KshKPC-M genome contains 91 open-reading frames. No tRNA, antibiotic resistance, toxin, virulence-related genes, or lysogen-forming gene clusters were detected in the phage genome. Comparative genomic analysis revealed that phage vB_KshKPC-M has sequence similarity to the Klebsiella phages, phage 13 (NC_049844.1), phage Sushi (NC_028774.1), phage vB_KpnD_PeteCarol (OL539448.1) and phage PWKp14 (MZ634345.1). CONCLUSION The broad host range and antibacterial activity make it a promising candidate for future phage therapy applications. The isolated phage was able to lyse most of the antibiotic-resistant clinical isolates. Therefore, this phage can be used alone or as a phage mixture in future studies to control and inhibit respiratory infections caused by these bacteria, especially in treating respiratory infections caused by resistant strains in sick patients.
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Affiliation(s)
- Mehrdad Mohammadi
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Pezeshk Blvd, Qotbe Ravandi Blvd, Kashan, 8715973449 Iran
| | - Mahmood Saffari
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Pezeshk Blvd, Qotbe Ravandi Blvd, Kashan, 8715973449 Iran
| | - Seyed Davar Siadat
- Tuberculosis and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Hossein Hejazi
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Shayestehpour
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Pezeshk Blvd, Qotbe Ravandi Blvd, Kashan, 8715973449 Iran
| | - Mitra Motallebi
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Pezeshk Blvd, Qotbe Ravandi Blvd, Kashan, 8715973449 Iran
| | - Milad Eidi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Bajiya N, Dhall A, Aggarwal S, Raghava GPS. Advances in the field of phage-based therapy with special emphasis on computational resources. Brief Bioinform 2023; 24:6961791. [PMID: 36575815 DOI: 10.1093/bib/bbac574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/07/2022] [Accepted: 11/25/2022] [Indexed: 12/29/2022] Open
Abstract
In the current era, one of the major challenges is to manage the treatment of drug/antibiotic-resistant strains of bacteria. Phage therapy, a century-old technique, may serve as an alternative to antibiotics in treating bacterial infections caused by drug-resistant strains of bacteria. In this review, a systematic attempt has been made to summarize phage-based therapy in depth. This review has been divided into the following two sections: general information and computer-aided phage therapy (CAPT). In the case of general information, we cover the history of phage therapy, the mechanism of action, the status of phage-based products (approved and clinical trials) and the challenges. This review emphasizes CAPT, where we have covered primary phage-associated resources, phage prediction methods and pipelines. This review covers a wide range of databases and resources, including viral genomes and proteins, phage receptors, host genomes of phages, phage-host interactions and lytic proteins. In the post-genomic era, identifying the most suitable phage for lysing a drug-resistant strain of bacterium is crucial for developing alternate treatments for drug-resistant bacteria and this remains a challenging problem. Thus, we compile all phage-associated prediction methods that include the prediction of phages for a bacterial strain, the host for a phage and the identification of interacting phage-host pairs. Most of these methods have been developed using machine learning and deep learning techniques. This review also discussed recent advances in the field of CAPT, where we briefly describe computational tools available for predicting phage virions, the life cycle of phages and prophage identification. Finally, we describe phage-based therapy's advantages, challenges and opportunities.
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Affiliation(s)
- Nisha Bajiya
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India
| | - Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India
| | - Suchet Aggarwal
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India
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Orozco-Ochoa AK, González-Gómez JP, Castro-Del Campo N, Lira-Morales JD, Martínez-Rodríguez CI, Gomez-Gil B, Chaidez C. Characterization and genome analysis of six novel Vibrio parahaemolyticus phages associated with acute hepatopancreatic necrosis disease (AHPND). Virus Res 2023; 323:198973. [PMID: 36272541 PMCID: PMC10194199 DOI: 10.1016/j.virusres.2022.198973] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022]
Abstract
Vibrio parahaemolyticus causes acute hepatopancreatic necrosis disease (AHPND) in farmed shrimp. Due to its damage potential, which could be as high as a 100% mortality rate, bacteriophages have emerged as a promising natural control intervention other than antibiotics, yet multiple roadblocks need to be overcome. In this study, six bacteriophages isolated from seafood samples, seawater, and estuary water in Sinaloa, Mexico, demonstrated a narrow host range among Mexican AHPND-causing V. parahaemolyticus. All bacteriophages are composed of a double-stranded DNA genome with lengths ranging between 43,268 and 57,805 bp. All six phages exhibited latency periods of 10-30 min and burst sizes of 34-168 viral particles per infected cell. The optimal MOI for bacteriophage propagation was 0.01-1. No transfer RNA (tRNA), virulence, or resistance genes were found in either genome, and the life cycle of these phages was classified as virulent by the PhageAI platform. Phylogenetic and comparative genomics analyzes assigned phages M3, C2, M9, and M83 as new species not yet reported within the genus Maculvirus, Autographiviridae family. ALK and CHI phages were assigned as new members of a new genus not yet classified within the subfamily Queuovirinae. The findings highlight the potential of CHI, ALK, M3, C2, M9, and M83 as promising alternatives against AHPND-causing V. parahaemolyticus from Mexico.
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Affiliation(s)
- Alma Karen Orozco-Ochoa
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Carretera a Eldorado Km 5.5, Campo El Diez, Culiacán, Sinaloa 80110, México
| | - Jean Pierre González-Gómez
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Carretera a Eldorado Km 5.5, Campo El Diez, Culiacán, Sinaloa 80110, México
| | - Nohelia Castro-Del Campo
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Carretera a Eldorado Km 5.5, Campo El Diez, Culiacán, Sinaloa 80110, México
| | - Juan Daniel Lira-Morales
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Carretera a Eldorado Km 5.5, Campo El Diez, Culiacán, Sinaloa 80110, México
| | - Célida Isabel Martínez-Rodríguez
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Carretera a Eldorado Km 5.5, Campo El Diez, Culiacán, Sinaloa 80110, México
| | - Bruno Gomez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Unidad Mazatlán en Acuicultura y Manejo Ambiental, Mazatlán, Sinaloa AP 711, México
| | - Cristóbal Chaidez
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Carretera a Eldorado Km 5.5, Campo El Diez, Culiacán, Sinaloa 80110, México.
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Taye MB. Biomedical applications of ion-doped bioactive glass: a review. APPLIED NANOSCIENCE 2022. [DOI: 10.1007/s13204-022-02672-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Plumet L, Ahmad-Mansour N, Dunyach-Remy C, Kissa K, Sotto A, Lavigne JP, Costechareyre D, Molle V. Bacteriophage Therapy for Staphylococcus Aureus Infections: A Review of Animal Models, Treatments, and Clinical Trials. Front Cell Infect Microbiol 2022; 12:907314. [PMID: 35782148 PMCID: PMC9247187 DOI: 10.3389/fcimb.2022.907314] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/23/2022] [Indexed: 01/22/2023] Open
Abstract
Staphylococcus aureus (S. aureus) is a common and virulent human pathogen causing several serious illnesses including skin abscesses, wound infections, endocarditis, osteomyelitis, pneumonia, and toxic shock syndrome. Antibiotics were first introduced in the 1940s, leading to the belief that bacterial illnesses would be eradicated. However, microorganisms, including S. aureus, began to develop antibiotic resistance from the increased use and abuse of antibiotics. Antibiotic resistance is now one of the most serious threats to global public health. Bacteria like methicillin-resistant Staphylococcus aureus (MRSA) remain a major problem despite several efforts to find new antibiotics. New treatment approaches are required, with bacteriophage treatment, a non-antibiotic strategy to treat bacterial infections, showing particular promise. The ability of S. aureus to resist a wide range of antibiotics makes it an ideal candidate for phage therapy studies. Bacteriophages have a relatively restricted range of action, enabling them to target pathogenic bacteria. Their usage, usually in the form of a cocktail of bacteriophages, allows for more focused treatment while also overcoming the emergence of resistance. However, many obstacles remain, particularly in terms of their effects in vivo, necessitating the development of animal models to assess the bacteriophage efficiency. Here, we provide a review of the animal models, the various clinical case treatments, and clinical trials for S. aureus phage therapy.
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Affiliation(s)
- Lucile Plumet
- Laboratory of Pathogen Host Interactions, Université de Montpellier, CNRS, UMR 5235, Montpellier, France
| | - Nour Ahmad-Mansour
- Laboratory of Pathogen Host Interactions, Université de Montpellier, CNRS, UMR 5235, Montpellier, France
| | - Catherine Dunyach-Remy
- Virulence Bactérienne et Infections Chroniques, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ Montpellier, Nîmes, France
| | - Karima Kissa
- Laboratory of Pathogen Host Interactions, Université de Montpellier, CNRS, UMR 5235, Montpellier, France
| | - Albert Sotto
- Virulence Bactérienne et Infections Chroniques, INSERM U1047, Department of Infectious and Tropical Diseases, CHU Nîmes, Univ Montpellier, Nîmes, France
| | - Jean-Philippe Lavigne
- Virulence Bactérienne et Infections Chroniques, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ Montpellier, Nîmes, France
| | - Denis Costechareyre
- Laboratory of Pathogen Host Interactions, Université de Montpellier, CNRS, UMR 5235, Montpellier, France
- Greenphage, Cap Alpha, Clapiers, France
| | - Virginie Molle
- Laboratory of Pathogen Host Interactions, Université de Montpellier, CNRS, UMR 5235, Montpellier, France
- *Correspondence: Virginie Molle,
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Drulis-Kawa Z, Augustyniak D. Special Issue: Phage-Bacteria Interplay in Health and Disease. Viruses 2022; 14:v14051054. [PMID: 35632795 PMCID: PMC9146416 DOI: 10.3390/v14051054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 12/10/2022] Open
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Knecht LE, Heinrich N, Born Y, Felder K, Pelludat C, Loessner MJ, Fieseler L. Bacteriophage S6 requires bacterial cellulose for Erwinia amylovora infection. Environ Microbiol 2022; 24:3436-3450. [PMID: 35289468 DOI: 10.1111/1462-2920.15973] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 01/21/2023]
Abstract
Bacteriophages are highly selective in targeting bacteria. This selectivity relies on the specific adsorption of phages to the host cell surface. In this study, a Tn5 transposon mutant library of Erwinia amylovora, the causative agent of fire blight, was screened to identify bacterial receptors required for infection by the podovirus S6. Phage S6 was unable to infect mutants with defects in the bacterial cellulose synthase operon (bcs). The Bcs complex produces and secretes bacterial cellulose, an extracellular polysaccharide associated with bacterial biofilms. Deletion of the bcs operon or associated genes (bcsA, bcsC and bcsZ) verified the crucial role of bacterial cellulose for S6 infection. Application of the cellulose binding dye Congo Red blocked infection by S6. We demonstrate that infective S6 virions degraded cellulose and that Gp95, a phage-encoded cellulase, is involved to catalyse the reaction. In planta S6 did not significantly inhibit fire blight symptom development. Moreover, deletion of bcs genes in E. amylovora did not affect bacterial virulence in blossom infections, indicating that sole application of cellulose targeting phages is less appropriate to biologically control E. amylovora. The interplay between cellulose synthesis, host cell infection and maintenance of the host cell population is discussed.
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Affiliation(s)
- Leandra E Knecht
- Food Microbiology Research Group, Institute of Food and Beverage Innovation, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.,Institute of Food, Nutrition and Health, ETH Zurich, Zürich, Switzerland
| | - Nadine Heinrich
- Institute of Food, Nutrition and Health, ETH Zurich, Zürich, Switzerland
| | - Yannick Born
- Food Microbiology Research Group, Institute of Food and Beverage Innovation, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Katja Felder
- Institute of Food, Nutrition and Health, ETH Zurich, Zürich, Switzerland
| | - Cosima Pelludat
- Agroscope, Plant Pathology and Zoology in Fruit and Vegetable Production, Wädenswil, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zürich, Switzerland
| | - Lars Fieseler
- Food Microbiology Research Group, Institute of Food and Beverage Innovation, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
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20
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Isolation and Identification of a Wastewater Siphoviridae Bacteriophage Targeting Multidrug-resistant Klebsiella pneumoniae. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.118910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Based on the WHO, multidrug-resistant Klebsiella pneumoniae is a priority pathogen that causes opportunistic infections and is widely spread in the environment. Phage therapy is considered a natural, safe, and very efficient alternative to treat difficult-to-treat infections. Objectives: This study aimed to isolate highly virulent, lytic bacteriophages and evaluate their efficacy for lysing multidrug-resistant K. pneumoniae. Methods: Municipal wastewater samples were collected and filtered using 0.22 µm syringe filters and cultivated with log-phase cultures of K. pneumoniae using enrichment media. After 48 h of incubation, the cultures were centrifuged, and the resultant supernatant was filtered (0.22 µm). The detection of the phage was done using the spot assay with K. pneumoniae as the host. One-step growth kinetics and bacterial reduction tests were conducted to assess the growth kinetics of the isolated phage. The stability of the isolated phage was characterized by subjecting it to various temperature and pH conditions. The chemical stability of the K. pneumoniae phage was determined by exposing it to various organic compounds. A panel of 20 bacterial strains was tested using the spot assay, as well as double agar overlying assay, to determine the host range of the isolated phage. Results: Out of 40 wastewater samples tested, only one sample was tested positive for the K. pneumoniae phage (2.5%) that was lytic against the host strain. The K. pneumoniae phage had a latent period of 15 min and a burst size of 100 virions per infected cell. It was most stable at 37°C and pH range of 6.0 to 10.0. Chemically, the K. pneumoniae phage was resistant to 10% chloroform treatment. Transmission electron micrograph indicated that the K. pneumoniae phage belonged to the order Caudovirales, family Siphoviridae, morphotype B1. Conclusions: Most of the characteristic features of the K. pneumoniae phage indicated the potential of this phage to be used in phage therapy. Hence, a comprehensive study is highly recommended to characterize the K. pneumoniae phage genome, detect its molecular interactions with the host cell, and determine its lytic activity in combination with other phages, which may lead to the efficient utilization of this phage in phage therapy against K. pneumoniae infections.
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21
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Abstract
Control of pathogenic bacteria by deliberate application of predatory phages has potential as a powerful therapy against antibiotic-resistant bacteria. The key advantages of phage biocontrol over antibacterial chemotherapy are: (1) an ability to self-propagate inside host bacteria, (2) targeted predation of specific species or strains of bacteria, (3) adaptive molecular machinery to overcome resistance in target bacteria. However, realizing the potential of phage biocontrol is dependent on harnessing or adapting these responses, as many phage species switch between lytic infection cycles (resulting in lysis) and lysogenic infection cycles (resulting in genomic integration) that increase the likelihood of survival of the phage in response to external stress or host depletion. Similarly, host range will need to be optimized to make phage therapy medically viable whilst avoiding the potential for deleteriously disturbing the commensal microbiota. Phage training is a new approach to produce efficient phages by capitalizing on the evolved response of wild-type phages to bacterial resistance. Here we will review recent studies reporting successful trials of training different strains of phages to switch into lytic replication mode, overcome bacterial resistance, and increase their host range. This review will also highlight the current knowledge of phage training and future implications in phage applications and phage therapy and summarize the recent pipeline of the magistral preparation to produce a customized phage for clinical trials and medical applications.
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22
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Mkwata HM, Omoregie AI, Nissom PM. Lytic bacteriophages isolated from limestone caves for biocontrol of Pseudomonas aeruginosa. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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