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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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2
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Zou X, Mo Z, Wang L, Chen S, Lee SY. Overcoming Bacteriophage Contamination in Bioprocessing: Strategies and Applications. SMALL METHODS 2024:e2400932. [PMID: 39359025 DOI: 10.1002/smtd.202400932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 09/14/2024] [Indexed: 10/04/2024]
Abstract
Bacteriophage contamination has a devastating impact on the viability of bacterial hosts and can significantly reduce the productivity of bioprocesses in biotechnological industries. The consequences range from widespread fermentation failure to substantial economic losses, highlighting the urgent need for effective countermeasures. Conventional prevention methods, which focus primarily on the physical removal of bacteriophages from equipment, bioprocess units, and the environment, have proven ineffective in preventing phage entry and contamination. The coevolutionary dynamics between phages and their bacterial hosts have spurred the development of a diverse repertoire of antiviral defense mechanisms within microbial communities. These naturally occurring defense strategies can be harnessed through genetic engineering to convert phage-sensitive hosts into robust, phage-resistant cell factories, providing a strategic approach to mitigate the threats posed by bacteriophages to industrial bacterial processes. In this review, an overview of the various defense strategies and immune systems that curb the propagation of bacteriophages and highlight their applications in fermentation bioprocesses to combat phage contamination is provided. Additionally, the tactics employed by phages to circumvent these defense strategies are also discussed, as preventing the emergence of phage escape mutants is a key component of effective contamination management.
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Affiliation(s)
- Xuan Zou
- Intensive Care Unit, Shenzhen Key Laboratory of Microbiology in Genomic Modification & Editing and Application, Shenzhen Institute of Translational Medicine, Medical Innovation Technology Transformation Center of Shenzhen Second People's Hospital, Shenzhen Univeristy Medical School, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, 518035, China
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Synthetic Biology Research Center, Shenzhen University, Shenzhen, Guangdong, 518035, China
| | - Ziran Mo
- Department of Respiratory Diseases, Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, 518026, China
- Department of Gastroenterology, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Taikang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Lianrong Wang
- Department of Respiratory Diseases, Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, 518026, China
- Department of Gastroenterology, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Taikang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Shi Chen
- Intensive Care Unit, Shenzhen Key Laboratory of Microbiology in Genomic Modification & Editing and Application, Shenzhen Institute of Translational Medicine, Medical Innovation Technology Transformation Center of Shenzhen Second People's Hospital, Shenzhen Univeristy Medical School, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, 518035, China
- Synthetic Biology Research Center, Shenzhen University, Shenzhen, Guangdong, 518035, China
- Department of Gastroenterology, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Taikang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
- BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea
- Graduate School of Engineering Biology, KAIST, Daejeon, 34141, Republic of Korea
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3
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Cui L, Watanabe S, Miyanaga K, Kiga K, Sasahara T, Aiba Y, Tan XE, Veeranarayanan S, Thitiananpakorn K, Nguyen HM, Wannigama DL. A Comprehensive Review on Phage Therapy and Phage-Based Drug Development. Antibiotics (Basel) 2024; 13:870. [PMID: 39335043 PMCID: PMC11428490 DOI: 10.3390/antibiotics13090870] [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: 08/23/2024] [Revised: 09/06/2024] [Accepted: 09/08/2024] [Indexed: 09/30/2024] Open
Abstract
Phage therapy, the use of bacteriophages (phages) to treat bacterial infections, is regaining momentum as a promising weapon against the rising threat of multidrug-resistant (MDR) bacteria. This comprehensive review explores the historical context, the modern resurgence of phage therapy, and phage-facilitated advancements in medical and technological fields. It details the mechanisms of action and applications of phages in treating MDR bacterial infections, particularly those associated with biofilms and intracellular pathogens. The review further highlights innovative uses of phages in vaccine development, cancer therapy, and as gene delivery vectors. Despite its targeted and efficient approach, phage therapy faces challenges related to phage stability, immune response, and regulatory approval. By examining these areas in detail, this review underscores the immense potential and remaining hurdles in integrating phage-based therapies into modern medical practices.
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Affiliation(s)
- Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Kazuhiko Miyanaga
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Kotaro Kiga
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Teppei Sasahara
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Yoshifumi Aiba
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Srivani Veeranarayanan
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Kanate Thitiananpakorn
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Huong Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke City 329-0498, Japan
| | - Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata 990-2292, Japan
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Hu Q, Huang L, Yang Y, Xiang Y, Liu J. Essential phage component induces resistance of bacterial community. SCIENCE ADVANCES 2024; 10:eadp5057. [PMID: 39231230 PMCID: PMC11373596 DOI: 10.1126/sciadv.adp5057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/30/2024] [Indexed: 09/06/2024]
Abstract
Despite extensive knowledge on phage resistance at bacterium level, the resistance of bacterial communities is still not well-understood. Given its ubiquity, it is essential to understand resistance at the community level. We performed quantitative investigations on the dynamics of phage infection in Klebsiella pneumoniae biofilms. We found that the biofilms quickly developed resistance and resumed growth. Instead of mutations, the resistance was caused by unassembled phage tail fibers released by the phage-lysed bacteria. The tail fibers degraded the bacterial capsule essential for infection and induced spreading of capsule loss in the biofilm, and tuning tail fiber and capsule levels altered the resistance. Latent infections sustained in the biofilm despite resistance, allowing stable phage-bacteria coexistence. Last, we showed that the resistance exposed vulnerabilities in the biofilm. Our findings indicate that phage lysate plays important roles in shaping phage-biofilm interactions and open more dimensions for the rational design of strategies to counter bacteria with phage.
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Affiliation(s)
- Qianyu Hu
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Liang Huang
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yaoyu Yang
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Ye Xiang
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jintao Liu
- Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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5
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Goh KJ, Altuvia Y, Argaman L, Raz Y, Bar A, Lithgow T, Margalit H, Gan YH. RIL-seq reveals extensive involvement of small RNAs in virulence and capsule regulation in hypervirulent Klebsiella pneumoniae. Nucleic Acids Res 2024; 52:9119-9138. [PMID: 38804271 PMCID: PMC11347178 DOI: 10.1093/nar/gkae440] [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: 09/13/2023] [Revised: 04/29/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) can infect healthy individuals, in contrast to classical strains that commonly cause nosocomial infections. The recent convergence of hypervirulence with carbapenem-resistance in K. pneumoniae can potentially create 'superbugs' that are challenging to treat. Understanding virulence regulation of hvKp is thus critical. Accumulating evidence suggest that posttranscriptional regulation by small RNAs (sRNAs) plays a role in bacterial virulence, but it has hardly been studied in K. pneumoniae. We applied RIL-seq to a prototypical clinical isolate of hvKp to unravel the Hfq-dependent RNA-RNA interaction (RRI) network. The RRI network is dominated by sRNAs, including predicted novel sRNAs, three of which we validated experimentally. We constructed a stringent subnetwork composed of RRIs that involve at least one hvKp virulence-associated gene and identified the capsule gene loci as a hub target where multiple sRNAs interact. We found that the sRNA OmrB suppressed both capsule production and hypermucoviscosity when overexpressed. Furthermore, OmrB base-pairs within kvrA coding region and partially suppresses translation of the capsule regulator KvrA. This agrees with current understanding of capsule as a major virulence and fitness factor. It emphasizes the intricate regulatory control of bacterial phenotypes by sRNAs, particularly of genes critical to bacterial physiology and virulence.
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Affiliation(s)
- Kwok Jian Goh
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yair Raz
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yunn-Hwen Gan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
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6
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Zeng Y, Li P, Liu S, Shen M, Liu Y, Zhou X. Salmonella enteritidis acquires phage resistance through a point mutation in rfbD but loses some of its environmental adaptability. Vet Res 2024; 55:85. [PMID: 38970094 PMCID: PMC11227202 DOI: 10.1186/s13567-024-01341-7] [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: 01/22/2024] [Accepted: 04/07/2024] [Indexed: 07/07/2024] Open
Abstract
Phage therapy holds promise as an alternative to antibiotics for combating multidrug-resistant bacteria. However, host bacteria can quickly produce progeny that are resistant to phage infection. In this study, we investigated the mechanisms of bacterial resistance to phage infection. We found that Rsm1, a mutant strain of Salmonella enteritidis (S. enteritidis) sm140, exhibited resistance to phage Psm140, which was originally capable of lysing its host at sm140. Whole genome sequencing analysis revealed a single nucleotide mutation at position 520 (C → T) in the rfbD gene of Rsm1, resulting in broken lipopolysaccharides (LPS), which is caused by the replacement of CAG coding glutamine with a stop codon TAG. The knockout of rfbD in the sm140ΔrfbD strain caused a subsequent loss of sensitivity toward phages. Furthermore, the reintroduction of rfbD in Rsm1 restored phage sensitivity. Moreover, polymerase chain reaction (PCR) amplification of rfbD in 25 resistant strains revealed a high percentage mutation rate of 64% within the rfbD locus. We assessed the fitness of four bacteria strains and found that the acquisition of phage resistance resulted in slower bacterial growth, faster sedimentation velocity, and increased environmental sensitivity (pH, temperature, and antibiotic sensitivity). In short, bacteria mutants lose some of their abilities while gaining resistance to phage infection, which may be a general survival strategy of bacteria against phages. This study is the first to report phage resistance caused by rfbD mutation, providing a new perspective for the research on phage therapy and drug-resistant mechanisms.
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Affiliation(s)
- Yukun Zeng
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Ping Li
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Shenglong Liu
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Mangmang Shen
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Yuqing Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Xin Zhou
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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7
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Bozidis P, Markou E, Gouni A, Gartzonika K. Does Phage Therapy Need a Pan-Phage? Pathogens 2024; 13:522. [PMID: 38921819 PMCID: PMC11206709 DOI: 10.3390/pathogens13060522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
The emergence of multidrug-resistant bacteria is undoubtedly one of the most serious global health threats. One response to this threat that has been gaining momentum over the past decade is 'phage therapy'. According to this, lytic bacteriophages are used for the treatment of bacterial infections, either alone or in combination with antimicrobial agents. However, to ensure the efficacy and broad applicability of phage therapy, several challenges must be overcome. These challenges encompass the development of methods and strategies for the host range manipulation and bypass of the resistance mechanisms developed by pathogenic bacteria, as has been the case since the advent of antibiotics. As our knowledge and understanding of the interactions between phages and their hosts evolves, the key issue is to define the host range for each application. In this article, we discuss the factors that affect host range and how this determines the classification of phages into different categories of action. For each host range group, recent representative examples are provided, together with suggestions on how the different groups can be used to combat certain types of bacterial infections. The available methodologies for host range expansion, either through sequential adaptation to a new pathogen or through genetic engineering techniques, are also reviewed.
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Affiliation(s)
- Petros Bozidis
- Department of Microbiology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Eleftheria Markou
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Athanasia Gouni
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Konstantina Gartzonika
- Department of Microbiology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
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8
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Zeng Y, Shen M, Liu S, Zhou X. Characterization and resistance mechanism of phage-resistant strains of Salmonella enteritidis. Poult Sci 2024; 103:103756. [PMID: 38652948 PMCID: PMC11063523 DOI: 10.1016/j.psj.2024.103756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/25/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024] Open
Abstract
In the face of the increasingly severe problem of antibiotic resistance, phage therapy is regarded as a highly potential alternative. Compared with traditional antimicrobial agents, a key research area of phage therapy is the study of phage-resistant mutant bacteria. To effectively monitor and prevent this resistance, it is crucial to conduct in-depth exploration of the mechanism behind phage resistance. In this study, a strain of Salmonella enteritidis (sm140) and the corresponding phage (Psm140) were isolated from chicken liver and sewage, respectively. Using the double-layer plate method, successfully screened out phage-resistant mutant strains. Whole-genome resequencing of 3 resistant strains found that the wbaP gene of all 3 strains had mutations at a specific position (1,118), with the base changing from G to A. This mutation causes the gene-encoded glycine to be replaced by aspartic acid. Subsequent studies found that the frequency of this gene mutation is extremely high, reaching 84%, and all mutations occur at the same position. To further explore the relationship between the wbaP gene and phage resistance, knockout strains and complement strains of the wbaP gene were constructed. The experimental results confirmed the association between the wbaP gene and phage resistance. At the same time, biological characteristics and virulence were evaluated for wild strains, resistant strains, knockout strains, and complement strains. It was found that mutations or deletions of the wbaP gene lead to a decrease in bacterial environmental adaptability and virulence. Through systematic research on the mechanism and biological characteristics of phage resistance, this study provides important references and guidance for the development of new phage therapies, promoting progress in the field of antimicrobial treatment. At the same time, the emergence of phage resistance due to wbaP gene mutations is reported for the first time in salmonella, providing a new perspective and ideas for further studying phage resistance mechanisms.
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Affiliation(s)
- Yukun Zeng
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Mangmang Shen
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Shenglong Liu
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Xin Zhou
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
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9
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Kraus S, Fletcher ML, Łapińska U, Chawla K, Baker E, Attrill EL, O'Neill P, Farbos A, Jeffries A, Galyov EE, Korbsrisate S, Barnes KB, Harding SV, Tsaneva-Atanasova K, Blaskovich MAT, Pagliara S. Phage-induced efflux down-regulation boosts antibiotic efficacy. PLoS Pathog 2024; 20:e1012361. [PMID: 38941361 PMCID: PMC11239113 DOI: 10.1371/journal.ppat.1012361] [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: 11/16/2023] [Revised: 07/11/2024] [Accepted: 06/21/2024] [Indexed: 06/30/2024] Open
Abstract
The interactions between a virus and its host vary in space and time and are affected by the presence of molecules that alter the physiology of either the host or the virus. Determining the molecular mechanisms at the basis of these interactions is paramount for predicting the fate of bacterial and phage populations and for designing rational phage-antibiotic therapies. We study the interactions between stationary phase Burkholderia thailandensis and the phage ΦBp-AMP1. Although heterogeneous genetic resistance to phage rapidly emerges in B. thailandensis, the presence of phage enhances the efficacy of three major antibiotic classes, the quinolones, the beta-lactams and the tetracyclines, but antagonizes tetrahydrofolate synthesis inhibitors. We discovered that enhanced antibiotic efficacy is facilitated by reduced antibiotic efflux in the presence of phage. This new phage-antibiotic therapy allows for eradication of stationary phase bacteria, whilst requiring reduced antibiotic concentrations, which is crucial for treating infections in sites where it is difficult to achieve high antibiotic concentrations.
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Affiliation(s)
- Samuel Kraus
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Megan L Fletcher
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Krina Chawla
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Evan Baker
- Department of Mathematics and Living Systems Institute, University of Exeter, Exeter, Devon, United Kingdom
- EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter, United Kingdom
| | - Erin L Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Paul O'Neill
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Audrey Farbos
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Aaron Jeffries
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Edouard E Galyov
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok Thailand
| | - Kay B Barnes
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Krasimira Tsaneva-Atanasova
- Department of Mathematics and Living Systems Institute, University of Exeter, Exeter, Devon, United Kingdom
- EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter, United Kingdom
| | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
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10
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Dicks LMT, Vermeulen W. Bacteriophage-Host Interactions and the Therapeutic Potential of Bacteriophages. Viruses 2024; 16:478. [PMID: 38543843 PMCID: PMC10975011 DOI: 10.3390/v16030478] [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: 02/05/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 05/23/2024] Open
Abstract
Healthcare faces a major problem with the increased emergence of antimicrobial resistance due to over-prescribing antibiotics. Bacteriophages may provide a solution to the treatment of bacterial infections given their specificity. Enzymes such as endolysins, exolysins, endopeptidases, endosialidases, and depolymerases produced by phages interact with bacterial surfaces, cell wall components, and exopolysaccharides, and may even destroy biofilms. Enzymatic cleavage of the host cell envelope components exposes specific receptors required for phage adhesion. Gram-positive bacteria are susceptible to phage infiltration through their peptidoglycan, cell wall teichoic acid (WTA), lipoteichoic acids (LTAs), and flagella. In Gram-negative bacteria, lipopolysaccharides (LPSs), pili, and capsules serve as targets. Defense mechanisms used by bacteria differ and include physical barriers (e.g., capsules) or endogenous mechanisms such as clustered regularly interspaced palindromic repeat (CRISPR)-associated protein (Cas) systems. Phage proteins stimulate immune responses against specific pathogens and improve antibiotic susceptibility. This review discusses the attachment of phages to bacterial cells, the penetration of bacterial cells, the use of phages in the treatment of bacterial infections, and the limitations of phage therapy. The therapeutic potential of phage-derived proteins and the impact that genomically engineered phages may have in the treatment of infections are summarized.
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Affiliation(s)
- Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa;
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11
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Haudiquet M, Le Bris J, Nucci A, Bonnin RA, Domingo-Calap P, Rocha EPC, Rendueles O. Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency. Nat Commun 2024; 15:2032. [PMID: 38448399 PMCID: PMC10918111 DOI: 10.1038/s41467-024-46147-5] [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: 05/31/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Bacterial evolution is affected by mobile genetic elements like phages and conjugative plasmids, offering new adaptive traits while incurring fitness costs. Their infection is affected by the bacterial capsule. Yet, its importance has been difficult to quantify because of the high diversity of confounding mechanisms in bacterial genomes such as anti-viral systems and surface receptor modifications. Swapping capsule loci between Klebsiella pneumoniae strains allowed us to quantify their impact on plasmid and phage infection independently of genetic background. Capsule swaps systematically invert phage susceptibility, revealing serotypes as key determinants of phage infection. Capsule types also influence conjugation efficiency in both donor and recipient cells, a mechanism shaped by capsule volume and conjugative pilus structure. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The least capsule-sensitive pili (F-like) are the most frequent in the species' plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.
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Affiliation(s)
- Matthieu Haudiquet
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
- Ecole Doctoral FIRE-Programme Bettencourt, CRI, Paris, France.
| | - Julie Le Bris
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
- Sorbonne Université, Collège Doctoral, Ecole Doctorale Complexité du Vivant, 75005, Paris, France
| | - Amandine Nucci
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | - Rémy A Bonnin
- Team Resist UMR1184 Université Paris Saclay, CEA, Inserm, Le Kremlin-Bicêtre, Paris, France
- Service de bactériologie, Hôpital Bicêtre, Université Paris Saclay, AP-HP, Le Kremlin-Bicêtre, Paris, France
- Centre National de Référence Associé de la Résistance aux Antibiotiques, Le Kremlin-Bicêtre, Paris, France
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, 46980, Paterna, Spain
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
| | - Olaya Rendueles
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
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12
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Young GR, Nelson A, Stewart CJ, Smith DL. Bacteriophage communities are a reservoir of unexplored microbial diversity in neonatal health and disease. Curr Opin Microbiol 2023; 75:102379. [PMID: 37647765 DOI: 10.1016/j.mib.2023.102379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 09/01/2023]
Abstract
Acquisition and development of the gut microbiome are vital for immune education in neonates, especially those born preterm. As such, microbial communities have been extensively studied in the context of postnatal health and disease. Bacterial communities have been the focus of research in this area due to the relative ease of targeted bacterial sequencing and the availability of databases to align and validate sequencing data. Recent increases in high-throughput metagenomic sequencing accessibility have facilitated research to investigate bacteriophages within the context of neonatal gut microbial communities. Focusing on unexplored viral diversity, has identified novel bacteriophage species and previously uncharacterised viral diversity. In doing so, studies have highlighted links between bacteriophages and bacterial community structure in the context of health and disease. However, much remains unknown about the complex relationships between bacteriophages, the bacteria they infect and their human host. With a particular focus on preterm infants, this review highlights opportunities to explore the influence of bacteriophages on developing microbial communities and the tripartite relationships between bacteriophages, bacteria and the neonatal human host. We suggest a focus on expanding collections of isolated bacteriophages that will further our understanding of the growing numbers of bacteriophages identified in metagenomes.
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Affiliation(s)
- Gregory R Young
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | - Andrew Nelson
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | | | - Darren L Smith
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK.
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13
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Georjon H, Bernheim A. The highly diverse antiphage defence systems of bacteria. Nat Rev Microbiol 2023; 21:686-700. [PMID: 37460672 DOI: 10.1038/s41579-023-00934-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 09/14/2023]
Abstract
Bacteria and their viruses have coevolved for billions of years. This ancient and still ongoing arms race has led bacteria to develop a vast antiphage arsenal. The development of high-throughput screening methods expanded our knowledge of defence systems from a handful to more than a hundred systems, unveiling many different molecular mechanisms. These findings reveal that bacterial immunity is much more complex than previously thought. In this Review, we explore recently discovered bacterial antiphage defence systems, with a particular focus on their molecular diversity, and discuss the ecological and evolutionary drivers and implications of the existing diversity of antiphage defence mechanisms.
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Affiliation(s)
- Héloïse Georjon
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France
| | - Aude Bernheim
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France.
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14
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Hong Y, Qin J, Forga XB, Totsika M. Extensive Diversity in Escherichia coli Group 3 Capsules Is Driven by Recombination and Plasmid Transfer from Multiple Species. Microbiol Spectr 2023; 11:e0143223. [PMID: 37358457 PMCID: PMC10433991 DOI: 10.1128/spectrum.01432-23] [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: 04/04/2023] [Accepted: 06/04/2023] [Indexed: 06/27/2023] Open
Abstract
Bacterial capsules provide protection against environmental challenges and host immunity. Historically, Escherichia coli K serotyping scheme, which relies on the hypervariable capsules, has identified around 80 K forms that fall into four distinct groups. Based on recent work by us and others, we predicted that E. coli capsular diversity is grossly underestimated. We exploited group 3 capsule gene clusters, the best genetically defined capsule group in E. coli, to analyze publicly available E. coli sequences for overlooked capsular diversity within the species. We report the discovery of seven novel group 3 clusters that fall into two distinct subgroups (3A and 3B). The majority of the 3B capsule clusters were found on plasmids, contrary to the defining feature of group 3 capsule genes localizing at the serA locus on the E. coli chromosome. Other new group 3 capsule clusters were derived from ancestral sequences through recombination events between shared genes found within the serotype variable central region 2. Intriguingly, flanking regions 1 and 3, known to be conserved areas among capsule clusters, showed considerable intra-subgroup variation in clusters from the 3B subgroup, containing genes of shared ancestry with other Enterobacteriaceae species. Variation of group 3 kps clusters within dominant E. coli lineages, including multidrug-resistant pathogenic lineages, further supports that E. coli capsules are undergoing rigorous change. Given the pivotal role of capsular polysaccharides in phage predation, our findings raise attention to the need of monitoring kps evolutionary dynamics in pathogenic E. coli in supporting phage therapy. IMPORTANCE Capsular polysaccharides protect pathogenic bacteria against environmental challenges, host immunity, and phage predations. The historical Escherichia coli K typing scheme, which relies on the hypervariable capsular polysaccharide, has identified around 80 different K forms that fall into four distinct groups. Taking advantage of the supposedly compact and genetically well-defined group 3 gene clusters, we analyzed published E. coli sequences to identify seven new gene clusters and revealed an unexpected capsular diversity. Genetic analysis revealed that group 3 gene clusters shared closely related serotype-specific region 2 and were diversified through recombination events and plasmid transfer between multiple Enterobacteriaceae species. Overall, capsular polysaccharides in E. coli are undergoing rigorous change. Given the pivotal role capsules play in phage interactions, this work highlighted the need to monitor the evolutionary dynamics of capsules in pathogenic E. coli for effective phage therapy.
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Affiliation(s)
- Yaoqin Hong
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Queensland, Australia
- Max Planck Queensland Centre, Queensland University of Technology, Queensland, Australia
| | - Jilong Qin
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Queensland, Australia
| | - Xavier Bertran Forga
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Queensland, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Queensland, Australia
- Max Planck Queensland Centre, Queensland University of Technology, Queensland, Australia
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15
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Jędrusiak A, Fortuna W, Majewska J, Górski A, Jończyk-Matysiak E. Phage Interactions with the Nervous System in Health and Disease. Cells 2023; 12:1720. [PMID: 37443756 PMCID: PMC10341288 DOI: 10.3390/cells12131720] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
The central nervous system manages all of our activities (e.g., direct thinking and decision-making processes). It receives information from the environment and responds to environmental stimuli. Bacterial viruses (bacteriophages, phages) are the most numerous structures occurring in the biosphere and are also found in the human organism. Therefore, understanding how phages may influence this system is of great importance and is the purpose of this review. We have focused on the effect of natural bacteriophages in the central nervous system, linking them to those present in the gut microbiota, creating the gut-brain axis network, as well as their interdependence. Importantly, based on the current knowledge in the field of phage application (e.g., intranasal) in the treatment of bacterial diseases associated with the brain and nervous system, bacteriophages may have significant therapeutic potential. Moreover, it was indicated that bacteriophages may influence cognitive processing. In addition, phages (via phage display technology) appear promising as a targeted therapeutic tool in the treatment of, among other things, brain cancers. The information collected and reviewed in this work indicates that phages and their impact on the nervous system is a fascinating and, so far, underexplored field. Therefore, the aim of this review is not only to summarize currently available information on the association of phages with the nervous system, but also to stimulate future studies that could pave the way for novel therapeutic approaches potentially useful in treating bacterial and non-bacterial neural diseases.
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Affiliation(s)
- Adam Jędrusiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
| | - Wojciech Fortuna
- Department of Neurosurgery, Wroclaw Medical University, Borowska 213, 54-427 Wroclaw, Poland;
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland
| | - Joanna Majewska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland
- Infant Jesus Hospital, The Medical University of Warsaw, 02-006 Warsaw, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
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16
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Arredondo-Alonso S, Blundell-Hunter G, Fu Z, Gladstone RA, Fillol-Salom A, Loraine J, Cloutman-Green E, Johnsen PJ, Samuelsen Ø, Pöntinen AK, Cléon F, Chavez-Bueno S, De la Cruz MA, Ares MA, Vongsouvath M, Chmielarczyk A, Horner C, Klein N, McNally A, Reis JN, Penadés JR, Thomson NR, Corander J, Taylor PW, McCarthy AJ. Evolutionary and functional history of the Escherichia coli K1 capsule. Nat Commun 2023; 14:3294. [PMID: 37322051 PMCID: PMC10272209 DOI: 10.1038/s41467-023-39052-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
Escherichia coli is a leading cause of invasive bacterial infections in humans. Capsule polysaccharide has an important role in bacterial pathogenesis, and the K1 capsule has been firmly established as one of the most potent capsule types in E. coli through its association with severe infections. However, little is known about its distribution, evolution and functions across the E. coli phylogeny, which is fundamental to elucidating its role in the expansion of successful lineages. Using systematic surveys of invasive E. coli isolates, we show that the K1-cps locus is present in a quarter of bloodstream infection isolates and has emerged in at least four different extraintestinal pathogenic E. coli (ExPEC) phylogroups independently in the last 500 years. Phenotypic assessment demonstrates that K1 capsule synthesis enhances E. coli survival in human serum independent of genetic background, and that therapeutic targeting of the K1 capsule re-sensitizes E. coli from distinct genetic backgrounds to human serum. Our study highlights that assessing the evolutionary and functional properties of bacterial virulence factors at population levels is important to better monitor and predict the emergence of virulent clones, and to also inform therapies and preventive medicine to effectively control bacterial infections whilst significantly lowering antibiotic usage.
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Affiliation(s)
- Sergio Arredondo-Alonso
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | - Zuyi Fu
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Rebecca A Gladstone
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Alfred Fillol-Salom
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | | | - Elaine Cloutman-Green
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - François Cléon
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Susana Chavez-Bueno
- University of Missouri Kansas City, Kansas City, USA
- Division of Infectious Diseases, Children's Mercy Hospital Kansas City, UMKC School of Medicine, Kansas City, USA
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Agnieszka Chmielarczyk
- Faculty of Medicine, Chair of Microbiology, Jagiellonian University Medical College, Czysta str. 18, 31-121, Kraków, Poland
| | - Carolyne Horner
- British Society for Antimicrobial Chemotherapy, Birmingham, UK
| | - Nigel Klein
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joice N Reis
- Laboratory of Pathology and Molecular Biology (LPBM), Gonçalo Moniz Research Institute, Oswaldo Cruz Foundation, Salvador, Brazil
- Faculdade de Farmácia, Universidade Federal da Bahia, Salvador, Brazil
| | - José R Penadés
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nicholas R Thomson
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
| | - Peter W Taylor
- School of Pharmacy, University College London, London, UK.
| | - Alex J McCarthy
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
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17
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Boyle TA, Hatoum-Aslan A. Recurring and emerging themes in prokaryotic innate immunity. Curr Opin Microbiol 2023; 73:102324. [PMID: 37163858 PMCID: PMC10360293 DOI: 10.1016/j.mib.2023.102324] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 05/12/2023]
Abstract
A resurgence of interest in the pathways that bacteria use to protect against their viruses (i.e. phages) has led to the discovery of dozens of new antiphage defenses. Given the sheer abundance and diversity of phages - the ever-evolving targets of immunity - it is not surprising that these newly described defenses are also remarkably diverse. However, as their mechanisms slowly come into focus, some common strategies and themes are also beginning to emerge. This review highlights recurring and emerging themes in the mechanisms of innate immunity in bacteria and archaea, with an emphasis on recently described systems that have undergone more thorough mechanistic characterization.
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Affiliation(s)
- Tori A Boyle
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL 61801, USA
| | - Asma Hatoum-Aslan
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL 61801, USA.
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18
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Smith WPJ, Wucher BR, Nadell CD, Foster KR. Bacterial defences: mechanisms, evolution and antimicrobial resistance. Nat Rev Microbiol 2023:10.1038/s41579-023-00877-3. [PMID: 37095190 DOI: 10.1038/s41579-023-00877-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 04/26/2023]
Abstract
Throughout their evolutionary history, bacteria have faced diverse threats from other microorganisms, including competing bacteria, bacteriophages and predators. In response to these threats, they have evolved sophisticated defence mechanisms that today also protect bacteria against antibiotics and other therapies. In this Review, we explore the protective strategies of bacteria, including the mechanisms, evolution and clinical implications of these ancient defences. We also review the countermeasures that attackers have evolved to overcome bacterial defences. We argue that understanding how bacteria defend themselves in nature is important for the development of new therapies and for minimizing resistance evolution.
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Affiliation(s)
- William P J Smith
- Division of Genomics, Infection and Evolution, University of Manchester, Manchester, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Benjamin R Wucher
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Carey D Nadell
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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19
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Williams J, Burton N, Dhanoa G, Sagona AP. Host-phage interactions and modeling for therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:127-158. [PMID: 37739552 DOI: 10.1016/bs.pmbts.2023.03.010] [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: 09/24/2023]
Abstract
Phage are drivers of numerous ecological processes on the planet and have the potential to be developed into a therapy alternative to antibiotics. Phage at all points of their life cycle, from initiation of infection to their release, interact with their host in some manner. More importantly, to harness their antimicrobial potential it is vital to understand how phage interact with the eukaryotic environment in the context of applying phage for therapy. In this chapter, the various mechanisms of phage interplay with their hosts as part of their natural life cycle are discussed in depth for Gram-positive and negative bacteria. Further, the literature surrounding the various models utilized to develop phage as a therapeutic are examined, and how these models may improve our understanding of phage-host interactions and current progress in utilizing phage for therapy in the clinical environment.
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Affiliation(s)
- Joshua Williams
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Nathan Burton
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Gurneet Dhanoa
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Coventry, United Kingdom.
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20
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Bleriot I, Blasco L, Pacios O, Fernández-García L, López M, Ortiz-Cartagena C, Barrio-Pujante A, Fernández-Cuenca F, Pascual Á, Martínez-Martínez L, Oteo-Iglesias J, Tomás M. Proteomic Study of the Interactions between Phages and the Bacterial Host Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0397422. [PMID: 36877024 PMCID: PMC10100988 DOI: 10.1128/spectrum.03974-22] [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: 10/03/2022] [Accepted: 02/08/2023] [Indexed: 03/07/2023] Open
Abstract
Phages and bacteria have acquired resistance mechanisms for protection. In this context, the aims of the present study were to analyze the proteins isolated from 21 novel lytic phages of Klebsiella pneumoniae in search of defense mechanisms against bacteria and also to determine the infective capacity of the phages. A proteomic study was also conducted to investigate the defense mechanisms of two clinical isolates of K. pneumoniae infected by phages. For this purpose, the 21 lytic phages were sequenced and de novo assembled. The host range was determined in a collection of 47 clinical isolates of K. pneumoniae, revealing the variable infective capacity of the phages. Genome sequencing showed that all of the phages were lytic phages belonging to the order Caudovirales. Phage sequence analysis revealed that the proteins were organized in functional modules within the genome. Although most of the proteins have unknown functions, multiple proteins were associated with defense mechanisms against bacteria, including the restriction-modification system, the toxin-antitoxin system, evasion of DNA degradation, blocking of host restriction and modification, the orphan CRISPR-Cas system, and the anti-CRISPR system. Proteomic study of the phage-host interactions (i.e., between isolates K3574 and K3320, which have intact CRISPR-Cas systems, and phages vB_KpnS-VAC35 and vB_KpnM-VAC36, respectively) revealed the presence of several defense mechanisms against phage infection (prophage, defense/virulence/resistance, oxidative stress and plasmid proteins) in the bacteria, and of the Acr candidate (anti-CRISPR protein) in the phages. IMPORTANCE Researchers, including microbiologists and infectious disease specialists, require more knowledge about the interactions between phages and their bacterial hosts and about their defense mechanisms. In this study, we analyzed the molecular mechanisms of viral and bacterial defense in phages infecting clinical isolates of K. pneumoniae. Viral defense mechanisms included restriction-modification system evasion, the toxin-antitoxin (TA) system, DNA degradation evasion, blocking of host restriction and modification, and resistance to the abortive infection system, anti-CRISPR and CRISPR-Cas systems. Regarding bacterial defense mechanisms, proteomic analysis revealed expression of proteins involved in the prophage (FtsH protease modulator), plasmid (cupin phosphomannose isomerase protein), defense/virulence/resistance (porins, efflux pumps, lipopolysaccharide, pilus elements, quorum network proteins, TA systems, and methyltransferases), oxidative stress mechanisms, and Acr candidates (anti-CRISPR protein). The findings reveal some important molecular mechanisms involved in the phage-host bacterial interactions; however, further study in this field is required to improve the efficacy of phage therapy.
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Affiliation(s)
- Inés Bleriot
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Lucia Blasco
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Olga Pacios
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Laura Fernández-García
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - María López
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Concha Ortiz-Cartagena
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Antonio Barrio-Pujante
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Felipe Fernández-Cuenca
- Clinical Unit of Infectious Diseases and Microbiology, Hospital Universitario Virgen Macarena, Institute of Biomedicine of Seville (University Hospital Virgen Macarena/CSIC/University of Seville), Seville, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Álvaro Pascual
- Clinical Unit of Infectious Diseases and Microbiology, Hospital Universitario Virgen Macarena, Institute of Biomedicine of Seville (University Hospital Virgen Macarena/CSIC/University of Seville), Seville, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Martínez-Martínez
- Clinical Unit of Microbiology, Reina Sofía University Hospital, Department of Agricultural Chemistry, Edaphology and Microbiology, University of Cordoba, Maimonides Biomedical Research Institute (IMIBIC), Cordoba, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - María Tomás
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
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21
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Beamud B, García-González N, Gómez-Ortega M, González-Candelas F, Domingo-Calap P, Sanjuan R. Genetic determinants of host tropism in Klebsiella phages. Cell Rep 2023; 42:112048. [PMID: 36753420 PMCID: PMC9989827 DOI: 10.1016/j.celrep.2023.112048] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/25/2022] [Accepted: 01/13/2023] [Indexed: 02/08/2023] Open
Abstract
Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates of Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show a narrow host range for most phages, with <2% of 6,319 phage-host combinations tested yielding detectable interactions. Bacterial capsule diversity is the main factor restricting phage host range. Consequently, phage-encoded depolymerases are key determinants of host tropism, and depolymerase sequence types are associated with the ability to infect specific capsular types across phage families. However, all phages with a broader host range found do not encode canonical depolymerases, suggesting alternative modes of entry. These findings expand our knowledge of the complex interactions between bacteria and their viruses and point out the feasibility of predicting the first steps of phage infection using bacterial and phage genome sequences.
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Affiliation(s)
- Beatriz Beamud
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Neris García-González
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Mar Gómez-Ortega
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
| | - Rafael Sanjuan
- Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
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22
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Teklemariam AD, Al-Hindi RR, Qadri I, Alharbi MG, Ramadan WS, Ayubu J, Al-Hejin AM, Hakim RF, Hakim FF, Hakim RF, Alseraihi LI, Alamri T, Harakeh S. The Battle between Bacteria and Bacteriophages: A Conundrum to Their Immune System. Antibiotics (Basel) 2023; 12:381. [PMID: 36830292 PMCID: PMC9952470 DOI: 10.3390/antibiotics12020381] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Bacteria and their predators, bacteriophages, or phages are continuously engaged in an arms race for their survival using various defense strategies. Several studies indicated that the bacterial immune arsenal towards phage is quite diverse and uses different components of the host machinery. Most studied antiphage systems are associated with phages, whose genomic matter is double-stranded-DNA. These defense mechanisms are mainly related to either the host or phage-derived proteins and other associated structures and biomolecules. Some of these strategies include DNA restriction-modification (R-M), spontaneous mutations, blocking of phage receptors, production of competitive inhibitors and extracellular matrix which prevent the entry of phage DNA into the host cytoplasm, assembly interference, abortive infection, toxin-antitoxin systems, bacterial retrons, and secondary metabolite-based replication interference. On the contrary, phages develop anti-phage resistance defense mechanisms in consortium with each of these bacterial phage resistance strategies with small fitness cost. These mechanisms allow phages to undergo their replication safely inside their bacterial host's cytoplasm and be able to produce viable, competent, and immunologically endured progeny virions for the next generation. In this review, we highlight the major bacterial defense systems developed against their predators and some of the phage counterstrategies and suggest potential research directions.
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Affiliation(s)
- Addisu D. Teklemariam
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rashad R. Al-Hindi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ishtiaq Qadri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mona G. Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Wafaa S. Ramadan
- Department of Anatomy, Faculty of Medicine (FM), King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Anatomy, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt
| | - Jumaa Ayubu
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed M. Al-Hejin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Microbiology Level 2 Laboratory, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| | | | - Fanar F. Hakim
- Department of Internal Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rahad F. Hakim
- Ibn Sina National College for Medical Studies, Jeddah 21418, Saudi Arabia
| | | | - Turki Alamri
- Family and Community Medicine Department, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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23
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Abedon ST. Ecology and Evolutionary Biology of Hindering Phage Therapy: The Phage Tolerance vs. Phage Resistance of Bacterial Biofilms. Antibiotics (Basel) 2023; 12:245. [PMID: 36830158 PMCID: PMC9952518 DOI: 10.3390/antibiotics12020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
As with antibiotics, we can differentiate various acquired mechanisms of bacteria-mediated inhibition of the action of bacterial viruses (phages or bacteriophages) into ones of tolerance vs. resistance. These also, respectively, may be distinguished as physiological insensitivities (or protections) vs. resistance mutations, phenotypic resistance vs. genotypic resistance, temporary vs. more permanent mechanisms, and ecologically vs. also near-term evolutionarily motivated functions. These phenomena can result from multiple distinct molecular mechanisms, many of which for bacterial tolerance of phages are associated with bacterial biofilms (as is also the case for the bacterial tolerance of antibiotics). The resulting inhibitions are relevant from an applied perspective because of their potential to thwart phage-based treatments of bacterial infections, i.e., phage therapies, as well as their potential to interfere more generally with approaches to the phage-based biological control of bacterial biofilms. In other words, given the generally low toxicity of properly chosen therapeutic phages, it is a combination of phage tolerance and phage resistance, as displayed by targeted bacteria, that seems to represent the greatest impediments to phage therapy's success. Here I explore general concepts of bacterial tolerance of vs. bacterial resistance to phages, particularly as they may be considered in association with bacterial biofilms.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
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24
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Leprince A, Mahillon J. Phage Adsorption to Gram-Positive Bacteria. Viruses 2023; 15:196. [PMID: 36680236 PMCID: PMC9863714 DOI: 10.3390/v15010196] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
The phage life cycle is a multi-stage process initiated by the recognition and attachment of the virus to its bacterial host. This adsorption step depends on the specific interaction between bacterial structures acting as receptors and viral proteins called Receptor Binding Proteins (RBP). The adsorption process is essential as it is the first determinant of phage host range and a sine qua non condition for the subsequent conduct of the life cycle. In phages belonging to the Caudoviricetes class, the capsid is attached to a tail, which is the central player in the adsorption as it comprises the RBP and accessory proteins facilitating phage binding and cell wall penetration prior to genome injection. The nature of the viral proteins involved in host adhesion not only depends on the phage morphology (i.e., myovirus, siphovirus, or podovirus) but also the targeted host. Here, we give an overview of the adsorption process and compile the available information on the type of receptors that can be recognized and the viral proteins taking part in the process, with the primary focus on phages infecting Gram-positive bacteria.
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25
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Dantas R, Brocchi M, Pacheco Fill T. Chemical-Biology and Metabolomics Studies in Phage-Host Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:71-100. [PMID: 37843806 DOI: 10.1007/978-3-031-41741-2_4] [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: 10/17/2023]
Abstract
For many years, several studies have explored the molecular mechanisms involved in the infection of bacteria by their specific phages to understand the main infection strategies and the host defense strategies. The modulation of the mechanisms involved in the infection, as well as the expression of key substances in the development of the different life cycles of phages, function as a natural source of strategies capable of promoting the control of different pathogens that are harmful to human and animal health. Therefore, this chapter aims to provide an overview of the mechanisms involved in virus-bacteria interaction to explore the main compounds produced or altered as a chemical survival strategy and the metabolism modulation when occurring a host-phage interaction. In this context, emphasis will be given to the chemistry of peptides/proteins and enzymes encoded by bacteriophages in the control of pathogenic bacteria and the use of secondary metabolites recently reported as active participants in the mechanisms of phage-bacteria interaction. Finally, metabolomics strategies developed to gain new insights into the metabolism involved in the phage-host interaction and the metabolomics workflow in host-phage interaction will be presented.
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Affiliation(s)
- Rodolfo Dantas
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | - Marcelo Brocchi
- Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Taícia Pacheco Fill
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil.
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26
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Abstract
EMBL-EBI The European Bioinformatics Institute; E. coli Escherichia coli; E. faecalis Enterobacter faecalis; B. fragilis Bacteroides fragilis; B. vulgatus Bacteroides vulgatus; SaPIs Staphylococcus aureus pathogenicity islands; ARGs Antibiotic resistance genes; STEC Shiga toxigenic E. coli; Stx Shiga toxin; BLAST Basic Local Alignment Search Tool; TSST-1 Toxic shock toxin 1; RBPs Receptor-binding proteins; LPS lipopolysaccharide; OMVs Outer membrane vesicles; PT Phosphorothioate; BREX Bacteriophage exclusion; OCR Overcome classical restriction; Pgl Phage growth limitation; DISARM Defense island system associated with restrictionmodification; R-M system Restriction-modification system; BREX system Bacteriophage exclusion system; CRISPR Clustered regularly interspaced short palindromic repeats; Cas CRISPR-associated; PAMs Prospacer adjacent motifs; crRNA CRISPR RNA; SIE; OMPs; Superinfection exclusion; Outer membrane proteins; Abi Abortive infection; TA Toxin-antitoxin; TLR Toll-like receptor; APCs Antigen-presenting cells; DSS Dextran sulfate sodium; IELs Intraepithelial lymphocytes; FMT Fecal microbiota transfer; IFN-γ Interferon-gamma; IBD Inflammatory bowel disease; AgNPs Silver nanoparticles; MDSC Myeloid-derived suppressor cell; CRC Colorectal cancer; VLPs Virus-like particles; TMP Tape measure protein; PSMB4 Proteasome subunit beta type-4; ALD Alcohol-related liver disease; GVHD Graft-versus-host disease; ROS Reactive oxygen species; RA Rheumatoid arthritis; CCP Cyclic citrullinated protein; AMGs Accessory metabolic genes; T1DM Type 1 diabetes mellitus; T2DM Type 2 diabetes mellitus; SCFAs Short-chain fatty acids; GLP-1 Glucagon-like peptide-1; A. baumannii Acinetobacter baumannii; CpG Deoxycytidylinate-phosphodeoxyguanosine; PEG Polyethylene glycol; MetS Metabolic syndrome; OprM Outer membrane porin M.
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Affiliation(s)
- Han Shuwen
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Department of Medical Oncology, Huzhou Central Hospital, Huzhou, China
| | - Ding Kefeng
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Department of Colorectal Surgery and Oncology, Cancer Center Zhejiang University, Hangzhou, China,CONTACT Ding Kefeng Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Building 6 room 2018, Hangzhou, Zhejiang310009, China
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27
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Knecht LE, Born Y, Pelludat C, Pothier JF, Smits THM, Loessner MJ, Fieseler L. Spontaneous Resistance of Erwinia amylovora Against Bacteriophage Y2 Affects Infectivity of Multiple Phages. Front Microbiol 2022; 13:908346. [PMID: 35979490 PMCID: PMC9376448 DOI: 10.3389/fmicb.2022.908346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Broad application of antibiotics gave rise to increasing numbers of antibiotic resistant bacteria. Therefore, effective alternatives are currently investigated. Bacteriophages, natural predators of bacteria, could work as such an alternative. Although phages can be highly effective at eliminating specific bacteria, phage resistance can be observed after application. The nature of this resistance, however, can differ depending on the phage. Exposing Erwinia amylovora CFBP 1430, the causative agent of fire blight, to the different phages Bue1, L1, S2, S6, or M7 led to transient resistance. The bacteria reversed to a phage sensitive state after the phage was eliminated. When wild type bacteria were incubated with Y2, permanently resistant colonies (1430Y2R) formed spontaneously. In addition, 1430Y2R revealed cross-resistance against other phages (Bue1) or lowered the efficiency of plating (L1, S2, and S6). Pull down experiments revealed that Y2 is no longer able to bind to the mutant suggesting mutation or masking of the Y2 receptor. Other phages tested were still able to bind to 1430Y2R. Bue1 was observed to still adsorb to the mutant, but no host lysis was found. These findings indicated that, in addition to the alterations of the Y2 receptor, the 1430Y2R mutant might block phage attack at different stage of infection. Whole genome sequencing of 1430Y2R revealed a deletion in the gene with the locus tag EAMY_2231. The gene, which encodes a putative galactosyltransferase, was truncated due to the resulting frameshift. The mutant 1430Y2R was monitored for potential defects or fitness loss. Weaker growth was observed in LB medium compared to the wild type but not in minimal medium. Strain 1430Y2R was still highly virulent in blossoms even though amylovoran production was observed to be reduced. Additionally, LPS structures were analyzed and were clearly shown to be altered in the mutant. Complementation of the truncated EAMY_2231 in trans restored the wild type phenotype. The truncation of EAMY_2231 can therefore be associated with manifold modifications in 1430Y2R, which can affect different phages simultaneously.
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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 Zürich, Zurich, Switzerland
| | - Yannick Born
- Food Microbiology Research Group, Institute of Food and Beverage Innovation, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Cosima Pelludat
- Agroscope, Plant Pathology and Zoology in Fruit and Vegetable Production, Wädenswil, Switzerland
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Theo H. M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Martin J. Loessner
- Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Lars Fieseler
- Food Microbiology Research Group, Institute of Food and Beverage Innovation, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
- *Correspondence: Lars Fieseler,
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Dhanoa GK, Kushnir I, Qimron U, Roper DI, Sagona AP. Investigating the effect of bacteriophages on bacterial FtsZ localisation. Front Cell Infect Microbiol 2022; 12:863712. [PMID: 35967845 PMCID: PMC9372555 DOI: 10.3389/fcimb.2022.863712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli is one of the most common Gram-negative pathogens and is responsible for infection leading to neonatal meningitis and sepsis. The FtsZ protein is a bacterial tubulin homolog required for cell division in most species, including E. coli. Several agents that block cell division have been shown to mislocalise FtsZ, including the bacteriophage λ-encoded Kil peptide, resulting in defective cell division and a filamentous phenotype, making FtsZ an attractive target for antimicrobials. In this study, we have used an in vitro meningitis model system for studying the effect of bacteriophages on FtsZ using fluorescent E. coli EV36/FtsZ-mCherry and K12/FtsZ-mNeon strains. We show localisation of FtsZ to the bacterial cell midbody as a single ring during normal growth conditions, and mislocalisation of FtsZ producing filamentous multi-ringed bacterial cells upon addition of the known inhibitor Kil peptide. We also show that when bacteriophages K1F-GFP and T7-mCherry were applied to their respective host strains, these phages can inhibit FtsZ and block bacterial cell division leading to a filamentous multi-ringed phenotype, potentially delaying lysis and increasing progeny number. This occurs in the exponential growth phase, as actively dividing hosts are needed. We present that ZapA protein is needed for phage inhibition by showing a phenotype recovery with a ZapA mutant strain, and we show that FtsI protein is also mislocalised upon phage infection. Finally, we show that the T7 peptide gp0.4 is responsible for the inhibition of FtsZ in K12 strains by observing a phenotype recovery with a T7Δ0.4 mutant.
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Affiliation(s)
- Gurneet K. Dhanoa
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Inbar Kushnir
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Antonia P. Sagona
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Antonia P. Sagona,
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29
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Phascinating Phages. Microorganisms 2022; 10:microorganisms10071365. [PMID: 35889083 PMCID: PMC9320029 DOI: 10.3390/microorganisms10071365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 02/01/2023] Open
Abstract
Treatment of infections caused by bacteria has become more complex due to the increasing number of bacterial strains that are resistant to conventional antimicrobial therapy. A highly promising alternative appears to be bacteriophage (phage) therapy, in which natural predators of bacteria, bacteriophages, play a role. Although these viruses were first discovered in 1917, the development of phage therapy was impacted by the discovery of antibiotics, which spread more quickly and effectively in medical practice. Despite this, phage therapy has a long history in Eastern Europe; however, Western countries are currently striving to reintroduce phage therapy as a tool in the fight against diseases caused by drug-resistant bacteria. This review describes phage biology, bacterial and phage competition mechanisms, and the benefits and drawbacks of phage therapy. The results of various laboratory experiments, and clinical cases where phage therapy was administered, are described.
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30
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Ongenae V, Mabrouk AS, Crooijmans M, Rozen D, Briegel A, Claessen D. Reversible bacteriophage resistance by shedding the bacterial cell wall. Open Biol 2022; 12:210379. [PMID: 35673854 PMCID: PMC9174709 DOI: 10.1098/rsob.210379] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/26/2022] [Indexed: 01/04/2023] Open
Abstract
Phages are highly abundant in the environment and pose a major threat for bacteria. Therefore, bacteria have evolved sophisticated defence systems to withstand phage attacks. Here, we describe a previously unknown mechanism by which mono- and diderm bacteria survive infection with diverse lytic phages. Phage exposure leads to a rapid and near-complete conversion of walled cells to a cell-wall-deficient state, which remains viable in osmoprotective conditions and can revert to the walled state. While shedding the cell wall dramatically reduces the number of progeny phages produced by the host, it does not always preclude phage infection. Altogether, these results show that the formation of cell-wall-deficient cells prevents complete eradication of the bacterial population and suggest that cell wall deficiency may potentially limit the efficacy of phage therapy, especially in highly osmotic environments or when used together with antibiotics that target the cell wall.
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Affiliation(s)
- Véronique Ongenae
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Adam Sidi Mabrouk
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Marjolein Crooijmans
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Daniel Rozen
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Ariane Briegel
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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A Putative Lipoprotein Mediates Cell-Cell Contact for Type VI Secretion System-Dependent Killing of Specific Competitors. mBio 2022; 13:e0308521. [PMID: 35404117 PMCID: PMC9040878 DOI: 10.1128/mbio.03085-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Interbacterial competition is prevalent in host-associated microbiota, where it can shape community structure and function, impacting host health in both positive and negative ways. However, the factors that permit bacteria to discriminate among their various neighbors for targeted elimination of competitors remain elusive. We identified a putative lipoprotein (TasL) in Vibrio species that mediates cell-cell attachment with a subset of target strains, allowing inhibitors to target specific competitors for elimination. Here, we describe this putative lipoprotein, which is associated with the broadly distributed type VI secretion system (T6SS), by studying symbiotic Vibrio fischeri, which uses the T6SS to compete for colonization sites in their squid host. We demonstrate that TasL allows V. fischeri cells to restrict T6SS-dependent killing to certain genotypes by selectively integrating competitor cells into aggregates while excluding other cell types. TasL is also required for T6SS-dependent competition within juvenile squid, indicating that the adhesion factor is active in the host. Because TasL homologs are found in other host-associated bacterial species, this newly described cell-cell attachment mechanism has the potential to impact microbiome structure within diverse hosts. IMPORTANCE T6SSs are broadly distributed interbacterial weapons that share an evolutionary history with bacteriophage. Because the T6SS can be used to kill neighboring cells, it can impact the spatial distribution and biological function of both free-living and host-associated microbial communities. Like their phage relatives, T6SS+ cells must sufficiently bind competitor cells to deliver their toxic effector proteins through the syringe-like apparatus. Although phage use receptor-binding proteins (RBPs) and tail fibers to selectively bind prey cells, the biophysical properties that mediate this cell-cell contact for T6SS-mediated killing remain unknown. Here, we identified a large, predicted lipoprotein that is coordinately expressed with T6SS proteins and facilitates the contact that is necessary for the T6SS-dependent elimination of competitors in a natural host. Similar to phage RBPs and tail fibers, this lipoprotein is required for T6SS+ cells to discriminate between prey and nonprey cell types, revealing new insight into prey selection during T6SS-mediated competition.
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Transposable Element Insertions into the Escherichia coli Polysialic Acid Gene Cluster Result in Resistance to the K1F Bacteriophage. Microbiol Spectr 2022; 10:e0211221. [PMID: 35467398 PMCID: PMC9241782 DOI: 10.1128/spectrum.02112-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Reviewing the genetics underlying the arms race between bacteria and bacteriophages can offer an interesting insight into the development of bacterial resistance and phage co-evolution. This study shows how the natural development of resistances to the K1F bacteriophage, a phage which targets the K1 capsule of pathogenic Escherichia coli, can come about through insertion sequences (IS). Of the K1F resistant mutants isolated, two were of particular interest. The first of these showed full resistance to K1F and was found to have disruptions to kpsE, the product of which is involved in polysialic acid translocation. The second, after showing an initial susceptibility to K1F which then developed to full resistance, had disruptions to neuC, a gene involved in one of the early steps of polysialic acid biosynthesis. Both of these mutations came with a fitness cost and produced considerable phenotypic differences in the completeness and location of the K1 capsule when compared with the wild type. Sequential treatment of these two K1F resistant mutants with T7 resulted in the production of a variety of isolates, many of which showed a renewed susceptibility to K1F, indicating that these insertion sequence mutations are reversible, as well as one isolate that developed resistance to both phages. IMPORTANCE Bacteriophages have many potential uses in industry and the clinical environment as an antibacterial control measure. One of their uses, phage therapy, is an appealing alternative to antibiotics due to their high specificity. However, as with the rise in antimicrobial resistance (AMR), it is critical to improve our understanding of how resistance develops against these viral agents. In the same way as bacteria will evolve and mutate antibiotic receptors so they can no longer be recognized, resistance to bacteriophages can come about via mutations to phage receptors, preventing phage binding and infection. We have shown that Escherichia coli will become resistant to the K1F bacteriophage via insertion element reshufflings causing null mutations to elements of the polysialic acid biosynthetic cluster. Exposure to the T7 bacteriophage then resulted in further changes in the position of these IS elements, further altering their resistance and sensitivity profiles.
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Acker M, Hogle SL, Berube PM, Hackl T, Coe A, Stepanauskas R, Chisholm SW, Repeta DJ. Phosphonate production by marine microbes: Exploring new sources and potential function. Proc Natl Acad Sci U S A 2022; 119:e2113386119. [PMID: 35254902 PMCID: PMC8931226 DOI: 10.1073/pnas.2113386119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/20/2022] [Indexed: 12/12/2022] Open
Abstract
SignificancePhosphonates are a class of phosphorus metabolites characterized by a highly stable C-P bond. Phosphonates accumulate to high concentrations in seawater, fuel a large fraction of marine methane production, and serve as a source of phosphorus to microbes inhabiting nutrient-limited regions of the oligotrophic ocean. Here, we show that 15% of all bacterioplankton in the surface ocean have genes phosphonate synthesis and that most belong to the abundant groups Prochlorococcus and SAR11. Genomic and chemical evidence suggests that phosphonates are incorporated into cell-surface phosphonoglycoproteins that may act to mitigate cell mortality by grazing and viral lysis. These results underscore the large global biogeochemical impact of relatively rare but highly expressed traits in numerically abundant groups of marine bacteria.
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Affiliation(s)
- Marianne Acker
- Massachusetts Institute of Technology-Woods Hole Oceanographic Institution Joint Program in Oceanography/Applied Ocean Science and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
- Department of Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Shane L. Hogle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, University of Turku, Turku 20500, Finland
| | - Paul M. Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Allison Coe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ramunas Stepanauskas
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Daniel J. Repeta
- Department of Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
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Mobile CRISPR-Cas9 based anti-phage system in E. coli. Front Chem Sci Eng 2022; 16:1281-1289. [PMID: 35251747 PMCID: PMC8882345 DOI: 10.1007/s11705-022-2141-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/03/2021] [Indexed: 10/26/2022]
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Marton HL, Styles KM, Kilbride P, Sagona AP, Gibson MI. Polymer-Mediated Cryopreservation of Bacteriophages. Biomacromolecules 2021; 22:5281-5289. [PMID: 34846863 PMCID: PMC8672357 DOI: 10.1021/acs.biomac.1c01187] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/06/2021] [Indexed: 12/11/2022]
Abstract
Bacteriophages (phages, bacteria-specific viruses) have biotechnological and therapeutic potential. To apply phages as pure or heterogeneous mixtures, it is essential to have a robust mechanism for transport and storage, with different phages having very different stability profiles across storage conditions. For many biologics, cryopreservation is employed for long-term storage and cryoprotectants are essential to mitigate cold-induced damage. Here, we report that poly(ethylene glycol) can be used to protect phages from cold damage, functioning at just 10 mg·mL-1 (∼1 wt %) and outperforms glycerol in many cases, which is a currently used cryoprotectant. Protection is afforded at both -20 and -80 °C, the two most common temperatures for frozen storage in laboratory settings. Crucially, the concentration of the polymer required leads to frozen solutions at -20 °C, unlike 50% glycerol (which results in liquid solutions). Post-thaw recoveries close to 100% plaque-forming units were achieved even after 2 weeks of storage with this method and kill assays against their bacterial host confirmed the lytic function of the phages. Initial experiments with other hydrophilic polymers also showed cryoprotection, but at this stage, the exact mechanism of this protection cannot be concluded but does show that water-soluble polymers offer an alternative tool for phage storage. Ice recrystallization inhibiting polymers (poly(vinyl alcohol)) were found to provide no additional protection, in contrast to their ability to protect proteins and microorganisms which are damaged by recrystallization. PEG's low cost, solubility, well-established low toxicity/immunogenicity, and that it is fit for human consumption at the concentrations used make it ideal to help translate new approaches for phage therapy.
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Affiliation(s)
- Huba L. Marton
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Kathryn M. Styles
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
| | - Peter Kilbride
- Asymptote,
Cytiva, Chivers Way, Cambridge CB24 9BZ, U.K.
| | - Antonia P. Sagona
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
| | - Matthew I. Gibson
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Medical School, University of Warwick, Coventry CV4 7AL, U.K.
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Sørensen PE, Baig S, Stegger M, Ingmer H, Garmyn A, Butaye P. Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli. Front Microbiol 2021; 12:782757. [PMID: 34966369 PMCID: PMC8711792 DOI: 10.3389/fmicb.2021.782757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/23/2021] [Indexed: 01/19/2023] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is one of the most important bacterial pathogens affecting poultry worldwide. The emergence of multidrug-resistant pathogens has renewed the interest in the therapeutic use of bacteriophages (phages). However, a major concern for the successful implementation of phage therapy is the emergence of phage-resistant mutants. The understanding of the phage-host interactions, as well as underlying mechanisms of resistance, have shown to be essential for the development of a successful phage therapy. Here, we demonstrate that the strictly lytic Escherichia phage vB_EcoM-P10 rapidly selected for resistance in the APEC ST95 O1 strain AM621. Whole-genome sequence analysis of 109 spontaneous phage-resistant mutant strains revealed 41 mutants with single-nucleotide polymorphisms (SNPs) in their core genome. In 32 of these, a single SNP was detected while two SNPs were identified in a total of nine strains. In total, 34 unique SNPs were detected. In 42 strains, including 18 strains with SNP(s), gene losses spanning 17 different genes were detected. Affected by genetic changes were genes known to be involved in phage resistance (outer membrane protein A, lipopolysaccharide-, O- antigen-, or cell wall-related genes) as well as genes not previously linked to phage resistance, including two hypothetical genes. In several strains, we did not detect any genetic changes. Infecting phages were not able to overcome the phage resistance in host strains. However, interestingly the initial infection was shown to have a great fitness cost for several mutant strains, with up to ∼65% decrease in overall growth. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in APEC. Although acquired resistance to phages is frequently observed in pathogenic E. coli, it may be associated with loss of fitness, which could be exploited in phage therapy.
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Affiliation(s)
- Patricia E. Sørensen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Sharmin Baig
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - An Garmyn
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
| | - Patrick Butaye
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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Antoine C, Laforêt F, Blasdel B, Fall A, Duprez JN, Mainil J, Delcenserie V, Thiry D. In Vitro Characterization and In Vivo Efficacy Assessment in Galleria mellonella Larvae of Newly Isolated Bacteriophages against Escherichia coli K1. Viruses 2021; 13:2005. [PMID: 34696434 PMCID: PMC8541614 DOI: 10.3390/v13102005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 01/04/2023] Open
Abstract
Extra-intestinal Escherichia coli express several virulence factors that increase their ability to colonize and survive in different localizations. The K1 capsular type is involved in several infections, including meningitis, urinary tract, and bloodstream infections. The aims of this work were to isolate, characterize, and assess the in vivo efficacy of phages targeting avian pathogenic E. coli (APEC) O18:K1, which shares many similarities with the human strains responsible for neonatal meningitis. Eleven phages were isolated against APEC O18:K1, and four of them presenting a narrow spectrum targeting E. coli K1 strains were further studied. The newly isolated phages vB_EcoS_K1-ULINTec2 were similar to the Siphoviridae family, and vB_EcoP_K1-ULINTec4, vB_EcoP_K1-ULINTec6, and vB_EcoP_K1-ULINTec7 to the Autographiviridae family. They are capsular type (K1) dependent and present several advantages characteristic of lytic phages, such as a short adsorption time and latent period. vB_EcoP_K1-ULINTec7 is able to target both K1 and K5 strains. This study shows that these phages replicate efficiently, both in vitro and in vivo in the Galleria mellonella model. Phage treatment increases the larvae survival rates, even though none of the phages were able to eliminate the bacterial load.
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Affiliation(s)
- Céline Antoine
- Bacteriology Laboratory, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; (C.A.); (F.L.); (J.-N.D.); (J.M.)
- Food Science Department, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium;
| | - Fanny Laforêt
- Bacteriology Laboratory, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; (C.A.); (F.L.); (J.-N.D.); (J.M.)
- Food Science Department, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium;
| | - Bob Blasdel
- Vésale Bioscience, Vésale Pharmaceutica, 5310 Noville-sur-Mehaigne, Belgium;
| | - Abdoulaye Fall
- Genalyse Partner SA, En Hayeneux 62, 4040 Herstal, Belgium;
| | - Jean-Noël Duprez
- Bacteriology Laboratory, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; (C.A.); (F.L.); (J.-N.D.); (J.M.)
| | - Jacques Mainil
- Bacteriology Laboratory, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; (C.A.); (F.L.); (J.-N.D.); (J.M.)
| | - Véronique Delcenserie
- Food Science Department, FARAH and Faculty of Veterinary Medicine, ULiège, 4000 Liège, Belgium;
| | - Damien Thiry
- Bacteriology Laboratory, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium; (C.A.); (F.L.); (J.-N.D.); (J.M.)
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Ongenae V, Briegel A, Claessen D. Cell wall deficiency as an escape mechanism from phage infection. Open Biol 2021; 11:210199. [PMID: 34465216 PMCID: PMC8437236 DOI: 10.1098/rsob.210199] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/09/2021] [Indexed: 01/04/2023] Open
Abstract
The cell wall plays a central role in protecting bacteria from some environmental stresses, but not against all. In fact, in some cases, an elaborate cell envelope may even render the cell more vulnerable. For example, it contains molecules or complexes that bacteriophages recognize as the first step of host invasion, such as proteins and sugars, or cell appendages such as pili or flagella. In order to counteract phages, bacteria have evolved multiple escape mechanisms, such as restriction-modification, abortive infection, CRISPR/Cas systems or phage inhibitors. In this perspective review, we present the hypothesis that bacteria may have additional means to escape phage attack. Some bacteria are known to be able to shed their cell wall in response to environmental stresses, yielding cells that transiently lack a cell wall. In this wall-less state, the bacteria may be temporarily protected against phages, since they lack the essential entities that are necessary for phage binding and infection. Given that cell wall deficiency can be triggered by clinically administered antibiotics, phage escape could be an unwanted consequence that limits the use of phage therapy for treating stubborn infections.
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Affiliation(s)
- Véronique Ongenae
- Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300 RA Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Ariane Briegel
- Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300 RA Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300 RA Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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Novel Host Recognition Mechanism of the K1 Capsule-Specific Phage of Escherichia coli: Capsular Polysaccharide as the First Receptor and Lipopolysaccharide as the Secondary Receptor. J Virol 2021; 95:e0092021. [PMID: 34191582 DOI: 10.1128/jvi.00920-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
K1 capsule-specific phages of Escherichia coli have been reported in recent years, but the molecular mechanism involved in host recognition of these phages remains unknown. In this study, the interactions between PNJ1809-36, a new K1-specific phage, and its host bacterium, E. coli DE058, were investigated. A transposon mutation library was used to screen for receptor-related genes. Gene deletion, lysis curve determination, plaque formation test, adsorption assay, and inhibition assay of phage by lipopolysaccharide (LPS) showed that capsular polysaccharide (CPS) was the first receptor for the initial adsorption of PNJ1809-36 to E. coli DE058 and that LPS was a secondary receptor for the irreversible binding of the phage. The penultimate galactose in the outer core was identified as the specific binding region on LPS. Through antibody blocking assay, fluorescence labeling and high-performance gel permeation chromatography, the tail protein ORF261 of phage PNJ1809-36 was identified as the receptor-binding protein on CPS. Given these findings, we propose a model for the recognition process of phage PNJ1809-36 on E. coli DE058: the phage PNJ1809-36 tail protein ORF261 recognizes and adsorbs to the K1 capsule, and then the K1 capsule is partially degraded, exposing the active site of LPS which is recognized by phage PNJ1809-36. This model provides insight into the molecular mechanisms between K1-specific phages and their host bacteria. IMPORTANCE It has been speculated that CPS is the main receptor of K1-specific phages belonging to Siphoviridae. In recent years, a new type of K1-specific phage belonging to Myoviridae has been reported, but its host recognition mechanisms remain unknown. Here, we studied the interactions between PNJ1809-36, a new type of K1 phage, and its host bacterium, E. coli DE058. Our research showed that the phage initially adsorbed to the K1 capsule mediated by ORF261 and then bound to the penultimate galactose of LPS to begin the infection process.
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Ngiam L, Schembri MA, Weynberg K, Guo J. Bacteriophage isolated from non-target bacteria demonstrates broad host range infectivity against multidrug-resistant bacteria. Environ Microbiol 2021; 23:5569-5586. [PMID: 34390602 DOI: 10.1111/1462-2920.15714] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/28/2021] [Accepted: 08/10/2021] [Indexed: 12/22/2022]
Abstract
Antibiotic resistance represents a global health challenge. The emergence of multidrug-resistant (MDR) bacteria such as uropathogenic Escherichia coli (UPEC) has attracted significant attention due to increased MDR properties, even against the last line of antibiotics. Bacteriophage, or simply phage, represents an alternative treatment to antibiotics. However, phage applications still face some challenges, such as host range specificity and development of phage resistant mutants. In this study, using both UPEC and non-UPEC hosts, five different phages were isolated from wastewater. We found that the inclusion of commensal Escherichia coli as target hosts during screening improved the capacity to select phage with desirable characteristics for phage therapy. Whole-genome sequencing revealed that four out of five phages adopt strictly lytic lifestyles and are taxonomically related to different phage families belonging to the Myoviridae and Podoviridae. In comparison to single phage treatment, the application of phage cocktails targeting different cell surface receptors significantly enhanced the suppression of UPEC hosts. The emergence of phage-resistant mutants after single phage treatment was attributed to mutational changes in outer membrane protein components, suggesting the potential receptors recognized by these phages. The findings highlight the use of commensal E. coli as target hosts to isolate broad host range phage with infectivity against MDR bacteria.
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Affiliation(s)
- Lyman Ngiam
- Advanced Water Management Centre, University of Queensland, Brisbane, Qld, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Qld, Australia
| | - Karen Weynberg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, University of Queensland, Brisbane, Qld, Australia
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Abstract
The horizontal transfer of mobile DNA is one of the signature moves of bacterial evolution, but the specific rules that govern this transfer remain elusive. In this PLOS Biology issue, Haudiquet and colleagues revealed that the interactions between mobile genetic elements and the bacterial capsule shape the horizontal flow of DNA in an important bacterial pathogen.
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Affiliation(s)
- Alfonso Santos-López
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
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Serwer P, Wright ET, De La Chapa J, Gonzales CB. Basics for Improved Use of Phages for Therapy. Antibiotics (Basel) 2021; 10:antibiotics10060723. [PMID: 34208477 PMCID: PMC8234457 DOI: 10.3390/antibiotics10060723] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/17/2022] Open
Abstract
Blood-borne therapeutic phages and phage capsids increasingly reach therapeutic targets as they acquire more persistence, i.e., become more resistant to non-targeted removal from blood. Pathogenic bacteria are targets during classical phage therapy. Metastatic tumors are potential future targets, during use of drug delivery vehicles (DDVs) that are phage derived. Phage therapy has, to date, only sometimes been successful. One cause of failure is low phage persistence. A three-step strategy for increasing persistence is to increase (1) the speed of lytic phage isolation, (2) the diversity of phages isolated, and (3) the effectiveness and speed of screening phages for high persistence. The importance of high persistence-screening is illustrated by our finding here of persistence dramatically higher for coliphage T3 than for its relative, coliphage T7, in murine blood. Coliphage T4 is more persistent, long-term than T3. Pseudomonas chlororaphis phage 201phi2-1 has relatively low persistence. These data are obtained with phages co-inoculated and separately assayed. In addition, highly persistent phage T3 undergoes dispersal to several murine organs and displays tumor tropism in epithelial tissue (xenografted human oral squamous cell carcinoma). Dispersal is an asset for phage therapy, but a liability for phage-based DDVs. We propose increased focus on phage persistence—and dispersal—screening.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Center, San Antonio, TX 78229-3900, USA;
- Correspondence: ; Tel.: +1-210-567-3765
| | - Elena T. Wright
- Department of Biochemistry and Structural Biology, The University of Texas Health Center, San Antonio, TX 78229-3900, USA;
| | - Jorge De La Chapa
- Department of Comprehensive Dentistry, The University of Texas Health Center, San Antonio, TX 78229-3900, USA; (J.D.L.C.); (C.B.G.)
| | - Cara B. Gonzales
- Department of Comprehensive Dentistry, The University of Texas Health Center, San Antonio, TX 78229-3900, USA; (J.D.L.C.); (C.B.G.)
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43
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Abd-Allah IM, El-Housseiny GS, Yahia IS, Aboshanab KM, Hassouna NA. Rekindling of a Masterful Precedent; Bacteriophage: Reappraisal and Future Pursuits. Front Cell Infect Microbiol 2021; 11:635597. [PMID: 34136415 PMCID: PMC8201069 DOI: 10.3389/fcimb.2021.635597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/13/2021] [Indexed: 12/30/2022] Open
Abstract
Antibiotic resistance is exuberantly becoming a deleterious health problem world-wide. Seeking innovative approaches is necessary in order to circumvent such a hazard. An unconventional fill-in to antibiotics is bacteriophage. Bacteriophages are viruses capable of pervading bacterial cells and disrupting their natural activity, ultimately resulting in their defeat. In this article, we will run-through the historical record of bacteriophage and its correlation with bacteria. We will also delineate the potential of bacteriophage as a therapeutic antibacterial agent, its supremacy over antibiotics in multiple aspects and the challenges that could arise on the way to its utilization in reality. Pharmacodynamics, pharmacokinetics and genetic engineering of bacteriophages and its proteins will be briefly discussed as well. In addition, we will highlight some of the in-use applications of bacteriophages, and set an outlook for their future ones. We will also overview some of the miscellaneous abilities of these tiny viruses in several fields other than the clinical one. This is an attempt to encourage tackling a long-forgotten hive. Perhaps, one day, the smallest of the creatures would be of the greatest help.
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Affiliation(s)
- Israa M. Abd-Allah
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Ghadir S. El-Housseiny
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Ibrahim S. Yahia
- Research Center for Advanced Materials Science (RCAMS), Advanced Functional Materials & Optoelectronic Laboratory (AFMOL), Department of Physics, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Nanoscience Laboratory for Environmental and Bio-Medical Applications (NLEBA), Semiconductor Lab., Metallurgical Lab, Physics Department, Faculty of Education, Ain Shams University, Cairo, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Nadia A. Hassouna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
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Chaudhry W, Lee E, Worthy A, Weiss Z, Grabowicz M, Vega N, Levin B. Mucoidy, a general mechanism for maintaining lytic phage in populations of bacteria. FEMS Microbiol Ecol 2021; 96:5897354. [PMID: 32845324 PMCID: PMC7532286 DOI: 10.1093/femsec/fiaa162] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022] Open
Abstract
We present evidence that phage resistance resulting from overproduction of exopolysaccharides, mucoidy, provides a general answer to the longstanding question of how lytic viruses are maintained in populations dominated by bacteria upon which they cannot replicate. In serial transfer culture, populations of mucoid Escherichia coli MG1655 that are resistant to lytic phages with different receptors, and thereby requiring independent mutations for surface resistance, are capable of maintaining these phages with little effect on their total density. Based on the results of our analysis of a mathematical model, we postulate that the maintenance of phage in populations dominated by mucoid cells can be attributed primarily to high rates of transition from the resistant mucoid states to susceptible non-mucoid states. Our tests with both population dynamic and single cell experiments as well as genomic analysis are consistent with this hypothesis. We discuss reasons for the generalized resistance of these mucoid E. coli, and the genetic and molecular mechanisms responsible for the high rate of transition from mucoid to sensitive states responsible for the maintenance of lytic phage in mucoid populations of E. coli.
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Affiliation(s)
- Waqas Chaudhry
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Esther Lee
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Andrew Worthy
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Zoe Weiss
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Marcin Grabowicz
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicole Vega
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Bruce Levin
- Department of Biology, Emory University, Atlanta, GA 30322, USA.,Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA
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45
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Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation. ISME JOURNAL 2020; 14:2980-2996. [PMID: 32732904 PMCID: PMC7784688 DOI: 10.1038/s41396-020-0726-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 01/21/2023]
Abstract
Klebsiella species are able to colonize a wide range of environments and include worrisome nosocomial pathogens. Here, we sought to determine the abundance and infectivity of prophages of Klebsiella to understand how the interactions between induced prophages and bacteria affect population dynamics and evolution. We identified many prophages in the species, placing these taxa among the top 5% of the most polylysogenic bacteria. We selected 35 representative strains of the Klebsiella pneumoniae species complex to establish a network of induced phage-bacteria interactions. This revealed that many prophages are able to enter the lytic cycle, and subsequently kill or lysogenize closely related Klebsiella strains. Although 60% of the tested strains could produce phages that infect at least one other strain, the interaction network of all pairwise cross-infections is very sparse and mostly organized in modules corresponding to the strains' capsule serotypes. Accordingly, capsule mutants remain uninfected showing that the capsule is a key factor for successful infections. Surprisingly, experiments in which bacteria are predated by their own prophages result in accelerated loss of the capsule. Our results show that phage infectiousness defines interaction modules between small subsets of phages and bacteria in function of capsule serotype. This limits the role of prophages as competitive weapons because they can infect very few strains of the species complex. This should also restrict phage-driven gene flow across the species. Finally, the accelerated loss of the capsule in bacteria being predated by their own phages, suggests that phages drive serotype switch in nature.
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46
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Møller-Olsen C, Ross T, Leppard KN, Foisor V, Smith C, Grammatopoulos DK, Sagona AP. Bacteriophage K1F targets Escherichia coli K1 in cerebral endothelial cells and influences the barrier function. Sci Rep 2020; 10:8903. [PMID: 32483257 PMCID: PMC7264188 DOI: 10.1038/s41598-020-65867-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
Bacterial neonatal meningitis results in high mortality and morbidity rates for those affected. Although improvements in diagnosis and treatment have led to a decline in mortality rates, morbidity rates have remained relatively unchanged. Bacterial resistance to antibiotics in this clinical setting further underlines the need for developing other technologies, such as phage therapy. We exploited an in vitro phage therapy model for studying bacterial neonatal meningitis based on Escherichia coli (E. coli) EV36, bacteriophage (phage) K1F and human cerebral microvascular endothelial cells (hCMECs). We show that phage K1F is phagocytosed and degraded by constitutive- and PAMP-dependent LC3-assisted phagocytosis and does not induce expression of inflammatory cytokines TNFα, IL-6, IL-8 or IFNβ. Additionally, we observed that phage K1F temporarily decreases the barrier resistance of hCMEC cultures, a property that influences the barrier permeability, which could facilitate the transition of immune cells across the endothelial vessel in vivo. Collectively, we demonstrate that phage K1F can infect intracellular E. coli EV36 within hCMECs without themselves eliciting an inflammatory or defensive response. This study illustrates the potential of phage therapy targeting infections such as bacterial neonatal meningitis and is an important step for the continued development of phage therapy targeting antibiotic-resistant bacterial infections generally.
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Affiliation(s)
| | - Toby Ross
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
| | - Keith N Leppard
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
| | - Veronica Foisor
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
| | - Corinne Smith
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
| | - Dimitris K Grammatopoulos
- Warwick Medical School, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
- Institute of Precision Diagnostics and Translational Medicine, Dept of Pathology, UHCW NHS Trust, Clifford Bridge Road, CV2 2DX, Coventry, UK
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK.
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV47AL, UK.
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Lelchat F, Mocaer PY, Ojima T, Michel G, Sarthou G, Bucciarelli E, Cérantola S, Colliec-Jouault S, Boisset C, Baudoux AC. Viral degradation of marine bacterial exopolysaccharides. FEMS Microbiol Ecol 2020; 95:5498295. [PMID: 31125051 DOI: 10.1093/femsec/fiz079] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/23/2019] [Indexed: 11/14/2022] Open
Abstract
The identification of the mechanisms by which marine dissolved organic matter (DOM) is produced and regenerated is critical to develop robust prediction of ocean carbon cycling. Polysaccharides represent one of the main constituents of marine DOM and their degradation is mainly attributed to polysaccharidases derived from bacteria. Here, we report that marine viruses can depolymerize the exopolysaccharides (EPS) excreted by their hosts using five bacteriophages that infect the notable EPS producer, Cobetia marina DSMZ 4741. Degradation monitorings as assessed by gel electrophoresis and size exclusion chromatography showed that four out of five phages carry structural enzymes that depolymerize purified solution of Cobetia marina EPS. The depolymerization patterns suggest that these putative polysaccharidases are constitutive, endo-acting and functionally diverse. Viral adsorption kinetics indicate that the presence of these enzymes provides a significant advantage for phages to adsorb onto their hosts upon intense EPS production conditions. The experimental demonstration that marine phages can display polysaccharidases active on bacterial EPS lead us to question whether viruses could also contribute to the degradation of marine DOM and modify its bioavailability. Considering the prominence of phages in the ocean, such studies may unveil an important microbial process that affects the marine carbon cycle.
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Affiliation(s)
- F Lelchat
- Laboratoire BMM, centre Ifremer de Brest, ZI pointe du diable, 29280 Plouzané, France
| | - P Y Mocaer
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - T Ojima
- Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, Minato-cho 3-1-1, Hakodate 041-8611, Japan
| | - G Michel
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Modèles Marins UMR 8227, Station Biologique de Roscoff, Roscoff, France
| | - G Sarthou
- CNRS, Université de Brest, IRD, Ifremer, UMR 6539/LEMAR/IUEM, Technopôle Brest Iroise, Place Nicolas Copernic, 29280 Plouzané, France
| | - E Bucciarelli
- CNRS, Université de Brest, IRD, Ifremer, UMR 6539/LEMAR/IUEM, Technopôle Brest Iroise, Place Nicolas Copernic, 29280 Plouzané, France
| | - S Cérantola
- Service commun de résonnance magnétique nucléaire, Faculté de science de Brest, Université de Bretagne Occidentale, 6 av. Victor Le Gorgeu, 29238 Brest Cedex 3, France
| | - S Colliec-Jouault
- Laboratoire EM3B, Centre Ifremer Atlantique - Rue de l'Ile d'Yeu - 44311 Nantes, France
| | - C Boisset
- Service commun de chromatographie, CERMAV-CNRS, 601 rue de la chimie, St Martin d'Hère, 38041 Grenoble, France
| | - A-C Baudoux
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
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Reuter M, Kruger DH. Approaches to optimize therapeutic bacteriophage and bacteriophage-derived products to combat bacterial infections. Virus Genes 2020; 56:136-149. [PMID: 32036540 PMCID: PMC7223754 DOI: 10.1007/s11262-020-01735-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/18/2020] [Indexed: 12/14/2022]
Abstract
The emerging occurrence of antibiotic-resistant bacterial pathogens leads to a recollection of bacteriophage as antimicrobial therapeutics. This article presents a short overview of the clinical phage application including their use in military medicine and discusses the genotypic and phenotypic properties of a potential "ideal" therapeutic phage. We describe current efforts to engineer phage for their improved usability in pathogen treatment. In addition, phage can be applied for pathogen detection, selective drug delivery, vaccine development, or food and surface decontamination. Instead of viable phage, (engineered) phage-derived enzymes, such as polysaccharide depolymerases or peptidoglycan-degrading enzymes, are considered as promising therapeutic candidates. Finally, we briefly summarize the use of phage for the detection and treatment of "Category A priority pathogens".
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Affiliation(s)
- Monika Reuter
- Institute of Virology, Helmut-Ruska-Haus, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Detlev H. Kruger
- Institute of Virology, Helmut-Ruska-Haus, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
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49
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Tan D, Zhang Y, Qin J, Le S, Gu J, Chen LK, Guo X, Zhu T. A Frameshift Mutation in wcaJ Associated with Phage Resistance in Klebsiella pneumoniae. Microorganisms 2020; 8:microorganisms8030378. [PMID: 32156053 PMCID: PMC7142929 DOI: 10.3390/microorganisms8030378] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/21/2023] Open
Abstract
Phage therapy is a potential and promising avenue for controlling the emergence and spread of multidrug-resistant (MDR) Klebsiella pneumoniae, however, the rapid development of anti-phage resistance has been identified as an obstacle to the development of phage therapy. Little is known about the mechanism employed by MDR K. pneumoniae strains and how they protect themselves from lytic phage predation in vitro and in vivo. In this study, comparative genomic analysis shows undecaprenyl-phosphate glucose-1-phosphate transferase (WcaJ), the initial enzyme catalyzing the biosynthesis of colanic acid, is necessary for the adsorption of phage 117 (Podoviridae) to the host strain Kp36 to complete its lytic life cycle. In-frame deletion of wcaJ alone was sufficient to provide phage 117 resistance in the Kp36 wild-type strain. Complementation assays demonstrated the susceptibility of phage 117, and the mucoid phenotype could be restored in the resistant strain Kp36-117R by expressing the wild-type version of wcaJ. Remarkably, we found that bacterial mobile genetic elements (insA and insB) block phage 117 infections by disrupting the coding region of wcaJ, thus preventing phage adsorption to its phage receptor. Further, we revealed that the wcaJ mutation likely occurred spontaneously rather than adapted by phage 117 predation under unfavorable environments. Taken together, our results address a crucial evolutionary question around the mechanisms of phage-host interactions, increasing our current understandings of anti-phage defense mechanisms in this important MDR pathogen.
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Affiliation(s)
- Demeng Tan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Correspondence: (D.T.); (T.Z.)
| | - Yiyuan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Jinhong Qin
- Institutes of Medical Sciences, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Shuai Le
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Jingmin Gu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Li-kuang Chen
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Xiaokui Guo
- Institutes of Medical Sciences, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Tongyu Zhu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Correspondence: (D.T.); (T.Z.)
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50
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Titze I, Lehnherr T, Lehnherr H, Krömker V. Efficacy of Bacteriophages Against Staphylococcus aureus Isolates from Bovine Mastitis. Pharmaceuticals (Basel) 2020; 13:ph13030035. [PMID: 32110980 PMCID: PMC7151712 DOI: 10.3390/ph13030035] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 02/05/2020] [Accepted: 02/24/2020] [Indexed: 01/16/2023] Open
Abstract
The lytic efficacy of bacteriophages against Staphylococcus aureus isolates from bovine milk was investigated in vitro, regarding possible applications in the therapy of udder inflammation caused by bacterial infections (mastitis). The host range of sequenced, lytic bacteriophages was determined against a collection of 92 Staphylococcus (S.) aureus isolates. The isolates originated from quarter foremilk samples of clinical and subclinical mastitis cases. A spot test and a subsequent plaque assay were used to determine the phage host range. According to their host range, propagation and storage properties, three phages, STA1.ST29, EB1.ST11, and EB1.ST27, were selected for preparing a bacteriophage mixture (1:1:1), which was examined for its lytic activity against S. aureus in pasteurized and raw milk. It was found that almost two thirds of the isolates could be lysed by at least one of the tested phages. The bacteriophage mixture was able to reduce the S. aureus germ density in pasteurized milk and its reduction ability was maintained in raw milk, with only a moderate decrease compared to the results in pasteurized milk. The significant reduction ability of the phage mixture in raw milk promotes further in vivo investigation.
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Affiliation(s)
- Isabel Titze
- Department of Bioprocess Engineering and Microbiology, University of Applied Sciences and Arts Hannover, D-30453 Hannover, Germany;
| | - Tatiana Lehnherr
- Phage Technology Center GmbH, D-59199 Bönen, Germany; (T.L.); (H.L.)
| | - Hansjörg Lehnherr
- Phage Technology Center GmbH, D-59199 Bönen, Germany; (T.L.); (H.L.)
| | - Volker Krömker
- Department of Bioprocess Engineering and Microbiology, University of Applied Sciences and Arts Hannover, D-30453 Hannover, Germany;
- Section for Production, Nutrition and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark
- Correspondence:
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