1
|
Ouyang R, Ongenae V, Muok A, Claessen D, Briegel A. Phage fibers and spikes: a nanoscale Swiss army knife for host infection. Curr Opin Microbiol 2024; 77:102429. [PMID: 38277900 DOI: 10.1016/j.mib.2024.102429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/19/2023] [Accepted: 01/08/2024] [Indexed: 01/28/2024]
Abstract
Bacteriophages are being rediscovered as potent agents for medical and industrial applications. However, finding a suitable phage relies on numerous factors, including host specificity, burst size, and infection cycle. The host range of a phage is, besides phage defense systems, initially determined by the recognition and attachment of receptor-binding proteins (RBPs) to the target receptors of susceptible bacteria. RBPs include tail (or occasionally head) fibers and tailspikes. Owing to the potential flexibility and heterogeneity of these structures, they are often overlooked during structural studies. Recent advances in cryo-electron microscopy studies and computational approaches have begun to unravel their structural and fundamental mechanisms during phage infection. In this review, we discuss the current state of research on different phage tail and head fibers, spike models, and molecular mechanisms. These details may facilitate the manipulation of phage-host specificity, which in turn will have important implications for science and society.
Collapse
Affiliation(s)
- Ruochen Ouyang
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xianning West Road 28, Xi'an 710049, China
| | - Véronique Ongenae
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Alise Muok
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Dennis Claessen
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Ariane Briegel
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands.
| |
Collapse
|
2
|
Rafiei S, Bouzari M. Genomic analysis of vB_PaS-HSN4 bacteriophage and its antibacterial activity (in vivo and in vitro) against Pseudomonas aeruginosa isolated from burn. Sci Rep 2024; 14:2007. [PMID: 38263187 PMCID: PMC10805781 DOI: 10.1038/s41598-023-50916-5] [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: 06/07/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024] Open
Abstract
The most frequent infections caused by Pseudomonas aeruginosa are local infections in soft tissues, including burns. Today, phage use is considered a suitable alternative to cure infections caused by multi-drug-resistant (MDR) and extensively drug-resistant (XDR) bacteria. We investigated the potential of a novel phage (vB_PaS-HSN4) belonging to Caudoviricetes class, against XDR and MDR P. aeruginosa strains in vivo and in vitro. Its biological and genetic characteristics were investigated. The phage burst size and latent were 119 and 20 min, respectively. It could tolerate a broad range of salt concentrations, pH values, and temperatures. The combination with ciprofloxacin significantly enhanced biofilm removal after 24 h. The genome was dsDNA with a size of 44,534 bp and encoded 61 ORFs with 3 tRNA and 5 promoters. No virulence factor was observed in the phage genome. In the in vivo infection model, treatment with vB_PaS-HSN4 increased Galleria mellonella larvae survival (80%, 66%, and 60%) (MOI 100) and (60%, 40%, and 26%) (MOI 1) in the pre-treatment, co-treatment, and post-treatment experiments, respectively. Based on these characteristics, it can be considered for the cure of infections of burns caused by P. aeruginosa.
Collapse
Affiliation(s)
- Solmaz Rafiei
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar-Jereeb Street, Isfahan, 81746-73441, Iran
| | - Majid Bouzari
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar-Jereeb Street, Isfahan, 81746-73441, Iran.
| |
Collapse
|
3
|
Lourenço M, Osbelt L, Passet V, Gravey F, Megrian D, Strowig T, Rodrigues C, Brisse S. Phages against Noncapsulated Klebsiella pneumoniae: Broader Host range, Slower Resistance. Microbiol Spectr 2023; 11:e0481222. [PMID: 37338376 PMCID: PMC10433977 DOI: 10.1128/spectrum.04812-22] [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: 11/22/2022] [Accepted: 05/23/2023] [Indexed: 06/21/2023] Open
Abstract
Klebsiella pneumoniae (Kp), a human gut colonizer and opportunistic pathogen, is a major contributor to the global burden of antimicrobial resistance. Virulent bacteriophages represent promising agents for decolonization and therapy. However, the majority of anti-Kp phages that have been isolated thus far are highly specific to unique capsular types (anti-K phages), which is a major limitation to phage therapy prospects due to the highly polymorphic capsule of Kp. Here, we report on an original anti-Kp phage isolation strategy, using capsule-deficient Kp mutants as hosts (anti-Kd phages). We show that anti-Kd phages have a broad host range, as the majority are able to infect noncapsulated mutants of multiple genetic sublineages and O-types. Additionally, anti-Kd phages induce a lower rate of resistance emergence in vitro and provide increased killing efficiency when in combination with anti-K phages. In vivo, anti-Kd phages are able to replicate in mouse guts colonized with a capsulated Kp strain, suggesting the presence of noncapsulated Kp subpopulations. The original strategy proposed here represents a promising avenue that circumvents the Kp capsule host restriction barrier, offering promise for therapeutic development. IMPORTANCE Klebsiella pneumoniae (Kp) is an ecologically generalist bacterium as well as an opportunistic pathogen that is responsible for hospital-acquired infections and a major contributor to the global burden of antimicrobial resistance. In the last decades, limited advances have been made in the use of virulent phages as alternatives or complements to antibiotics that are used to treat Kp infections. This work demonstrates the potential value of an anti-Klebsiella phage isolation strategy that addresses the issue of the narrow host range of anti-K phages. Anti-Kd phages may be active in infection sites in which capsule expression is intermittent or repressed or in combination with anti-K phages, which often induce the loss of capsule in escape mutants.
Collapse
Affiliation(s)
- Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Virginie Passet
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - François Gravey
- Dynamycure Inserm UM1311 Normandie Univ, UNICAEN, UNIROUEN, Caen, France
| | - Daniela Megrian
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Carla Rodrigues
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| |
Collapse
|
4
|
Tisalema-Guanopatín E, Cabezas-Mera F, Nolivos-Rodríguez K, Fierro I, Pazmiño L, Garzon-Chavez D, Debut A, Vizuete K, Reyes JA. New Bacteriophages Members of the Ackermannviridae Family Specific for Klebsiella pneumoniae ST258. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:99-107. [PMID: 37350993 PMCID: PMC10282792 DOI: 10.1089/phage.2022.0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
Background Carbapenem-resistant Klebsiella pneumoniae, particularly isolates classified as sequence-type 258 (ST258), are multidrug-resistant strains that are strongly associated with poor-prognosis nosocomial infections, as current therapeutic options are limited and ineffective. In recent years, phage therapy has emerged as a promising treatment option for these scenarios. Methodology and Results We report the isolation and characterization of three new phages against Klebsiella pneumoniae ST258 strains recovered from Machángara river wastewater. These new members of the Ackermannviridae family showed stability over a wide temperature and pH range and burst sizes ranging from 6 to 44 plaque-forming units per bacteria. Their genomes were about 157 kilobases, with an average guanine-cytosine content of 46.4% and showed presence of several transfer RNAs, which also allowed us to predict in silico a lytic replicative cycle due to the presence of endolysins and lysozymes. Conclusion Three lytic phages of Ackermannviridae family were recovered against Klebsiella pneumoniae ST258 strains from sewage; however, further characterization is needed for future consideration as therapeutic alternatives.
Collapse
Affiliation(s)
- Estefanía Tisalema-Guanopatín
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
- Faculty of Engineering and Applied Sciences, Universidad Internacional SEK, Quito, Ecuador
| | - Fausto Cabezas-Mera
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Diego de Robles y Vía Interoceánica, Quito, Ecuador
| | - Karla Nolivos-Rodríguez
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
| | - Isabel Fierro
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
| | - Lourdes Pazmiño
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
| | - Daniel Garzon-Chavez
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud (COCSA), Diego de Robles y Vía Interoceánica, Quito, Ecuador
| | - Alexis Debut
- Centro de Nanociencia y Nanotecnología (CENCINAT), Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Karla Vizuete
- Centro de Nanociencia y Nanotecnología (CENCINAT), Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Jorge Aníbal Reyes
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
- Departamento de Microbiología, Hospital del IESS Quito Sur, Avenida Moraspungo, Quito, Ecuador
| |
Collapse
|
5
|
Khambhati K, Bhattacharjee G, Gohil N, Dhanoa GK, Sagona AP, Mani I, Bui NL, Chu DT, Karapurkar JK, Jang SH, Chung HY, Maurya R, Alzahrani KJ, Ramakrishna S, Singh V. Phage engineering and phage-assisted CRISPR-Cas delivery to combat multidrug-resistant pathogens. Bioeng Transl Med 2023; 8:e10381. [PMID: 36925687 PMCID: PMC10013820 DOI: 10.1002/btm2.10381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/30/2022] [Accepted: 07/16/2022] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance ranks among the top threats to humanity. Due to the frequent use of antibiotics, society is facing a high prevalence of multidrug resistant pathogens, which have managed to evolve mechanisms that help them evade the last line of therapeutics. An alternative to antibiotics could involve the use of bacteriophages (phages), which are the natural predators of bacterial cells. In earlier times, phages were implemented as therapeutic agents for a century but were mainly replaced with antibiotics, and considering the menace of antimicrobial resistance, it might again become of interest due to the increasing threat of antibiotic resistance among pathogens. The current understanding of phage biology and clustered regularly interspaced short palindromic repeats (CRISPR) assisted phage genome engineering techniques have facilitated to generate phage variants with unique therapeutic values. In this review, we briefly explain strategies to engineer bacteriophages. Next, we highlight the literature supporting CRISPR-Cas9-assisted phage engineering for effective and more specific targeting of bacterial pathogens. Lastly, we discuss techniques that either help to increase the fitness, specificity, or lytic ability of bacteriophages to control an infection.
Collapse
Affiliation(s)
- Khushal Khambhati
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Gargi Bhattacharjee
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Nisarg Gohil
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Gurneet K Dhanoa
- School of Life Sciences University of Warwick, Gibbet Hill Campus Coventry United Kindgom
| | - Antonia P Sagona
- School of Life Sciences University of Warwick, Gibbet Hill Campus Coventry United Kindgom
| | - Indra Mani
- Department of Microbiology Gargi College, University of Delhi New Delhi India
| | - Nhat Le Bui
- Center for Biomedicine and Community Health International School, Vietnam National University Hanoi Vietnam
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health International School, Vietnam National University Hanoi Vietnam.,Faculty of Applied Sciences International School, Vietnam National University Hanoi Vietnam
| | | | - Su Hwa Jang
- Graduate School of Biomedical Science and Engineering Hanyang University Seoul South Korea.,Hanyang Biomedical Research Institute Hanyang University Seoul South Korea
| | - Hee Yong Chung
- Graduate School of Biomedical Science and Engineering Hanyang University Seoul South Korea.,Hanyang Biomedical Research Institute Hanyang University Seoul South Korea.,College of Medicine Hanyang University Seoul South Korea
| | - Rupesh Maurya
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences College of Applied Medical Sciences, Taif University Taif Saudi Arabia
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering Hanyang University Seoul South Korea.,College of Medicine Hanyang University Seoul South Korea
| | - Vijai Singh
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| |
Collapse
|
6
|
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: 11] [Impact Index Per Article: 11.0] [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.
Collapse
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.
| |
Collapse
|
7
|
Characteristics of Environmental Klebsiella pneumoniae and Klebsiella oxytoca Bacteriophages and Their Therapeutic Applications. Pharmaceutics 2023; 15:pharmaceutics15020434. [PMID: 36839755 PMCID: PMC9960720 DOI: 10.3390/pharmaceutics15020434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
In recent years, multidrug-resistant (MDR) strains of Klebsiella pneumoniae have spread globally, being responsible for the occurrence and severity of nosocomial infections. The NDM-1-kp, VIM-1 carbapenemase-producing isolates as well as extended-spectrum beta lactamase-producing (ESBL) isolates along with Klebsiella oxytoca strains have become emerging pathogens. Due to the growing problem of antibiotic resistance, bacteriophage therapy may be a potential alternative to combat such multidrug-resistant Klebsiella strains. Here, we present the results of a long-term study on the isolation and biology of bacteriophages active against K. pneumoniae, as well as K. oxytoca strains. We evaluated biological properties, morphology, host specificity, lytic spectrum and sensitivity of these phages to chemical agents along with their life cycle parameters such as adsorption, latent period, and burst size. Phages designated by us, vB_KpnM-52N (Kpn52N) and VB_KpnM-53N (Kpn53N), demonstrated relatively broad lytic spectra among tested Klebsiella strains, high burst size, adsorption rates and stability, which makes them promising candidates for therapeutic purposes. We also examined selected Klebsiella phages from our historical collection. Notably, one phage isolated nearly 60 years ago was successfully used in purulent cerebrospinal meningitis in a new-born and has maintained lytic activity to this day. Genomic sequences of selected phages were determined and analyzed. The phages of the sequenced genomes belong to the Slopekvirus and Jiaodavirus genus, a group of phages related to T4 at the family level. They share several features of T4 making them suitable for antibacterial therapies: the obligatorily lytic lifestyle, a lack of homologs of known virulence or antibiotic resistance genes, and a battery of enzymes degrading host DNA at infection.
Collapse
|
8
|
Bumunang EW, McAllister TA, Polo RO, Ateba CN, Stanford K, Schlechte J, Walker M, MacLean K, Niu YD. Genomic Profiling of Non-O157 Shiga Toxigenic Escherichia coli-Infecting Bacteriophages from South Africa. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:221-230. [PMID: 36793886 PMCID: PMC9917312 DOI: 10.1089/phage.2022.0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Background Non-O157 Shiga toxigenic Escherichia coli (STEC) are one of the most important food and waterborne pathogens worldwide. Although bacteriophages (phages) have been used for the biocontrol of these pathogens, a comprehensive understanding of the genetic characteristics and lifestyle of potentially effective candidate phages is lacking. Materials and Methods In this study, 10 non-O157-infecting phages previously isolated from feedlot cattle and dairy farms in the North-West province of South Africa were sequenced, and their genomes were analyzed. Results Comparative genomics and proteomics revealed that the phages were closely related to other E. coli-infecting Tunaviruses, Seuratviruses, Carltongylesviruses, Tequatroviruses, and Mosigviruses from the National Center for Biotechnology Information GenBank database. Phages lacked integrases associated with a lysogenic cycle and genes associated with antibiotic resistance and Shiga toxins. Conclusions Comparative genomic analysis identified a diversity of unique non-O157-infecting phages, which could be used to mitigate the abundance of various non-O157 STEC serogroups without safety concerns.
Collapse
Affiliation(s)
- Emmanuel W. Bumunang
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
| | - Rodrigo Ortega Polo
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
| | - Collins N. Ateba
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Kim Stanford
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Canada
| | - Jared Schlechte
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Matthew Walker
- Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada, Winnipeg, Canada
| | - Kellie MacLean
- Cumming School of Medicine, Faculty of Science, University of Calgary, Calgary, Canada
| | - Yan D. Niu
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| |
Collapse
|
9
|
Ouyang R, Costa AR, Cassidy CK, Otwinowska A, Williams VCJ, Latka A, Stansfeld PJ, Drulis-Kawa Z, Briers Y, Pelt DM, Brouns SJJ, Briegel A. High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers. Nat Commun 2022; 13:7241. [PMID: 36433970 PMCID: PMC9700779 DOI: 10.1038/s41467-022-34972-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, microbiological and machine learning approaches to explore the capsid, tail, and tail fibers of ϕKp24. We determine the structure of the capsid and tail at 4.1 Å and 3.0 Å resolution. We observe the tail fibers are branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide ϕKp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types of Klebsiella pneumoniae. Our study provides structural and functional insight into how ϕKp24 adapts to the variable surfaces of capsulated bacterial pathogens, which is useful for the development of phage therapy approaches against pan-drug resistant K. pneumoniae strains.
Collapse
Affiliation(s)
- Ruochen Ouyang
- grid.43169.390000 0001 0599 1243MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xianning West Road 28, Xi’an, 710049 China ,grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ana Rita Costa
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands ,grid.5292.c0000 0001 2097 4740Kavli Institute of Nanoscience, Delft, The Netherlands
| | - C. Keith Cassidy
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, UK
| | - Aleksandra Otwinowska
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland
| | - Vera C. J. Williams
- grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Agnieszka Latka
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland ,grid.5342.00000 0001 2069 7798Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Phill J. Stansfeld
- grid.7372.10000 0000 8809 1613School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
| | - Zuzanna Drulis-Kawa
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland
| | - Yves Briers
- grid.5342.00000 0001 2069 7798Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Daniël M. Pelt
- grid.5132.50000 0001 2312 1970Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333CA Leiden, The Netherlands
| | - Stan J. J. Brouns
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands ,grid.5292.c0000 0001 2097 4740Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Ariane Briegel
- grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| |
Collapse
|
10
|
Genomic Characterization of Twelve Lytic Bacteriophages Infecting Midgut Bacteria of Aedes aegypti. Curr Microbiol 2022; 79:385. [DOI: 10.1007/s00284-022-03092-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022]
|
11
|
Wójcicki M, Średnicka P, Błażejak S, Gientka I, Kowalczyk M, Emanowicz P, Świder O, Sokołowska B, Juszczuk-Kubiak E. Characterization and Genome Study of Novel Lytic Bacteriophages against Prevailing Saprophytic Bacterial Microflora of Minimally Processed Plant-Based Food Products. Int J Mol Sci 2021; 22:12460. [PMID: 34830335 PMCID: PMC8624825 DOI: 10.3390/ijms222212460] [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: 11/03/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
The food industry is still searching for novel solutions to effectively ensure the microbiological safety of food, especially fresh and minimally processed food products. Nowadays, the use of bacteriophages as potential biological control agents in microbiological food safety and preservation is a promising strategy. The aim of the study was the isolation and comprehensive characterization of novel bacteriophages with lytic activity against saprophytic bacterial microflora of minimally processed plant-based food products, such as mixed leaf salads. From 43 phages isolated from municipal sewage, four phages, namely Enterobacter phage KKP 3263, Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 have lytic activity against Enterobacter ludwigii KKP 3083, Citrobacter freundii KKP 3655, Enterobacter cloacae KKP 3082, and Serratia fonticola KKP 3084 bacterial strains, respectively. Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) identified Enterobacter phage KKP 3263 as an Autographiviridae, and Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 as members of the Myoviridae family. Genome sequencing revealed that these phages have linear double-stranded DNA (dsDNA) with sizes of 39,418 bp (KKP 3263), 61,608 bp (KKP 3664), 84,075 bp (KKP 3262), and 148,182 bp (KKP 3264). No antibiotic resistance genes, virulence factors, integrase, recombinase, or repressors, which are the main markers of lysogenic viruses, were annotated in phage genomes. Serratia phage KKP 3264 showed the greatest growth inhibition of Serratia fonticola KKP 3084 strain. The use of MOI 1.0 caused an almost 5-fold decrease in the value of the specific growth rate coefficient. The phages retained their lytic activity in a wide range of temperatures (from -20 °C to 50 °C) and active acidity values (pH from 4 to 11). All phages retained at least 70% of lytic activity at 60 °C. At 80 °C, no lytic activity against tested bacterial strains was observed. Serratia phage KKP 3264 was the most resistant to chemical factors, by maintaining high lytic activity across a broader range of pH from 3 to 11. The results indicated that these phages could be a potential biological control agent against saprophytic bacterial microflora of minimally processed plant-based food products.
Collapse
Affiliation(s)
- Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Paulina Średnicka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Stanisław Błażejak
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland; (S.B.); (I.G.)
| | - Iwona Gientka
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland; (S.B.); (I.G.)
| | - Monika Kowalczyk
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Paulina Emanowicz
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland;
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland;
| | - Edyta Juszczuk-Kubiak
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| |
Collapse
|
12
|
Liu S, Wang X, Ge J, Wu X, Zhao Q, Li YM, Wang R. Analysis of Carbapenemase-Resistant Genotypes of Highly Virulent Klebsiella pneumoniae and Clinical Infection Characteristics of Different MLST Types. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:3455121. [PMID: 34630606 PMCID: PMC8497112 DOI: 10.1155/2021/3455121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022]
Abstract
Carbapenemase-resistant Klebsiella pneumoniae (CR-KP) has become one of the nosocomial infections that seriously threaten the lives of patients, greatly increasing the burden on patients. In order to explore the resistance mechanism of clinically isolated CR-KP to carbapenems and perform multilocus sequence typing (MLST), to study the clinical characteristics of patients with different ST types of infection, we collected 74 CR-KP strains clinically isolated from the main 6 hospitals in Zhejiang province from January 2018 to July 2020. The sensitivity of the tested strains to 23 antibacterial drugs was determined by the microbroth dilution method, and PCR was applied. Gene amplification technology and DNA sequencing methods were used to detect the carbapenemase gene of the tested strains. Through the MLST of the tested strains, the clonal correlation and molecular epidemiological characteristics of the tested strains were explored, and the characteristics of CR-KP resistance, resistance mechanisms, and clinical characteristics of bacterial infections under different MLST types were analyzed at the same time. The results showed that 74 carbapenem-resistant Klebsiella pneumoniae strains showed high resistance to 21 commonly used antibacterial drugs, and all carbapenemase phenotypic screening tests were positive. MLST typing showed that 74 CR-KP strains had 17 ST typings, and ST11 was the dominant type (54.05%). The study also found that these ST11 strains are more likely to be resistant to carbapenem antibiotics. Most of them produce KPC carbapenemase, and a few are IMP, VIM, and NDM. Univariate analysis suggested that the proportion of patients in the ST11 group receiving treatment in ICU, the use rate of mechanical ventilation, and the proportion of drainage tube indwelling were higher than those in the non-ST11 group, and the survival rate of the ST11 group was lower than that of the non-ST11 group. Clinical data suggested that the same hospital was dominated by the same clonal epidemic in the same period. In view of the analysis of clinical data suggesting that patients who have received ICU treatment, mechanical ventilation, and drainage tube indwelling are prone to the risk of CR-KP strain (especially ST11) infection and low survival rate, such patients should arouse extensive clinical attention.
Collapse
Affiliation(s)
- Shuli Liu
- Department of Critical Care Medicine, Wenzhou Central Hospital, Wenzhou, Zhejiang 325099, China
| | - Xiaobo Wang
- Department of Critical Care Medicine, Wenzhou Central Hospital, Wenzhou, Zhejiang 325099, China
| | - Jingjing Ge
- Clinical Laboratory Center, Qingyuan Maternal and Child Health Hospital, Qingyuan, Guangdong 511500, China
| | - XiangBing Wu
- Department of Laboratory Medicine, Wenzhou Central Hospital, Wenzhou, Zhejiang 325100, China
| | - Qiu Zhao
- Department of Emergency, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325099, China
| | - Yue Man Li
- Department of Critical Care Medicine, Wenzhou Central Hospital, Wenzhou, Zhejiang 325099, China
| | - Renshu Wang
- Department of Critical Care Medicine, Wenzhou Central Hospital, Wenzhou, Zhejiang 325099, China
| |
Collapse
|