1
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Kunisch F, Campobasso C, Wagemans J, Yildirim S, Chan BK, Schaudinn C, Lavigne R, Turner PE, Raschke MJ, Trampuz A, Gonzalez Moreno M. Targeting Pseudomonas aeruginosa biofilm with an evolutionary trained bacteriophage cocktail exploiting phage resistance trade-offs. Nat Commun 2024; 15:8572. [PMID: 39362854 PMCID: PMC11450229 DOI: 10.1038/s41467-024-52595-w] [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: 05/29/2023] [Accepted: 09/12/2024] [Indexed: 10/05/2024] Open
Abstract
Spread of multidrug-resistant Pseudomonas aeruginosa strains threatens to render currently available antibiotics obsolete, with limited prospects for the development of new antibiotics. Lytic bacteriophages, the viruses of bacteria, represent a path to combat this threat. In vitro-directed evolution is traditionally applied to expand the bacteriophage host range or increase bacterial suppression in planktonic cultures. However, while up to 80% of human microbial infections are biofilm-associated, research towards targeted improvement of bacteriophages' ability to combat biofilms remains scarce. This study aims at an in vitro biofilm evolution assay to improve multiple bacteriophage parameters in parallel and the optimisation of bacteriophage cocktail design by exploiting a bacterial bacteriophage resistance trade-off. The evolved bacteriophages show an expanded host spectrum, improved antimicrobial efficacy and enhanced antibiofilm performance, as assessed by isothermal microcalorimetry and quantitative polymerase chain reaction, respectively. Our two-phage cocktail reveals further improved antimicrobial efficacy without incurring dual-bacteriophage-resistance in treated bacteria. We anticipate this assay will allow a better understanding of phenotypic-genomic relationships in bacteriophages and enable the training of bacteriophages against other desired pathogens. This, in turn, will strengthen bacteriophage therapy as a treatment adjunct to improve clinical outcomes of multidrug-resistant bacterial infections.
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Affiliation(s)
- Fabian Kunisch
- Faculty of Medicine, Universität Münster, Münster, Germany
- Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
| | - Claudia Campobasso
- Department of Biosystems, KU Leuven, Leuven, Belgium
- Department of Biology, Università di Pisa, Pisa, Italy
| | | | - Selma Yildirim
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Berlin, Germany
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
| | - Christoph Schaudinn
- Advanced Light and Electron Microscopy (Zentrum für Biologische Gefahren und Spezielle Pathogene 4), Robert Koch Institute, Berlin, Germany
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT, USA
| | - Michael J Raschke
- Faculty of Medicine, Universität Münster, Münster, Germany
- Department of Trauma, Hand and Reconstructive Surgery, Universitätsklinikum Münster, Münster, Germany
| | - Andrej Trampuz
- Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Berlin, Germany.
| | - Mercedes Gonzalez Moreno
- Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Berlin, Germany
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2
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Wei T, Lu C, Du H, Yang Q, Qi X, Liu Y, Zhang Y, Chen C, Li Y, Tang Y, Zhang WH, Tao X, Jiang N. DeepPBI-KG: a deep learning method for the prediction of phage-bacteria interactions based on key genes. Brief Bioinform 2024; 25:bbae484. [PMID: 39344712 PMCID: PMC11440089 DOI: 10.1093/bib/bbae484] [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: 05/30/2024] [Revised: 08/18/2024] [Accepted: 09/13/2024] [Indexed: 10/01/2024] Open
Abstract
Phages, the natural predators of bacteria, were discovered more than 100 years ago. However, increasing antimicrobial resistance rates have revitalized phage research. Methods that are more time-consuming and efficient than wet-laboratory experiments are needed to help screen phages quickly for therapeutic use. Traditional computational methods usually ignore the fact that phage-bacteria interactions are achieved by key genes and proteins. Methods for intraspecific prediction are rare since almost all existing methods consider only interactions at the species and genus levels. Moreover, most strains in existing databases contain only partial genome information because whole-genome information for species is difficult to obtain. Here, we propose a new approach for interaction prediction by constructing new features from key genes and proteins via the application of K-means sampling to select high-quality negative samples for prediction. Finally, we develop DeepPBI-KG, a corresponding prediction tool based on feature selection and a deep neural network. The results show that the average area under the curve for prediction reached 0.93 for each strain, and the overall AUC and area under the precision-recall curve reached 0.89 and 0.92, respectively, on the independent test set; these values are greater than those of other existing prediction tools. The forward and reverse validation results indicate that key genes and key proteins regulate and influence the interaction, which supports the reliability of the model. In addition, intraspecific prediction experiments based on Klebsiella pneumoniae data demonstrate the potential applicability of DeepPBI-KG for intraspecific prediction. In summary, the feature engineering and interaction prediction approaches proposed in this study can effectively improve the robustness and stability of interaction prediction, can achieve high generalizability, and may provide new directions and insights for rapid phage screening for therapy.
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Affiliation(s)
- Tongqing Wei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Shanghai, 200433, China
| | - Chenqi Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Shanghai, 200433, China
| | - Hanxiao Du
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Shanghai, 200433, China
| | - Qianru Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Shanghai, 200433, China
| | - Xin Qi
- Shanghai Sci-Tech Inno Center for Infection & Immunity, No. 1688 Guoquan Bei Road, Shanghai, China
| | - Yankun Liu
- Shanghai Sci-Tech Inno Center for Infection & Immunity, No. 1688 Guoquan Bei Road, Shanghai, China
| | - Yi Zhang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai, China
| | - Chen Chen
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai, China
| | - Yutong Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Shanghai, 200433, China
| | - Yuanhao Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Shanghai, 200433, China
| | - Wen-Hong Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Shanghai, 200433, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, No. 1688 Guoquan Bei Road, Shanghai, China
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai, China
| | - Xu Tao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Shanghai, 200433, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, No. 1688 Guoquan Bei Road, Shanghai, China
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Shanghai, 200433, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, No. 1688 Guoquan Bei Road, Shanghai, China
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai, China
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3
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Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Crawford KD, Shipman SL. An experimental census of retrons for DNA production and genome editing. Nat Biotechnol 2024:10.1038/s41587-024-02384-z. [PMID: 39289529 DOI: 10.1038/s41587-024-02384-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 08/12/2024] [Indexed: 09/19/2024]
Abstract
Retrons are bacterial immune systems that use reverse-transcribed DNA (RT-DNA) to detect phage infection. They are also deployed for genome editing, where they are modified so that the RT-DNA encodes an editing donor. Retrons are common in bacterial genomes, and thousands of unique retrons have been predicted bioinformatically. However, few have been characterized experimentally. We add to the corpus of experimentally studied retrons, finding 62 empirically determined, natural RT-DNAs that are not predictable from the retron sequence alone. We synthesize >100 previously untested retrons to identify the natural sequence of RT-DNA they produce, quantify their RT-DNA production and test the relative efficacy of editing using retron-derived donors to edit bacterial, phage and human genomes. We observe large diversity in RT-DNA production and editing rates across retrons, finding that top-performing editors are drawn from a subset of the retron phylogeny and outperform those used in previous studies, reaching precise editing rates of up to 40% in human cells.
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Affiliation(s)
- Asim G Khan
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | | | | | - Santiago C Lopez
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco, San Francisco and University of California, Berkeley, Berkeley, CA, USA
| | - Rebecca F Fang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Neuroscience, University of California, San Francisco, San Francisco, CA, USA
| | - Kate D Crawford
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco, San Francisco and University of California, Berkeley, Berkeley, CA, USA
| | - Seth L Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
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4
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Zulkarneev ER, Laishevtsevtsev AI, Kiseleva IA, Efimova OG, Mizaeva TE, Pasivkina MA, Zubkova ES, Aleshkin AV, Karaulov AV. Assessment of the Safety of Anti-Salmonella Disinfectant for Veterinary Use Based on a Cocktail of Bacteriophages. Bull Exp Biol Med 2024:10.1007/s10517-024-06225-6. [PMID: 39287723 DOI: 10.1007/s10517-024-06225-6] [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: 12/12/2023] [Indexed: 09/19/2024]
Abstract
The toxicity and safety of a veterinary anti-salmonella disinfectant based on three highly virulent bacteriophage strains (titers 1010 PFU/ml) were studied. Acute, chronic, and inhalation toxicity, as well as local irritancy of the disinfectant were evaluated on outbred white mice CD1 (n=65), Soviet chinchilla rabbits (n=20), and rats (n=20). No toxic effects of the disinfectant was observed after its intraperitoneal or intragastric administration to mice and intragastric administration to rats; in rabbits, application on the skin and eyes produced no local irritation effect. Inhalation of 10% of the disinfectant did not cause any pathologies in mice. Thus, the tests confirmed the high level of safety of the disinfectant based on a mixture of bacteriophages for use as an additional specific disinfection agent against Salmonella in veterinary and livestock facilities.
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Affiliation(s)
- E R Zulkarneev
- Gabrichevsky Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia.
- Antiplague Center, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia.
| | - A I Laishevtsevtsev
- Gabrichevsky Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
- Federal State Budget Scientific Institution "Federal Scientific Center VIEV", Moscow, Russia
| | - I A Kiseleva
- Gabrichevsky Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
| | - O G Efimova
- Gabrichevsky Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
| | - T E Mizaeva
- Gabrichevsky Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
| | - M A Pasivkina
- Gabrichevsky Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
| | - E S Zubkova
- Gabrichevsky Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
| | - A V Aleshkin
- Gabrichevsky Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
| | - A V Karaulov
- I. M. Sechenov First Moscow State Medical University, Ministry of Health of the Russian Federation (Sechenovsky University), Moscow, Russia
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5
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Nuytten M, Leprince A, Goulet A, Mahillon J. Deciphering the adsorption machinery of Deep-Blue and Vp4, two myophages targeting members of the Bacillus cereus group. J Virol 2024; 98:e0074524. [PMID: 39177355 PMCID: PMC11406892 DOI: 10.1128/jvi.00745-24] [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: 04/24/2024] [Accepted: 07/11/2024] [Indexed: 08/24/2024] Open
Abstract
In tailed phages, the baseplate is the macromolecular structure located at the tail distal part, which is directly implicated in host recognition and cell wall penetration. In myophages (i.e., with contractile tails), the baseplate is complex and comprises a central puncturing device and baseplate wedges connecting the hub to the receptor-binding proteins (RBPs). In this work, we investigated the structures and functions of adsorption-associated tail proteins of Deep-Blue and Vp4, two Herelleviridae phages infecting members of the Bacillus cereus group. Their interest resides in their different host spectrum despite a high degree of similarity. Analysis of their tail module revealed that the gene order is similar to that of the Listeria phage A511. Among their tail proteins, Gp185 (Deep-Blue) and Gp112 (Vp4) had no structural homolog, but the C-terminal variable parts of these proteins were able to bind B. cereus strains, confirming their implication in the phage adsorption. Interestingly, Vp4 and Deep-Blue adsorption to their hosts was also shown to require polysaccharides, which are likely to be bound by the arsenal of carbohydrate-binding modules (CBMs) of these phages' baseplates, suggesting that the adsorption does not rely solely on the RBPs. In particular, the BW Gp119 (Vp4), harboring a CBM fold, was shown to effectively bind to bacterial cells. Finally, we also showed that the putative baseplate hub proteins (i.e., Deep-Blue Gp189 and Vp4 Gp110) have a bacteriolytic activity against B. cereus strains, which supports their role as ectolysins locally degrading the peptidoglycan to facilitate genome injection. IMPORTANCE The Bacillus cereus group comprises closely related species, including some with pathogenic potential (e.g., Bacillus anthracis and Bacillus cytotoxicus). Their toxins represent the most frequently reported cause of food poisoning outbreaks at the European level. Bacteriophage research is undergoing a remarkable renaissance for its potential in the biocontrol and detection of such pathogens. As the primary site of phage-bacteria interactions and a prerequisite for successful phage infection, adsorption is a crucial process that needs further investigation. The current knowledge about B. cereus phage adsorption is currently limited to siphoviruses and tectiviruses. Here, we present the first insights into the adsorption process of Herelleviridae Vp4 and Deep-Blue myophages preying on B. cereus hosts, highlighting the importance of polysaccharide moieties in this process and confirming the binding to the host surface of Deep-Blue Gp185 and Vp4 Gp112 receptor-binding proteins and Gp119 baseplate wedge.
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Affiliation(s)
- Manon Nuytten
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Audrey Leprince
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Adeline Goulet
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), CNRS and Aix-Marseille Université UMR7255, Marseille, France
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
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6
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Kolenda C, Jourdan J, Roussel-Gaillard T, Medina M, Laurent F. Phage susceptibility testing methods or 'phagograms': where do we stand and where should we go? J Antimicrob Chemother 2024:dkae325. [PMID: 39271114 DOI: 10.1093/jac/dkae325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024] Open
Abstract
Phage therapy is a highly promising approach to address the challenge that is presented by the global burden of antimicrobial resistance. Given the natural specificity of phages, phage susceptibility testing (PST) is a prerequisite for successful personalized therapy, allowing the selection of active phages from large and diverse collections. However, the issue of an easy-to-use and standardized technique remains. In this review, we describe the principles, advantages and drawbacks of two routinely used PST techniques: plaque and growth kinetic assays. These are labour-intensive and time-consuming methods that require automation of one or more steps, including preparation of test panels, incubation, reading and analysis of results. In addition to automation, there is an urgent need to establish a reference method to enable efficient of PST techniques selection of therapeutic phages. We discuss knowledge gaps and parameters that need to be investigated to work towards this goal.
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Affiliation(s)
- Camille Kolenda
- Service de bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Team StaPath, CIRI-Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Julie Jourdan
- Service de bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | | | - Mathieu Medina
- Service de bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Team StaPath, CIRI-Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Frédéric Laurent
- Service de bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Team StaPath, CIRI-Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
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7
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Fishman CB, Crawford KD, Bhattarai-Kline S, Poola D, Zhang K, González-Delgado A, Rojas-Montero M, Shipman SL. Continuous multiplexed phage genome editing using recombitrons. Nat Biotechnol 2024:10.1038/s41587-024-02370-5. [PMID: 39237706 DOI: 10.1038/s41587-024-02370-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 07/27/2024] [Indexed: 09/07/2024]
Abstract
Bacteriophage genome editing can enhance the efficacy of phages to eliminate pathogenic bacteria in patients and in the environment. However, current methods for editing phage genomes require laborious screening, counterselection or in vitro construction of modified genomes. Here, we present a scalable approach that uses modified bacterial retrons called recombitrons to generate recombineering donor DNA paired with single-stranded binding and annealing proteins for integration into phage genomes. This system can efficiently create genome modifications in multiple phages without the need for counterselection. The approach also supports larger insertions and deletions, which can be combined with simultaneous counterselection for >99% efficiency. Moreover, we show that the process is continuous, with more edits accumulating the longer the phage is cultured with the host, and multiplexable. We install up to five distinct mutations on a single lambda phage genome without counterselection in only a few hours of hands-on time and identify a residue-level epistatic interaction in the T7 gp17 tail fiber.
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Affiliation(s)
- Chloe B Fishman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Kate D Crawford
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA
| | - Santi Bhattarai-Kline
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Darshini Poola
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Indian Institute of Science Education and Research (IISER), Pune, India
| | - Karen Zhang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA
| | | | | | - Seth L Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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8
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Borkowski A, Działak P, Berent K, Gajewska M, Syczewski MD, Słowakiewicz M. Mechanism of bacteriophage-induced vaterite formation. Sci Rep 2024; 14:20481. [PMID: 39227688 PMCID: PMC11372193 DOI: 10.1038/s41598-024-71638-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/29/2024] [Indexed: 09/05/2024] Open
Abstract
This study shows how bacterial viruses (bacteriophages, phages) interact with calcium carbonate during precipitation from aqueous solution. Using electron microscopy, epifluorescence microscopy, X-ray diffraction, and image analysis, we demonstrate that bacteriophages can strongly influence the formation of the vaterite phase. Importantly, bacteriophages may selectively bind both amorphous calcium carbonate (ACC) and vaterite, and indirectly affect the formation of structural defects in calcite crystallites. Consequently, the surface properties of calcium carbonate phases precipitating in the presence of viruses may exhibit different characteristics. These findings may have significant implications in determining the role of bacterial viruses in modern microbially-rich carbonate sedimentary environments, as well as in biomedical technologies. Finally, the phage-vaterite system, as a biocompatible material, may serve as a basis for the development of promising drug delivery carriers.
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Affiliation(s)
- Andrzej Borkowski
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Krakow, Al. Mickiewicza 30, 30-059, Kraków, Poland.
| | - Paweł Działak
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Krakow, Al. Mickiewicza 30, 30-059, Kraków, Poland
| | - Katarzyna Berent
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Al. Mickiewicza 30, 30-059, Kraków, Poland
| | - Marta Gajewska
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Al. Mickiewicza 30, 30-059, Kraków, Poland
| | - Marcin D Syczewski
- GFZ German Research Centre for Geosciences, 14473, Telegrafenberg, Potsdam, Germany
| | - Mirosław Słowakiewicz
- Faculty of Geology, University of Warsaw, Ul. Żwirki i Wigury 93, 02-089, Warsaw, Poland
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9
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Wang C, Wang S, Jing S, Zeng Y, Yang L, Mu Y, Ding Z, Song Y, Sun Y, Zhang G, Wei D, Li M, Ma Y, Zhou H, Wu L, Feng J. Data-Driven Engineering of Phages with Tunable Capsule Tropism for Klebsiella pneumoniae. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309972. [PMID: 38937990 PMCID: PMC11434222 DOI: 10.1002/advs.202309972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/26/2024] [Indexed: 06/29/2024]
Abstract
Klebsiella pneumoniae, a major clinical pathogen known for causing severe infections, is attracting heightened attention due to its escalating antibiotic resistance. Phages are emerging as a promising alternative to antibiotics; however, their specificity to particular hosts often restricts their use. In this study, a collection of 114 phages is obtained and subjected to analysis against 238 clinical K. pneumoniae strains, revealing a spectrum of lytic behaviors. A correlation between putative tail protein clusters and lysis patterns leads to the discovery of six receptor-binding protein (RBP) clusters that determine host capsule tropism. Significantly, RBPs with cross-capsular lysis capabilities are identified. The newly-identified RBPs provide a toolbox for customizing phages to target diverse capsular types. Building on the toolbox, the engineered phages with altered RBPs successfully shifted and broadened their host capsule tropism, setting the stage for tunable phage that offer a precise and flexible solution to combat K. pneumoniae infections.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest UniversityXi'an710069China
| | - Shisong Jing
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijing100049China
| | - Yuan Zeng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
| | - Lili Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
- Shandong First Medical University & Shandong Academy of Medical SciencesJinan250117China
| | - Yongqi Mu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijing100049China
| | - Zixuan Ding
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
- Shandong First Medical University & Shandong Academy of Medical SciencesJinan250117China
| | - Yuqin Song
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
| | - Yanmei Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest UniversityXi'an710069China
| | - Gang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
| | - Dawei Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
| | - Yingfei Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of SciencesShenzhen518000China
| | - Haijian Zhou
- State Key Laboratory for Infectious Diseases Prevention and ControlNational Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing102206China
| | - Linhuan Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing100101China
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10
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Wang X, Xu Z, Xia Y, Chen Z, Zong R, Meng Q, Wang W, Zhuang W, Meng X, Chen G. Characterization of an Escherichia coli phage Tequatrovirus YZ2 and its application in bacterial wound infection. Virology 2024; 597:110155. [PMID: 38943783 DOI: 10.1016/j.virol.2024.110155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/05/2024] [Accepted: 06/20/2024] [Indexed: 07/01/2024]
Abstract
The increasing prevalence of drug-resistant Escherichia coli (E. coli) resulting from the excessive utilization of antibiotics necessitates the immediate exploration of alternative approaches to counteract pathogenic E. coli. Phages, with their unique antibacterial mechanisms, are considered promising candidates for treating bacterial infections. Herein, we isolated a lytic Escherichia phage Tequatrovirus YZ2 (phage YZ2), which belongs to the genus Tequatrovirus. The genome of phage YZ2 consists of 168,356 base pairs with a G + C content of 35.34% and 269 putative open reading frames (ORFs). Of these, 146 ORFs have been annotated as functional proteins associated with nucleotide metabolism, structure, transcription, DNA replication, translation, and lysis. In the mouse model of a skin wound infected by E. coli, phage YZ2 therapy significantly promoted the wound healing. Furthermore, histopathological analysis revealed reductions in IL-1β and TNF-α and increased VEGF levels, indicating the potential of phages as effective antimicrobial agents against E. coli infection.
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Affiliation(s)
- Xuewen Wang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, 266024, PR China
| | - Zhou Xu
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, 266024, PR China
| | - Yinhe Xia
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, 266024, PR China
| | - Zhiling Chen
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, 266024, PR China
| | - Rongling Zong
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, 266024, PR China
| | - Qingye Meng
- School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, 266024, PR China
| | - Weijie Wang
- School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, 266024, PR China
| | - Wenzhen Zhuang
- Office of International Cooperation and Exchange, Weifang People's Hospital, Weifang, 261000, PR China.
| | - Xiangjun Meng
- School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, 266024, PR China.
| | - Gang Chen
- School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, 266024, PR China.
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11
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Pedersen JS, Carstens AB, Rothgard MM, Roy C, Viry A, Papudeshi B, Kot W, Hille F, Franz CMAP, Edwards R, Hansen LH. A novel genus of Pectobacterium bacteriophages display broad host range by targeting several species of Danish soft rot isolates. Virus Res 2024; 347:199435. [PMID: 38986742 PMCID: PMC11445585 DOI: 10.1016/j.virusres.2024.199435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/28/2024] [Accepted: 07/07/2024] [Indexed: 07/12/2024]
Abstract
The bacterial diseases black leg and soft rot in potatoes cause heavy losses of potatoes worldwide. Bacteria within the genus Pectobacteriaceae are the causative agents of black leg and soft rot. The use of antibiotics in agriculture is heavily regulated and no other effective treatment currently exists, but bacteriophages (phages) have shown promise as potential biocontrol agents. In this study we isolated soft rot bacteria from potato tubers and plant tissue displaying soft rot or black leg symptoms collected in Danish fields. We then used the isolated bacterial strains as hosts for phage isolation. Using organic waste, we isolated phages targeting different species within Pectobacterium. Here we focus on seven of these phages representing a new genus primarily targeting P. brasiliense; phage Ymer, Amona, Sabo, Abuela, Koroua, Taid and Pappous. TEM image of phage Ymer showed siphovirus morphotype, and the proposed Ymer genus belongs to the class Caudoviricetes, with double-stranded DNA genomes varying from 39 kb to 43 kb. In silico host range prediction using a CRISPR-Cas spacer database suggested both P. brasiliense, P. polaris and P. versatile as natural hosts for phages within the proposed Ymer genus. A following host range experiment, using 47 bacterial isolates from Danish tubers and plants symptomatic with soft rot or black leg disease verified the in silico host range prediction, as the genus as a group were able to infect all three Pectobacterium species. Phages did, however, primarily target P. brasiliense isolates and displayed differences in host range even within the species level. Two of the phages were able to infect two or more Pectobacterium species. Despite no nucleotide similarity with any phages in the NCBI database, the proposed Ymer genus did share some similarity at the protein level, as well as gene synteny, with currently known phages. None of the phages encoded integrases or other genes typically associated with lysogeny. Similarly, no virulence factors nor antimicrobial resistance genes were found, and combined with their ability to infect several soft rot-causing Pectobacterium species from Danish fields, demonstrates their potential as biocontrol agents against soft rot and black leg diseases in potatoes.
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Affiliation(s)
- Julie Stenberg Pedersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Alexander Byth Carstens
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Magnus Mulbjerg Rothgard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Chayan Roy
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Anouk Viry
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Frank Hille
- Department of Microbiology and Biotechnology, Max Rubner-Institute, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institute, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Robert Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark.
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12
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Zhu HX, Wright BW, Logel DY, Needham P, Yehl K, Molloy MP, Jaschke PR. IbpAB small heat shock proteins are not host factors for bacteriophage ϕX174 replication. Virology 2024; 597:110169. [PMID: 38996611 DOI: 10.1016/j.virol.2024.110169] [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: 02/01/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024]
Abstract
Bacteriophage ϕX174 is a small icosahedral virus of the Microviridae with a rapid replication cycle. Previously, we found that in ϕX174 infections of Escherichia coli, the most highly upregulated host proteins are two small heat shock proteins, IbpA and IbpB, belonging to the HSP20 family, which is a universally conserved group of stress-induced molecular chaperones that prevent irreversible aggregation of proteins. Heat shock proteins were found to protect against ϕX174 lysis, but IbpA/B have not been studied. In this work, we disrupted the ibpA and ibpB genes and measured the effects on ϕX174 replication. We found that in contrast to other E. coli heat shock proteins, they are not necessary for ϕX174 replication; moreover, their absence has no discernible effect on ϕX174 fecundity. These results suggest IbpA/B upregulation is a response to ϕX174 protein expression but does not play a role in phage replication, and they are not Microviridae host factors.
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Affiliation(s)
- Hannah X Zhu
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Bradley W Wright
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Dominic Y Logel
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Patrick Needham
- Miami University, Department of Chemistry and Biochemistry, Oxford, 45056, USA
| | - Kevin Yehl
- Miami University, Department of Chemistry and Biochemistry, Oxford, 45056, USA
| | - Mark P Molloy
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; Kolling Institute, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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13
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Torkashvand N, Kamyab H, Shahverdi AR, Khoshayand MR, Karimi Tarshizi MA, Sepehrizadeh Z. Characterization and genome analysis of a broad host range lytic phage vB_SenS_TUMS_E19 against Salmonella enterica and its efficiency evaluation in the liquid egg. Can J Microbiol 2024; 70:358-369. [PMID: 38990097 DOI: 10.1139/cjm-2024-0013] [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] [Indexed: 07/12/2024]
Abstract
Salmonella enterica serovars are zoonotic bacterial that cause foodborne enteritis. Due to bacteria's antibiotic resistance, using bacteriophages for biocontrol and treatment is a new therapeutic approach. In this study, we isolated, characterized, and analyzed the genome of vB_SenS_TUMS_E19 (E19), a broad host range Salmonella bacteriophage, and evaluated the influence of E19 on liquid eggs infected with Salmonella enterica serovar Enteritidis. Transmission electron microscopy showed that the isolated bacteriophage had a siphovirus morphotype. E19 showed rapid adsorption (92% in 5 min), a short latent period (18 min), a large burst size (156 PFU per cell), and a broad host range against different Salmonella enterica serovars. Whole-genome sequencing analysis indicated that the isolated phage had a 42 813 bp long genome with 49.8% G + C content. Neither tRNA genes nor those associated with antibiotic resistance, virulence factors, or lysogenic formation were detected in the genome. The efficacy of E19 was evaluated in liquid eggs inoculated with S. Enteritidis at 4 and 25 °C, and results showed that it could effectively eradicate S. Enteritidis in just 30 min and prevented its growth up to 72 h. Our findings indicate that E19 can be an alternative to a preservative to control Salmonella in food samples and help prevent and treat salmonellosis.
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Affiliation(s)
- Narges Torkashvand
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Haniyeh Kamyab
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Reza Shahverdi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Khoshayand
- Department of Food and Drug Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Zargham Sepehrizadeh
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
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14
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Kaşkatepe B, Erol HB, Sönmez VZ, Arikan M, Unal EM, Keskin E, Sivri N. Adapting nature's own solution: The effect of rhamnolipid and lytic bacteriophage cocktail on enteric pathogens that proliferate in mucilage. MARINE POLLUTION BULLETIN 2024; 206:116810. [PMID: 39116759 DOI: 10.1016/j.marpolbul.2024.116810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
The mucilage event witnessed in the Sea of Marmara in 2021 has emerged as a prominent environmental concern, capturing public attention due to its detrimental effects on ecological, economic, and aesthetic dimensions. Addressing the multifaceted impacts of mucilage demands a nature-centric scientific approach, given its global ramifications spanning economy, public health, international relations, and tourism. Consequently, this study sought to explore alternative approaches for the removal of pathogenic enteric bacteria associated with mucilage occurrences, diverging from conventional methodologies. Specifically, the primary objective was to assess the efficacy of rhamnolipid and a bacteriophage cocktail in mitigating the proliferation of enteric pathogens within mucilaginous environments. During the study, 91 phage isolations were obtained from 45 water samples taken and 10 phages were selected for the broad host range and because of the efficacy tests, a phage cocktail was created with 5 phages. It was found that the mixture of rhamnolipid, phage cocktail and rhamnolipid-phage cocktail reduced bacterial load by 7-9 log10, 9-12 log10 and 9-11 log10 respectively under laboratory conditions. When the study was carried out in seawater, reductions of 4-5 log10, 3 log10 and 4 log10 were achieved. This study has shown that the combined use of rhamnolipid, phage cocktail and rhamnolipid-phage cocktail can be considered as the most effective natural solution proposal for reducing bacterial load, both in laboratory conditions and in sea surface water.
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Affiliation(s)
- Banu Kaşkatepe
- Department of Pharmaceutical Microbiology, Ankara University, Turkey.
| | - Hilal Başak Erol
- Department of Pharmaceutical Microbiology, Ankara University, Turkey
| | | | - Metehan Arikan
- Ankara University, Faculty of Agriculture, Department of Fisheries and Aquaculture, Evolutionary Genetics Laboratory (eGL), Ankara, Turkey; AgriGenomics Hub: Animal and PlantGenomics Research Innovation Center, Ankara, Turkey; Ankara University, Biotechnology Institute, Ankara, Turkey
| | - Esra Mine Unal
- Ankara University, Faculty of Agriculture, Department of Fisheries and Aquaculture, Evolutionary Genetics Laboratory (eGL), Ankara, Turkey; AgriGenomics Hub: Animal and PlantGenomics Research Innovation Center, Ankara, Turkey
| | - Emre Keskin
- Ankara University, Faculty of Agriculture, Department of Fisheries and Aquaculture, Evolutionary Genetics Laboratory (eGL), Ankara, Turkey; AgriGenomics Hub: Animal and PlantGenomics Research Innovation Center, Ankara, Turkey
| | - Nüket Sivri
- Department of Environmental Engineering, Istanbul University-Cerrahpasa, Istanbul, Turkey
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15
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Senhaji-Kacha A, Bernabéu-Gimeno M, Domingo-Calap P, Aguilera-Correa JJ, Seoane-Blanco M, Otaegi-Ugartemendia S, van Raaij MJ, Esteban J, García-Quintanilla M. Isolation and characterization of two novel bacteriophages against carbapenem-resistant Klebsiella pneumoniae. Front Cell Infect Microbiol 2024; 14:1421724. [PMID: 39268483 PMCID: PMC11390652 DOI: 10.3389/fcimb.2024.1421724] [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: 04/22/2024] [Accepted: 08/07/2024] [Indexed: 09/15/2024] Open
Abstract
The increase of antibiotic-resistant bacteria has become a global health emergency and the need to explore alternative therapeutic options arises. Phage therapy uses bacteriophages to target specific bacterial strains. Phages are highly specific and can target resistant bacteria. Currently, research in this regard is focused on ensuring reliability and safety to bring this tool into clinical practice. The first step is to conduct comprehensive preclinical research. In this work, we present two novel bacteriophages vB_Kpn_F13 and vB_Kpn_F14 isolated against clinical carbapenem-resistant Klebsiella pneumoniae strains obtained from hospital sewage. Multiple studies in vitro were conducted, such as sequencing, electron microscopy, stability, host range infectivity, planktonic effect and biofilm inhibition in order to discover their ability to be used against carbapenem-resistant K. pneumoniae pathogens causing difficult-to-treat infections.
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Affiliation(s)
- Abrar Senhaji-Kacha
- Department of Clinical Microbiology, Health Research Institute or Instituto de Investigación Sanitaria (IIS)-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- CIBERINFEC-CIBER of Infectious Diseases, Madrid, Spain
| | - Mireia Bernabéu-Gimeno
- Institute of Biología Integrativa de Sistemas, Universitat de València-The Spanish National Research Council or Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Spain
| | - Pilar Domingo-Calap
- Institute of Biología Integrativa de Sistemas, Universitat de València-The Spanish National Research Council or Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Spain
| | - John Jairo Aguilera-Correa
- Department of Clinical Microbiology, Health Research Institute or Instituto de Investigación Sanitaria (IIS)-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- CIBERINFEC-CIBER of Infectious Diseases, Madrid, Spain
| | - Mateo Seoane-Blanco
- Department of Macromolecular Structure, Centro Nacional de Biotecnología-The Spanish National Research Council or Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Sara Otaegi-Ugartemendia
- Department of Macromolecular Structure, Centro Nacional de Biotecnología-The Spanish National Research Council or Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Mark J van Raaij
- Department of Macromolecular Structure, Centro Nacional de Biotecnología-The Spanish National Research Council or Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, Health Research Institute or Instituto de Investigación Sanitaria (IIS)-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- CIBERINFEC-CIBER of Infectious Diseases, Madrid, Spain
| | - Meritxell García-Quintanilla
- Department of Clinical Microbiology, Health Research Institute or Instituto de Investigación Sanitaria (IIS)-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- CIBERINFEC-CIBER of Infectious Diseases, Madrid, Spain
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16
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Yang L, Wang C, Zeng Y, Song Y, Zhang G, Wei D, Li Y, Feng J. Characterization of a novel phage against multidrug-resistant Klebsiella pneumoniae. Arch Microbiol 2024; 206:379. [PMID: 39143367 DOI: 10.1007/s00203-024-04106-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024]
Abstract
Multidrug-resistant Klebsiella pneumoniae (MDR-KP) poses a significant challenge in global healthcare, underscoring the urgency for innovative therapeutic approaches. Phage therapy emerges as a promising strategy amidst rising antibiotic resistance, emphasizing the crucial need to identify and characterize effective phage resources for clinical use. In this study, we introduce a novel lytic phage, RCIP0100, distinguished by its classification into the Chaoyangvirus genus and Fjlabviridae family based on International Committee on Taxonomy of Viruses (ICTV) criteria due to low genetic similarity to known phage families. Our findings demonstrate that RCIP0100 exhibits broad lytic activity against 15 out of 27 tested MDR-KP strains, including diverse profiles such as carbapenem-resistant K. pneumoniae (CR-KP). This positions phage RCIP0100 as a promising candidate for phage therapy. Strains resistant to RCIP0100 also showed increased susceptibility to various antibiotics, implying the potential for synergistic use of RCIP0100 and antibiotics as a strategic countermeasure against MDR-KP.
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Affiliation(s)
- Lili Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Qilu Medical University, Zibo, China
| | - Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuan Zeng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuqin Song
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Gang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dawei Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yalin Li
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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17
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Paranos P, Pournaras S, Meletiadis J. A single-layer spot assay for easy, fast, and high-throughput quantitation of phages against multidrug-resistant Gram-negative pathogens. J Clin Microbiol 2024; 62:e0074324. [PMID: 39072625 PMCID: PMC11323465 DOI: 10.1128/jcm.00743-24] [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: 05/17/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024] Open
Abstract
Double-layer agar (DLA) overlay plaque assay is the gold standard for phage enumeration. However, it is cumbersome and time-consuming. Given the great interest in phage therapy, we explored alternative assays for phage quantitation. A total of 16 different phages belonging to Myoviridae, Siphoviridae, and Podoviridae families were quantitated with five K. pneumoniae, eight P. aeruginosa, and three A. baumannii host isolates. Phages were quantitated with the standard DLA assay (10 mL of LB soft agar 0.7% on LB hard agar 1.5%) and the new single-layer agar (SLA) assay (10 mL of LB soft agar 0.7%) with phages spread (spread) into or spotted (spot) onto soft agar. Phage concentrations with each assay were correlated with the standard assay, and the relative and absolute differences between each assay and the standard double-layer agar spread were calculated. Phage concentrations 1 × 104-8.3 x1012 PFU/mL with the standard DLA assay were quantitated with SLA-spread, SLA-spot, and DLA-spot assays, and the median (range) relative and absolute differences were <10% and <0.98 log10PFU/mL, respectively, for all phage/bacterial species (ANOVA P = 0.1-0.43), and they were highly correlated (r > 0.77, P < 0.01). Moreover, plaques could be quantified at 37°C after 4-h incubation for K. pneumoniae phages and 6-h incubation for P. aeruginosa and A. baumannii phages, and estimated concentrations remained the same over 24 hours. Compared to DLA assay, the SLA-spot assay required less media, it was 10 times faster, and generated same-day results. The SLA-spot assay was cheaper, faster, easier to perform, and generated similar phage concentrations as the standard DLA-spread assay.
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Affiliation(s)
- Paschalis Paranos
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Spyros Pournaras
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Joseph Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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18
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Yang XY, Shen Z, Xie J, Greenwald J, Marathe I, Lin Q, Xie WJ, Wysocki VH, Fu TM. Molecular basis of Gabija anti-phage supramolecular assemblies. Nat Struct Mol Biol 2024; 31:1243-1250. [PMID: 38627580 PMCID: PMC11418746 DOI: 10.1038/s41594-024-01283-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 03/22/2024] [Indexed: 05/15/2024]
Abstract
As one of the most prevalent anti-phage defense systems in prokaryotes, Gabija consists of a Gabija protein A (GajA) and a Gabija protein B (GajB). The assembly and function of the Gabija system remain unclear. Here we present cryo-EM structures of Bacillus cereus GajA and GajAB complex, revealing tetrameric and octameric assemblies, respectively. In the center of the complex, GajA assembles into a tetramer, which recruits two sets of GajB dimer at opposite sides of the complex, resulting in a 4:4 GajAB supramolecular complex for anti-phage defense. Further biochemical analysis showed that GajA alone is sufficient to cut double-stranded DNA and plasmid DNA, which can be inhibited by ATP. Unexpectedly, the GajAB displays enhanced activity for plasmid DNA, suggesting a role of substrate selection by GajB. Together, our study defines a framework for understanding anti-phage immune defense by the GajAB complex.
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Affiliation(s)
- Xiao-Yuan Yang
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Program of OSBP, The Ohio State University, Columbus, OH, USA
| | - Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Jiale Xie
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Program of OSBP, The Ohio State University, Columbus, OH, USA
| | - Jacelyn Greenwald
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Ila Marathe
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Qingpeng Lin
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Wen Jun Xie
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- Program of OSBP, The Ohio State University, Columbus, OH, USA.
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19
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Wang WX, Wu JZ, Zhang BL, Yu JY, Han LM, Lu XL, Li H, Fu SY, Ren YY, Dong H, Xu Y, Wang GT, Gao JH, Wang C, Chen XZ, Liu DX, Huang Y, Yu JH, Wang SW, Yang YF, Chen W. Phage therapy combats pan drug-resistant Acinetobacter baumannii infection safely and efficiently. Int J Antimicrob Agents 2024; 64:107220. [PMID: 38810939 DOI: 10.1016/j.ijantimicag.2024.107220] [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: 07/12/2023] [Revised: 04/20/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Phage therapy offers a promising approach to combat the growing threat of antimicrobial resistance. Yet, key questions remain regarding dosage, administration routes, combination therapy, and the causes of therapeutic failure. In this study, we focused on a novel lytic phage, ФAb4B, which specifically targeted the Acinetobacter baumannii strains with KL160 capsular polysaccharide, including the pan-drug resistant A. baumannii YQ4. ФAb4B exhibited the ability to effectively inhibit biofilm formation and eradicate mature biofilms independently of dosage. Additionally, it demonstrated a wide spectrum of antibiotic-phage synergy and did not show any cytotoxic or haemolytic effects. Continuous phage injections, both intraperitoneally and intravenously over 7 d, showed no acute toxicity in vivo. Importantly, phage therapy significantly improved neutrophil counts, outperforming ciprofloxacin. However, excessive phage injections suppressed neutrophil levels. The combinatorial treatment of phage-ciprofloxacin rescued 91% of the mice, a superior outcome compared to phage alone (67%). The efficacy of the combinatorial treatment was independent of phage dosage. Notably, prophylactic administration of the combinatorial regimen provided no protection, but even when combined with a delayed therapeutic regimen, it saved all the mice. Bacterial resistance to the phage was not a contributing factor to treatment failure. Our preclinical study systematically describes the lytic phage's effectiveness in both in vitro and in vivo settings, filling in crucial details about phage treatment against bacteriemia caused by A. baumannii, which will provide a robust foundation for the future of phage therapy.
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Affiliation(s)
- Wei-Xiao Wang
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Jia-Zhen Wu
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China; Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Bai-Ling Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiao-Yang Yu
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China; Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Li-Mei Han
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiao-Liang Lu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Hui Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shi-Yong Fu
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Yun-Yao Ren
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Dong
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Yi Xu
- Department of Geriatric Medicine, Jiangxi Provincial People's Hospital, Nanchang, China
| | - Gong-Ting Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Jing-Han Gao
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Chun Wang
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiu-Zhen Chen
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Du-Xian Liu
- Department of pathology, the Second Hospital of Nanjing, Affiliated Hospital to Nanjing University of Chinese Medicine, Nanjing, China
| | - Ying Huang
- Department of Infection Control and Management, the Second Hospital of Nanjing, Affiliated Hospital to Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Hong Yu
- Department of Clinical Laboratory, the Second Hospital of Nanjing, Affiliated Hospital to Nanjing University of Chinese Medicine, Nanjing, China
| | - Shi-Wei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Yong-Feng Yang
- The Clinical Infectious Disease Center of Nanjing, Nanjing, China.
| | - Wei Chen
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China.
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20
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Chen Q, Zhang F, Bai J, Che Q, Xiang L, Zhang Z, Wang Y, Sjöling Å, Martín-Rodríguez AJ, Zhu B, Fu L, Zhou Y. Bacteriophage-resistant carbapenem-resistant Klebsiella pneumoniae shows reduced antibiotic resistance and virulence. Int J Antimicrob Agents 2024; 64:107221. [PMID: 38810938 DOI: 10.1016/j.ijantimicag.2024.107221] [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: 07/23/2023] [Revised: 04/21/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Phage therapy has shown great promise in the treatment of bacterial infections. However, the effectiveness of phage therapy is compromised by the inevitable emergence of phage-resistant strains. In this study, a phage-resistant carbapenem-resistant Klebsiella pneumoniae strain SWKP1711R, derived from parental carbapenem-resistant K. pneumoniae strain SWKP1711 was identified. The mechanism of bacteriophage resistance in SWKP1711R was investigated and the molecular determinants causing altered growth characteristics, antibiotic resistance, and virulence of SWKP1711R were tested. Compared to SWKP1711, SWKP1711R showed slower growth, smaller colonies, filamentous cells visible under the microscope, reduced production of capsular polysaccharide (CPS) and lipopolysaccharide, and reduced resistance to various antibiotics accompanied by reduced virulence. Adsorption experiments showed that phage vB_kpnM_17-11 lost the ability to adsorb onto SWKP1711R, and the adsorption receptor was identified to be bacterial surface polysaccharides. Genetic variation analysis revealed that, compared to the parental strain, SWKP1711R had only one thymine deletion at position 78 of the open reading frame of the lpcA gene, resulting in a frameshift mutation that caused alteration of the bacterial surface polysaccharide and inhibition of phage adsorption, ultimately leading to phage resistance. Transcriptome analysis and quantitative reverse transcriptase PCR revealed that genes encoding lipopolysaccharide synthesis, ompK35, blaTEM-1, and type II and Hha-TomB toxin-antitoxin systems, were all downregulated in SWKP1711R. Taken together, the evidence presented here indicates that the phenotypic alterations and phage resistance displayed by the mutant may be related to the frameshift mutation of lpcA and altered gene expression. While evolution of phage resistance remains an issue, our study suggests that the reduced antibiotic resistance and virulence of phage-resistant strain derivatives might be beneficial in alleviating the burden caused by multidrug-resistant bacteria.
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Affiliation(s)
- Qiao Chen
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Feiyang Zhang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Jiawei Bai
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Qian Che
- Sichuan Center For Disease Control And Prevention, Chengdu, 610000, China
| | - Li Xiang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Zhikun Zhang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Ying Wang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Stockholm, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, 413 90 Gothenburg, Sweden
| | - Alberto J Martín-Rodríguez
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Stockholm, Sweden; Department of Clinical Sciences, University of Las Palmas de Gran Canaria, 35016, Las Palmas de Gran Canaria, Spain
| | - Baoli Zhu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Li Fu
- The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, China.
| | - Yingshun Zhou
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China; Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, 646000, China.
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21
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Sun X, Xue F, Cong C, Murtaza B, Wang L, Li X, Li S, Xu Y. Characterization of two virulent Salmonella phages and transient application in egg, meat and lettuce safety. Food Res Int 2024; 190:114607. [PMID: 38945617 DOI: 10.1016/j.foodres.2024.114607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/13/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024]
Abstract
Salmonella, a prominent foodborne pathogen, has posed enduring challenges to the advancement of food safety and global public health. The escalating concern over antibiotic misuse, resulting in the excessive presence of drug residues in animal-derived food products, necessitates urgent exploration of alternative strategies for Salmonella control. Bacteriophages emerge as promising green biocontrol agents against pathogenic bacteria. This study delineates the identification of two novel virulent Salmonella phages, namely phage vB_SalS_ABTNLsp11241 (referred to as sp11241) and phage 8-19 (referred to as 8-19). Both phages exhibited efficient infectivity against Salmonella enterica serotype Enteritidis (SE). Furthermore, this study evaluated the effectiveness of two phages to control SE in three different foods (whole chicken eggs, raw chicken meat, and lettuce) at different MOIs (1, 100, and 10000) at 4°C. It's worth noting that sp11241 and 8-19 achieved complete elimination of SE on eggs after 3 h and 6 h at MOI = 100, and after 2 h and 5 h at MOI = 10000, respectively. After 12 h of treatment with sp11241, a maximum reduction of 3.17 log10 CFU/mL in SE was achieved on raw chicken meat, and a maximum reduction of 3.00 log10 CFU/mL was achieved on lettuce. Phage 8-19 has the same effect on lettuce as sp11241, but is slightly less effective than sp11241 on chicken meat (a maximum 2.69 log10 CFU/mL reduction). In conclusion, sp11241 and 8-19 exhibit considerable potential for controlling Salmonella contamination in food at a low temperature and represent viable candidates as green antibacterial agents for food applications.
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Affiliation(s)
- XiaoWen Sun
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Fan Xue
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Cong Cong
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Bilal Murtaza
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China
| | - LiLi Wang
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian 116600, China
| | - XiaoYu Li
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian 116600, China
| | - ShuYing Li
- Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China
| | - YongPing Xu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China; Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian 116600, China.
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22
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Li H, Zhong W, Zhang X, Rui Z, Yang Y, Xu J, Gao J, Zhou X, Wu J, Xu J. Isolation and Characterization of a Novel Vibrio Phage vB_ValA_R15Z. Curr Microbiol 2024; 81:285. [PMID: 39073500 DOI: 10.1007/s00284-024-03736-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/08/2024] [Indexed: 07/30/2024]
Abstract
Vibrio phages have emerged as a potential alternative to antibiotic therapy for treating Vibrio infections. In this study, a lytic Vibrio phage, vB_ValA_R15Z against Vibrio alginolyticus ATCC 17749T, was isolated from an aquatic water sample collected in Xiamen, China. The phage had an icosahedral head (diameter 69 ± 2 nm) and a short, non-contractile tail measuring 16 ± 2 nm. The genome of vB_ValA_R15Z was found to be a double-stranded DNA consisting of 43, 552 bp, containing 54 coding sequences (CDSs) associated with phage packaging, structure, DNA metabolism, lysis and additional functions. The BLASTN results indicated that vB_ValA_R15Z shared less than 90.18% similarity with known phages recorded in the NCBI GenBank database, suggesting that vB_ValA_R15Z was a novel Vibrio phage. Furthermore, phylogenetic analysis revealed that vB_ValA_R15Z belongs to the genus Kaohsiungvirus. In addition, a typical lytic mechanism (holin-endolysim) was found in the genome of vB_ValA_R15Z, while no antibiotic resistance- or virulence factor-related gene was detected. Overall, the study provides valuable insights into the isolation and characterization of vB_ValA_R15Z, highlighting its potential as an effective phage therapy option for combating Vibrio alginolyticus infections.
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Affiliation(s)
- Huifang Li
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China.
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China.
| | - Wanxuan Zhong
- State Key Laboratory of Trophic Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xinyu Zhang
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Zhang Rui
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518061, Guangdong, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518061, Guangdong, China
| | - Juntian Xu
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jie Gao
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Xing Zhou
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jie Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China.
| | - Jie Xu
- Centre for Regional Oceans, Department of Ocean Science and Technology, Faculty of Science and Technology, University of Macau, Macau, 999078, China.
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23
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Camacho-Beltrán E, Morales-Aguilar JJ, López-Meyer M, Rincón-Enríquez G, Quiñones-Aguilar EE. Complete genome sequence of the Exiguobacterium bacteriophage. Microbiol Resour Announc 2024; 13:e0034224. [PMID: 38860812 PMCID: PMC11256790 DOI: 10.1128/mra.00342-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024] Open
Abstract
We purified a lytic bacteriophage from soil collected in Guasave, Sinaloa: phiExGM16. This bacteriophage was isolated using the host, Exiguobacterium acetilycum. Its 17.6 kb genome contains 33 putative genes and shows a cover of 64% with 76.37% of nucleotide identity to Microbacterium phage Noelani.
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Affiliation(s)
- Erika Camacho-Beltrán
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Zapopan, Jalisco, Mexico
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR-Unidad Sinaloa), Guasave, Sinaloa, Mexico
| | - Juan José Morales-Aguilar
- Universidad Autónoma de Occidente, Unidad Regional Guasave. Avenida Universidad S/N Colonia Villa Universidad, Guasave, Sinaloa, Mexico
| | - Melina López-Meyer
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR-Unidad Sinaloa), Guasave, Sinaloa, Mexico
| | - Gabriel Rincón-Enríquez
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Zapopan, Jalisco, Mexico
| | - Evangelina Esmeralda Quiñones-Aguilar
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Zapopan, Jalisco, Mexico
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24
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Das S, Kaledhonkar S. Physiochemical characterization of a potential Klebsiella phage MKP-1 and analysis of its application in reducing biofilm formation. Front Microbiol 2024; 15:1397447. [PMID: 39086652 PMCID: PMC11288805 DOI: 10.3389/fmicb.2024.1397447] [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: 03/08/2024] [Accepted: 06/20/2024] [Indexed: 08/02/2024] Open
Abstract
The common intestinal pathogen Klebsiella pneumoniae (K. pneumoniae) is one of the leading causes of fatal superbug infections that can resist the effects of commonly prescribed medicines. The uncontrolled use or misuse of antibiotics has increased the prevalence of drug-resistant K. pneumoniae strains in the environment. In the quest to search for alternative therapeutics for treating these drug-resistant infections, bacteriophages (bacterial viruses) emerged as potential candidates for in phage therapy against Klebsiella. The effective formulation of phage therapy against drug-resistant Klebsiella infections demands thorough characterization and screening of many bacteriophages. To contribute effectively to the formulation of successful phage therapy against superbug infections by K. pneumoniae, this study includes the isolation and characterization of a novel lytic bacteriophage MKP-1 to consider its potential to be used as therapeutics in treating drug-resistant Klebsiella infections. Morphologically, having a capsid attached to a long non-contractile tail, it was found to be a siphovirus that belongs to the class Caudoviricetes and showed infectivity against different strains of the target host bacterium. Comparatively, this double-stranded DNA phage has a large burst size and is quite stable in various physiological conditions. More interestingly, it has the potential to degrade the tough biofilms formed by K. pneumoniae (Klebsiella pneumoniae subsp. pneumoniae (Schroeter) Trevisan [ATCC 15380]) significantly. Thus, the following study would contribute effectively to considering phage MKP-1 as a potential candidate for phage therapy against Klebsiella infection.
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Affiliation(s)
| | - Sandip Kaledhonkar
- Department of Bioscience and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
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25
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Villicaña C, Rubí-Rangel LM, Amarillas L, Lightbourn-Rojas LA, Carrillo-Fasio JA, León-Félix J. Isolation and Characterization of Two Novel Genera of Jumbo Bacteriophages Infecting Xanthomonas vesicatoria Isolated from Agricultural Regions in Mexico. Antibiotics (Basel) 2024; 13:651. [PMID: 39061333 PMCID: PMC11273794 DOI: 10.3390/antibiotics13070651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/27/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Bacterial spot is a serious disease caused by several species of Xanthomonas affecting pepper and tomato production worldwide. Since the strategies employed for disease management have been inefficient and pose a threat for environmental and human health, the development of alternative methods is gaining relevance. The aim of this study is to isolate and characterize lytic phages against Xanthomonas pathogens. Here, we isolate two jumbo phages, named XaC1 and XbC2, from water obtained from agricultural irrigation channels by the enrichment technique using X. vesicatoria as a host. We determined that both phages were specific for inducing the lysis of X. vesicatoria strains, but not of other xanthomonads. The XaC1 and XbC2 phages showed a myovirus morphology and were classified as jumbo phages due to their genomes being larger than 200 kb. Phylogenetic and comparative analysis suggests that XaC1 and XbC2 represent both different and novel genera of phages, where XaC1 possesses a low similarity to other phage genomes reported before. Finally, XaC1 and XbC2 exhibited thermal stability up to 45 °C and pH stability from 5 to 9. All these results indicate that the isolated phages are promising candidates for the development of formulations against bacterial spot, although further characterization is required.
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Affiliation(s)
- Claudia Villicaña
- CONAHCYT—Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo, A. C., Culiacán 80110, Sinaloa, Mexico;
| | - Lucía M. Rubí-Rangel
- Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo, A. C., Culiacán 80110, Sinaloa, Mexico;
| | - Luis Amarillas
- Laboratorio de Genética, Instituto de Investigación Lightbourn, A. C., Cd. Jimenez 33981, Chihuahua, Mexico; (L.A.)
| | | | - José Armando Carrillo-Fasio
- Laboratorio de Nematología Agrícola, Centro de Investigación en Alimentación y Desarrollo, A. C., Culiacán 80110, Sinaloa, Mexico;
| | - Josefina León-Félix
- Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo, A. C., Culiacán 80110, Sinaloa, Mexico;
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26
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Suchithra KV, Hameed A, Surya S, Mahammad S, Arun AB. Dual phage-incorporated electrospun polyvinyl alcohol-eudragit nanofiber matrix for rapid healing of diabetic wound infected by Pseudomonas aeruginosa and Staphylococcus aureus. Drug Deliv Transl Res 2024:10.1007/s13346-024-01660-4. [PMID: 38980574 DOI: 10.1007/s13346-024-01660-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2024] [Indexed: 07/10/2024]
Abstract
Diabetic wound healing remains a healthcare challenge due to co-occurring multidrug-resistant (MDR) bacterial infections and the constraints associated with sustained drug delivery. Here, we integrate two new species of phages designated as PseuPha1 and RuSa1 respectively lysing multiple clinical MDR strains of P. aeruginosa and S. aureus into a novel polyvinyl alcohol-eudragit (PVA-EU†) nanofiber matrix through electrospinning for rapid diabetic wound healing. PVA-EU† evaluated for characteristic changes that occurred due to electrospinning and subjected to elution, stability and antibacterial assays. The biocompatibility and wound healing ability of PVA-EU† were assessed through mouse fibroblast cell line NIH3T3, followed by validation through diabetic mice excision wound co-infected with P. aeruginosa and S. aureus. The electrospinning resulted in the incorporation of ~ 75% active phages at PVA-EU†, which were stable at 25 °C for 30 days and at 4 °C for 90 days. PVA-EU† showed sustained release of phages for 18 h and confirmed to be detrimental to both mono- and mixed-cultures of target pathogens. The antibacterial activity of PVA-EU† remained unaltered in the presence of high amounts of glucose, whereas alkaline pH promoted the activity. The matrix exerted no cytotoxicity on NIH3T3, but showed significant (p < 0.0001) wound healing in vitro and the process was rapid as validated through a diabetic mice model. The sustained release, quick wound closure, declined abundance of target MDR bacteria in situ and histopathological signs of recovery corroborated the therapeutic efficacy of PVA-EU†. Taken together, our data signify the potential application of PVA-EU† in the rapid treatment of diabetic wounds without the aid of antibiotics.
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Affiliation(s)
- Kokkarambath Vannadil Suchithra
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore-575018, India
| | - Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore-575018, India.
| | - Suprith Surya
- Advanced Surgical Skill Enhancement Division (ASSEND), Yenepoya (Deemed to Be University), Deralakatte, Mangalore-575018, India
| | - Sajida Mahammad
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore-575018, India
| | - Ananthapadmanabha Bhagwath Arun
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore-575018, India.
- Yenepoya Institute of Arts, Science, Commerce and Management, Balmatta, Mangalore-575002, India.
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27
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Lyytinen OL, Dapuliga C, Wallinger D, Patpatia S, Audu BJ, Kiljunen SJ. Three novel Enterobacter cloacae bacteriophages for therapeutic use from Ghanaian natural waters. Arch Virol 2024; 169:156. [PMID: 38967872 PMCID: PMC11226500 DOI: 10.1007/s00705-024-06081-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 05/15/2024] [Indexed: 07/06/2024]
Abstract
Infections caused by multidrug-resistant (MDR) bacteria are a growing global concern. Enterobacter cloacae complex (ECC) species are particularly adept at developing antibiotic resistance. Phage therapy is proposed as an alternative treatment for pathogens that no longer respond to antibiotics. Unfortunately, ECC phages are understudied when compared to phages of many other bacterial species. In this Ghanaian-Finnish study, we isolated two ECC strains from ready-to-eat food samples and three novel phages from natural waters against these strains. We sequenced the genomic DNA of the novel Enterobacter phages, fGh-Ecl01, fGh-Ecl02, and fGh-Ecl04, and assessed their therapeutic potential. All of the phages were found to be lytic, easy to propagate, and lacking any toxic, integrase, or antibiotic resistance genes and were thus considered suitable for therapy purposes. They all were found to be related to T4-type viruses: fGh-Ecl01 and fGh-Ecl04 to karamviruses and fGh-Ecl02 to agtreviruses. Testing of Finnish clinical ECC strains showed promising susceptibility to these novel phages. As many as 61.1% of the strains were susceptible to fGh-Ecl01 and fGh-Ecl04, and 7.4% were susceptible to fGh-Ecl02. Finally, we investigated the susceptibility of the newly isolated ECC strains to three antibiotics - meropenem, ciprofloxacin, and cefepime - in combination with the novel phages. The use of phages and antibiotics together had synergistic effects. When using an antibiotic-phage combination, even low concentrations of antibiotics fully inhibited the growth of bacteria.
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Affiliation(s)
- O L Lyytinen
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - C Dapuliga
- Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - D Wallinger
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - S Patpatia
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - B J Audu
- National Veterinary Research Institute, Vom, Nigeria
| | - S J Kiljunen
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
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28
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Chakraborty S, Rohit A, Prasanthi SJ, Chauhan A. A New Casjensviridae Bacteriophage Isolated from Hospital Sewage for Inactivation of Biofilms of Carbapenem Resistant Klebsiella pneumoniae Clinical Isolates. Pharmaceutics 2024; 16:904. [PMID: 39065601 PMCID: PMC11280391 DOI: 10.3390/pharmaceutics16070904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Klebsiella pneumoniae, a member of the ESKAPE pathogen group, is a prominent cause of hospital-acquired infections. The WHO has recognized carbapenem-resistant K. pneumoniae as a critical-one priority pathogen. These resilient superbugs have the ability to form biofilms and present a significant global threat. In the present study, we isolated and characterized a bacteriophage SAKp02, from hospital sewage, infectious to carbapenem-resistant K. pneumoniae patient isolates. SAKp02 could infect 43 of 72 clinical isolates, indicating a broad host spectrum. Whole genome analysis classified SAKp02 within the family Casjensviridae, with a 59,343 bp genome encoding 82 ORFs. Comparative genomic analysis revealed significant differences between SAKp02 and its closest viruses, indicating a distinct genetic makeup positioning it as a novel phage strain within the lineage. The SAKp02 genome comprises bacteriolytic enzymes, including holin, endolysin, and phage depolymerase, crucial for bacterial lysis and biofilm disruption. It reduced biofilm biomass by over threefold compared to the control and eradicated 99% of viable cells within a 4 h treatment period. Scanning electron microscopy corroborated the ability of the phage to dismantle biofilm matrices and lyse bacterial cells. Safe and effective treatments are warranted, and hence, the fully characterized lytic phages with therapeutic potential against drug-resistant clinical isolates of bacteria are needed. Our study is the first to report the antibacterial and antibiofilm activity of Casjensviridae phages, and our discovery of a novel K. pneumoniae phage broadens the arsenal against the bacteria.
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Affiliation(s)
- Sambuddha Chakraborty
- Department of Microbiology, Tripura University, Suryamaninagar 799022, India
- Department of Microbiology, University of Delhi South Campus, Benito Jaurez Marg, New Delhi 110021, India
| | - Anusha Rohit
- Madras Medical Mission Hospital, Chennai 600037, India
| | | | - Ashwini Chauhan
- Department of Microbiology, Tripura University, Suryamaninagar 799022, India
- Department of Microbiology, University of Delhi South Campus, Benito Jaurez Marg, New Delhi 110021, India
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Berryhill BA, Burke KB, Fontaine J, Brink CE, Harvill MG, Goldberg DA, Konstantinidis KT, Levin BR, Woodworth MH. Enteric Populations of Escherichia coli are Likely to be Resistant to Phages Due to O Antigen Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.08.566299. [PMID: 37986824 PMCID: PMC10659284 DOI: 10.1101/2023.11.08.566299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
There is a surfeit of bioinformatic data showing that bacteriophages abound in the enteric microbiomes of humans. What is the contribution of these viruses in shaping the bacterial strain and species composition of the gut microbiome and how are these phages maintained over time? To address these questions, we performed experiments with Escherichia coli and phages isolated from four fecal microbiota transplantation (FMT) doses as representative samples of non-dysbiotic enteric microbiota and develop and analyze the properties of a mathematical model of the population and evolutionary dynamics of bacteria and phage. Our models predict and experiments confirm that due to production of the O antigen, E. coli in the enteric microbiome are likely to be resistant to infection with co-occurring phages. Furthermore, our modeling suggests that the phages can be maintained in the population due to the high rates of host transition between resistant and sensitive states, which we call leaky resistance. Based on our observations and model predictions, we postulate that the phages found in the human gut are likely to play little role in shaping the composition of E. coli at the strain level in the enteric microbiome in healthy individuals. How general this is for other species of bacteria in the enteric flora is not yet clear, although O antigen expression is common across many taxa.
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Affiliation(s)
- Brandon A. Berryhill
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
- Program in Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Laney Graduate School, Emory University; Atlanta, Georgia, 30322, USA
| | - Kylie B. Burke
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Jake Fontaine
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Catherine E. Brink
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mason G. Harvill
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - David A. Goldberg
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Konstantinos T. Konstantinidis
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bruce R. Levin
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Michael H. Woodworth
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
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30
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Ragab S, Gouda SM, Abdelmoteleb M, El-Shibiny A. The role of identified and characterized bacteriophage ZCEC13 in controlling pathogenic and multidrug-resistant Escherichia coli in wastewater: in vitro study. ENVIRONMENTAL TECHNOLOGY 2024; 45:3544-3558. [PMID: 37255221 DOI: 10.1080/09593330.2023.2220886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 05/20/2023] [Indexed: 06/01/2023]
Abstract
The spread and development of Multi-Drug Resistant (MDR) bacteria in wastewater became beyond control and a global public health concern. The conventional disinfectants used in wastewater treatment methods have been becoming increasingly ineffective against a range of pathogenic and MDR bacteria. Bacteriophages are considered a novel approach to microbial control. Therefore, this study aims to explore the possibility of using phages against pathogenic and MDR Escherichia coli strains isolated from wastewater treatment plants. The wastewater samples were collected from two different treatment plants for E. coli isolation. The antibiotic sensitivity profile and occurrence of virulence and resistant genes were tested in 28 E. coli isolates. Phage ZCEC13 was selected based on its promising activity and host range to undergo identification and characterization. ZCEC13 was evaluated by transmission electron microscopy, genomic sequencing, in vitro lytic activity and tested for its stability under different conditions such as pH, Ultraviolet light exposure, and temperature. The results reported that ZCEC13 belongs to the Caudoviricetes class, with a high antibacterial dynamic. Phage ZCEC13 displayed high stability at different pH values ranging from 2 to 12, good tolerance to temperatures from -4 to 65°C, and high stability at UV exposure for 120 min. Respectively, the findings showed stability of the phage under several conditions and high efficiency in killing MDR bacteria isolated from the treatment plants. Further studies are encouraged to analyse the efficacy of phages as a microbial control agent in wastewater treatment plants.
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Affiliation(s)
- Samar Ragab
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Shrouk Mohamed Gouda
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | | | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
- Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt
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31
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Bekircan Eski D, Gencer D, Darcan C. Whole-genome sequence of a novel lytic bacteriophage infecting Clavibacter michiganensis subsp. michiganensis from Turkey. J Gen Virol 2024; 105. [PMID: 39007232 DOI: 10.1099/jgv.0.002006] [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] [Indexed: 07/16/2024] Open
Abstract
Clavibacter michiganensis subsp. michiganensis (Cmm) is an important plant-pathogenic bacterium that causes canker and wilt diseases. Biological control of the disease with bacteriophages is an alternative to conventional methods. In this study, Phage33 infecting Cmm was characterized based on morphological and genomic properties. Morphological characteristics such as shape and size were investigated using electron microscopy. The whole genome was sequenced using the Illumina Novaseq 6000 platform and the sequence was assembled and annotated. VICTOR and VIRIDIC were used for determining the phylogeny and comparing viral genomes, respectively. Electron microscopy showed that Phage33 has an icosahedral head with a diameter of ~55 nm and a long, thin, non-contractile tail ~169 nm in length. The genome of Phage33 is 56 324 bp in size, has a GC content of 62.49 % and encodes 67 open reading frames. Thirty-seven ORFs showed high homology to functionally annotated bacteriophage proteins in the NCBI database. The remaining 30 ORFs were identified as hypothetical with unknown functions. The genome contains no antimicrobial resistance, no lysogenicity and no virulence signatures, suggesting that it is a suitable candidate for biocontrol agents. The results of a blastn search showed similarity to the previously reported Xylella phage Sano, with an average nucleotide sequence identity of 92.37 % and query coverage of 91 %. This result was verified using VICTOR and VIRIDIC analysis, and suggests that Phage33 is a new member of the genus Sanovirus under the class Caudoviricetes.
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Affiliation(s)
- Duygu Bekircan Eski
- Department of Biotechnology, Bilecik Seyh Edebali University, 11100 Bilecik, Turkey
| | - Donus Gencer
- Department of Property Protection and Security, Şalpazarı Vocational School, Trabzon University, 61670 Şalpazarı, Trabzon, Turkey
| | - Cihan Darcan
- Department of Molecular Biology and Genetics, Bilecik Seyh Edebali University, 11100 Bilecik, Turkey
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32
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Parra B, Lutz VT, Brøndsted L, Carmona JL, Palomo A, Nesme J, Van Hung Le V, Smets BF, Dechesne A. Characterization and Abundance of Plasmid-Dependent Alphatectivirus Bacteriophages. MICROBIAL ECOLOGY 2024; 87:85. [PMID: 38935220 PMCID: PMC11211187 DOI: 10.1007/s00248-024-02401-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Antimicrobial resistance (AMR) is a major public health threat, exacerbated by the ability of bacteria to rapidly disseminate antimicrobial resistance genes (ARG). Since conjugative plasmids of the incompatibility group P (IncP) are ubiquitous mobile genetic elements that often carry ARG and are broad-host-range, they are important targets to prevent the dissemination of AMR. Plasmid-dependent phages infect plasmid-carrying bacteria by recognizing components of the conjugative secretion system as receptors. We sought to isolate plasmid-dependent phages from wastewater using an avirulent strain of Salmonella enterica carrying the conjugative IncP plasmid pKJK5. Irrespective of the site, we only obtained bacteriophages belonging to the genus Alphatectivirus. Eleven isolates were sequenced, their genomes analyzed, and their host range established using S. enterica, Escherichia coli, and Pseudomonas putida carrying diverse conjugative plasmids. We confirmed that Alphatectivirus are abundant in domestic and hospital wastewater using culture-dependent and culture-independent approaches. However, these results are not consistent with their low or undetectable occurrence in metagenomes. Therefore, overall, our results emphasize the importance of performing phage isolation to uncover diversity, especially considering the potential of plasmid-dependent phages to reduce the spread of ARG carried by conjugative plasmids, and to help combat the AMR crisis.
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Affiliation(s)
- Boris Parra
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Laboratorio de Investigación de Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Concepción, Chile
| | - Veronika T Lutz
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Javiera L Carmona
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alejandro Palomo
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vuong Van Hung Le
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Barth F Smets
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark.
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofs Plads, Building 221, Kgs. Lyngby, 2800, Denmark.
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33
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Han NS, Harada M, Pham-Khanh NH, Kamei K. Isolation, Characterization, and Complete Genome Sequence of Escherichia Phage KIT06 Which Infects Nalidixic Acid-Resistant Escherichia coli. Antibiotics (Basel) 2024; 13:581. [PMID: 39061264 PMCID: PMC11274021 DOI: 10.3390/antibiotics13070581] [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: 05/17/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Escherichia coli (E. coli) is one of the most common sources of infection in humans and animals. The emergence of E. coli which acquires resistance to various antibiotics has made treatment difficult. Bacteriophages can be considered promising agents to expand the options for the treatment of antibiotic-resistant bacteria. This study describes the isolation and characterization of Escherichia phage KIT06, which can infect E. coli resistant to the quinolone antibiotic nalidixic acid. Phage virions possess an icosahedral head that is 93 ± 8 nm in diameter and a contractile tail (116 ± 12 nm × 13 ± 5 nm). The phage was found to be stable under various thermal and pH conditions. A one-step growth curve showed that the latent time of the phage was 20 min, with a burst size of 28 particles per infected cell. Phage KIT06 infected 7 of 12 E. coli strains. It inhibited the growth of the host bacterium and nalidixic acid-resistant E. coli. The lipopolysaccharide and outer membrane proteins of E. coli, tsx and btuB, are phage receptors. Phage KIT06 is a new species of the genus Tequatrovirus with a genome of 167,059 bp consisting of 264 open reading frames (ORFs) that encode gene products related to morphogenesis, replication, regulation, and host lysis. The lack of genes encoding integrase or excisionase indicated that this phage was lytic. Thus, KIT06 could potentially be used to treat antibiotic-resistant E. coli using phage therapy. However, further studies are essential to understand its use in combination with other antimicrobial agents and its safe use in such applications.
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Affiliation(s)
- Nguyen Song Han
- Department of Functional Chemistry, Kyoto Institute of Technology, Kyoto 606-8585, Japan; (N.S.H.); (M.H.)
| | - Mana Harada
- Department of Functional Chemistry, Kyoto Institute of Technology, Kyoto 606-8585, Japan; (N.S.H.); (M.H.)
| | - Nguyen Huan Pham-Khanh
- Department of Biology, College of Natural Sciences, Can Tho University, Can Tho City 900000, Vietnam;
| | - Kaeko Kamei
- Department of Functional Chemistry, Kyoto Institute of Technology, Kyoto 606-8585, Japan; (N.S.H.); (M.H.)
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34
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Ahmad S, Leng Q, Hou G, Liang Y, Li Y, Qu Y. Biological Traits and Comprehensive Genomic Analysis of Novel Enterococcus faecalis Bacteriophage EFP6. Microorganisms 2024; 12:1202. [PMID: 38930584 PMCID: PMC11206139 DOI: 10.3390/microorganisms12061202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 05/21/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Enterococcus faecalis is a prevalent opportunistic pathogen associated with chicken embryonic and neonatal chick mortality, posing a significant challenge in poultry farming. In the current study, E. faecalis strain EF6, isolated from a recent hatchery outbreak, served as the host bacterium for the isolation of a novel phage EFP6, capable of lysing E. faecalis. Transmission electron microscopy revealed a hexagonal head and a short tail, classifying EFP6 as a member of the Autographiviridae family. EFP6 showed sensitivity to ultraviolet radiation and resistance to chloroform. The lytic cycle duration of EFP6 was determined to be 50 min, highlighting its efficacy in host eradication. With an optimal multiplicity of infection of 0.001, EFP6 exhibited a narrow lysis spectrum and strong specificity towards host strains. Additionally, EFP6 demonstrated optimal growth conditions at 40 °C and pH 8.0. Whole genome sequencing unveiled a genome length of 18,147 bp, characterized by a GC concentration of 33.21% and comprising 25 open reading frames. Comparative genomic assessment underscored its collinearity with related phages, notably devoid of lysogenic genes, thus ensuring genetic stability. This in-depth characterization forms the basis for understanding the biological attributes of EFP6 and its potential utilization in phage therapy, offering promising prospects for mitigating E. faecalis-associated poultry infections.
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Affiliation(s)
| | | | | | | | | | - Yonggang Qu
- College of Animal Science and Technology, Shihezi University, Shihezi 832003, China; (S.A.); (Q.L.); (G.H.); (Y.L.); (Y.L.)
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35
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Al-Anany AM, Fatima R, Nair G, Mayol JT, Hynes AP. Temperate phage-antibiotic synergy across antibiotic classes reveals new mechanism for preventing lysogeny. mBio 2024; 15:e0050424. [PMID: 38757974 PMCID: PMC11237771 DOI: 10.1128/mbio.00504-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
A recent demonstration of synergy between a temperate phage and the antibiotic ciprofloxacin suggested a scalable approach to exploiting temperate phages in therapy, termed temperate phage-antibiotic synergy, which specifically interacted with the lysis-lysogeny decision. To determine whether this would hold true across antibiotics, we challenged Escherichia coli with the phage HK97 and a set of 13 antibiotics spanning seven classes. As expected, given the conserved induction pathway, we observed synergy with classes of drugs known to induce an SOS response: a sulfa drug, other quinolones, and mitomycin C. While some β-lactams exhibited synergy, this appeared to be traditional phage-antibiotic synergy, with no effect on the lysis-lysogeny decision. Curiously, we observed a potent synergy with antibiotics not known to induce the SOS response: protein synthesis inhibitors gentamicin, kanamycin, tetracycline, and azithromycin. The synergy results in an eightfold reduction in the effective minimum inhibitory concentration of gentamicin, complete eradication of the bacteria, and, when administered at sub-optimal doses, drastically decreases the frequency of lysogens emerging from the combined challenge. However, lysogens exhibit no increased sensitivity to the antibiotic; synergy was maintained in the absence of RecA; and the antibiotic reduced the initial frequency of lysogeny rather than selecting against formed lysogens. Our results confirm that SOS-inducing antibiotics broadly result in temperate-phage-specific synergy, but that other antibiotics can interact with temperate phages specifically and result in synergy. This is the first report of a means of chemically blocking entry into lysogeny, providing a new means for manipulating the key lysis-lysogeny decision.IMPORTANCEThe lysis-lysogeny decision is made by most bacterial viruses (bacteriophages, phages), determining whether to kill their host or go dormant within it. With over half of the bacteria containing phages waiting to wake, this is one of the most important behaviors in all of biology. These phages are also considered unusable for therapy because of this behavior. In this paper, we show that many antibiotics bias this behavior to "wake" the dormant phages, forcing them to kill their host, but some also prevent dormancy in the first place. These will be important tools to study this critical decision point and may enable the therapeutic use of these phages.
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Affiliation(s)
- Amany M Al-Anany
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rabia Fatima
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gayatri Nair
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jordan T Mayol
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Alexander P Hynes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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36
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Camacho-Beltrán E, Morales-Aguilar JJ, López-Meyer M, Rincón-Enríquez G, Quiñones-Aguilar EE. Complete genome sequence of the Microbacterium enclense bacteriophage phiMiGM15. Microbiol Resour Announc 2024; 13:e0030224. [PMID: 38700345 PMCID: PMC11237405 DOI: 10.1128/mra.00302-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 04/23/2024] [Indexed: 05/05/2024] Open
Abstract
We characterized the complete genome sequence of phiMiGM15, a lytic bacteriophage with siphovirus morphology that infects Microbacterium enclense. Its 48.6 kb genome contains 81 putative genes and shows coverage of 28% with 82.26% of nucleotide identity to Microbacterium phage Caron accession number OQ190481.1.
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Affiliation(s)
- Erika Camacho-Beltrán
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan, Jalisco, Mexico
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR-Unidad Sinaloa), Juan de Dios Bátiz Paredes 250, Guasave, Sinaloa, Mexico
| | - Juan José Morales-Aguilar
- Universidad Autónoma de Occidente, Unidad Regional Guasave. Avenida Universidad S/N Colonia Villa Universidad, Guasave, Sinaloa, Mexico
| | - Melina López-Meyer
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR-Unidad Sinaloa), Juan de Dios Bátiz Paredes 250, Guasave, Sinaloa, Mexico
| | - Gabriel Rincón-Enríquez
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan, Jalisco, Mexico
| | - Evangelina Esmeralda Quiñones-Aguilar
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan, Jalisco, Mexico
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37
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Vukovic D, Gostimirovic S, Cvetanovic J, Gavric D, Aleksic Sabo V, Todorovic D, Medic D, Knezevic P. Antibacterial Potential of Non-Tailed Icosahedral Phages Alone and in Combination with Antibiotics. Curr Microbiol 2024; 81:215. [PMID: 38849666 DOI: 10.1007/s00284-024-03705-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/13/2024] [Indexed: 06/09/2024]
Abstract
Non-tailed icosahedral phages belonging to families Fiersviridae (phages MS2 and Qbeta), Tectiviridae (PRD1) and Microviridae (phiX174) have not been considered in detail so far as potential antibacterial agents. The aim of the study was to examine various aspects of the applicability of these phages as antibacterial agents. Antibacterial potential of four phages was investigated via bacterial growth and biofilm formation inhibition, lytic spectra determination, and phage safety examination. The phage phiX174 was combined with different classes of antibiotics to evaluate potential synergistic interactions. In addition, the incidence of phiX174-insensitive mutants was analyzed. The results showed that only phiX174 out of four phages tested against their corresponding hosts inhibited bacterial growth for > 90% at different multiplicity of infection and that only this phage considerably prevented biofilm formation. Although all phages show the absence of potentially undesirable genes, they also have extremely narrow lytic spectra. The synergism was determined between phage phiX174 and ceftazidime, ceftriaxone, ciprofloxacin, macrolides, and chloramphenicol. It was shown that the simultaneous application of agents is more effective than successive treatment, where one agent is applied first. The analysis of the appearance of phiX174 bacteriophage-insensitive mutants showed that mutations occur with a frequency of 10-3. The examined non-tailed phages have a limited potential for use as antibacterial agents, primarily due to a very narrow lytic spectrum and the high frequency of resistant mutants appearance, but Microviridae can be considered in the future as biocontrol agents against susceptible strains of E. coli in combinations with conventional antimicrobial agents.
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Affiliation(s)
- Darija Vukovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Sonja Gostimirovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Jelena Cvetanovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Damir Gavric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Verica Aleksic Sabo
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | | | - Deana Medic
- Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | - Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia.
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Uskudar-Guclu A, Unlu S, Salih-Dogan H, Yalcin S, Basustaoglu A. Biological and genomic characteristics of three novel bacteriophages and a phage-plasmid of Klebsiella pneumoniae. Can J Microbiol 2024; 70:213-225. [PMID: 38447122 DOI: 10.1139/cjm-2023-0188] [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] [Indexed: 03/08/2024]
Abstract
Bacteriophages have emerged as promising candidates for the treatment of difficult-to-treat bacterial infections. The aim of this study is to isolate and characterize phages infecting carbapenem-resistant and extended-spectrum beta-lactamase producer Klebsiella pneumoniae isolates. Water samples were taken for the isolation of bacteriophages. One-step growth curve, the optimal multiplicity of infection (MOI), thermal and pH stabilities, transmission electron microscopy and whole-genome sequencing of phages were studied. Four phages were isolated and named Klebsiella phage Kpn02, Kpn17, Kpn74, and Kpn13. The optimal MOI and latent periods of phage Kpn02, Kpn17, Kpn74, and Kpn13 were 10, 1, 0.001, and 100 PFU/CFU and 20, 10, 20, and 30 min, respectively. Burst sizes ranged from 811 to 2363. No known antibiotic resistance and virulence genes were identified. No tRNAs were detected except Klebsiella phage Kpn02 which encodes 24 tRNAs. Interestingly, Klebsiella phage Kpn74 was predicted to be a lysogenic phage whose prophage is a linear plasmid molecule with covalently closed ends. Of the Klebsiella-infecting phages presented in current study, virulent phages suggest that they may represent candidate therapeutic agents against MDR K. pneumoniae, based on short latent period, high burst sizes and no known antibiotic resistance and virulence genes in their genomes.
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Affiliation(s)
- Aylin Uskudar-Guclu
- Baskent University, Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkiye
| | - Sezin Unlu
- Baskent University, Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkiye
| | - Hanife Salih-Dogan
- Aydin Adnan Menderes University, Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydin, Turkiye
| | - Suleyman Yalcin
- Ministry of Health General Directorate of Public Health, Microbiology References Laboratory, Ankara, Turkiye
| | - Ahmet Basustaoglu
- Baskent University, Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkiye
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Jhandai P, Mittal D, Gupta R, Kumar M, Khurana R. Therapeutics and prophylactic efficacy of novel lytic Escherichia phage vB_EcoS_PJ16 against multidrug-resistant avian pathogenic E. coli using in vivo study. Int Microbiol 2024; 27:673-687. [PMID: 37632591 DOI: 10.1007/s10123-023-00420-7] [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: 05/19/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/28/2023]
Abstract
Avian pathogenic Escherichia coli (APEC) is the causative agent of avian colibacillosis, which causes significant economic losses to the poultry industry. The growing resistance of bacteria to antibiotics is a major global public health concern. However, there is limited data on the efficacy of phage therapy in effectively controlling and treating APEC infections. In this study, a novel lytic Escherichia phage, vB_EcoS_PJ16, was isolated from poultry farm wastewater and characterized in both in vitro and in vivo conditions. Transmission electron microscopy analysis revealed the presence of an icosahedral head and a long non-contractile tail, classifying the phage under the Caudoviricetes class. Host range determination showed that Escherichia phage vB_EcoS_PJ16 exhibited lytic activity against multiple strains of pathogenic E. coli, while no significant signs of lysis for Klebsiella pneumoniae, Salmonella Typhimurium, Listeria monocytogenes, and Staphylococcus aureus. Biophysical characterization revealed that the isolated phage was sturdy, as it remained viable for up to 300 days at temperatures of 30 °C, 37 °C, and 42 °C and for up to 24 h at pH 5 to 11, with only minor changes in titer. Kinetic analysis at multiplicity of infection (MOI) 0.1 showed a latency period of about 20 min and a burst size of 26.5 phage particles per infected cell for phage vB_EcoS_PJ16. Whole genome sequencing unveiled that the phage vB_EcoS_PJ16 genome consists of a double-stranded linear DNA molecule with 57,756 bp and a GC content of 43.58%. The Escherichia phage vB_EcoS_PJ16 genome consisted of 98 predicted putative ORFs, with no transfer RNA identified in the genome. Among these 98 genes, 34 genes were predicted to have known functions. A significant reduction in APEC viability was observed at MOI 100 during in vitro bacterial challenge tests conducted at different MOIs (0.01, 1, and 100). In vivo oral evaluation of the isolated phage to limit E. coli infections in day-old chicks indicated a decrease in mortality within both the therapeutic (20%) and prophylactic (30%) groups, when compared to the control group. The findings of this study contribute to our current knowledge of Escherichia phages and suggest a potentially effective role of phages in the therapeutic and prophylactic control of antibiotic-resistant APEC strains.
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Affiliation(s)
- Punit Jhandai
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125004, India
| | - Dinesh Mittal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125004, India.
| | - Renu Gupta
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125004, India
| | - Manesh Kumar
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125004, India
| | - Rajesh Khurana
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125004, India
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Feltin C, Garneau JR, Morris CE, Bérard A, Torres-Barceló C. Novel phages of Pseudomonas syringae unveil numerous potential auxiliary metabolic genes. J Gen Virol 2024; 105:001990. [PMID: 38833289 PMCID: PMC11256456 DOI: 10.1099/jgv.0.001990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/07/2024] [Indexed: 06/06/2024] Open
Abstract
Relatively few phages that infect plant pathogens have been isolated and investigated. The Pseudomonas syringae species complex is present in various environments, including plants. It can cause major crop diseases, such as bacterial canker on apricot trees. This study presents a collection of 25 unique phage genomes that infect P. syringae. These phages were isolated from apricot orchards with bacterial canker symptoms after enrichment with 21 strains of P. syringae. This collection comprises mostly virulent phages, with only three being temperate. They belong to 14 genera, 11 of which are newly discovered, and 18 new species, revealing great genetic diversity within this collection. Novel DNA packaging systems have been identified bioinformatically in one of the new phage species, but experimental confirmation is required to define the precise mechanism. Additionally, many phage genomes contain numerous potential auxiliary metabolic genes with diversified putative functions. At least three phages encode genes involved in bacterial tellurite resistance, a toxic metalloid. This suggests that viruses could play a role in bacterial stress tolerance. This research emphasizes the significance of continuing the search for new phages in the agricultural ecosystem to unravel novel ecological diversity and new gene functions. This work contributes to the foundation for future fundamental and applied research on phages infecting phytopathogenic bacteria.
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Affiliation(s)
- Chloé Feltin
- INRAE, Pathologie Végétale, F-84140, Montfavet, France
| | - Julian R. Garneau
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
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Sabri M, El Handi K, Cara O, De Stradis A, Valentini F, Elbeaino T. Xylella phage MATE 2: a novel bacteriophage with potent lytic activity against Xylella fastidiosa subsp. pauca. Front Microbiol 2024; 15:1412650. [PMID: 38863752 PMCID: PMC11165191 DOI: 10.3389/fmicb.2024.1412650] [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: 04/05/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Xylella fastidiosa (Xf) is a major phytosanitary threat to global agricultural production. The complexity and difficulty of controlling Xf underscore the pressing need for novel antibacterial agents, i.e., bacteriophages, which are natural predators of bacteria. In this study, a novel lytic bacteriophage of Xf subsp. pauca, namely Xylella phage MATE 2 (MATE 2), was isolated from sewage water in southern Italy. Biological characterization showed that MATE 2 possessed a broad-spectrum of antibacterial activity against various phytobacteria within the family Xanthomonadaceae, a rapid adsorption time (10 min), and high resistance to a broad range of pH (4-10) and temperatures (4-60°C). Most importantly, MATE 2 was able to suppress the growth of Xf subsp. pauca cells in liquid culture for 7 days, demonstrating its potential as an effective antibacterial agent against Xf. The genomic and electron microscopy analyses revealed that MATE 2 is a new species tentatively belonging to the genus Carpasinavirus within the class Caudoviricetes, with an isometric capsid head of 60 ± 5 nm along with a contractile tail of 120 ± 7.5 nm. Furthermore, the high-throughput sequencing and de novo assembly generated a single contig of 63,695 nucleotides in length; representing a complete genome composed of 95 Open Reading Frames. Bioinformatics analysis performed on MATE 2 genome revealed the absence of lysogenic mediated genes, and genes encoding virulence factors, antibiotic resistance, and toxins. This study adds a new phage to the very short list of Xf-infecting lytic phages, whose in-vitro antibacterial activity has been ascertained, while its efficacy on Xf-infected olive trees in the field has yet to be determined.
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Affiliation(s)
- Miloud Sabri
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
| | - Kaoutar El Handi
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
| | - Orges Cara
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
- Department of Soil, Plant and Food Science, University of Bari, Bari, Italy
| | - Angelo De Stradis
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), University of Bari, Bari, Italy
| | - Franco Valentini
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
| | - Toufic Elbeaino
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Portici, Italy
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Greenrod STE, Cazares D, Johnson S, Hector TE, Stevens EJ, MacLean RC, King KC. Warming alters life-history traits and competition in a phage community. Appl Environ Microbiol 2024; 90:e0028624. [PMID: 38624196 PMCID: PMC11107170 DOI: 10.1128/aem.00286-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024] Open
Abstract
Host-parasite interactions are highly susceptible to changes in temperature due to mismatches in species thermal responses. In nature, parasites often exist in communities, and responses to temperature are expected to vary between host-parasite pairs. Temperature change thus has consequences for both host-parasite dynamics and parasite-parasite interactions. Here, we investigate the impact of warming (37°C, 40°C, and 42°C) on parasite life-history traits and competition using the opportunistic bacterial pathogen Pseudomonas aeruginosa (host) and a panel of three genetically diverse lytic bacteriophages (parasites). We show that phages vary in their responses to temperature. While 37°C and 40°C did not have a major effect on phage infectivity, infection by two phages was restricted at 42°C. This outcome was attributed to disruption of different phage life-history traits including host attachment and replication inside hosts. Furthermore, we show that temperature mediates competition between phages by altering their competitiveness. These results highlight phage trait variation across thermal regimes with the potential to drive community dynamics. Our results have important implications for eukaryotic viromes and the design of phage cocktail therapies.IMPORTANCEMammalian hosts often elevate their body temperatures through fevers to restrict the growth of bacterial infections. However, the extent to which fever temperatures affect the communities of phages with the ability to parasitize those bacteria remains unclear. In this study, we investigate the impact of warming across a fever temperature range (37°C, 40°C, and 42°C) on phage life-history traits and competition using a bacterium (host) and bacteriophage (parasite) system. We show that phages vary in their responses to temperature due to disruption of different phage life-history traits. Furthermore, we show that temperature can alter phage competitiveness and shape phage-phage competition outcomes. These results suggest that fever temperatures have the potential to restrict phage infectivity and drive phage community dynamics. We discuss implications for the role of temperature in shaping host-parasite interactions more widely.
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Affiliation(s)
| | - Daniel Cazares
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Serena Johnson
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Tobias E. Hector
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Emily J. Stevens
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - R. Craig MacLean
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Kayla C. King
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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43
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Karami M, Goudarztalejerdi A, Mohammadzadeh A, Berizi E. In vitro evaluation of two novel Escherichia bacteriophages against multiple drug resistant avian pathogenic Escherichia coli. BMC Infect Dis 2024; 24:497. [PMID: 38755537 PMCID: PMC11100137 DOI: 10.1186/s12879-024-09402-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND In recent years, there has been a growing interest in phage therapy as an effective therapeutic tool against colibacillosis caused by avian pathogenic Escherichia coli (APEC) which resulted from the increasing number of multidrug resistant (MDR) APEC strains. METHODS In the present study, we reported the characterization of a new lytic bacteriophage (Escherichia phage AG- MK-2022. Basu) isolated from poultry slaughterhouse wastewater. In addition, the in vitro bacteriolytic activity of the newly isolated phage (Escherichia phage AG- MK-2022. Basu) and the Escherichia phage VaT-2019a isolate PE17 (GenBank: MK353636.1) were assessed against MDR- APEC strains (n = 100) isolated from broiler chickens with clinical signs of colibacillosis. RESULTS Escherichia phage AG- MK-2022. Basu belongs to the Myoviridae family and exhibits a broad host range. Furthermore, the phage showed stability under a wide range of temperatures, pH values and different concentrations of NaCl. Genome analysis of the Escherichia phage AG- MK-2022. Basu revealed that the phage possesses no antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and any E. coli virulence associated genes. In vitro bacterial challenge tests demonstrated that two phages, the Escherichia phage VaT-2019a isolate PE17 and the Escherichia phage AG- MK-2022. Basu exhibited high bactericidal activity against APEC strains and lysed 95% of the tested APEC strains. CONCLUSIONS The current study findings indicate that both phages could be suggested as safe biocontrol agents and alternatives to antibiotics for controlling MDR-APEC strains isolated from broilers.
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Affiliation(s)
- Mobina Karami
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, 6517658978, Iran
| | - Ali Goudarztalejerdi
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, 6517658978, Iran.
| | - Abdolmajid Mohammadzadeh
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, 6517658978, Iran
| | - Enayat Berizi
- Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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Chen W, Han LM, Chen XZ, Yi PC, Li H, Ren YY, Gao JH, Zhang CY, Huang J, Wang WX, Hu ZL, Hu CM. Engineered endolysin of Klebsiella pneumoniae phage is a potent and broad-spectrum bactericidal agent against "ESKAPEE" pathogens. Front Microbiol 2024; 15:1397830. [PMID: 38784808 PMCID: PMC11112412 DOI: 10.3389/fmicb.2024.1397830] [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: 03/08/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
The rise of antimicrobial resistance in ESKAPEE pathogens poses significant clinical challenges, especially in polymicrobial infections. Bacteriophage-derived endolysins offer promise in combating this crisis, but face practical hurdles. Our study focuses on engineering endolysins from a Klebsiella pneumoniae phage, fusing them with ApoE23 and COG133 peptides. We assessed the resulting chimeric proteins' bactericidal activity against ESKAPEE pathogens in vitro. ApoE23-Kp84B (CHU-1) reduced over 3 log units of CFU for A. baumannii, E. faecalis, K. pneumoniae within 1 h, while COG133-Kp84B (CHU-2) showed significant efficacy against S. aureus. COG133-L1-Kp84B, with a GS linker insertion in CHU-2, exhibited outstanding bactericidal activity against E. cloacae and P. aeruginosa. Scanning electron microscopy revealed alterations in bacterial morphology after treatment with engineered endolysins. Notably, CHU-1 demonstrated promising anti-biofilm and anti-persister cell activity against A. baumannii and E. faecalis but had limited efficacy in a bacteremia mouse model of their coinfection. Our findings advance the field of endolysin engineering, facilitating the customization of these proteins to target specific bacterial pathogens. This approach holds promise for the development of personalized therapies tailored to combat ESKAPEE infections effectively.
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Affiliation(s)
- Wei Chen
- Department of Tuberculosis, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Li-Mei Han
- Department of Tuberculosis, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiu-Zhen Chen
- Department of Infectious Diseases, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Peng-Cheng Yi
- Department of Tuberculosis, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yun-Yao Ren
- Department of Tuberculosis, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Jing-Han Gao
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Cai-Yun Zhang
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Jing Huang
- Department of Clinical Laboratory, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei-Xiao Wang
- Department of Infectious Diseases, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhi-Liang Hu
- Department of Infectious Diseases, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chun-Mei Hu
- Department of Tuberculosis, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
- Innovation Center for Infectious Diseases of Jiangsu Province, Nanjing, China
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Berryhill BA, Burke KB, Smith AP, Morgan JS, Tarabay J, Mamora J, Varkey JB, Mumma JM, Kraft CS. A bacteriophage-based validation of a personal protective equipment doffing procedure to be used with high-consequence pathogens. Infect Control Hosp Epidemiol 2024:1-7. [PMID: 38706211 DOI: 10.1017/ice.2024.84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
OBJECTIVE To determine if the high-level personal protective equipment used in the treatment of high-consequence infectious diseases is effective at stopping the spread of pathogens to healthcare personnel (HCP) while doffing. BACKGROUND Personal protective equipment (PPE) is fundamental to the safety of HCPs. HCPs treating patients with high-consequence infectious diseases use several layers of PPE, forming complex protective ensembles. With high-containment PPE, step-by-step procedures are often used for donning and doffing to minimize contamination risk to the HCP, but these procedures are rarely empirically validated and instead rely on following infection prevention best practices. METHODS A doffing protocol video for a high-containment PPE ensemble was evaluated to determine potential contamination pathways. These potential pathways were tested using fluorescence and genetically marked bacteriophages. RESULTS The experiments revealed existing protocols permit contamination pathways allowing for transmission of bacteriophages to HCPs. Updates to the doffing protocols were generated based on the discovered contamination pathways. This updated doffing protocol eliminated the movement of viable bacteriophages from the outside of the PPE to the skin of the HCP. CONCLUSIONS Our results illustrate the need for quantitative, scientific investigations of infection prevention practices, such as doffing PPE.
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Affiliation(s)
- Brandon A Berryhill
- Department of Biology, Emory University, Atlanta, GA, USA
- Program in Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Laney Graduate School, Emory University, Atlanta, GA, USA
| | - Kylie B Burke
- Department of Biology, Emory University, Atlanta, GA, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Andrew P Smith
- Department of Biology, Emory University, Atlanta, GA, USA
| | | | | | | | - Jay B Varkey
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Healthcare, Atlanta, GA, USA
| | - Joel M Mumma
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Healthcare, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
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Thanki AM, Osei EK, Whenham N, Salter MG, Bedford MR, Masey O’Neill HV, Clokie MRJ. Broad host range phages target global Clostridium perfringens bacterial strains and clear infection in five-strain model systems. Microbiol Spectr 2024; 12:e0378423. [PMID: 38511948 PMCID: PMC11064546 DOI: 10.1128/spectrum.03784-23] [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: 10/26/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024] Open
Abstract
Clostridium perfringens is a prevalent bacterial pathogen in poultry, and due to the spread of antimicrobial resistance, alternative treatments are needed to prevent and treat infection. Bacteriophages (phages), viruses that kill bacteria, offer a viable option and can be used therapeutically to treat C. perfringens infections. The aim of this study was to isolate phages against C. perfringens strains currently circulating on farms across the world and establish their virulence and development potential using host range screening, virulence assays, and larva infection studies. We isolated 32 phages of which 19 lysed 80%-92% of our global C. perfringens poultry strain collection (n = 97). The virulence of these individual phages and 32 different phage combinations was quantified in liquid culture at multiple doses. We then developed a multi-strain C. perfringens larva infection model, to mimic an effective poultry model used by the industry. We tested the efficacy of 16/32 phage cocktails in the larva model. From this, we identified that our phage cocktail consisting of phages CPLM2, CPLM15, and CPLS41 was the most effective at reducing C. perfringens colonization in infected larvae when administered before bacterial challenge. These data suggest that phages do have significant potential to prevent and treat C. perfringens infection in poultry. IMPORTANCE Clostridium perfringens causes foodborne illness worldwide, and 95% of human infections are linked to the consumption of contaminated meat, including chicken products. In poultry, C. perfringens infection causes necrotic enteritis, and associated mortality rates can be up to 50%. However, treating infections is difficult as the bacterium is becoming antibiotic-resistant. Furthermore, the poultry industry is striving toward reduced antibiotic usage. Bacteriophages (phages) offer a promising alternative, and to progress this approach, robust suitable phages and laboratory models that mimic C. perfringens infections in poultry are required. In our study, we isolated phages targeting C. perfringens and found that many lyse C. perfringens strains isolated from chickens worldwide. Consistent with other published studies, in the model systems we assayed here, when some phages were combined as cocktails, the infection was cleared most effectively compared to individual phage use.
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Affiliation(s)
- Anisha M. Thanki
- Department of Genetics and Genome Biology, Leicester Centre for Phage Research, University of Leicester, Leicester, United Kingdom
| | - Emmanuel K. Osei
- Department of Agriculture, Food and the Marine, Teagasc Food Research Centre, Moorepark, Ireland
- APC Microbiome Ireland, University College, Cork, Ireland
| | - Natasha Whenham
- AB Agri, Innovation Way, Peterborough Business Park, Peterborough, United Kingdom
| | - Michael G. Salter
- AB Agri, Innovation Way, Peterborough Business Park, Peterborough, United Kingdom
| | - Mike R. Bedford
- AB Vista, Woodstock Court, Marlborough Business Park, Marlborough, Wiltshire, United Kingdom
| | | | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, Leicester Centre for Phage Research, University of Leicester, Leicester, United Kingdom
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47
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Li J, Cheng R, Wang Z, Yuan W, Xiao J, Zhao X, Du X, Xia S, Wang L, Zhu B, Wang L. Structures and activation mechanism of the Gabija anti-phage system. Nature 2024; 629:467-473. [PMID: 38471529 DOI: 10.1038/s41586-024-07270-x] [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: 06/15/2023] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Prokaryotes have evolved intricate innate immune systems against phage infection1-7. Gabija is a highly widespread prokaryotic defence system that consists of two components, GajA and GajB8. GajA functions as a DNA endonuclease that is inactive in the presence of ATP9. Here, to explore how the Gabija system is activated for anti-phage defence, we report its cryo-electron microscopy structures in five states, including apo GajA, GajA in complex with DNA, GajA bound by ATP, apo GajA-GajB, and GajA-GajB in complex with ATP and Mg2+. GajA is a rhombus-shaped tetramer with its ATPase domain clustered at the centre and the topoisomerase-primase (Toprim) domain located peripherally. ATP binding at the ATPase domain stabilizes the insertion region within the ATPase domain, keeping the Toprim domain in a closed state. Upon ATP depletion by phages, the Toprim domain opens to bind and cleave the DNA substrate. GajB, which docks on GajA, is activated by the cleaved DNA, ultimately leading to prokaryotic cell death. Our study presents a mechanistic landscape of Gabija activation.
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Affiliation(s)
- Jing Li
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Rui Cheng
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiming Wang
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Wuliu Yuan
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jun Xiao
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xinyuan Zhao
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xinran Du
- School of Electronic Information, Wuhan University, Wuhan, China
| | - Shiyu Xia
- Divison of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Lianrong Wang
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Longfei Wang
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
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48
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Nithiya P, Alagarsamy G, Sathish PB, Rajarathnam D, Li X, Jeyaraj S, Satheesh M, Selvakumar R. Impact of effluent parameters and vancomycin concentration on vancomycin resistant Escherichia coli and its host specific bacteriophage lytic activity in hospital effluent. ENVIRONMENTAL RESEARCH 2024; 247:118334. [PMID: 38316381 DOI: 10.1016/j.envres.2024.118334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/07/2024]
Abstract
Vancomycin resistance in bacteria has been classified under high priority category by World Health Organization (WHO) and its presence in hospital effluent is reported to be increasing owing to excess antibiotics use. Among various strategies, bacteriophage has been recently considered as a promising biological agent for combating such antimicrobial resistant bacteria (ARB). However, the influence of effluent's properties on phage-ARB interaction in actual hospital effluent is not completely understood. The present works intends to study this influence of hospital effluent and its parameters on the interaction between vancomycin resistant E. coli (VRE) and its host specific bacteriophage. The isolated VRE was identified by 16S rRNA sequencing, matrix-assisted laser desorption/ionization-time of flight (MALDI - TOF) and whole genome sequencing. The infectivity of phage onto host bacteria was investigated using electron microscopic techniques, dynamic light scattering (DLS), spectrofluorophotometer and confirmed using double agar overlay method. The monovalency and polyvalency of isolated phage against various bacterial species were determined. The phage morphology was identical to T7 phage belonging to Podoviridae. The phage lysis was maximum at pH 7 (90.2%), 37 °C (91.6%) and vancomycin concentration of 50 μg/mL in both synthetic media (89.13%) and effluent (100%). At a maximum vancomycin concentration of 100 μg/mL, decrease in Ca, K, Mg and P (up to 19.70, 14.18, 28, and 15.82% respectively) concentration in effluent was observed due to phage infectivity when compared to control. The whole genome sequencing was performed and the bioinformatics analysis presented the role of mdfA gene encoding the efflux pump in causing vancomycin resistance in E. coli. It also depicted the presence of multiple genes responsible for mercury, cobalt, zinc and cadmium resistance in VRE. These results clearly indicate that bacteriophage mediated combating of VRE is possible in actual hospital effluent and can be used as one of the treatment methods.
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Affiliation(s)
- P Nithiya
- Department of Nanobiotechnology, PSG Institute of Advanced Studies, Coimbatore, 641004, India
| | - G Alagarsamy
- Department of Nanobiotechnology, PSG Institute of Advanced Studies, Coimbatore, 641004, India
| | - P B Sathish
- Department of Nanobiotechnology, PSG Institute of Advanced Studies, Coimbatore, 641004, India
| | - D Rajarathnam
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sankarganesh Jeyaraj
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, 641004, India; PSG Center for Genetics and Molecular Biology, Off Avinashi Road, Coimbatore, 641004, India
| | - Manjima Satheesh
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, 641004, India; PSG Center for Genetics and Molecular Biology, Off Avinashi Road, Coimbatore, 641004, India
| | - R Selvakumar
- Department of Nanobiotechnology, PSG Institute of Advanced Studies, Coimbatore, 641004, India.
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49
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Quinones-Olvera N, Owen SV, McCully LM, Marin MG, Rand EA, Fan AC, Martins Dosumu OJ, Paul K, Sanchez Castaño CE, Petherbridge R, Paull JS, Baym M. Diverse and abundant phages exploit conjugative plasmids. Nat Commun 2024; 15:3197. [PMID: 38609370 PMCID: PMC11015023 DOI: 10.1038/s41467-024-47416-z] [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: 01/04/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 65 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the evolutionarily promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.
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Affiliation(s)
- Natalia Quinones-Olvera
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Siân V Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Lucy M McCully
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Maximillian G Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eleanor A Rand
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Alice C Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Boston University, Boston, MA, 02215, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Oluremi J Martins Dosumu
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Kay Paul
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Cleotilde E Sanchez Castaño
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Rachel Petherbridge
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jillian S Paull
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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50
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Aslam S, Roach D, Nikolich MP, Biswas B, Schooley RT, Lilly-Bishop KA, Rice GK, Cer RZ, Hamilton T, Henry M, Luong T, Salabarria AC, Sisk-Hackworth L, Filippov AA, Lebreton F, Hall L, Nir-Paz R, Onallah H, Livni G, Shostak E, Wieder-Finesod A, Yahav D, Yerushalmy O, Alkalay-Oren S, Braunstein R, Khalifa L, Rimon A, Gelman D, Hazan R. Pseudomonas aeruginosa ventricular assist device infections: findings from ineffective phage therapies in five cases. Antimicrob Agents Chemother 2024; 68:e0172823. [PMID: 38470133 PMCID: PMC10989018 DOI: 10.1128/aac.01728-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
Left ventricular assist devices (LVAD) are increasingly used for management of heart failure; infection remains a frequent complication. Phage therapy has been successful in a variety of antibiotic refractory infections and is of interest in treating LVAD infections. We performed a retrospective review of four patients that underwent five separate courses of intravenous (IV) phage therapy with concomitant antibiotic for treatment of endovascular Pseudomonas aeruginosa LVAD infection. We assessed phage susceptibility, bacterial strain sequencing, serum neutralization, biofilm activity, and shelf-life of phage preparations. Five treatments of one to four wild-type virulent phage(s) were administered for 14-51 days after informed consent and regulatory approval. There was no successful outcome. Breakthrough bacteremia occurred in four of five treatments. Two patients died from the underlying infection. We noted a variable decline in phage susceptibility following three of five treatments, four of four tested developed serum neutralization, and prophage presence was confirmed in isolates of two tested patients. Two phage preparations showed an initial titer drop. Phage biofilm activity was confirmed in two. Phage susceptibility alone was not predictive of clinical efficacy in P. aeruginosa endovascular LVAD infection. IV phage was associated with serum neutralization in most cases though lack of clinical effect may be multifactorial including presence of multiple bacterial isolates with varying phage susceptibility, presence of prophages, decline in phage titers, and possible lack of biofilm activity. Breakthrough bacteremia occurred frequently (while the organism remained susceptible to administered phage) and is an important safety consideration.
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Affiliation(s)
- Saima Aslam
- Division of Infectious Diseases and Global Public Health and the Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Dwayne Roach
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Mikeljon P. Nikolich
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Biswajit Biswas
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
| | - Robert T. Schooley
- Division of Infectious Diseases and Global Public Health and the Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, California, USA
| | | | - Gregory K. Rice
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
- Leidos, Inc, Reston, Virginia, USA
| | - Regina Z. Cer
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
| | - Theron Hamilton
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
| | - Matthew Henry
- Naval Medical Research Command – Frederick, Fort Detrick, Maryland, USA
- The Geneva Foundation, Tacoma, Washington, USA
| | - Tiffany Luong
- Department of Biology, San Diego State University, San Diego, California, USA
| | | | | | - Andrey A. Filippov
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Francois Lebreton
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Lindsey Hall
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ran Nir-Paz
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Hadil Onallah
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Gilat Livni
- Schneider Children’s Medical Center, Petah Tikva, Israel
| | - Eran Shostak
- Schneider Children’s Medical Center, Petah Tikva, Israel
| | - Anat Wieder-Finesod
- The Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Dafna Yahav
- The Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Ortal Yerushalmy
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sivan Alkalay-Oren
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ron Braunstein
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Leron Khalifa
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Rimon
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Gelman
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ronen Hazan
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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