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Maffei E, Woischnig AK, Burkolter MR, Heyer Y, Humolli D, Thürkauf N, Bock T, Schmidt A, Manfredi P, Egli A, Khanna N, Jenal U, Harms A. Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication. Nat Commun 2024; 15:175. [PMID: 38168031 PMCID: PMC10761892 DOI: 10.1038/s41467-023-44157-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Bacteriophages are ubiquitous viral predators that have primarily been studied using fast-growing laboratory cultures of their bacterial hosts. However, microbial life in nature is mostly in a slow- or non-growing, dormant state. Here, we show that diverse phages can infect deep-dormant bacteria and suspend their replication until the host resuscitates ("hibernation"). However, a newly isolated Pseudomonas aeruginosa phage, named Paride, can directly replicate and induce the lysis of deep-dormant hosts. While non-growing bacteria are notoriously tolerant to antibiotic drugs, the combination with Paride enables the carbapenem meropenem to eradicate deep-dormant cultures in vitro and to reduce a resilient bacterial infection of a tissue cage implant in mice. Our work might inspire new treatments for persistent bacterial infections and, more broadly, highlights two viral strategies to infect dormant bacteria (hibernation and direct replication) that will guide future studies on phage-host interactions.
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Affiliation(s)
- Enea Maffei
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | - Anne-Kathrin Woischnig
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Marco R Burkolter
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | - Yannik Heyer
- Biozentrum, University of Basel, Basel, Switzerland
| | - Dorentina Humolli
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | | | - Thomas Bock
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University and University Hospital of Basel, Basel, Switzerland
| | - Nina Khanna
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
| | - Alexander Harms
- Biozentrum, University of Basel, Basel, Switzerland.
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland.
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Friedrich I, Neubauer H, Kuritsyn A, Bodenberger B, Tskhay F, Hartmann S, Poehlein A, Bömeke M, Hoppert M, Schneider D, Hertel R, Daniel R. Brevundimonas and Serratia as host systems for assessing associated environmental viromes and phage diversity by complementary approaches. Front Microbiol 2023; 14:1095850. [PMID: 37025643 PMCID: PMC10070969 DOI: 10.3389/fmicb.2023.1095850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 04/08/2023] Open
Abstract
Focusing on visible plaques for phage isolation leaves the question if we miss the diversity of non-plaque forming phages. We addressed this question through direct plaque-based isolation by employing the new hosts Brevundimonas pondensis LVF1 and Serratia marcescens LVF3 dsDNA, ssDNA, dsRNA, and ssRNA host-associated metavirome analysis. Of the 25 distinctive dsDNA phage isolates, 14 were associated with Brevundimonas and 11 with Serratia. TEM analysis revealed that 6 were myoviruses, 18 siphoviruses and 1 podovirus, while phages infecting Brevundimonas belonged all to siphoviruses. The associated viromes suggested a higher phage diversity in summer than in winter, and dsDNA phages were the dominant group. Isolation of vB_SmaP-Kaonashi was possible after investigating the viromes associated with Serratia, demonstrating the great potential of accompanying host-associated metavirome analysis. The ssDNA virome analysis showed that the B. pondensis LVF1 host is associated with Microviridae and Inoviridae phages, although none of them were isolated. The results demonstrated that the classical isolation technique is not exhausted, leading to the isolation of new dsDNA phages. It can be further improved by combination with metavirome techniques, which revealed further diversity.
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Affiliation(s)
- Ines Friedrich
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Hannes Neubauer
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Alisa Kuritsyn
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Bernhard Bodenberger
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Faina Tskhay
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Sara Hartmann
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Mechthild Bömeke
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Michael Hoppert
- General Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Robert Hertel
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- FG Synthetic Microbiology, Institute of Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- *Correspondence: Rolf Daniel,
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Florent P, Cauchie H, Herold M, Ogorzaly L. Bacteriophages pass through candle-shaped porous ceramic filters: Application for the collection of viruses in soil water. Microbiologyopen 2022; 11:e1314. [PMID: 36314760 PMCID: PMC9490336 DOI: 10.1002/mbo3.1314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/26/2022] [Indexed: 11/15/2022] Open
Abstract
Despite the ubiquity of viruses in soils, their diversity in soil water has not been explored, mainly due to the difficulty of collecting them. In hydrology, soil water is usually collected using porous candles. This study proposes using these porous candles as a new tool for sampling viruses in soil water to analyze their passage through the ceramic part of the candles. The recovery of the viruses was determined after filtration under laboratory conditions using three model bacteriophages (MS2, ΦX174, and Φ6) and Escherichia coli, at neutral and acidic pH. Then, a field experiment was carried out where soil water filtration and viral identification by metagenomic shotgun were performed. At neutral pH, all bacteriophages tested successfully passed through the porous candles during the filtration process, with reductions of 0.02 log, 0.16 log, and 0.55 log for MS2 ΦX174 and Φ6, respectively. At pH 4.4, the passage of MS2 was not affected while ΦX174 underwent a slight reduction in recovery, probably caused by adsorption onto the filter material. Regarding the application of the porous candles in the field, the results obtained allowed the successful recovery of viruses, exposing porous candles as a new method suitable for the collection of viruses from soil water in the context of the study of viral communities.
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Affiliation(s)
- Perrine Florent
- Environmental Research and Innovation Department (ERIN)Luxembourg Institute of Science and Technology (LIST)BelvauxLuxembourg
- Faculté des Sciences, de la Technologie et de la Communication (FSTC), Doctoral School in Science and Engineering (DSSE)University of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Henry‐Michel Cauchie
- Environmental Research and Innovation Department (ERIN)Luxembourg Institute of Science and Technology (LIST)BelvauxLuxembourg
| | - Malte Herold
- Environmental Research and Innovation Department (ERIN)Luxembourg Institute of Science and Technology (LIST)BelvauxLuxembourg
| | - Leslie Ogorzaly
- Environmental Research and Innovation Department (ERIN)Luxembourg Institute of Science and Technology (LIST)BelvauxLuxembourg
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Nazir A, Ali A, Qing H, Tong Y. Emerging Aspects of Jumbo Bacteriophages. Infect Drug Resist 2021; 14:5041-5055. [PMID: 34876823 PMCID: PMC8643167 DOI: 10.2147/idr.s330560] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/30/2021] [Indexed: 01/21/2023] Open
Abstract
The bacteriophages have been explored at a huge scale as a model system for their applications in many biological-related fields. Jumbo phages with a large genome size from 200 to 500 kbp were not previously assigned a great value, and characterized by complex structures coupled with large virions with a wide variety of hosts. The origin of most of the jumbo phages was not well understood; however, many other prominent features have been discovered recently. In the current review, we strive to unearth the most advanced characteristics of jumbo phages, particularly their significance and structural organization that holds immense value to the viral life cycle. The unique characteristics of jumbo phages are the basis of variations in different types of phages concerning their organization at the genomic level, virion structure, evolution, and progeny propagation. The presence of tRNA and additional translation-related genes along with chaperonin genes mark the ability of these phages for being independent of host molecular machinery enabling them to have wide host options. A large number of jumbo phages have been isolated from various sources through advanced standard screening methods. The current review has summarized the available data on jumbo phages and discussed the genome orientation of jumbo phages, translational machinery, diversity and evolution of jumbo phages. In the studies conducted, jumbo phages possessed special additional genes that helps to reduce the dependence of jumbo phages on their hosts. Furthermore, their genomes might have evolved from smaller genome phages.
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Affiliation(s)
- Amina Nazir
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, People’s Republic of China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Azam Ali
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, People’s Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
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Saremi B, Kohls M, Liebig P, Siebert U, Jung K. Measuring reproducibility of virus metagenomics analyses using bootstrap samples from FASTQ-files. Bioinformatics 2021; 37:1068-1075. [PMID: 33135067 DOI: 10.1093/bioinformatics/btaa926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/24/2020] [Accepted: 10/20/2020] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION High-throughput sequencing data can be affected by different technical errors, e.g. from probe preparation or false base calling. As a consequence, reproducibility of experiments can be weakened. In virus metagenomics, technical errors can result in falsely identified viruses in samples from infected hosts. We present a new resampling approach based on bootstrap sampling of sequencing reads from FASTQ-files in order to generate artificial replicates of sequencing runs which can help to judge the robustness of an analysis. In addition, we evaluate a mixture model on the distribution of read counts per virus to identify potentially false positive findings. RESULTS The evaluation of our approach on an artificially generated dataset with known viral sequence content shows in general a high reproducibility of uncovering viruses in sequencing data, i.e. the correlation between original and mean bootstrap read count was highly correlated. However, the bootstrap read counts can also indicate reduced or increased evidence for the presence of a virus in the biological sample. We also found that the mixture-model fits well to the read counts, and furthermore, it provides a higher accuracy on the original or on the bootstrap read counts than on the difference between both. The usefulness of our methods is further demonstrated on two freely available real-world datasets from harbor seals. AVAILABILITY AND IMPLEMENTATION We provide a Phyton tool, called RESEQ, available from https://github.com/babaksaremi/RESEQ that allows efficient generation of bootstrap reads from an original FASTQ-file. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Babak Saremi
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover D-30559, Germany
| | - Moritz Kohls
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover D-30559, Germany
| | - Pamela Liebig
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover D-30559, Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Hannover D-30559, Germany
| | - Klaus Jung
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover D-30559, Germany
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Amarillas L, Villicaña C, Lightbourn-Rojas L, González-Robles A, León-Félix J. The complete genome and comparative analysis of the phage phiC120 infecting multidrug-resistant Escherichia coli and Salmonella strains. G3-GENES GENOMES GENETICS 2021; 11:6114451. [PMID: 33598707 PMCID: PMC8022965 DOI: 10.1093/g3journal/jkab014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/06/2021] [Indexed: 11/25/2022]
Abstract
Phages infecting Salmonella and Escherichia coli are promising agents for therapeutics and biological control of these foodborne pathogens, in particular those strains with resistance to several antibiotics. In an effort to assess the potential of the phage phiC120, a virulent phage isolated from horse feces in Mexico, we characterized its morphology, host range and complete genome. Herein, we showed that phiC120 possesses strong lytic activity against several multidrug-resistant E. coli O157: H7 and Salmonella strains, and its morphology indicated that is a member of Myoviridae family. The phiC120 genome is double-stranded DNA and consists of 186,570 bp in length with a 37.6% G + C content. A total of 281 putative open reading frames (ORFs) and two tRNAs were found, where 150 ORFs encoded hypothetical proteins with unknown function. Comparative analysis showed that phiC120 shared high similarity at nucleotide and protein levels with coliphages RB69 and phiE142. Detailed phiC120 analysis revealed that ORF 94 encodes a putative depolymerase, meanwhile genes encoding factors associated with lysogeny, toxins, and antibiotic resistance were absent; however, ORF 95 encodes a putative protein with potential allergenic and pro-inflammatory properties, making needed further studies to guarantee the safety of phiC120 for human use. The characterization of phiC120 expands our knowledge about the biology of coliphages and provides novel insights supporting its potential for the development of phage-based applications to control unwanted bacteria.
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Affiliation(s)
- Luis Amarillas
- Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo, Sinaloa 80110, México.,Laboratorio de Genética, Instituto de Investigación Lightbourn, Chihuahua 33981, México
| | - Claudia Villicaña
- Laboratorio de Biología Molecular y Genómica Funcional, CONACYT-Centro de Investigación en Alimentación y Desarrollo, Sinaloa 80110, México
| | - Luis Lightbourn-Rojas
- Laboratorio de Genética, Instituto de Investigación Lightbourn, Chihuahua 33981, México
| | - Arturo González-Robles
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Instituto Politécnico Nacional, Ciudad de México 07360, México
| | - Josefina León-Félix
- Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo, Sinaloa 80110, México
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Krylov V, Bourkaltseva M, Pleteneva E, Shaburova O, Krylov S, Karaulov A, Zhavoronok S, Svitich O, Zverev V. Phage phiKZ-The First of Giants. Viruses 2021; 13:149. [PMID: 33498475 PMCID: PMC7909554 DOI: 10.3390/v13020149] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
The paper covers the history of the discovery and description of phiKZ, the first known giant bacteriophage active on Pseudomonas aeruginosa. It also describes its unique features, especially the characteristic manner of DNA packing in the head around a cylinder-shaped structure ("inner body"), which probably governs an ordered and tight packaging of the phage genome. Important properties of phiKZ-like phages include a wide range of lytic activity and the blue opalescence of their negative colonies, and provide a background for the search and discovery of new P. aeruginosa giant phages. The importance of the phiKZ species and of other giant phage species in practical phage therapy is noted given their broad use in commercial phage preparations.
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Affiliation(s)
- Victor Krylov
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Maria Bourkaltseva
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Elena Pleteneva
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Olga Shaburova
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Sergey Krylov
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Alexander Karaulov
- Department of Clinical Immunology and Allergy, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia;
| | - Sergey Zhavoronok
- Department of Infectious Diseases, Belarusian State Medical University, 220116 Minsk, Belarus;
| | - Oxana Svitich
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
- Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
| | - Vitaly Zverev
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
- Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
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Lood C, Danis‐Wlodarczyk K, Blasdel BG, Jang HB, Vandenheuvel D, Briers Y, Noben J, van Noort V, Drulis‐Kawa Z, Lavigne R. Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages. Environ Microbiol 2020; 22:2165-2181. [PMID: 32154616 PMCID: PMC7318152 DOI: 10.1111/1462-2920.14979] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 03/06/2020] [Indexed: 11/28/2022]
Abstract
Pseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage-bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA-Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four non-coding RNAs (ncRNAs) and 93 virion-associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA-Seq revealed a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA-pncB1-nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position our isolate amongst other phages using a gene-sharing network. This integrative omics study illustrates the molecular diversity of jumbo viruses and raises new questions towards cellular regulation and phage-encoded hijacking mechanisms.
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Affiliation(s)
- Cédric Lood
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
- Department of Microbial and Molecular Systems, Laboratory of Computational Systems Biology, KU LeuvenLeuvenBelgium
| | - Katarzyna Danis‐Wlodarczyk
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
- Department of Pathogen Biology and ImmunologyInstitute of Genetics and Microbiology, University of WroclawWroclawPoland
| | - Bob G. Blasdel
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Ho Bin Jang
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Dieter Vandenheuvel
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Yves Briers
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Jean‐Paul Noben
- Biomedical Research Institute and Transnational University LimburgHasselt UniversityDiepenbeekBelgium
| | - Vera van Noort
- Department of Microbial and Molecular Systems, Laboratory of Computational Systems Biology, KU LeuvenLeuvenBelgium
- Institute of Biology, Leiden UniversityLeidenThe Netherlands
| | - Zuzanna Drulis‐Kawa
- Department of Pathogen Biology and ImmunologyInstitute of Genetics and Microbiology, University of WroclawWroclawPoland
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
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9
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Wagemans J, Tsonos J, Holtappels D, Fortuna K, Hernalsteens JP, De Greve H, Estrozi LF, Bacia-Verloop M, Moriscot C, Noben JP, Schoehn G, Lavigne R. Structural Analysis of Jumbo Coliphage phAPEC6. Int J Mol Sci 2020; 21:ijms21093119. [PMID: 32354127 PMCID: PMC7247149 DOI: 10.3390/ijms21093119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 01/24/2023] Open
Abstract
The phAPEC6 genome encodes 551 predicted gene products, with the vast majority (83%) of unknown function. Of these, 62 have been identified as virion-associated proteins by mass spectrometry (ESI-MS/MS), including the major capsid protein (Gp225; present in 1620 copies), which shows a HK97 capsid protein-based fold. Cryo-electron microscopy experiments showed that the 350-kbp DNA molecule of Escherichia coli virus phAPEC6 is packaged in at least 15 concentric layers in the phage capsid. A capsid inner body rod is also present, measuring about 91 nm by 18 nm and oriented along the portal axis. In the phAPEC6 contractile tail, 25 hexameric stacked rings can be distinguished, built of the identified tail sheath protein (Gp277). Cryo-EM reconstruction reveals the base of the unique hairy fibers observed during an initial transmission electron microscopy (TEM) analysis. These very unusual filaments are ordered at three annular positions along the contractile sheath, as well as around the capsid, and may be involved in host interaction.
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Affiliation(s)
- Jeroen Wagemans
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | - Jessica Tsonos
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
- Department of Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium;
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium;
| | - Dominique Holtappels
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | - Kiandro Fortuna
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | | | - Henri De Greve
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium;
- VIB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium
| | - Leandro F. Estrozi
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
| | - Maria Bacia-Verloop
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
| | - Christine Moriscot
- Univ. Grenoble Alpes, CNRS, CEA, EMBL, Integrated Structural Biology Grenoble (ISBG), F-38042 Grenoble, France;
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Agoralaan D, 3590 Hasselt, Belgium;
| | - Guy Schoehn
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
- Correspondence: (G.S.); (R.L.); Tel.: +33-4-5742-8568 (G.S.); +32-16-3795-24 (R.L.)
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
- Correspondence: (G.S.); (R.L.); Tel.: +33-4-5742-8568 (G.S.); +32-16-3795-24 (R.L.)
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10
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Yuan Y, Xi H, Dai J, Zhong Y, Lu S, Wang T, Yang L, Guan Y, Wang P. The characteristics and genome analysis of the novel Y. pestis phage JC221. Virus Res 2020; 283:197982. [PMID: 32315702 DOI: 10.1016/j.virusres.2020.197982] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 10/24/2022]
Abstract
The pathogen of plague is Yersinia pestis (Y. pestis), one of the deadliest pathogens in the world and belonging to the family Enterobacteriaceae. In this work, the biological characteristics and complete genome sequence analysis of a novel lytic Y. pestis-specific phage JC221 isolated from Yunnan Province, China, was studied. JC221 belongs to the Myoviridae family and has a regular icosahedral head and a long contractile tail. The double-stranded DNA genome of JC221 contains 174,931 bp, and the G + C content is 41.23 %. There are 274 predicted genes, of which only 103 hits of genes or gene products are found in database searches, and there are no known virulence-related or antibiotic resistance genes. The genome sequence of JC221 showed <80 % identity to other phages, and evolutionary analysis revealed that bacteriophage JC221 belongs to the Yersinia phage cluster. Furthermore, the bacteriophage could completely lyse most of the tested Y. pestis strains (12/13) at 28 °C and 37 °C, and some Shigella strains could be lysed at 37°C. Morphological and genomic analysis indicated that JC221 is a new Y. pestis phage and a new member of the Tequatrovirus phages. The novel Y. pestis phage JC221 has important reference value for the study of environmental microecology and epidemiology of plague foci.
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Affiliation(s)
- Yue Yuan
- School of Public Health, Kunming Medical University, Kunming, 650106, PR China; Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, PR China.
| | - Hengyu Xi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, PR China.
| | - Jiaxin Dai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, PR China.
| | - Youhong Zhong
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, PR China.
| | - Shuguang Lu
- Department of Microbiology, School of Basic Medical Sciences, Army Military Medical University, Chongqing, 400030, PR China.
| | - Tianqi Wang
- College of Clinical Medicine, Jilin University, Changchun, 130021, PR China.
| | - Lihua Yang
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, PR China.
| | - Yuan Guan
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, PR China.
| | - Peng Wang
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, PR China.
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11
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Imam M, Alrashid B, Patel F, Dowah ASA, Brown N, Millard A, Clokie MRJ, Galyov EE. vB_PaeM_MIJ3, a Novel Jumbo Phage Infecting Pseudomonas aeruginosa, Possesses Unusual Genomic Features. Front Microbiol 2019; 10:2772. [PMID: 31849908 PMCID: PMC6892783 DOI: 10.3389/fmicb.2019.02772] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/13/2019] [Indexed: 01/06/2023] Open
Abstract
Phages are the most abundant biological entity on Earth. There are many variants in phage virion sizes, morphology, and genome sizes. Large virion sized phages, with genome sizes greater than 200 kbp have been identified and termed as Jumbo phages. These phages exhibit certain characteristics that have not been reported in phages with smaller genomes. In this work, a jumbo phage named MIJ3 (vB_PaeM_MIJ3) that infects Pseudomonas aeruginosa PAO1 was isolated from an equine livery yard in Leicestershire, United Kingdom. The genome and biological characteristics of this phage have been investigated. MIJ3 is a Myovirus with multiple long tail fibers. Assessment of the host range of MIJ3 revealed that it has the ability to infect many clinical isolates of P. aeruginosa. Bioinformatics analysis of the phage genome indicated that MIJ3 is closely related to the Pseudomonas phage, PA5oct. MIJ3 possesses several unusual features that are either rarely present in other phages or have not yet been reported. In particular, MIJ3 encodes a FtsH-like protein, and a putative lysidine synthase, TilS. These two proteins have not been reported in phages. MIJ3 also possesses a split DNA polymerase B with a novel intein. Of particular interest, unlike other jumbo phages infecting Pseudomonas spp., MIJ3 lacks the genetic elements required for the formation of the phage nucleus, which was believed to be conserved across jumbo Pseudomonas phages.
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Affiliation(s)
- Mohammed Imam
- Department of Respiratory Sciences, College of Life Sciences, University of Leicester, Leicester, United Kingdom.,Laboratory Department, University Medical Center, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Bandar Alrashid
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom.,King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Faizal Patel
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Ahmed S A Dowah
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Nathan Brown
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Edouard E Galyov
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
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12
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Olszak T, Danis-Wlodarczyk K, Arabski M, Gula G, Maciejewska B, Wasik S, Lood C, Higgins G, Harvey BJ, Lavigne R, Drulis-Kawa Z. Pseudomonas aeruginosa PA5oct Jumbo Phage Impacts Planktonic and Biofilm Population and Reduces Its Host Virulence. Viruses 2019; 11:E1089. [PMID: 31771160 PMCID: PMC6950013 DOI: 10.3390/v11121089] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
The emergence of phage-resistant mutants is a key aspect of lytic phages-bacteria interaction and the main driver for the co-evolution between both organisms. Here, we analyze the impact of PA5oct jumbo phage treatment on planktonic/cell line associated and sessile P. aeruginosa population. Besides its broad-spectrum activity and efficient bacteria reduction in both airway surface liquid (ASL) model, and biofilm matrix degradation, PA5oct appears to persist in most of phage-resistant clones. Indeed, a high percentage of resistance (20/30 clones) to PA5oct is accompanied by the presence of phage DNA within bacterial culture. Moreover, the maintenance of this phage in the bacterial population correlates with reduced P. aeruginosa virulence, coupled with a sensitization to innate immune mechanisms, and a significantly reduced growth rate. We observed rather unusual consequences of PA5oct infection causing an increased inflammatory response of monocytes to P. aeruginosa. This phenomenon, combined with the loss or modification of the phage receptor, makes most of the phage-resistant clones significantly less pathogenic in in vivo model. These findings provide new insights into the general knowledge of giant phages biology and the impact of their application in phage therapy.
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Affiliation(s)
- Tomasz Olszak
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Katarzyna Danis-Wlodarczyk
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Michal Arabski
- Department of Biochemistry and Genetics, Institute of Biology, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Grzegorz Gula
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Slawomir Wasik
- Department of Molecular Physics, Institute of Physics, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Cédric Lood
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
- Laboratory of Computational Systems Biology, KU Leuven, 3000 Leuven, Belgium
| | - Gerard Higgins
- National Children Research Centre, Our Lady’s Children’s Hospital, Crumlin, 12 Dublin, Ireland;
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Brian J. Harvey
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
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13
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Colistin-resistance-mediated bacterial surface modification sensitizes phage infection. Antimicrob Agents Chemother 2019:AAC.01609-19. [PMID: 31570405 DOI: 10.1128/aac.01609-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Colistin is a drug of last resort for the treatment of many multidrug resistant Gram-negative bacteria, including Klebsiella pneumoniae However, bacteria readily acquire resistance to this antibiotic via lipopolysaccharide modifications caused by spontaneous mutations or from enzymes acquired by lateral gene transfer. The fitness cost associated with these modifications remains poorly understood. In this study, we show that colistin-resistant K. pneumoniae are more susceptible to killing by a newly isolated lytic phage than the colistin sensitive parent strain. We observe this behavior for colistin-resistance conferred by a horizontally transferred mcr-1 containing plasmid and also from the inactivation of the chromosomal gene mgrB By measuring zeta potentials, we found that the phage particles were negatively charged at neutral pH and that colistin-resistant bacteria had less negative zeta potentials than did wildtype. These results suggest that the decreased negative surface charge of colistin-resistant cells lowers the electrostatic repulsion between the phage and bacteria, thereby promoting phage adherence and subsequent infection. To further explore this, we tested the effect of phage treatment on K. pneumoniae growing in several different environments. We found that colistin-resistant cells were more susceptible to phage than were the wildtype cells when growing in biofilms or infected moth larvae and when colonizing the mammalian gut. A better understanding of these fitness costs may lead to new treatment approaches that minimize the emergence and spread of colistin-resistant pathogens in human and environmental reservoirs.
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14
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Ramírez-Vargas G, Goh S, Rodríguez C. The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile. Front Microbiol 2018; 9:26. [PMID: 29403466 PMCID: PMC5786514 DOI: 10.3389/fmicb.2018.00026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/08/2018] [Indexed: 12/27/2022] Open
Abstract
Until recently, Clostridium difficile phages were limited to Myoviruses and Siphoviruses of medium genome length (32–57 kb). Here we report the finding of phiCD5763, a Siphovirus with a large extrachromosomal circular genome (132.5 kb, 172 ORFs) and a large capsid (205.6 ± 25.6 nm in diameter) infecting MLST Clade 1 strains of C. difficile. Two subgroups of big phage genomes similar to phiCD5763 were identified in 32 NAPCR1/RT012/ST-54 C. difficile isolates from Costa Rica and in whole genome sequences (WGS) of 41 C. difficile isolates of Clades 1, 2, 3, and 4 from Canada, USA, UK, Belgium, Iraq, and China. Through comparative genomics we discovered another putative big phage genome in a non-NAPCR1 isolate from Costa Rica, phiCD2955, which represents other big phage genomes found in 130 WGS of MLST Clade 1 and 2 isolates from Canada, USA, Hungary, France, Austria, and UK. phiCD2955 (131.6 kb, 172 ORFs) is related to a previously reported C. difficile phage genome, phiCD211/phiCDIF1296T. Detailed genome analyses of phiCD5763, phiCD2955, phiCD211/phiCDIF1296T, and seven other putative C. difficile big phage genome sequences of 131–136 kb reconstructed from publicly available WGS revealed a modular gene organization and high levels of sequence heterogeneity at several hotspots, suggesting that these genomes correspond to biological entities undergoing recombination. Compared to other C. difficile phages, these big phages have unique predicted terminase, capsid, portal, neck and tail proteins, receptor binding proteins (RBPs), recombinases, resolvases, primases, helicases, ligases, and hypothetical proteins. Moreover, their predicted gene load suggests a complex regulation of both phage and host functions. Overall, our results indicate that the prevalence of C. difficile big bacteriophages is more widespread than realized and open new avenues of research aiming to decipher how these viral elements influence the biology of this emerging pathogen.
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Affiliation(s)
- Gabriel Ramírez-Vargas
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Shan Goh
- Pathobiology and Population Studies, Royal Veterinary College, Hatfield, United Kingdom
| | - César Rodríguez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
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15
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Abstract
Tailed bacteriophages with genomes larger than 200 kbp are classified as Jumbo phages, and are rarely isolated by conventional methods. These phages are designated “jumbo” owing to their most notable features of a large phage virion and large genome size. However, in addition to these, jumbo phages also exhibit several novel characteristics that have not been observed for phages with smaller genomes, which differentiate jumbo phages in terms of genome organization, virion structure, progeny propagation, and evolution. In this review, we summarize available reports on jumbo phages and discuss the differences between jumbo phages and small-genome phages. We also discuss data suggesting that jumbo phages might have evolved from phages with smaller genomes by acquiring additional functional genes, and that these additional genes reduce the dependence of the jumbo phages on the host bacteria.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, PR, China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, PR, China
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16
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Buttimer C, Hendrix H, Oliveira H, Casey A, Neve H, McAuliffe O, Ross RP, Hill C, Noben JP, O'Mahony J, Lavigne R, Coffey A. Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB. Front Microbiol 2017; 8:44. [PMID: 28174560 PMCID: PMC5259590 DOI: 10.3389/fmicb.2017.00044] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/06/2017] [Indexed: 11/30/2022] Open
Abstract
Enterobacteria phage vB_PcaM_CBB is a "jumbo" phage belonging to the family Myoviridae. It possesses highly atypical whisker-like structures along the length of its contractile tail. It has a broad host range with the capability of infecting species of the genera Erwinia, Pectobacterium, and Cronobacter. With a genome of 355,922 bp, excluding a predicted terminal repeat of 22,456 bp, phage CBB is the third largest phage sequenced to date. Its genome was predicted to encode 554 ORFs with 33 tRNAs. Based on prediction and proteome analysis of the virions, 29% of its predicted ORFs could be functionally assigned. Protein comparison shows that CBB shares between 33-38% of its proteins with Cronobacter phage GAP32, coliphages PBECO4 and 121Q as well as Klebsiella phage vB_KleM_Rak2. This work presents a detailed and comparative analysis of vB_PcaM_CBB of a highly atypical jumbo myoviridae phage, contributing to a better understanding of phage diversity and biology.
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Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of TechnologyCork, Ireland
| | - Hanne Hendrix
- Laboratory of Gene Technology, KU LeuvenLeuven, Belgium
| | - Hugo Oliveira
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of MinhoBraga, Portugal
| | - Aidan Casey
- Teagasc Food Research Centre, Moorepark Fermoy, Co.Cork, Ireland
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-InstitutKiel, Germany
| | - Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark Fermoy, Co.Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark Fermoy, Co.Cork, Ireland
| | - Colin Hill
- APC Microbiome Institute and School of Microbiology, University CollegeCork, Ireland
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt UniversityDiepenbeek, Belgium
| | - Jim O'Mahony
- Department of Biological Sciences, Cork Institute of TechnologyCork, Ireland
| | - Rob Lavigne
- Laboratory of Gene Technology, KU LeuvenLeuven, Belgium
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of TechnologyCork, Ireland
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17
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Yuan Y, Gao M. Characteristics and complete genome analysis of a novel jumbo phage infecting pathogenic Bacillus pumilus causing ginger rhizome rot disease. Arch Virol 2016; 161:3597-3600. [PMID: 27619796 DOI: 10.1007/s00705-016-3053-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/05/2016] [Indexed: 01/22/2023]
Abstract
Tailed phages with genomes larger than 200 kbp are classified as jumbo phage and exhibit extremely high diversity. In this study, a novel jumbo phage, vB_BpuM_BpSp, infecting pathogenic Bacillus pumilus, the cause of ginger rhizome rot disease, was isolated. Notable features of phage vB_BpuM_BpSp are the large phage capsid of 137 nm and baseplate-attached curly tail fibers. The genome of the phage is 255,569 bp in size with G+C content of 25.9 %, and it shows low similarity to known biological entities. The phage genome contains 318 predicted coding sequences. Among these predicted coding sequences, 26 genes responsible for nucleotide metabolism were found, and seven structural genes could be identified. The findings of this study provide new understanding of the genetic diversity of phages.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
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18
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A proposed integrated approach for the preclinical evaluation of phage therapy in Pseudomonas infections. Sci Rep 2016; 6:28115. [PMID: 27301427 PMCID: PMC4908380 DOI: 10.1038/srep28115] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/27/2016] [Indexed: 12/29/2022] Open
Abstract
Bacteriophage therapy is currently resurging as a potential complement/alternative to antibiotic treatment. However, preclinical evaluation lacks streamlined approaches. We here focus on preclinical approaches which have been implemented to assess bacteriophage efficacy against Pseudomonas biofilms and infections. Laser interferometry and profilometry were applied to measure biofilm matrix permeability and surface geometry changes, respectively. These biophysical approaches were combined with an advanced Airway Surface Liquid infection model, which mimics in vitro the normal and CF lung environments, and an in vivo Galleria larvae model. These assays have been implemented to analyze KTN4 (279,593 bp dsDNA genome), a type-IV pili dependent, giant phage resembling phiKZ. Upon contact, KTN4 immediately disrupts the P. aeruginosa PAO1 biofilm and reduces pyocyanin and siderophore production. The gentamicin exclusion assay on NuLi-1 and CuFi-1 cell lines revealed the decrease of extracellular bacterial load between 4 and 7 logs and successfully prevents wild-type Pseudomonas internalization into CF epithelial cells. These properties and the significant rescue of Galleria larvae indicate that giant KTN4 phage is a suitable candidate for in vivo phage therapy evaluation for lung infection applications.
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19
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Drulis-Kawa Z, Majkowska-Skrobek G, Maciejewska B. Bacteriophages and phage-derived proteins--application approaches. Curr Med Chem 2016; 22:1757-73. [PMID: 25666799 PMCID: PMC4468916 DOI: 10.2174/0929867322666150209152851] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/29/2014] [Accepted: 02/02/2015] [Indexed: 12/17/2022]
Abstract
Currently, the bacterial resistance, especially to most commonly used antibiotics has proved to be a severe therapeutic problem. Nosocomial and community-acquired infections are usually caused by multidrug resistant strains. Therefore, we are forced to develop an alternative or supportive treatment for successful cure of life-threatening infections. The idea of using natural bacterial pathogens such as bacteriophages is already well known. Many papers have been published proving the high antibacterial efficacy of lytic phages tested in animal models as well as in the clinic. Researchers have also investigated the application of non-lytic phages and temperate phages, with promising results. Moreover, the development of molecular biology and novel generation methods of sequencing has opened up new possibilities in the design of engineered phages and recombinant phage-derived proteins. Encouraging performances were noted especially for phage enzymes involved in the first step of viral infection responsible for bacterial envelope degradation, named depolymerases. There are at least five major groups of such enzymes – peptidoglycan hydrolases, endosialidases, endorhamnosidases, alginate lyases and hyaluronate lyases – that have application potential. There is also much interest in proteins encoded by lysis cassette genes (holins, endolysins, spanins) responsible for progeny release during the phage lytic cycle. In this review, we discuss several issues of phage and phage-derived protein application approaches in therapy, diagnostics and biotechnology in general.
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Affiliation(s)
- Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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20
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Khawaja KA, Rauf M, Abbas Z, Rehman SU. A virulent phage JHP against Pseudomonas aeruginosa showed infectivity against multiple genera. J Basic Microbiol 2016; 56:1090-1097. [PMID: 27106788 DOI: 10.1002/jobm.201500764] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/09/2016] [Indexed: 01/08/2023]
Abstract
The resistance to antibiotics in clinically important bacteria is one of the major global health concerns. Phage therapy could be one reliable alternative therapeutic strategy to combat these superbugs. In this study, we assessed host range of a novel bacteriophage, JHP, and characterized for its potential use in phage therapy. The bacteriophage demonstrated infectivity over a broad range of genera including multidrug resistant clinical isolates of Pseudomonas aeruginosa, members of family Enterobacteracae, and other important human pathogens. The antibacterial activity was highest at pH 7, and at temperature of 37 °C. The phage lytic activity gradually decreased till 60 °C and showed no activity when temperature was further raised. The bacteriophage could safely be stored at 4 °C or -20 °C. The latent period of the bacteriophage was 25 min and showed a burst size of 433 virions per cell. The size of JHP genome was approximately 30 kb. Family, Siphoviridae was assigned to JHP based on its icosahedral head with non-contractile tail. The diameter of JHP head and tail length was found 115 and 152 nm, respectively. To sum up, the broad spectrum Siphoviridae phage JHP is an ingenious candidate for phage therapy.
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Affiliation(s)
- Komal Ameer Khawaja
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Mahd Rauf
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Zaigham Abbas
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Shafiq Ur Rehman
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan.
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21
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Essoh C, Latino L, Midoux C, Blouin Y, Loukou G, Nguetta SPA, Lathro S, Cablanmian A, Kouassi AK, Vergnaud G, Pourcel C. Investigation of a Large Collection of Pseudomonas aeruginosa Bacteriophages Collected from a Single Environmental Source in Abidjan, Côte d'Ivoire. PLoS One 2015; 10:e0130548. [PMID: 26115051 PMCID: PMC4482731 DOI: 10.1371/journal.pone.0130548] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/22/2015] [Indexed: 12/12/2022] Open
Abstract
Twenty two distinct bacteriophages were isolated from sewage water from five locations in the city of Abidjan, Côte d'Ivoire over a two-year period, using a collection of Pseudomonas aeruginosa strains with diverse genotypes. The phages were characterized by their virulence spectrum on a panel of selected P. aeruginosa strains from cystic fibrosis patients and by whole genome sequencing. Twelve virions representing the observed diversity were visualised by electron microscopy. The combined observations showed that 17 phages, distributed into seven genera, were virulent, and that five phages were related to temperate phages belonging to three genera. Some showed similarity with known phages only at the protein level. The vast majority of the genetic variations among virulent phages from the same genus resulted from seemingly non-random horizontal transfer events, inside a population of P. aeruginosa phages with limited diversity. This suggests the existence of a single environmental reservoir or ecotype in which continuous selection is taking place. In contrast, mostly point mutations were observed among phages potentially capable of lysogenisation. This is the first study of P. aeruginosa phage diversity in an African city and it shows that a large variety of phage species can be recovered in a limited geographical site at least when different bacterial strains are used. The relative temporal and spatial stability of the Abidjan phage population might reflect equilibrium in the microbial community from which they are released.
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Affiliation(s)
- Christiane Essoh
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Libera Latino
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Cédric Midoux
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Yann Blouin
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Guillaume Loukou
- Laboratoire National de Santé Publique, Abidjan, Côte d’Ivoire
- Laboratoire de Bactériologie-Virologie, département de Sciences pharmaceutiques et Biologiques, Univ Félix Houphouët-Boigny, Abidjan, Côte d’Ivoire
| | - Simon-Pierre A. Nguetta
- Laboratoire de Génétique, Département des Biosciences, Univ Félix Houphouet-Boigny, Abidjan, Côte d’Ivoire
| | - Serge Lathro
- Laboratoire National de Santé Publique, Abidjan, Côte d’Ivoire
| | | | | | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
- ENSTA ParisTech, Université Paris-Saclay, Palaiseau, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
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Olszak T, Zarnowiec P, Kaca W, Danis-Wlodarczyk K, Augustyniak D, Drevinek P, de Soyza A, McClean S, Drulis-Kawa Z. In vitro and in vivo antibacterial activity of environmental bacteriophages against Pseudomonas aeruginosa strains from cystic fibrosis patients. Appl Microbiol Biotechnol 2015; 99:6021-33. [PMID: 25758956 PMCID: PMC4480334 DOI: 10.1007/s00253-015-6492-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 02/03/2015] [Accepted: 02/14/2015] [Indexed: 01/20/2023]
Abstract
The goal of the study was to determine the relationship between in vitro/in vivo efficacy of environmental Pseudomonas phages and certain phenotypical properties of Pseudomonas aeruginosa (PA) strains. We studied the diversity between particular isolates and determined phage sensitivity in vitro and in vivo in the Galleria mellonella insect model. Twenty-eight lytic bacteriophages specific for PA were tested against 121 CF PA isolates including 29 mucoid PA strains. Most strains from cystic fibrosis (CF) patients were lysed by at least three phages (93.6 %), but completely insensitive strains were also present (6.4 %). Two phages PA5oct and KT28 exhibited high rates of lytic potency on 55–68 % of PA strains (72–86 % of mucoid isolates). We further explored phage activity against six PA strains (CF and non-CF) in vitro, comparing clonal differences in phage susceptibility with bacterial properties such as the ability to form biofilms, mucosity, twitching motility, and biochemical profiles. We observed the relationship between variation in phage susceptibility and Fourier transform infrared spectroscopy (FTIR) analysis in the spectra window of carbohydrates. The protective efficacy of two selected phages against PA PAO1 and 0038 infection was confirmed in vivo in G. mellonella larvae. Generally, the wax moth model results confirmed the data from in vitro assays, but in massive infection of CF isolates, the application of lytic phages probably led to the release of toxic compound causing an increase in larvae mortality. We assumed that apart of in vitro phage activity testing, a simple and convenient wax moth larvae model should be applied for the evaluation of in vivo effectiveness of particular phage preparations.
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Affiliation(s)
- Tomasz Olszak
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
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