1
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Robins WP, Meader BT, Toska J, Mekalanos JJ. DdmABC-dependent death triggered by viral palindromic DNA sequences. Cell Rep 2024; 43:114450. [PMID: 39002129 DOI: 10.1016/j.celrep.2024.114450] [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: 05/08/2023] [Revised: 04/24/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024] Open
Abstract
Defense systems that recognize viruses provide important insights into both prokaryotic and eukaryotic innate immunity mechanisms. Such systems that restrict foreign DNA or trigger cell death have recently been recognized, but the molecular signals that activate many of these remain largely unknown. Here, we characterize one such system in pandemic Vibrio cholerae responsible for triggering cell density-dependent death (CDD) of cells in response to the presence of certain genetic elements. We show that the key component is the Lamassu DdmABC anti-phage/plasmid defense system. We demonstrate that signals that trigger CDD were palindromic DNA sequences in phages and plasmids that are predicted to form stem-loop hairpins from single-stranded DNA. Our results suggest that agents that damage DNA also trigger DdmABC activation and inhibit cell growth. Thus, any infectious process that results in damaged DNA, particularly during DNA replication, can in theory trigger DNA restriction and death through the DdmABC abortive infection system.
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Affiliation(s)
- William P Robins
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Bradley T Meader
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jonida Toska
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - John J Mekalanos
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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2
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Chong Qui E, Habtehyimer F, Germroth A, Grant J, Kosanovic L, Singh I, Hancock SP. Mycobacteriophage Alexphander Gene 94 Encodes an Essential dsDNA-Binding Protein during Lytic Infection. Int J Mol Sci 2024; 25:7466. [PMID: 39000573 PMCID: PMC11242194 DOI: 10.3390/ijms25137466] [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: 05/31/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Mycobacteriophages are viruses that specifically infect bacterial species within the genera Mycobacterium and Mycolicibacterium. Over 2400 mycobacteriophages have been isolated on the host Mycolicibacterium smegmatis and sequenced. This wealth of genomic data indicates that mycobacteriophage genomes are diverse, mosaic, and contain numerous (35-60%) genes for which there is no predicted function based on sequence similarity to characterized orthologs, many of which are essential to lytic growth. To fully understand the molecular aspects of mycobacteriophage-host interactions, it is paramount to investigate the function of these genes and gene products. Here we show that the temperate mycobacteriophage, Alexphander, makes stable lysogens with a frequency of 2.8%. Alexphander gene 94 is essential for lytic infection and encodes a protein predicted to contain a C-terminal MerR family helix-turn-helix DNA-binding motif (HTH) and an N-terminal DinB/YfiT motif, a putative metal-binding motif found in stress-inducible gene products. Full-length and C-terminal gp94 constructs form high-order nucleoprotein complexes on 100-500 base pair double-stranded DNA fragments and full-length phage genomic DNA with little sequence discrimination for the DNA fragments tested. Maximum gene 94 mRNA levels are observed late in the lytic growth cycle, and gene 94 is transcribed in a message with neighboring genes 92 through 96. We hypothesize that gp94 is an essential DNA-binding protein for Alexphander during lytic growth. We proposed that gp94 forms multiprotein complexes on DNA through cooperative interactions involving its HTH DNA-binding motif at sites throughout the phage chromosome, facilitating essential DNA transactions required for lytic propagation.
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Affiliation(s)
| | | | | | | | | | | | - Stephen P. Hancock
- Department of Chemistry, Towson University, Towson, MD 21252, USA; (E.C.Q.); (F.H.); (A.G.); (J.G.); (L.K.); (I.S.)
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3
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Casters Y, Bäcker LE, Broux K, Aertsen A. Phage transmission strategies: are phages farming their host? Curr Opin Microbiol 2024; 79:102481. [PMID: 38677076 DOI: 10.1016/j.mib.2024.102481] [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: 12/20/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/29/2024]
Abstract
Extensive coevolution has led to utterly intricate interactions between phages and their bacterial hosts. While both the (short-term) intracellular molecular host-subversion mechanisms during a phage infection cycle and the (long-term) mutational arms race between phages and host cells have traditionally received a lot of attention, there has been an underestimating neglect of (mid-term) transmission strategies by which phages manage to cautiously spread throughout their host population. However, recent findings underscore that phages encode mechanisms to avoid host cell scarcity and promote coexistence with the host, giving the impression that some phages manage to 'farm' their host population to ensure access to host cells for lytic consumption. Given the tremendous impact of phages on bacterial ecology, charting and understanding the complexity of such transmission strategies is of key importance.
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Affiliation(s)
- Yorben Casters
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium
| | - Leonard E Bäcker
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium
| | - Kevin Broux
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium.
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4
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Brauer A, Rosendahl S, Kängsep A, Lewańczyk AC, Rikberg R, Hõrak R, Tamman H. Isolation and characterization of a phage collection against Pseudomonas putida. Environ Microbiol 2024; 26:e16671. [PMID: 38863081 DOI: 10.1111/1462-2920.16671] [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: 03/22/2024] [Accepted: 05/31/2024] [Indexed: 06/13/2024]
Abstract
The environmental bacterium, Pseudomonas putida, possesses a broad spectrum of metabolic pathways. This makes it highly promising for use in biotechnological production as a cell factory, as well as in bioremediation strategies to degrade various aromatic pollutants. For P. putida to flourish in its environment, it must withstand the continuous threats posed by bacteriophages. Interestingly, until now, only a handful of phages have been isolated for the commonly used laboratory strain, P. putida KT2440, and no phage defence mechanisms have been characterized. In this study, we present a new Collection of Environmental P. putida Phages from Estonia, or CEPEST. This collection comprises 67 double-stranded DNA phages, which belong to 22 phage species and 9 phage genera. Our findings reveal that most phages in the CEPEST collection are more infectious at lower temperatures, have a narrow host range, and require an intact lipopolysaccharide for P. putida infection. Furthermore, we show that cryptic prophages present in the P. putida chromosome provide strong protection against the infection of many phages. However, the chromosomal toxin-antitoxin systems do not play a role in the phage defence of P. putida. This research provides valuable insights into the interactions between P. putida and bacteriophages, which could have significant implications for biotechnological and environmental applications.
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Affiliation(s)
- Age Brauer
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Sirli Rosendahl
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Anu Kängsep
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Alicja Cecylia Lewańczyk
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Roger Rikberg
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Rita Hõrak
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Hedvig Tamman
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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5
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Kennedy JW, Jones JD, Meek RMD. Phage therapy. Bone Joint J 2024; 106-B:522-524. [PMID: 38821504 DOI: 10.1302/0301-620x.106b6.bjj-2023-0878.r2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
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6
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Liu K, Wang C, Zhou X, Guo X, Yang Y, Liu W, Zhao R, Song H. Bacteriophage therapy for drug-resistant Staphylococcus aureus infections. Front Cell Infect Microbiol 2024; 14:1336821. [PMID: 38357445 PMCID: PMC10864608 DOI: 10.3389/fcimb.2024.1336821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Drug-resistant Staphylococcus aureus stands as a prominent pathogen in nosocomial and community-acquired infections, capable of inciting various infections at different sites in patients. This includes Staphylococcus aureus bacteremia (SaB), which exhibits a severe infection frequently associated with significant mortality rate of approximately 25%. In the absence of better alternative therapies, antibiotics is still the main approach for treating infections. However, excessive use of antibiotics has, in turn, led to an increase in antimicrobial resistance. Hence, it is imperative that new strategies are developed to control drug-resistant S. aureus infections. Bacteriophages are viruses with the ability to infect bacteria. Bacteriophages, were used to treat bacterial infections before the advent of antibiotics, but were subsequently replaced by antibiotics due to limited theoretical understanding and inefficient preparation processes at the time. Recently, phages have attracted the attention of many researchers again because of the serious problem of antibiotic resistance. This article provides a comprehensive overview of phage biology, animal models, diverse clinical case treatments, and clinical trials in the context of drug-resistant S. aureus phage therapy. It also assesses the strengths and limitations of phage therapy and outlines the future prospects and research directions. This review is expected to offer valuable insights for researchers engaged in phage-based treatments for drug-resistant S. aureus infections.
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Affiliation(s)
- Kaixin Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chao Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xudong Zhou
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- College of Public Health, China Medical University, Shenyang, China
| | - Xudong Guo
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yi Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Wanying Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Rongtao Zhao
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- College of Public Health, Zhengzhou University, Zhengzhou, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- College of Public Health, China Medical University, Shenyang, China
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7
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Yan Y, Zheng J, Zhang X, Yin Y. dbAPIS: a database of anti-prokaryotic immune system genes. Nucleic Acids Res 2024; 52:D419-D425. [PMID: 37889074 PMCID: PMC10767833 DOI: 10.1093/nar/gkad932] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/20/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Anti-prokaryotic immune system (APIS) proteins, typically encoded by phages, prophages, and plasmids, inhibit prokaryotic immune systems (e.g. restriction modification, toxin-antitoxin, CRISPR-Cas). A growing number of APIS genes have been characterized and dispersed in the literature. Here we developed dbAPIS (https://bcb.unl.edu/dbAPIS), as the first literature curated data repository for experimentally verified APIS genes and their associated protein families. The key features of dbAPIS include: (i) experimentally verified APIS genes with their protein sequences, functional annotation, PDB or AlphaFold predicted structures, genomic context, sequence and structural homologs from different microbiome/virome databases; (ii) classification of APIS proteins into sequence-based families and construction of hidden Markov models (HMMs); (iii) user-friendly web interface for data browsing by the inhibited immune system types or by the hosts, and functions for searching and batch downloading of pre-computed data; (iv) Inclusion of all types of APIS proteins (except for anti-CRISPRs) that inhibit a variety of prokaryotic defense systems (e.g. RM, TA, CBASS, Thoeris, Gabija). The current release of dbAPIS contains 41 verified APIS proteins and ∼4400 sequence homologs of 92 families and 38 clans. dbAPIS will facilitate the discovery of novel anti-defense genes and genomic islands in phages, by providing a user-friendly data repository and a web resource for an easy homology search against known APIS proteins.
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Affiliation(s)
- Yuchen Yan
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA
| | | | - Xinpeng Zhang
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA
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8
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [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: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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9
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Loney RE, Delesalle VA, Chaudry BE, Czerpak M, Guffey AA, Goubet-McCall L, McCarty M, Strine MS, Tanke NT, Vill AC, Krukonis GP. A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations. Viruses 2023; 15:2267. [PMID: 38005943 PMCID: PMC10674732 DOI: 10.3390/v15112267] [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: 10/14/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range assays, our data suggest that these phages are adapting to hosts with different cell walls.
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Affiliation(s)
- Rachel E. Loney
- University Program in Genetics and Genomics, School of Medicine, Duke University, Durham, NC 27708, USA
| | - Véronique A. Delesalle
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | | | - Megan Czerpak
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | - Alexandra A. Guffey
- Janssen Scientific Affairs, LLC. 200 Tournament Dr., Horsham, PA 19044, USA;
| | - Leo Goubet-McCall
- Department of Biology, The Pennsylvania State University, 201 Huck Life Sciences Building, University Park, PA 16802, USA;
| | - Michael McCarty
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | - Madison S. Strine
- Department of Immunobiology, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA;
| | - Natalie T. Tanke
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Albert C. Vill
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA;
| | - Greg P. Krukonis
- Department of Biology, Angelo State University, Cavness Science Building 101, ASU Station #10890, San Angelo, TX 76909, USA;
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10
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Bens L, Green SI, Jansen D, Hillary T, Vanhoutvin T, Matthijnssens J, Sabino J, Vermeire S, Van Laethem A, Wagemans J, Lavigne R. Phage therapy for hidradenitis suppurativa: a unique challenge and possible opportunity for personalized treatment of a complex, inflammatory disease. Clin Exp Dermatol 2023; 48:1221-1229. [PMID: 37315154 DOI: 10.1093/ced/llad207] [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: 04/25/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023]
Abstract
Phage therapy is an emerging antimicrobial treatment for critical multidrug-resistant pathogens. In this review, the specific potential and challenges of phage therapy for patients with hidradenitis suppurativa (HS) are discussed. This represents a unique challenge as HS is a chronic inflammatory disease, but presenting with acute exacerbations, which have an enormous negative impact on patient's quality of life. The therapeutic arsenal for HS has expanded in the past decade, for example, with adalimumab and several other biologicals that are currently under investigation. However, treatment of HS remains challenging for dermatologists because there are individuals who do not respond to any classes of the current treatment options when used for a first or second time. Furthermore, after several courses of treatment, a patient may lose their response to therapy, meaning long-term use is not always an option. Culturing studies and 16S ribosomal RNA profiling highlight the complex polymicrobial nature of HS lesions. Despite the detection of various bacterial species in lesion samples, several key pathogens, including Staphylococcus, Corynebacterium and Streptococcus, may be potential targets for phage therapy. Using phage therapy for the treatment of a chronic inflammatory disease could potentially provide new insights into the role of bacteria and the immune system in HS development. In addition, it is possible more details on the immunomodulatory effects of phages may come to light.
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Affiliation(s)
| | | | - Daan Jansen
- Microbiology, Immunology and Transplantation, Rega Institute, KU LeuvenBelgium
| | | | | | - Jelle Matthijnssens
- Microbiology, Immunology and Transplantation, Rega Institute, KU LeuvenBelgium
| | - João Sabino
- Gastroenterology and Hepatology, UZ Leuven, Leuven, Belgium
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11
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Thabet MA, Penadés JR, Haag AF. The ClpX protease is essential for inactivating the CI master repressor and completing prophage induction in Staphylococcus aureus. Nat Commun 2023; 14:6599. [PMID: 37852980 PMCID: PMC10584840 DOI: 10.1038/s41467-023-42413-0] [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: 09/22/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Bacteriophages (phages) are the most abundant biological entities on Earth, exerting a significant influence on the dissemination of bacterial virulence, pathogenicity, and antimicrobial resistance. Temperate phages integrate into the bacterial chromosome in a dormant state through intricate regulatory mechanisms. These mechanisms repress lytic genes while facilitating the expression of integrase and the CI master repressor. Upon bacterial SOS response activation, the CI repressor undergoes auto-cleavage, producing two fragments with the N-terminal domain (NTD) retaining significant DNA-binding ability. The process of relieving CI NTD repression, essential for prophage induction, remains unknown. Here we show a specific interaction between the ClpX protease and CI NTD repressor fragment of phages Ф11 and 80α in Staphylococcus aureus. This interaction is necessary and sufficient for prophage activation after SOS-mediated CI auto-cleavage, defining the final stage in the prophage induction cascade. Our findings unveil unexpected roles of bacterial protease ClpX in phage biology.
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Affiliation(s)
- Mohammed A Thabet
- School of Infection & Immunity, University of Glasgow, G12 8TA, Glasgow, UK
- Department of Biology, Faculty of Science, Al-Baha University, Al-Baha city, Al Aqiq, 65779, Kingdom of Saudi Arabia
| | - José R Penadés
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Andreas F Haag
- School of Infection & Immunity, University of Glasgow, G12 8TA, Glasgow, UK.
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK.
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12
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Mallawaarachchi V, Roach MJ, Decewicz P, Papudeshi B, Giles SK, Grigson SR, Bouras G, Hesse RD, Inglis LK, Hutton ALK, Dinsdale EA, Edwards RA. Phables: from fragmented assemblies to high-quality bacteriophage genomes. Bioinformatics 2023; 39:btad586. [PMID: 37738590 PMCID: PMC10563150 DOI: 10.1093/bioinformatics/btad586] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/14/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023] Open
Abstract
MOTIVATION Microbial communities have a profound impact on both human health and various environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of challenges in viral assembly, fragmentation of genomes can occur, and existing tools may recover incomplete genome fragments. Therefore, the identification and characterization of novel phage genomes remain a challenge, leading to the need of improved approaches for phage genome recovery. RESULTS We introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make. AVAILABILITY AND IMPLEMENTATION Phables is available on GitHub at https://github.com/Vini2/phables.
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Affiliation(s)
- Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Michael J Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Przemyslaw Decewicz
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Sarah K Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Susanna R Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- The Department of Surgery—Otolaryngology Head and Neck Surgery, Central Adelaide Local Health Network, Adelaide, South Australia 5000, Australia
| | - Ryan D Hesse
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Laura K Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Abbey L K Hutton
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Elizabeth A Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
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13
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Mallawaarachchi V, Roach MJ, Decewicz P, Papudeshi B, Giles SK, Grigson SR, Bouras G, Hesse RD, Inglis LK, Hutton ALK, Dinsdale EA, Edwards RA. Phables: from fragmented assemblies to high-quality bacteriophage genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535632. [PMID: 37066369 PMCID: PMC10104058 DOI: 10.1101/2023.04.04.535632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Microbial communities influence both human health and different environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies, and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of the challenges in viral assembly, fragmentation of genomes can occur, leading to the need for new approaches in viral identification. Therefore, the identification and characterisation of novel phages remain a challenge. We introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make. Phables is available on GitHub at https://github.com/Vini2/phables.
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Affiliation(s)
- Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Michael J Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Sarah K Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Susanna R Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - George Bouras
- Adelaide Medical School, The University of Adelaide, North Tce, Adelaide, SA, 5000, Australia
| | - Ryan D Hesse
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Laura K Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Abbey L K Hutton
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Elizabeth A Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
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14
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Prosdocimi F, Cortines JR, José MV, Farias ST. Decoding viruses: An alternative perspective on their history, origins and role in nature. Biosystems 2023; 231:104960. [PMID: 37437771 DOI: 10.1016/j.biosystems.2023.104960] [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: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/14/2023]
Abstract
This article provides an alternative perspective on viruses, exploring their origins, ecology, and evolution. Viruses are recognized as the most prevalent biological entities on Earth, permeating nearly all environments and forming the virosphere-a significant biological layer. They play a crucial role in regulating bacterial populations within ecosystems and holobionts, influencing microbial communities and nutrient recycling. Viruses are also key drivers of molecular evolution, actively participating in the maintenance and regulation of ecosystems and cellular organisms. Many eukaryotic genomes contain genomic elements with viral origins, which contribute to organismal equilibrium and fitness. Viruses are involved in the generation of species-specific orphan genes, facilitating adaptation and the development of unique traits in biological lineages. They have been implicated in the formation of vital structures like the eukaryotic nucleus and the mammalian placenta. The presence of virus-specific genes absent in cellular organisms suggests that viruses may pre-date cellular life. Like progenotes, viruses are ribonucleoprotein entities with simpler capsid architectures compared to proteolipidic membranes. This article presents a comprehensive scenario describing major transitions in prebiotic evolution and proposes that viruses emerged prior to the Last Universal Common Ancestor (LUCA) during the progenote era. However, it is important to note that viruses do not form a monophyletic clade, and many viral taxonomic groups originated more recently as reductions of cellular structures. Thus, viral architecture should be seen as an ancient and evolutionarily stable strategy adopted by biological systems. The goal of this article is to reshape perceptions of viruses, highlighting their multifaceted significance in the complex tapestry of life and fostering a deeper understanding of their origins, ecological impact, and evolutionary dynamics.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Juliana Reis Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, CDMX, Mexico
| | - Sávio Torres Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK
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15
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Flint R, Laucirica DR, Chan HK, Chang BJ, Stick SM, Kicic A. Stability Considerations for Bacteriophages in Liquid Formulations Designed for Nebulization. Cells 2023; 12:2057. [PMID: 37626867 PMCID: PMC10453214 DOI: 10.3390/cells12162057] [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: 07/13/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Pulmonary bacterial infections present a significant health risk to those with chronic respiratory diseases (CRDs) including cystic fibrosis (CF) and chronic-obstructive pulmonary disease (COPD). With the emergence of antimicrobial resistance (AMR), novel therapeutics are desperately needed to combat the emergence of resistant superbugs. Phage therapy is one possible alternative or adjunct to current antibiotics with activity against antimicrobial-resistant pathogens. How phages are administered will depend on the site of infection. For respiratory infections, a number of factors must be considered to deliver active phages to sites deep within the lung. The inhalation of phages via nebulization is a promising method of delivery to distal lung sites; however, it has been shown to result in a loss of phage viability. Although preliminary studies have assessed the use of nebulization for phage therapy both in vitro and in vivo, the factors that determine phage stability during nebulized delivery have yet to be characterized. This review summarizes current findings on the formulation and stability of liquid phage formulations designed for nebulization, providing insights to maximize phage stability and bactericidal activity via this delivery method.
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Affiliation(s)
- Rohan Flint
- School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia;
- Wal-yan Respiratory Research Center, Telethon Kids Institute, The University of Western Australia, Perth, WA 6009, Australia; (D.R.L.); (S.M.S.)
| | - Daniel R. Laucirica
- Wal-yan Respiratory Research Center, Telethon Kids Institute, The University of Western Australia, Perth, WA 6009, Australia; (D.R.L.); (S.M.S.)
| | - Hak-Kim Chan
- Advanced Drug Delivery Group, School of Pharmacy, University of Sydney, Sydney, NSW 2050, Australia;
| | - Barbara J. Chang
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia;
| | - Stephen M. Stick
- Wal-yan Respiratory Research Center, Telethon Kids Institute, The University of Western Australia, Perth, WA 6009, Australia; (D.R.L.); (S.M.S.)
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Perth, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Anthony Kicic
- Wal-yan Respiratory Research Center, Telethon Kids Institute, The University of Western Australia, Perth, WA 6009, Australia; (D.R.L.); (S.M.S.)
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Perth, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA 6009, Australia
- School of Population Health, Curtin University, Perth, WA 6102, Australia
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16
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Marshall K, Marsella R. Topical Bacteriophage Therapy for Staphylococcal Superficial Pyoderma in Horses: A Double-Blind, Placebo-Controlled Pilot Study. Pathogens 2023; 12:828. [PMID: 37375518 DOI: 10.3390/pathogens12060828] [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: 05/22/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Increased antimicrobial resistance highlights the need for alternatives to antibiotics. Bacteriophages, which are benign viruses that kill bacteria, are promising. We studied the efficacy of topical bacteriophages for treating equine staphylococcal superficial pyodermas. Eight Staphylococcus aureus isolates were tested against a bacteriophage bank, and a cocktail consisting of two bacteriophages was prepared. Twenty horses with clinical and cytological evidence of superficial pyoderma and confirmed S. aureus infection based on swabbed culture were enrolled in the study. Each horse received both the bacteriophage cocktail and the placebo at two different infection sites, once daily for four weeks. Clinical lesions and cytology were evaluated weekly by an investigator who was unaware of the treatment sites. All infection sites were swabbed and cultured at the end of the study. A linear mixed model showed no significant differences between the placebo and treatment sites in terms of clinical signs, cytological scores of inflammation, and bacterial counts at the end of the study. It is possible that the bacteriophage cocktail killed S. aureus, but cytology scores did not change as new populations of cocci took over. The study limitations included a small sample size and inconsistent control of the underlying causes of pyodermas.
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Affiliation(s)
- Kalie Marshall
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, 2015 SW 16th Avenue, Gainesville, FL 32610, USA
| | - Rosanna Marsella
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, 2015 SW 16th Avenue, Gainesville, FL 32610, USA
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17
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Liu H, Kheirvari M, Tumban E. Potential Applications of Thermophilic Bacteriophages in One Health. Int J Mol Sci 2023; 24:8222. [PMID: 37175929 PMCID: PMC10179064 DOI: 10.3390/ijms24098222] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/26/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Bacteriophages have a wide range of applications such as combating antibiotic resistance, preventing food contamination for food safety, and as biomarkers to indirectly assess the quality of water. Additionally, bacteriophage components (endolysins and coat proteins) have a lot of applications in food processing, vaccine design, and the delivery of cargo to the body. Therefore, bacteriophages/components have a multitude of applications in human, plant/veterinary, and environmental health (One Health). Despite their versatility, bacteriophage/component use is mostly limited to temperatures within 4-40 °C. This limits their applications (e.g., in food processing conditions, pasteurization, and vaccine design). Advances in thermophilic bacteriophage research have uncovered novel thermophilic endolysins (e.g., ΦGVE2 amidase and MMPphg) that can be used in food processing and in veterinary medicine. The endolysins are thermostable at temperatures > 65 °C and have broad antimicrobial activities. In addition to thermophilic endolysins, enzymes (DNA polymerase and ligases) derived from thermophages have different applications in molecular biology/biotechnology: to generate DNA libraries and develop diagnostics for human and animal pathogens. Furthermore, coat proteins from thermophages are being explored to develop virus-like particle platforms with versatile applications in human and animal health. Overall, bacteriophages, especially those that are thermophilic, have a plethora of applications in One Health.
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Affiliation(s)
| | | | - Ebenezer Tumban
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA
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18
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Gómez MC, Mondragon EI, Molano EL, Hidalgo-Troya A, Mármol-Martínez MA, Guerrero-Ceballos DL, Pantoja MA, Paz-García C, Gómez-Arrieta J, Burbano-Rosero M. Mathematical model of interaction Escherichia coli and Coliphages. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:9712-9727. [PMID: 37322908 DOI: 10.3934/mbe.2023426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We propose a mathematical model based in ordinary differential equations between bacterial pathogen and Bacteriophages to describe the infection dynamics of these populations, for which we use a nonlinear function with an inhibitory effect. We study the stability of the model using the Lyapunov theory and the second additive compound matrix and perform a global sensitivity analysis to elucidate the most influential parameters in the model, besides we make a parameter estimation using growth data of Escherichia coli (E.coli) bacteria in presence of Coliphages (bacteriophages that infect E.coli) with different multiplicity of infection. We found a threshold that indicates whether the bacteriophage concentration will coexist with the bacterium (the coexistence equilibrium) or become extinct (phages extinction equilibrium), the first equilibrium is locally asymptotically stable while the other is globally asymptotically stable depending on the magnitude of this threshold. Beside we found that the dynamics of the model is particularly affected by infection rate of bacteria and Half-saturation phages density. Parameter estimation show that all multiplicities of infection are effective in eliminating infected bacteria but the smaller one leaves a higher number of bacteriophages at the end of this elimination.
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Affiliation(s)
- Miller Cerón Gómez
- Department of Mathematics, University of Narño, Pasto, Clle 18 - Cra 50, Colombia
| | | | - Eddy Lopez Molano
- Department of Biology, University of Narño, Pasto, Clle 18 - Cra 50, Colombia
| | | | | | | | - Mario A Pantoja
- Department of Biology, University of Narño, Pasto, Clle 18 - Cra 50, Colombia
| | - Camilo Paz-García
- Department of Biology, University of Narño, Pasto, Clle 18 - Cra 50, Colombia
| | - Jenny Gómez-Arrieta
- Department of Biology, University of Narño, Pasto, Clle 18 - Cra 50, Colombia
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19
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Jones JD, Trippett C, Suleman M, Clokie MRJ, Clark JR. The Future of Clinical Phage Therapy in the United Kingdom. Viruses 2023; 15:721. [PMID: 36992430 PMCID: PMC10053292 DOI: 10.3390/v15030721] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Bacteriophage (phage) therapy is a promising alternative antimicrobial strategy with the potential to transform the way bacterial infections are treated. In the United Kingdom, phages are classed as a biological medicine. Although no phages are licensed for UK use, they may be used as unlicensed medicinal products where licensed alternatives cannot meet a patient's clinical needs. In the last 2 years, 12 patients in the UK have received phage therapy, and there is burgeoning clinical interest. Currently, clinical phage provision in the UK is ad hoc and relies upon networking with international sources of phages. The provision of phage therapy in the UK will not progress beyond an increasing number of ad hoc cases until an onshore sustainable and scalable source of well-characterised phages manufactured in accordance with Good Manufacturing Practice (GMP) is established. Here, we present an exciting new collaboration between UK Phage Therapy, the Centre for Phage Research at University of Leicester, CPI, and Fixed Phage. These partners, and others as we develop, will establish sustainable, scalable, and equitable phage therapy provision in the UK. We set out a vision for how phage therapy will be integrated into the NHS and healthcare more broadly, including the complementarity between licensed (cocktail) and unlicensed (personalised) phage preparations. Key elements of phage therapy infrastructure in the UK will be GMP phage manufacturing, a national phage library, and a national clinical phage centre. Together, this infrastructure will support NHS microbiology departments to develop and oversee phage therapy provision across the UK. As it will take time to deliver this, we also describe considerations for clinicians seeking to use unlicensed phage therapy in the interim. In summary, this review sets out a roadmap for the delivery of clinical phage therapy to the UK, the benefits of which we hope will reverberate for patients for decades to come.
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Affiliation(s)
| | - Clare Trippett
- CPI, 1 Union Square, Central Park, Darlington DL1 1GL, UK
| | - Mehrunisha Suleman
- The Ethox Centre, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford OX3 7LF, UK
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Jason R. Clark
- Fixed Phage, West of Scotland Science Park, Block 2, Kelvin Campus, 2317 Maryhill Road, Glasgow G20 0SP, UK
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20
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Pardo-Freire M, Domingo-Calap P. Phages and Nanotechnology: New Insights against Multidrug-Resistant Bacteria. BIODESIGN RESEARCH 2023; 5:0004. [PMID: 37849463 PMCID: PMC10521656 DOI: 10.34133/bdr.0004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/21/2022] [Indexed: 10/19/2023] Open
Abstract
Bacterial infections are a major threat to the human healthcare system worldwide, as antibiotics are becoming less effective due to the emergence of multidrug-resistant strains. Therefore, there is a need to explore nontraditional antimicrobial alternatives to support rapid interventions and combat the spread of pathogenic bacteria. New nonantibiotic approaches are being developed, many of them at the interface of physics, nanotechnology, and microbiology. While physical factors (e.g., pressure, temperature, and ultraviolet light) are typically used in the sterilization process, nanoparticles and phages (bacterial viruses) are also applied to combat pathogenic bacteria. Particularly, phage-based therapies are rising due to the unparalleled specificity and high bactericidal activity of phages. Despite the success of phages mostly as compassionate use in clinical cases, some drawbacks need to be addressed, mainly related to their stability, bioavailability, and systemic administration. Combining phages with nanoparticles can improve their performance in vivo. Thus, the combination of nanotechnology and phages might provide tools for the rapid and accurate detection of bacteria in biological samples (diagnosis and typing), and the development of antimicrobials that combine the selectivity of phages with the efficacy of targeted therapy, such as photothermal ablation or photodynamic therapies. In this review, we aim to provide an overview of how phage-based nanotechnology represents a step forward in the fight against multidrug-resistant bacteria.
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Affiliation(s)
- Marco Pardo-Freire
- Institute for Integrative Systems Biology, I2SysBio, Universitat de València-CSIC, 46980 Paterna, Spain
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology, I2SysBio, Universitat de València-CSIC, 46980 Paterna, Spain
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21
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Jones JD, Varghese D, Pabary R, Langley RJ. The potential of bacteriophage therapy in the treatment of paediatric respiratory infections. Paediatr Respir Rev 2022; 44:70-77. [PMID: 35241371 DOI: 10.1016/j.prrv.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/14/2022]
Abstract
The looming antibiotic resistance crisis is forcing clinicians to consider alternative approaches to treating bacterial infections. As the window of use for current antimicrobial agents becomes ever narrower, we consider if looking back will now be the way forward. Conceptually, phage therapy is simple and specific; a targeted treatment to control bacterial overgrowth. In this article we discuss bacteriophage and potential use in future therapy.
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Affiliation(s)
- J D Jones
- Infection Medicine, University of Edinburgh, United Kingdom
| | - D Varghese
- Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children, Glasgow, United Kingdom
| | - R Pabary
- Department of Paediatric Respiratory and Sleep Medicine, Royal Brompton Hospital, London, United Kingdom
| | - R J Langley
- Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children, Glasgow, United Kingdom; School of Medicine, Dentistry & Nursing, University of Glasgow, United Kingdom.
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22
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Complete Genome Sequence of Gordonia rubripertincta Bacteriophage Hexbug Suggests Potential for a New CT Subcluster. Microbiol Resour Announc 2022; 11:e0077322. [DOI: 10.1128/mra.00773-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Through the SEA-PHAGES program at Tufts University, a bacteriophage infecting
Gordonia rubripertincta
NRRL B-16540 was isolated and characterized. Hexbug is a lytic phage and is currently one of 44 phages belonging to cluster CT. The Hexbug genome shares >96% nucleotide identity with cluster CT phage Orla.
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23
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Cunliffe T, Parker AL, Jaramillo A. Pseudotyping Bacteriophage P2 Tail Fibers to Extend the Host Range for Biomedical Applications. ACS Synth Biol 2022; 11:3207-3215. [PMID: 36084285 PMCID: PMC9594776 DOI: 10.1021/acssynbio.1c00629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Bacteriophages (phages) represent powerful potential treatments against antibiotic-resistant bacterial infections. Antibiotic-resistant bacteria represent a significant threat to global health, with an estimated 70% of infection-causing bacteria being resistant to one or more antibiotics. Developing novel antibiotics against the limited number of cellular targets is expensive and time-consuming, and bacteria can rapidly develop resistance. While bacterial resistance to phage can evolve, bacterial resistance to phage does not appear to spread through lateral gene transfer, and phage may similarly adapt through mutation to recover infectivity. Phages have been identified for all known bacteria, allowing the strain-selective killing of pathogenic bacteria. Here, we re-engineered the Escherichia coli phage P2 to alter its tropism toward pathogenic bacteria. Chimeric tail fibers formed between P2 and S16 genes were designed and generated through two approaches: homology- and literature-based. By presenting chimeric P2:S16 fibers on the P2 particle, our data suggests that the resultant phages were effectively detargeted from the native P2 cellular target, lipopolysaccharide, and were instead able to infect via the proteinaceous receptor, OmpC, the natural S16 receptor. Our work provides evidence that pseudotyping P2 is feasible and can be used to extend the host range of P2 to alternative receptors. Extension of this work could produce alternative chimeric tail fibers to target pathogenic bacterial threats. Our engineering of P2 allows adsorption through a heterologous outer-membrane protein without culturing in its native host, thus providing a potential means of engineering designer phages against pathogenic bacteria from knowledge of their surface proteome.
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Affiliation(s)
- Tabitha
G. Cunliffe
- Division
of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14
4XN, U.K.,School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
| | - Alan L. Parker
- Division
of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14
4XN, U.K.,Systems
Immunity University Research Institute, School of Medicine, Cardiff University, Heath Park, Cardiff CF14
4XN, U.K.,. Phone: +44 2922 510 231
| | - Alfonso Jaramillo
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.,De
Novo Synthetic Biology Laboratory, I2SysBio, CSIC-University of Valencia, Parc Científic Universitat de València, Calle Catedrático Agustín
Escardino, 9, 46980 Paterna, Spain,. Phone: +34 963 543 056
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24
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Complete Genome Sequences of
Microbacterium
Phages Clayda5 and Gshelby23 and
Gordonia
Phages Wrigley and Santhid. Microbiol Resour Announc 2022; 11:e0078922. [DOI: 10.1128/mra.00789-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteriophages Clayda5, Gshelby23, Wrigley, and Santhid were isolated from soil samples collected in Iowa, with genomes typical of actinobacteriophages from clusters EB, EM, CY, and DY, respectively. Wrigley and Santhid were isolated on
Gordonia terrae
and are likely to be temperate. Clayda5 and Gshelby23 were isolated on
Microbacterium foliorum
.
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25
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Local Treatment of Driveline Infection with Bacteriophages. Antibiotics (Basel) 2022; 11:antibiotics11101310. [PMID: 36289968 PMCID: PMC9598463 DOI: 10.3390/antibiotics11101310] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
Drive line infections (DLI) are common infectious complications after left ventricular assist devices (LVAD) implantation. In case of severe or persistent infections, when conservative management fails, the exchange of the total LVAD may become necessary. We present a case of successful treatment of DL infection with a combination of antibiotics, debridement and local bacteriophage treatment.
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26
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Singh S, Pitchers R, Hassard F. Coliphages as viral indicators of sanitary significance for drinking water. Front Microbiol 2022; 13:941532. [PMID: 35958148 PMCID: PMC9362991 DOI: 10.3389/fmicb.2022.941532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Coliphages are virus that infect coliform bacteria and are used in aquatic systems for risk assessment for human enteric viruses. This mini-review appraises the types and sources of coliphage and their fate and behavior in source waters and engineered drinking water treatment systems. Somatic (cell wall infection) and F+ (male specific) coliphages are abundant in drinking water sources and are used as indicators of fecal contamination. Coliphage abundances do not consistently correlate to human enteric virus abundance, but they suitably reflect the risks of exposure to human enteric viruses. Coliphages have highly variable surface characteristics with respect to morphology, size, charge, isoelectric point, and hydrophobicity which together interact to govern partitioning and removal characteristics during water treatment. The groups somatic and F+ coliphages are valuable for investigating the virus elimination during water treatment steps and as indicators for viral water quality assessment. Strain level analyses (e.g., Qβ or GA-like) provide more information about specific sources of viral pollution but are impractical for routine monitoring. Consistent links between rapid online monitoring tools (e.g., turbidity, particle counters, and flow cytometry) and phages in drinking water have yet to be established but are recommended as a future area of research activity. This could enable the real-time monitoring of virus and improve the process understanding during transient operational events. Exciting future prospects for the use of coliphages in aquatic microbiology are also discussed based on current scientific evidence and practical needs.
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Affiliation(s)
- Suniti Singh
- Cranfield Water Science Institute, Cranfield University, Bedford, United Kingdom
| | | | - Francis Hassard
- Cranfield Water Science Institute, Cranfield University, Bedford, United Kingdom
- Institute for Nanotechnology and Water Sustainability, University of South Africa, Johannesburg, South Africa
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Advancing bacteriophages as a treatment of antibiotic-resistant bacterial pulmonary infections. Curr Opin Pulm Med 2022; 28:225-231. [PMID: 35165237 DOI: 10.1097/mcp.0000000000000864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW The current article summarizes the recent advances in the use of bacteriophages to treat pulmonary infections, particularly those caused by Gram-negative drug-resistant bacteria, including Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae and Burkholderia species. It provides an updated overview of the current available evidence, with a summary of published clinical cases, case series and clinical trials currently underway.Recent finding Personalized treatment with bacteriophages is still in its infancy in Europe and the USA, despite extensive experience in Eastern countries. However, more patients are expected to be treated with clinical trials in progress and others planned. SUMMARY Despite very promising initial results and the confirmation of phage safety, there are still many ethical and practical implications to be considered, from the necessary regulatory approval to optimization of dose and route of administration, to developing strategies to tackle bacterial resistance. Patients with cystic fibrosis are a group where phage therapy, if successful, could have a major impact.
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28
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Ibarra-Chávez R, Brady A, Chen J, Penadés JR, Haag AF. Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis. PLoS Genet 2022; 18:e1010146. [PMID: 35344558 PMCID: PMC8989297 DOI: 10.1371/journal.pgen.1010146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 04/07/2022] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
Phage-inducible chromosomal islands (PICIs) are a widespread family of highly mobile genetic elements that disseminate virulence and toxin genes among bacterial populations. Since their life cycle involves induction by helper phages, they are important players in phage evolution and ecology. PICIs can interfere with the lifecycle of their helper phages at different stages resulting frequently in reduced phage production after infection of a PICI-containing strain. Since phage defense systems have been recently shown to be beneficial for the acquisition of exogenous DNA via horizontal gene transfer, we hypothesized that PICIs could provide a similar benefit to their hosts and tested the impact of PICIs in recipient strains on host cell viability, phage propagation and transfer of genetic material. Here we report an important role for PICIs in bacterial evolution by promoting the survival of phage-mediated transductants of chromosomal or plasmid DNA. The presence of PICIs generates favorable conditions for population diversification and the inheritance of genetic material being transferred, such as antibiotic resistance and virulence genes. Our results show that by interfering with phage reproduction, PICIs can protect the bacterial population from phage attack, increasing the overall survival of the bacterial population as well as the transduced cells. Moreover, our results also demonstrate that PICIs reduce the frequency of lysogenization after temperate phage infection, creating a more genetically diverse bacterial population with increased bet-hedging opportunities to adapt to new niches. In summary, our results identify a new role for the PICIs and highlight them as important drivers of bacterial evolution.
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Affiliation(s)
- Rodrigo Ibarra-Chávez
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Aisling Brady
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, United Kingdom
| | - John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, United Kingdom
- Universidad CEU Cardenal Herrera, Moncada, Spain
- * E-mail: (JRP); (AFH)
| | - Andreas F. Haag
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Medicine, University of St Andrews, North Haugh, St Andrews, United Kingdom
- * E-mail: (JRP); (AFH)
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29
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Transcriptional Organization of the Salmonella Typhimurium Phage P22 pid ORFan Locus. Int J Mol Sci 2022; 23:ijms23031253. [PMID: 35163175 PMCID: PMC8835761 DOI: 10.3390/ijms23031253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/20/2022] Open
Abstract
Many phage genes lack sequence similarity to any other open reading frame (ORF) in current databases. These enigmatic ORFan genes can have a tremendous impact on phage propagation and host interactions but often remain experimentally unexplored. We previously revealed a novel interaction between phage P22 and its Salmonella Typhimurium host, instigated by the ORFan gene pid (for phage P22 encoded instigator of dgo expression) and resulting in derepression of the host dgoRKAT operon. The pid gene is highly expressed in phage carrier cells that harbor a polarly located P22 episome that segregates asymmetrically among daughter cells. Here, we discovered that the pid locus is fitted with a weak promoter, has an exceptionally long 5′ untranslated region that is instructive for a secondary pid mRNA species, and has a 3′ Rho-independent termination loop that is responsible for stability of the pid transcript.
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30
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Morcinek-Orłowska J, Zdrojewska K, Węgrzyn A. Bacteriophage-Encoded DNA Polymerases-Beyond the Traditional View of Polymerase Activities. Int J Mol Sci 2022; 23:635. [PMID: 35054821 PMCID: PMC8775771 DOI: 10.3390/ijms23020635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
DNA polymerases are enzymes capable of synthesizing DNA. They are involved in replication of genomes of all cellular organisms as well as in processes of DNA repair and genetic recombination. However, DNA polymerases can also be encoded by viruses, including bacteriophages, and such enzymes are involved in viral DNA replication. DNA synthesizing enzymes are grouped in several families according to their structures and functions. Nevertheless, there are examples of bacteriophage-encoded DNA polymerases which are significantly different from other known enzymes capable of catalyzing synthesis of DNA. These differences are both structural and functional, indicating a huge biodiversity of bacteriophages and specific properties of their enzymes which had to evolve under certain conditions, selecting unusual properties of the enzymes which are nonetheless crucial for survival of these viruses, propagating as special kinds of obligatory parasites. In this review, we present a brief overview on DNA polymerases, and then we discuss unusual properties of different bacteriophage-encoded enzymes, such as those able to initiate DNA synthesis using the protein-priming mechanisms or even start this process without any primer, as well as able to incorporate untypical nucleotides. Apart from being extremely interesting examples of biochemical biodiversity, bacteriophage-encoded DNA polymerases can also be useful tools in genetic engineering and biotechnology.
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Affiliation(s)
- Joanna Morcinek-Orłowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.M.-O.); (K.Z.)
| | - Karolina Zdrojewska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.M.-O.); (K.Z.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland
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31
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Kazantseva OA, Buzikov RM, Pilipchuk TA, Valentovich LN, Kazantsev AN, Kalamiyets EI, Shadrin AM. The Bacteriophage Pf-10-A Component of the Biopesticide "Multiphage" Used to Control Agricultural Crop Diseases Caused by Pseudomonas syringae. Viruses 2021; 14:42. [PMID: 35062246 PMCID: PMC8779105 DOI: 10.3390/v14010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Phytopathogenic pseudomonads are widespread in the world and cause a wide range of plant diseases. In this work, we describe the Pseudomonas phage Pf-10, which is a part of the biopesticide "Multiphage" used for bacterial diseases of agricultural crops caused by Pseudomonas syringae. The Pf-10 chromosome is a dsDNA molecule with two direct terminal repeats (DTRs). The phage genomic DNA is 39,424 bp long with a GC-content of 56.5%. The Pf-10 phage uses a packaging mechanism based on T7-like short DTRs, and the length of each terminal repeat is 257 bp. Electron microscopic analysis has shown that phage Pf-10 has the podovirus morphotype. Phage Pf-10 is highly stable at pH values from 5 to 10 and temperatures from 4 to 60 °C and has a lytic activity against Pseudomonas strains. Phage Pf-10 is characterized by fast adsorption rate (80% of virions attach to the host cells in 10 min), but has a relatively small number of progeny (37 ± 8.5 phage particles per infected cell). According to the phylogenetic analysis, phage Pf-10 can be classified as a new phage species belonging to the genus Pifdecavirus, subfamily Studiervirinae, family Autographiviridae, order Caudovirales.
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Affiliation(s)
- Olesya A. Kazantseva
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
| | - Rustam M. Buzikov
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
| | - Tatsiana A. Pilipchuk
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
| | - Leonid N. Valentovich
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
- Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus
| | - Andrey N. Kazantsev
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Pushchino Radio Astronomy Observatory, 142290 Pushchino, Russia;
| | - Emilia I. Kalamiyets
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
| | - Andrey M. Shadrin
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
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32
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Mompeán M, Oroz J, Laurents DV. Do polyproline II helix associations modulate biomolecular condensates? FEBS Open Bio 2021; 11:2390-2399. [PMID: 33934561 PMCID: PMC8409303 DOI: 10.1002/2211-5463.13163] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/29/2021] [Accepted: 04/09/2021] [Indexed: 12/22/2022] Open
Abstract
Biomolecular condensates are microdroplets that form inside cells and serve to selectively concentrate proteins, RNAs and other molecules for a variety of physiological functions, but can contribute to cancer, neurodegenerative diseases and viral infections. The formation of these condensates is driven by weak, transient interactions between molecules. These weak associations can operate at the level of whole protein domains, elements of secondary structure or even moieties composed of just a few atoms. Different types of condensates do not generally combine to form larger microdroplets, suggesting that each uses a distinct class of attractive interactions. Here, we address whether polyproline II (PPII) helices mediate condensate formation. By combining with PPII-binding elements such as GYF, WW, profilin, SH3 or OCRE domains, PPII helices help form lipid rafts, nuclear speckles, P-body-like neuronal granules, enhancer complexes and other condensates. The number of PPII helical tracts or tandem PPII-binding domains can strongly influence condensate stability. Many PPII helices have a low content of proline residues, which hinders their identification. Recently, we characterized the NMR spectral properties of a Gly-rich, Pro-poor protein composed of six PPII helices. Based on those results, we predicted that many Gly-rich segments may form PPII helices and interact with PPII-binding domains. This prediction is being tested and could join the palette of verified interactions contributing to biomolecular condensate formation.
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Affiliation(s)
- Miguel Mompeán
- Departamento de Química Física BiológicaInstituto de Química Física RocasolanoCSICMadridEspaña
| | - Javier Oroz
- Departamento de Química Física BiológicaInstituto de Química Física RocasolanoCSICMadridEspaña
| | - Douglas V. Laurents
- Departamento de Química Física BiológicaInstituto de Química Física RocasolanoCSICMadridEspaña
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33
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Tamma PD, Suh GA. Phage Are All the Rage: Bacteriophage in Clinical Practice. J Pediatric Infect Dis Soc 2021; 10:749-753. [PMID: 33755148 DOI: 10.1093/jpids/piab012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 02/12/2021] [Indexed: 01/17/2023]
Affiliation(s)
- Pranita D Tamma
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Gina A Suh
- Department of Medicine, Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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34
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Comparative Genomics of Three Novel Jumbo Bacteriophages Infecting Staphylococcus aureus. J Virol 2021; 95:e0239120. [PMID: 34287047 DOI: 10.1128/jvi.02391-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The majority of previously described Staphylococcus aureus bacteriophages belong to three major groups: P68-like podophages, Twort-like or K-like myophages, and a more diverse group of temperate siphophages. Here we present three novel S. aureus "jumbo" phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade of S. aureus myophage. The average genome size for these phages is ∼269 kb with each genome encoding ∼263 predicted protein-coding genes. Phage genome organization and content is similar to known jumbo phages of Bacillus, including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete virion and non-virion RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect human S. aureus isolates. Importance of work: This study describes the comparative genomics of three novel S. aureus jumbo phages: MarsHill, Madawaska, and Machias. These three S. aureus myophages represent an emerging class of S. aureus phage. These genomes contain abundant introns which show a pattern consistent with repeated acquisition rather than vertical inheritance, suggesting intron acquisition and loss is an active process in the evolution of these phages. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, these phages also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. In particular, such hypermodified genomes may be missed by metagenomic studies due to their resistance to standard sequencing techniques. Phage MarsHill was found to be able to transduce host DNA at levels comparable to that found for other transducing S. aureus phages, making them a potential vector for horizontal gene transfer in the environment.
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35
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Kazantseva OA, Piligrimova EG, Shadrin AM. vB_BcM_Sam46 and vB_BcM_Sam112, members of a new bacteriophage genus with unusual small terminase structure. Sci Rep 2021; 11:12173. [PMID: 34108535 PMCID: PMC8190038 DOI: 10.1038/s41598-021-91289-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
One of the serious public health concerns is food contaminated with pathogens and their vital activity products such as toxins. Bacillus cereus group of bacteria includes well-known pathogenic species such as B. anthracis, B. cereus sensu stricto (ss), B. cytotoxicus and B. thuringiensis. In this report, we describe the Bacillus phages vB_BcM_Sam46 and vB_BcM_Sam112 infecting species of this group. Electron microscopic analyses indicated that phages Sam46 and Sam112 have the myovirus morphotype. The genomes of Sam46 and Sam112 comprise double-stranded DNA of 45,419 bp and 45,037 bp in length, respectively, and have the same GC-content. The genome identity of Sam46 and Sam112 is 96.0%, indicating that they belong to the same phage species. According to the phylogenetic analysis, these phages form a distinct clade and may be members of a new phage genus, for which we propose the name 'Samaravirus'. In addition, an interesting feature of the Sam46 and Sam112 phages is the unusual structure of their small terminase subunit containing N-terminal FtsK_gamma domain.
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Affiliation(s)
- Olesya A Kazantseva
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia.
| | - Emma G Piligrimova
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia
| | - Andrey M Shadrin
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia.
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36
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van Steensel MAM, Goh BC. Cutibacterium acnes: Much ado about maybe nothing much. Exp Dermatol 2021; 30:1471-1476. [PMID: 34009698 DOI: 10.1111/exd.14394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/08/2021] [Accepted: 05/13/2021] [Indexed: 12/28/2022]
Abstract
Cutibacterium acnes (also known as Propionibacterium acnes) has long been implicated in the pathogenesis of acne, inspiring both therapeutic and personal care approaches aiming to control the disease by controlling the bacterium. The purported association has made people with acne feel dirty and led to the-at times excessive-use of cleansers, antiseptics and antibiotics for the condition. However, recent evidence seems to weaken the case for C. acnes' involvement. New genetics and molecular biology findings strongly suggest that abnormal differentiation of sebaceous progenitor cells causes comedones, the primary lesions in acne. Comodegenesis is initiated by androgens and is unlikely to be triggered by C. acnes, which probably doesn't affect sebaceous differentiation. Is there still a place for it in this understanding of acne? It is necessary to critically address this question because it has consequences for treatment. Antibiotic use for acne noticeably contributes to microbial drug resistance, which we can ill afford. In this Viewpoint, we explore if and how C. acnes (still) fits into the developing view on acne. We also briefly discuss the implications for therapy in the light of antibiotic resistance and the need for more targeted therapies.
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Affiliation(s)
- Maurice A M van Steensel
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Skin Research Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Boon Chong Goh
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre Center, Singapore, Singapore
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37
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Villarreal LP, Witzany G. Social Networking of Quasi-Species Consortia drive Virolution via Persistence. AIMS Microbiol 2021; 7:138-162. [PMID: 34250372 PMCID: PMC8255905 DOI: 10.3934/microbiol.2021010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the history and context of social RNA networks become crucial for survival and function. History and context of social RNA networks also lead to the emergence of a natural genetic code. Indeed, this QS-C thinking can also provide us with a transition point between the chemical world of RNA replicators and the living world of RNA agents that actively differentiate self from non-self and generate group identity with membership roles. Importantly the social force of a consortia to solve complex, multilevel problems also depend on using opposing and minority functions. The consortial action of social networks of RNA stem-loops subsequently lead to the evolution of cellular organisms representing a tree of life.
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Janousek S, Vlkova A, Jirova G, Kejlova K, Krsek D, Jirova D, Kandarova H, Wittlingerova Z, Heinonen T, Mannerstrom M, Maly M. Qualitative and Quantitative Analysis of Certain Aspects of the Cytotoxic and Genotoxic Hazard of Hospital Wastewaters by Using a Range of In Vitro Assays. Altern Lab Anim 2021; 49:33-48. [PMID: 33910377 DOI: 10.1177/02611929211004956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Health care facilities and hospitals generate significant amounts of wastewater which are released into the sewage system, either after a preliminary treatment or without any further treatment. Hospital wastewater may contain large amounts of hazardous chemicals and pharmaceuticals, some of which cannot be eliminated entirely by wastewater treatment plants. Moreover, hospital effluents may be loaded with a plethora of pathogenic microorganisms or other microbiota and microbiome residues. The need to monitor hospital effluents for their genotoxic hazard is of high importance, as detailed information is scarce. DNA-based information can be acquired directly from samples through the application of various molecular methods, while cell-based biomonitoring assays can provide important information about impaired cellular pathways or mechanisms of toxicity without prior knowledge of the identity of each toxicant. In our study, we evaluated samples of chlorinated hospital wastewater discharged into the sewage system after this disinfection process. The assessment of cytotoxicity, genotoxicity and mutagenicity of the hospital effluents was performed in vitro by using a broad battery of biomonitoring assays that are relevant for human health effects. All the tested hospital wastewater samples could be classified as potentially genotoxic, and it is concluded that the microbiota present in hospital wastewater might contribute to this genotoxic potential.
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Affiliation(s)
- Stanislav Janousek
- Centre of Toxicology and Health Safety, 37739National Institute of Public Health, Prague, Czech Republic
| | - Alena Vlkova
- Centre of Toxicology and Health Safety, 37739National Institute of Public Health, Prague, Czech Republic.,Faculty of Environmental Sciences, 48371Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Gabriela Jirova
- Centre of Toxicology and Health Safety, 37739National Institute of Public Health, Prague, Czech Republic.,Faculty of Environmental Sciences, 48371Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Kristina Kejlova
- Centre of Toxicology and Health Safety, 37739National Institute of Public Health, Prague, Czech Republic
| | - Daniel Krsek
- Centre of Toxicology and Health Safety, 37739National Institute of Public Health, Prague, Czech Republic
| | - Dagmar Jirova
- Centre of Toxicology and Health Safety, 37739National Institute of Public Health, Prague, Czech Republic
| | - Helena Kandarova
- Centre of Experimental Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zdenka Wittlingerova
- Faculty of Environmental Sciences, 48371Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Tuula Heinonen
- FICAM, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Marika Mannerstrom
- FICAM, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Marek Maly
- Centre of Toxicology and Health Safety, 37739National Institute of Public Health, Prague, Czech Republic
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Scattolini S, D’Angelantonio D, Boni A, Mangone I, Marcacci M, Battistelli N, D’Agostino K, Pomilio F, Camma C, Migliorati G, Aprea G. Characterization and In Vitro Efficacy against Listeria monocytogenes of a Newly Isolated Bacteriophage, ɸIZSAM-1. Microorganisms 2021; 9:731. [PMID: 33807487 PMCID: PMC8065603 DOI: 10.3390/microorganisms9040731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022] Open
Abstract
Listeria monocytogenes is a bacterial pathogen responsible of listeriosis, a disease that in humans is often related to the contamination of ready-to-eat foods. Phages are candidate biodecontaminants of pathogenic bacteria thanks to their ability to lyse prokaryotes while being safe for eukaryotic cells. In this study, ɸIZSAM-1 was isolated from the drain-waters of an Italian blue cheese plant and showed lytic activity against antimicrobial resistant Listeria monocytogenes strains. This phage was subjected to purification and in vitro efficacy tests. The results showed that at multiplicities of infection (MOIs) ≤ 1, phages were able to keep Listeria monocytogenes at low optical density values up to 8 h, with bacterial counts ranging from 1.02 to 3.96 log10 units lower than the control. Besides, ɸIZSAM-1 was further characterized, showing 25 principal proteins (sodium dodecyl sulfate polyacrylamide gel electrophoresis profile) and a genome of approximately 50 kilo base pairs. Moreover, this study describes a new approach to phage isolation for applications in Listeriamonocytogenes biocontrol in food production. In particular, the authors believe that the selection of phages from the same environments where pathogens live could represent a new approach to successfully integrating the control measures in an innovative, cost effective, safe and environmentally friendly way.
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Affiliation(s)
- Silvia Scattolini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Daniela D’Angelantonio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Arianna Boni
- Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Noemi Battistelli
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy;
| | - Krizia D’Agostino
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Cesare Camma
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Giacomo Migliorati
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
| | - Giuseppe Aprea
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (S.S.); (D.D.); (I.M.); (M.M.); (K.D.); (F.P.); (C.C.); (G.M.)
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Tan CW, Rukayadi Y, Hasan H, Abdul-Mutalib NA, Jambari NN, Hara H, Thung TY, Lee E, Radu S. Isolation and Characterization of Six Vibrio parahaemolyticus Lytic Bacteriophages From Seafood Samples. Front Microbiol 2021; 12:616548. [PMID: 33776954 PMCID: PMC7987779 DOI: 10.3389/fmicb.2021.616548] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/19/2021] [Indexed: 01/21/2023] Open
Abstract
Vibrio parahaemolyticus is a foodborne pathogen that is frequently isolated from a variety of seafood. To control this pathogenic Vibrio spp., the implementation of bacteriophages in aquaculture and food industries have shown a promising alternative to antibiotics. In this study, six bacteriophages isolated from the seafood samples demonstrated a narrow host range specificity that infecting only the V. parahaemolyticus strains. Morphological analysis revealed that bacteriophages Vp33, Vp22, Vp21, and Vp02 belong to the Podoviridae family, while bacteriophages Vp08 and Vp11 were categorized into the Siphoviridae family. All bacteriophages were composed of DNA genome and showed distinctive restriction fragment length polymorphism. The optimal MOI for bacteriophage propagation was determined to be 0.001 to 1. One-step growth curve revealed that the latent period ranged from 10 to 20 min, and the burst size of bacteriophage was approximately 17 to 51 PFU/cell. The influence of temperature and pH levels on the stability of bacteriophages showed that all bacteriophages were optimally stable over a wide range of temperatures and pH levels. In vitro lytic activity of all bacteriophages demonstrated to have a significant effect against V. parahaemolyticus. Besides, the application of a bacteriophage cocktail instead of a single bacteriophage suspension was observed to have a better efficiency to control the growth of V. parahaemolyticus. Results from this study provided a basic understanding of the physiological and biological properties of the isolated bacteriophages before it can be readily used as a biocontrol agent against the growth of V. parahaemolyticus.
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Affiliation(s)
- Chia Wanq Tan
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Yaya Rukayadi
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Hanan Hasan
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Noor-Azira Abdul-Mutalib
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia.,Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security (ITAFoS), Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Nuzul Noorahya Jambari
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia.,Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security (ITAFoS), Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Hirofumi Hara
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Kuala Lumpur, Malaysia
| | - Tze Young Thung
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Epeng Lee
- Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security (ITAFoS), Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Son Radu
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia.,Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security (ITAFoS), Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
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Hashemi Shahraki A, Mirsaeidi M. Phage Therapy for Mycobacterium Abscessus and Strategies to Improve Outcomes. Microorganisms 2021; 9:microorganisms9030596. [PMID: 33799414 PMCID: PMC7999966 DOI: 10.3390/microorganisms9030596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/16/2022] Open
Abstract
Members of Mycobacterium abscessus complex are known for causing severe, chronic infections. Members of M. abscessus are a new "antibiotic nightmare" as one of the most resistant organisms to chemotherapeutic agents. Treatment of these infections is challenging due to the either intrinsic or acquired resistance of the M. abscessus complex to the available antibiotics. Recently, successful phage therapy with a cocktail of three phages (one natural lytic phage and two engineered phages) every 12 h for at least 32 weeks has been reported against a severe case of the disseminated M. abscessus subsp. massiliense infection, which underlines the high value of phages against drug-resistant superbugs. This report also highlighted the limitations of phage therapy, such as the absence of lytic phages with a broad host-range against all strains and subspecies of the M. abscessus complex and also the risk of phage resistant bacteria over treatment. Cutting-edge genomic technologies have facilitated the development of engineered phages for therapeutic purposes by introducing new desirable properties, changing host-range and arming the phages with additional killing genes. Here, we review the available literature and suggest new potential solutions based on the progress in phage engineering that can help to overcome the present limitations of M. abscessus treatment.
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Kittler S, Steffan S, Peh E, Plötz M. Phage Biocontrol of Campylobacter: A One Health Approach. Curr Top Microbiol Immunol 2021; 431:127-168. [PMID: 33620651 DOI: 10.1007/978-3-030-65481-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human infections by Campylobacter species are among the most reported bacterial gastrointestinal diseases in the European Union and worldwide with severe outcomes in rare cases. Considering the transmission routes and farm animal reservoirs of these zoonotic pathogens, a comprehensive One Health approach will be necessary to reduce human infection rates. Bacteriophages are viruses that specifically infect certain bacterial genera, species, strains or isolates. Multiple studies have demonstrated the general capacity of phage treatments to reduce Campylobacter loads in the chicken intestine. However, phage treatments are not yet approved for extensive use in the agro-food industry in Europe. Technical inconvenience is mainly related to the efficacy of phages, depending on the optimal choice of phages and their combination, as well as application route, concentration and timing. Additionally, regulatory uncertainties have been a major concern for investment in commercial phage-based products. This review addresses the question as to how phages can be put into practice and can help to solve the issue of human campylobacteriosis in a sustainable One Health approach. By compiling the reported findings from the literature in a standardized manner, we enabled inter-experimental comparisons to increase our understanding of phage infection in Campylobacter spp. and practical on-farm studies. Further, we address some of the hurdles that still must be overcome before this new methodology can be adapted on an industrial scale. We envisage that phage treatment can become an integrated and standardized part of a multi-hurdle anti-bacterial strategy in food production. The last part of this chapter deals with some of the issues raised by legal authorities, bringing together current knowledge on Campylobacter-specific phages and the biosafety requirements for approval of phage treatment in the food industry.
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Affiliation(s)
- Sophie Kittler
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany.
| | - Severin Steffan
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - Elisa Peh
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - Madeleine Plötz
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
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cDNA-Derived RNA Phage Assembly Reveals Critical Residues in the Maturation Protein of the Pseudomonas aeruginosa Leviphage PP7. J Virol 2021; 95:JVI.01643-20. [PMID: 33177196 DOI: 10.1128/jvi.01643-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/30/2020] [Indexed: 11/20/2022] Open
Abstract
PP7 is a leviphage, with a single-stranded RNA genome, that infects Pseudomonas aeruginosa PAO1. A reverse genetic system for PP7 was previously created by using reverse-transcribed cDNA (PP7O) from a virion-derived RNA genome. Here, we have found that the PP7O cDNA contained 20 nucleotide differences from the PP7 genome sequence deposited in the database. We created another reverse genetic system exploiting chemically synthesized cDNA (PP7S) based on the database sequence. Unlike PP7O, which yielded infectious PP7 virions, PP7S-derived particles were incapable of plaque formation on PAO1 cells, which was restored in the PAO1 cells expressing the maturation protein (MP) from PP7O Using this reverse genetic system, we revealed two amino acid residues involved in the known roles of MP (i.e., adsorption and genome replication), fortuitously providing a lesson that the viral RNA genome sequencing needs functional verification, possibly by a reverse genetic system.IMPORTANCE The biological significance of RNA phages has been largely ignored, ironically, because few studies have focused on RNA phages. As an initial attempt to properly represent RNA phages in the phageome, we previously created, by using reverse-transcribed cDNA, a reverse genetic system for the small RNA phage PP7, which infects the opportunistic human pathogen Pseudomonas aeruginosa We report another system by using chemically synthesized cDNA based on the database genome that has 20 nucleotide differences from the previous cDNA. Investigation of those cDNA-derived phage virions revealed that two amino acids of the maturation protein are crucial for the normal phage lifecycle at different steps. Our study provides insight into the molecular basis for the RNA phage lifecycle and a lesson that the RNA genome sequencing needs to be carefully validated by cDNA-based phage assembly systems.
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Macdonald KE, Stacey HJ, Harkin G, Hall LML, Young MJ, Jones JD. Patient perceptions of phage therapy for diabetic foot infection. PLoS One 2020; 15:e0243947. [PMID: 33315926 PMCID: PMC7735629 DOI: 10.1371/journal.pone.0243947] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/30/2020] [Indexed: 01/04/2023] Open
Abstract
Infections of diabetic foot ulcers are common, generally recalcitrant and often complicated by antibiotic resistance. Alternative antimicrobial strategies are needed. Phage therapy is a promising alternative that is being rediscovered. Despite phage therapy's 100-year history, there have been no investigations into patient thoughts and concerns. This study aimed to explore patient awareness of and concern about antibiotic resistance and gain insight into the perceptions of phage therapy among a patient group that could potentially benefit from phage therapy. Patients with an active or resolved (healed or amputated) diabetic foot ulcer were eligible to participate. A survey was distributed digitally to eligible patients across Scotland via the NHS Research Scotland Diabetes Network and hard copies were available in diabetic foot clinics at the Royal Infirmary of Edinburgh and Queen Elizabeth University Hospital, Glasgow. A focus group of five survey respondents was held in Glasgow. Fifty-five survey responses were obtained. There was a high level of awareness (76.4%; N = 55) and concern (83.3%; N = 54) about antibiotic resistance. While largely aware of viruses, most patients had not heard of phage or phage therapy. Patients were no more concerned about phage than antibiotic therapy, with most suggesting more information could alleviate any concerns. Patient acceptability of phage therapy was high, a finding confirmed by the focus group. Patients are concerned about antibiotic resistance and supportive of 'new' antimicrobials. We have demonstrated that patients are supportive, enthusiastic and accepting of phage therapy. Although 'Western' phage therapy remains in its infancy, an understanding of patient ideas, concerns and expectations will be important in eventually shaping and successfully reintroducing phage therapy.
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Affiliation(s)
- Katherine E. Macdonald
- Infection Medicine, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Helen J. Stacey
- Edinburgh Medical School, University of Edinburgh, Edinburgh, United Kingdom
| | - Gillian Harkin
- Diabetes and Endocrinology, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Lesley M. L. Hall
- Diabetes and Endocrinology, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Matthew J. Young
- Diabetic Foot Clinic, Outpatient Department 2, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Joshua D. Jones
- Infection Medicine, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
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The Safety and Efficacy of Phage Therapy for Bone and Joint Infections: A Systematic Review. Antibiotics (Basel) 2020; 9:antibiotics9110795. [PMID: 33182795 PMCID: PMC7697170 DOI: 10.3390/antibiotics9110795] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/29/2022] Open
Abstract
Bacterial resistance to antibiotics has catalysed interest in alternative antimicrobial strategies. Bacteriophages (phages) are viruses of bacteria with a long history of successful therapeutic use. Phage therapy is a promising antibacterial strategy for infections with a biofilm component, including recalcitrant bone and joint infections, which have significant social, financial and human impacts. Here, we report a systematic review of the safety and efficacy of phage therapy for the treatment of bone and joint infections. Three electronic databases were systematically searched for articles that reported primary data about human phage therapy for bone and joint infections. Two authors independently assessed study eligibility and performed data extraction. Seventeen reports were eligible for inclusion in this review, representing the treatment of 277 patients. A cautionary, crude, efficacy estimate revealed that 93.1% (n = 258/277) achieved clinical resolution, 3.3% (n = 9/277) had improvement and 3.6% (n = 10/277) showed no improvement. Seven of the nine reports that directly commented on the safety of phage therapy did not express safety concerns. The adverse effects reported in the remaining two were not severe and were linked to the presence of contaminating endotoxins and pre-existing liver pathology in a patient treated with high-titre intravenous phage therapy. Three other reports, from 1940-1987, offered general comments on the safety of phage therapy and documented adverse effects consistent with endotoxin co-administration concomitant with the use of raw phage lysates. Together, the reports identified by this review suggest that appropriately purified phages represent a safe and highly efficacious treatment option for complex and intractable bone and joint infections.
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Topka-Bielecka G, Bloch S, Nejman-Faleńczyk B, Grabski M, Jurczak-Kurek A, Górniak M, Dydecka A, Necel A, Węgrzyn G, Węgrzyn A. Characterization of the Bacteriophage vB_EfaS-271 Infecting Enterococcus faecalis. Int J Mol Sci 2020; 21:ijms21176345. [PMID: 32882938 PMCID: PMC7503890 DOI: 10.3390/ijms21176345] [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: 07/21/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022] Open
Abstract
A newly isolated bacteriophage infecting Enterococcus faecalis strains has been characterized, including determination of its molecular features. This phage, named vB_EfaS-271, has been classified as a Siphoviridae member, according to electron microscopy characterization of the virions, composed of a 50 nm-diameter head and a long, flexible, noncontractable tail (219 × 12.5 nm). Analysis of the whole dsDNA genome of this phage showed that it consists of 40,197 bp and functional modules containing genes coding for proteins that are involved in DNA replication (including DNA polymerase/primase), morphogenesis, packaging and cell lysis. Mass spectrometry analysis allowed us to identify several phage-encoded proteins. vB_EfaS-271 reveals a relatively narrow host range, as it is able to infect only a few E. faecalis strains. On the other hand, it is a virulent phage (unable to lysogenize host cells), effectively and quickly destroying cultures of sensitive host bacteria, with a latent period as short as 8 min and burst size of approximately 70 phages per cell at 37 °C. This phage was also able to destroy biofilms formed by E. faecalis. These results contribute to our understanding of the biodiversity of bacteriophages, confirming the high variability among these viruses and indicating specific genetic and functional features of vB_EfaS-271.
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Affiliation(s)
- Gracja Topka-Bielecka
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
| | - Sylwia Bloch
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland;
| | - Bożena Nejman-Faleńczyk
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
| | - Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
- Laboratory of Marine Biogeochemistry, Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Agata Jurczak-Kurek
- Department of Molecular Evolution, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (A.J.-K.); (M.G.)
| | - Marcin Górniak
- Department of Molecular Evolution, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (A.J.-K.); (M.G.)
| | - Aleksandra Dydecka
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
| | - Agnieszka Necel
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland;
- Correspondence: ; Tel.: +48-58-523-6040
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Kisil OV, Efimenko TA, Gabrielyan NI, Efremenkova OV. Development of Antimicrobial Therapy Methods to Overcome the Antibiotic Resistance of Acinetobacter baumannii. Acta Naturae 2020; 12:34-45. [PMID: 33173595 PMCID: PMC7604900 DOI: 10.32607/actanaturae.10955] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/19/2020] [Indexed: 12/29/2022] Open
Abstract
The spread of antibiotic resistance among pathogens represents a threat to human health around the world. In 2017, the World Health Organization published a list of 12 top-priority antibiotic-resistant pathogenic bacteria for which new effective antibiotics or new ways of treating the infections caused by them are needed. This review focuses on Acinetobacter baumannii, one of these top-priority pathogens. The pathogenic bacterium A. baumannii is one of the most frequently encountered infectious agents in the world; its clinically significant features include resistance to UV light, drying, disinfectants, and antibiotics. This review looks at the various attempts that have been made to tackle the problem of drug resistance relating to A. baumannii variants without the use of antibiotics. The potential of bacteriophages and antimicrobial peptides in the treatment of infections caused by A. baumannii in both planktonic and biofilm form is assessed. Such topics as research into the development of vaccines based on the outer membrane proteins of A. baumannii and the use of silver nanoparticles, as well as photodynamic and chelate therapy, are also covered.
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Affiliation(s)
- O. V. Kisil
- Gause Institute of New Antibiotics, Moscow, 119021 Russia
| | - T. A. Efimenko
- Gause Institute of New Antibiotics, Moscow, 119021 Russia
| | - N. I. Gabrielyan
- V.I. Shumakov Federal Research Center of Transplantology and Artificial Organs, Ministry of Healthcare of the Russian Federation, Moscow, 1123182 Russia
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Gerstmans H, Grimon D, Gutiérrez D, Lood C, Rodríguez A, van Noort V, Lammertyn J, Lavigne R, Briers Y. A VersaTile-driven platform for rapid hit-to-lead development of engineered lysins. SCIENCE ADVANCES 2020; 6:eaaz1136. [PMID: 32537492 PMCID: PMC7269649 DOI: 10.1126/sciadv.aaz1136] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
Health care authorities are calling for new antibacterial therapies to cope with the global emergence of antibiotic-resistant bacteria. Bacteriophage-encoded lysins are a unique class of antibacterials with promising (pre)clinical progress. Custom engineering of lysins allows for the creation of variants against potentially any bacterial pathogen. We here present a high-throughput hit-to-lead development platform for engineered lysins. The platform is driven by VersaTile, a new DNA assembly method for the rapid construction of combinatorial libraries of engineered lysins. We constructed approximately 10,000 lysin variants. Using an iterative screening procedure, we identified a lead variant with high antibacterial activity against Acinetobacter baumannii in human serum and an ex vivo pig burn wound model. This generic platform could offer new opportunities to populate the preclinical pipeline with engineered lysins for diverse (therapeutic) applications.
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Affiliation(s)
- H. Gerstmans
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Gent, Belgium
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
- Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - D. Grimon
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Gent, Belgium
| | - D. Gutiérrez
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Gent, Belgium
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, s/n, 33300 Villaviciosa, Asturias, Spain
| | - C. Lood
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 23, 3001 Leuven, Belgium
| | - A. Rodríguez
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, s/n, 33300 Villaviciosa, Asturias, Spain
| | - V. van Noort
- Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 23, 3001 Leuven, Belgium
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 Leiden, Netherlands
| | - J. Lammertyn
- Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - R. Lavigne
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Y. Briers
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Gent, Belgium
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Love MJ, Abeysekera GS, Muscroft-Taylor AC, Billington C, Dobson RC. On the catalytic mechanism of bacteriophage endolysins: Opportunities for engineering. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140302. [DOI: 10.1016/j.bbapap.2019.140302] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/03/2019] [Accepted: 10/10/2019] [Indexed: 10/25/2022]
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