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Mäkelä K, Laanto E, Sundberg LR. Determinants in the phage life cycle: The dynamic nature of ssDNA phage FLiP and host interactions under varying environmental conditions and growth phases. Environ Microbiol 2024; 26:e16670. [PMID: 38952172 DOI: 10.1111/1462-2920.16670] [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: 12/20/2023] [Accepted: 05/24/2024] [Indexed: 07/03/2024]
Abstract
The influence of environmental factors on the interactions between phages and bacteria, particularly single-stranded DNA (ssDNA) phages, has been largely unexplored. In this study, we used Finnlakevirus FLiP, the first known ssDNA phage species with a lipid membrane, as our model phage. We examined the infectivity of FLiP with three Flavobacterium host strains, B330, B167 and B114. We discovered that FLiP infection is contingent on the host strain and conditions such as temperature and bacterial growth phase. FLiP can infect its hosts across a wide temperature range, but optimal phage replication varies with each host. We uncovered some unique aspects of phage infectivity: FLiP has limited infectivity in liquid-suspended cells, but it improves when cells are surface-attached. Moreover, FLiP infects stationary phase B167 and B114 cells more rapidly and efficiently than exponentially growing cells, a pattern not observed with the B330 host. We also present the first experimental evidence of endolysin function in ssDNA phages. The activity of FLiP's lytic enzymes was found to be condition-dependent. Our findings underscore the importance of studying phage ecology in contexts that are relevant to the environment, as both the host and the surrounding conditions can significantly alter the outcome of phage-host interactions.
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Affiliation(s)
- Kati Mäkelä
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Elina Laanto
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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2
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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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3
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Kraus S, Fletcher ML, Łapińska U, Chawla K, Baker E, Attrill EL, O'Neill P, Farbos A, Jeffries A, Galyov EE, Korbsrisate S, Barnes KB, Harding SV, Tsaneva-Atanasova K, Blaskovich MAT, Pagliara S. Phage-induced efflux down-regulation boosts antibiotic efficacy. PLoS Pathog 2024; 20:e1012361. [PMID: 38941361 PMCID: PMC11239113 DOI: 10.1371/journal.ppat.1012361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 07/11/2024] [Accepted: 06/21/2024] [Indexed: 06/30/2024] Open
Abstract
The interactions between a virus and its host vary in space and time and are affected by the presence of molecules that alter the physiology of either the host or the virus. Determining the molecular mechanisms at the basis of these interactions is paramount for predicting the fate of bacterial and phage populations and for designing rational phage-antibiotic therapies. We study the interactions between stationary phase Burkholderia thailandensis and the phage ΦBp-AMP1. Although heterogeneous genetic resistance to phage rapidly emerges in B. thailandensis, the presence of phage enhances the efficacy of three major antibiotic classes, the quinolones, the beta-lactams and the tetracyclines, but antagonizes tetrahydrofolate synthesis inhibitors. We discovered that enhanced antibiotic efficacy is facilitated by reduced antibiotic efflux in the presence of phage. This new phage-antibiotic therapy allows for eradication of stationary phase bacteria, whilst requiring reduced antibiotic concentrations, which is crucial for treating infections in sites where it is difficult to achieve high antibiotic concentrations.
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Affiliation(s)
- Samuel Kraus
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Megan L Fletcher
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Krina Chawla
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Evan Baker
- Department of Mathematics and Living Systems Institute, University of Exeter, Exeter, Devon, United Kingdom
- EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter, United Kingdom
| | - Erin L Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Paul O'Neill
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Audrey Farbos
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Aaron Jeffries
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Edouard E Galyov
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok Thailand
| | - Kay B Barnes
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Krasimira Tsaneva-Atanasova
- Department of Mathematics and Living Systems Institute, University of Exeter, Exeter, Devon, United Kingdom
- EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter, United Kingdom
| | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
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4
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Roughgarden J. Lytic/Lysogenic Transition as a Life-History Switch. Virus Evol 2024; 10:veae028. [PMID: 38756985 PMCID: PMC11097211 DOI: 10.1093/ve/veae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 05/18/2024] Open
Abstract
The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.
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Affiliation(s)
- Joan Roughgarden
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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Wiebe KG, Cook BWM, Lightly TJ, Court DA, Theriault SS. Investigation into scalable and efficient enterotoxigenic Escherichia coli bacteriophage production. Sci Rep 2024; 14:3618. [PMID: 38351153 PMCID: PMC10864315 DOI: 10.1038/s41598-024-53276-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
As the demand for bacteriophage (phage) therapy increases due to antibiotic resistance in microbial pathogens, strategies and methods for increased efficiency, large-scale phage production need to be determined. To date, very little has been published on how to establish scalable production for phages, while achieving and maintaining a high titer in an economical manner. The present work outlines a phage production strategy using an enterotoxigenic Escherichia coli-targeting phage, 'Phage75', and accounts for the following variables: infection load, multiplicity of infection, temperature, media composition, harvest time, and host bacteria. To streamline this process, variables impacting phage propagation were screened through a high-throughput assay monitoring optical density at 600 nm (OD600) to indirectly infer phage production from host cell lysis. Following screening, propagation conditions were translated in a scalable fashion in shake flasks at 0.01 L, 0.1 L, and 1 L. A final, proof-of-concept production was then carried out in a CellMaker bioreactor to represent practical application at an industrial level. Phage titers were obtained in the range of 9.5-10.1 log10 PFU/mL with no significant difference between yields from shake flasks and CellMaker. Overall, this suggests that the methodology for scalable processing is reliable for translating into large-scale phage production.
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Affiliation(s)
- Katie G Wiebe
- Cytophage Technologies Inc., Winnipeg, MB, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | | | | | - Deborah A Court
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Steven S Theriault
- Cytophage Technologies Inc., Winnipeg, MB, Canada.
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada.
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Aviram N, Shilton AK, Lyn NG, Reis BS, Brivanlou A, Marraffini LA. The Cas10 nuclease activity relieves host dormancy to facilitate spacer acquisition and retention during type III-A CRISPR immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579731. [PMID: 38405743 PMCID: PMC10888962 DOI: 10.1101/2024.02.11.579731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A hallmark of CRISPR immunity is the acquisition of short viral DNA sequences, known as spacers, that are transcribed into guide RNAs to recognize complementary sequences. The staphylococcal type III-A CRISPR-Cas system uses guide RNAs to locate viral transcripts and start a response that displays two mechanisms of immunity. When immunity is triggered by an early-expressed phage RNA, degradation of viral ssDNA can cure the host from infection. In contrast, when the RNA guide targets a late-expressed transcript, defense requires the activity of Csm6, a non-specific RNase. Here we show that Csm6 triggers a growth arrest of the host that provides immunity at the population level which hinders viral propagation to allow the replication of non-infected cells. We demonstrate that this mechanism leads to defense against not only the target phage but also other viruses present in the population that fail to replicate in the arrested cells. On the other hand, dormancy limits the acquisition and retention of spacers that trigger it. We found that the ssDNase activity of type III-A systems is required for the re-growth of a subset of the arrested cells, presumably through the degradation of the phage DNA, ending target transcription and inactivating the immune response. Altogether, our work reveals a built-in mechanism within type III-A CRISPR-Cas systems that allows the exit from dormancy needed for the subsistence of spacers that provide broad-spectrum immunity.
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Affiliation(s)
- Naama Aviram
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Amanda K Shilton
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Nia G Lyn
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Bernardo S Reis
- Laboratory of Mucosal Immunology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Amir Brivanlou
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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Brenner T, Schultze DM, Mahoney D, Wang S. Reduction of Nontyphoidal Salmonella enterica in Broth and on Raw Chicken Breast by a Broad-spectrum Bacteriophage Cocktail. J Food Prot 2024; 87:100207. [PMID: 38142823 DOI: 10.1016/j.jfp.2023.100207] [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: 07/11/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
Globally, nontyphoidal Salmonella (NTS) causes approximately 150 million foodborne illnesses annually; many of which are linked to poultry products. Thus, improving food safety interventions in the poultry sector can reduce foodborne illness associated with prevalent NTS serotypes. Bacteriophages (phages) have shown promise as food-safe alternatives to current antimicrobial practices. However, challenges such as limited host range, bactericidal effectiveness in practical production settings, and the risk of developing host resistance remain as barriers for the widespread use of phages in commercial poultry operations. A broad-spectrum three-phage cocktail was evaluated against S. enterica subsp. enterica serotypes Enteritidis, Typhimurium, and Kentucky. The impact of multiplicity of infection (MOI) on NTS growth was assessed in broth at 22°C for 18 hours (h). Then, phage cocktail efficacy was evaluated on raw chicken breast samples inoculated with the NTS cocktail and stored at 10°C or 22°C for 0, 1, and 5 days or 0, 4, 8, and 16 h, respectively. Most probable number (MPN) calculations were performed for NTS counts on chicken after phage treatment and storage at 10°C to account for samples with NTS counts below the detection limit. In general, a higher MOI corresponded to reduced NTS growth; however, residual nutrition in growth media and initial NTS contamination level affected samples treated with the phage cocktail at identical MOIs. On chicken, phage cocktail treatment significantly reduced NTS counts at 10°C and 22°C. After storage at 10°C for 5 days, NTS counts were reduced by >3.2 log compared to the control. After storage at 22°C for 16 h, NTS counts were reduced by >1.7 log compared to the control. Overall, the phage cocktail was effective at reducing a diverse set of prominent NTS strains in broth and on raw chicken breast, highlighting its potential for commercialization and use alongside other hurdles in poultry production.
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Affiliation(s)
- Thomas Brenner
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Danielle Morgan Schultze
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - David Mahoney
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Siyun Wang
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada.
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Ngiam L, Weynberg K, Guo J. Evolutionary and co-evolutionary phage training approaches enhance bacterial suppression and delay the emergence of phage resistance. ISME COMMUNICATIONS 2024; 4:ycae082. [PMID: 38988700 PMCID: PMC11234896 DOI: 10.1093/ismeco/ycae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 03/18/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
The development of phage resistance by bacteria is a major barrier that impedes the therapeutic use of phages. Phage training has been proposed as a novel tool that harnesses the evolutionary potential of phages to improve phage infectivity. Both evolutionary and co-evolutionary phage training models have been previously reported to train phages. However, both of these phage training models have been reported able to effectively suppress the emergence of phage-resistant bacteria mutants, thus presenting a contradictory phenomenon. Therefore, in this study, we set out to systematically compare the effectiveness of both evolutionary and co-evolutionary phage training models with regard to phage physiology, infectivity, and genotype. To this end, a natural lytic phage capable of infecting a Klebsiella pneumonia strain was isolated from wastewater and subjected to evolutionary and co-evolutionary phage training for 30 days. After the phage training, the physiology and genomic characteristics of evolved and co-evolved phages were assessed. Our results demonstrated that both evolved and co-evolved phages exhibit improved bacterial suppression activity and are able to delay the emergence of phage resistance. Furthermore, both phages harbored unique genome mutational changes in different functionally associated phage proteins. Similarly, evolved and co-evolved phage-resistant bacteria mutants that arose post phage infection displayed varying phage resistance sensitivities, which may be correlated to the unique genome mutational change identified in cell membrane structure. In particular, co-evolved phage-resistant bacteria mutants exhibited less phage resistance compared to evolved phage-resistant bacteria mutants. These results highlighted the finding that the co-evolutionary phage training model serves as a better phage training model as it endows phage with improved infectivity, but also selects for phage-resistant bacteria with a lower phage resistance when compared to evolutionary phage training.
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Affiliation(s)
- Lyman Ngiam
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, 4 Gehrmann Laboratories Building, Research Road, St Lucia, Queensland 4072, Australia
| | - Karen Weynberg
- Australian Centre for Ecogenomics, The University of Queensland, Chemistry Building 68, Cooper Road, St Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, 4 Gehrmann Laboratories Building, Research Road, St Lucia, Queensland 4072, Australia
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