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Oechslin F, Zhu X, Morency C, Somerville V, Shi R, Moineau S. Fermentation Practices Select for Thermostable Endolysins in Phages. Mol Biol Evol 2024; 41:msae055. [PMID: 38489607 PMCID: PMC10980517 DOI: 10.1093/molbev/msae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/12/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024] Open
Abstract
Endolysins are produced by (bacterio)phages and play a crucial role in degrading the bacterial cell wall and the subsequent release of new phage progeny. These lytic enzymes exhibit a remarkable diversity, often occurring in a multimodular form that combines different catalytic and cell wall-binding domains, even in phages infecting the same species. Yet, our current understanding lacks insight into how environmental factors and ecological niches may have influenced the evolution of these enzymes. In this study, we focused on phages infecting Streptococcus thermophilus, as this bacterial species has a well-defined and narrow ecological niche, namely, dairy fermentation. Among the endolysins found in phages targeting this species, we observed limited diversity, with a singular structural type dominating in most of identified S. thermophilus phages. Within this prevailing endolysin type, we discovered a novel and highly conserved calcium-binding motif. This motif proved to be crucial for the stability and activity of the enzyme at elevated temperatures. Ultimately, we demonstrated its positive selection within the host's environmental conditions, particularly under the temperature profiles encountered in the production of yogurt, mozzarella, and hard cheeses that rely on S. thermophilus.
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Affiliation(s)
- Frank Oechslin
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Canada
| | - Xiaojun Zhu
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Canada
| | - Carlee Morency
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Canada
| | - Vincent Somerville
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Canada
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Rong Shi
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Canada
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Oechslin F, Zhu X, Dion MB, Shi R, Moineau S. Phage endolysins are adapted to specific hosts and are evolutionarily dynamic. PLoS Biol 2022; 20:e3001740. [PMID: 35913996 PMCID: PMC9371310 DOI: 10.1371/journal.pbio.3001740] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/11/2022] [Accepted: 07/01/2022] [Indexed: 01/21/2023] Open
Abstract
Endolysins are produced by (bacterio)phages to rapidly degrade the bacterial cell wall and release new viral particles. Despite sharing a common function, endolysins present in phages that infect a specific bacterial species can be highly diverse and vary in types, number, and organization of their catalytic and cell wall binding domains. While much is now known about the biochemistry of phage endolysins, far less is known about the implication of their diversity on phage–host adaptation and evolution. Using CRISPR-Cas9 genome editing, we could genetically exchange a subset of different endolysin genes into distinct lactococcal phage genomes. Regardless of the type and biochemical properties of these endolysins, fitness costs associated to their genetic exchange were marginal if both recipient and donor phages were infecting the same bacterial strain, but gradually increased when taking place between phage that infect different strains or bacterial species. From an evolutionary perspective, we observed that endolysins could be naturally exchanged by homologous recombination between phages coinfecting a same bacterial strain. Furthermore, phage endolysins could adapt to their new phage/host environment by acquiring adaptative mutations. These observations highlight the remarkable ability of phage lytic systems to recombine and adapt and, therefore, explain their large diversity and mosaicism. It also indicates that evolution should be considered to act on functional modules rather than on bacteriophages themselves. Furthermore, the extensive degree of evolvability observed for phage endolysins offers new perspectives for their engineering as antimicrobial agents. Endolysins are produced by bacteriophages to degrade the host cell wall and release new particles, but the implications of their diversity on phage-host adaptation and evolution is unknown. This study uses CRISPR-Cas9 genome editing to reveal novel insights into bacteriophage endolysin diversity and phage-bacteria interactions as well as into endolysin adaptation towards a new bacterial host.
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Affiliation(s)
- Frank Oechslin
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Canada
- * E-mail:
| | - Xiaojun Zhu
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
| | - Moira B. Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Canada
| | - Rong Shi
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Canada
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3
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Holtappels D, Fortuna KJ, Moons L, Broeckaert N, Bäcker LE, Venneman S, Rombouts S, Lippens L, Baeyen S, Pollet S, Noben JP, Oechslin F, Vallino M, Aertsen A, Maes M, Van Vaerenbergh J, Lavigne R, Wagemans J. The potential of bacteriophages to control Xanthomonas campestris pv. campestris at different stages of disease development. Microb Biotechnol 2022; 15:1762-1782. [PMID: 35084112 PMCID: PMC9151335 DOI: 10.1111/1751-7915.14004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/23/2022] Open
Abstract
Xanthomonas campestris pv. campestris (Xcc) is a vascular pathogen that invades the xylem of Brassica crops. Current chemical and antibiotics‐based control measures for this bacterium are unsustainable and inefficient. After establishing a representative collection of Xcc strains, we isolated and characterized bacteriophages from two clades of phages to assess their potential in phage‐based biocontrol. The most promising phages, FoX2 and FoX6, specifically recognize (lipo) polysaccharides, associated with the wxc gene cluster, on the surface of the bacterial cell wall. Next, we determined and optimized the applicability of FoX2 and FoX6 in an array of complementary bioassays, ranging from seed decontamination to irrigation‐ and spray‐based applications. Here, an irrigation‐based application showed promising results. In a final proof‐of‐concept, a CaCl2‐formulated phage cocktail was shown to control the outbreak of Xcc in the open field. This comprehensive approach illustrates the potential of phage biocontrol of black rot disease in Brassica and serves as a reference for the broader implementation of phage biocontrol in integrated pest management strategies.
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Affiliation(s)
| | | | - Lauren Moons
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | | | - Léon E Bäcker
- Laboratory of Food Microbiology, KU Leuven, Leuven, Belgium
| | - Sofie Venneman
- Proefstation voor de groenteteelt, Sint-Katelijne-Waver, Belgium
| | - Sofie Rombouts
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium.,Flanders Research Institute for Agriculture, Fisheries and Food, Ghent, Belgium
| | - Louis Lippens
- Provinciaal Proefcentrum voor de Groenteteelt Oost-Vlaanderen, Kruishoutem, Belgium
| | - Steve Baeyen
- Flanders Research Institute for Agriculture, Fisheries and Food, Ghent, Belgium
| | | | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Hasselt, Belgium
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Counsil of Italy, Turin, Italy
| | - Abram Aertsen
- Laboratory of Food Microbiology, KU Leuven, Leuven, Belgium
| | | | | | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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4
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Oechslin F, Menzi C, Moreillon P, Resch G. The multidomain architecture of a bacteriophage endolysin enables intramolecular synergism and regulation of bacterial lysis. J Biol Chem 2021; 296:100639. [PMID: 33838182 PMCID: PMC8144678 DOI: 10.1016/j.jbc.2021.100639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/29/2021] [Accepted: 04/05/2021] [Indexed: 01/07/2023] Open
Abstract
Endolysins are peptidoglycan hydrolases produced at the end of the bacteriophage (phage) replication cycle to lyse the host cell. Endolysins in Gram-positive phages come in a variety of multimodular forms that combine different catalytic and cell wall binding domains. However, the reason why phages adopt endolysins with such complex multidomain architecture is not well understood. In this study, we used the Streptococcus dysgalactiae phage endolysin PlySK1249 as a model to investigate the role of multidomain architecture in phage-induced bacterial lysis and lysis regulation. PlySK1249 consists of an amidase (Ami) domain that lyses bacterial cells, a nonbacteriolytic endopeptidase (CHAP) domain that acts as a dechaining enzyme, and a central LysM cell wall binding domain. We observed that the Ami and CHAP domains synergized for peptidoglycan digestion and bacteriolysis in the native enzyme or when expressed individually and reunified. The CHAP endopeptidase resolved complex polymers of stem-peptides to dimers and helped the Ami domain to digest peptidoglycan to completion. We also found that PlySK1249 was subject to proteolytic cleavage by host cell wall proteases both in vitro and after phage induction. Cleavage disconnected the different domains by hydrolyzing their linker regions, thus hindering their bacteriolytic cooperation and possibly modulating the lytic activity of the enzyme. PlySK1249 cleavage by cell-wall-associated proteases may represent another example of phage adaptation toward the use of existing bacterial regulation mechanism for their own advantage. In addition, understanding more thoroughly the multidomain interplay of PlySK1249 broadens our knowledge on the ideal architecture of therapeutic antibacterial endolysins.
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Affiliation(s)
- Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Carmen Menzi
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Philippe Moreillon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gregory Resch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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5
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Abstract
Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes.
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Affiliation(s)
- Moïra B Dion
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Frank Oechslin
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada. .,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada. .,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada.
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6
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Leshkasheli L, Kutateladze M, Balarjishvili N, Bolkvadze D, Save J, Oechslin F, Que YA, Resch G. Efficacy of newly isolated and highly potent bacteriophages in a mouse model of extensively drug-resistant Acinetobacter baumannii bacteraemia. J Glob Antimicrob Resist 2019; 19:255-261. [DOI: 10.1016/j.jgar.2019.05.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/15/2019] [Accepted: 05/06/2019] [Indexed: 02/02/2023] Open
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Testa S, Berger S, Piccardi P, Oechslin F, Resch G, Mitri S. Spatial structure affects phage efficacy in infecting dual-strain biofilms of Pseudomonas aeruginosa. Commun Biol 2019; 2:405. [PMID: 31701033 PMCID: PMC6828766 DOI: 10.1038/s42003-019-0633-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
Bacterial viruses, or phage, are key members of natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Here we explored how bacterial diversity affects the success of lytic phage in structured communities. We infected a sensitive Pseudomonas aeruginosa strain PAO1 with a lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies on agar. We found that both in liquid and in colonies, inter-strain competition reduced resistance evolution in the susceptible strain and decreased phage population size. However, while all sensitive bacteria died in liquid, bacteria in colonies could remain sensitive yet escape phage infection, due mainly to reduced growth in colony centers. In sum, spatial structure can protect bacteria against phage infection, while the presence of competing strains reduces the evolution of resistance to phage.
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Affiliation(s)
- Samuele Testa
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Sarah Berger
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Philippe Piccardi
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec City, QC Canada
| | - Grégory Resch
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
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Laumay F, Corvaglia AR, Diene SM, Girard M, Oechslin F, van der Mee-Marquet N, Entenza JM, François P. Temperate Prophages Increase Bacterial Adhesin Expression and Virulence in an Experimental Model of Endocarditis Due to Staphylococcus aureus From the CC398 Lineage. Front Microbiol 2019; 10:742. [PMID: 31105650 PMCID: PMC6492496 DOI: 10.3389/fmicb.2019.00742] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/25/2019] [Indexed: 01/13/2023] Open
Abstract
Until 2007, Staphylococcus aureus from clonal complex 398 (CC398) was exclusively associated with livestock species and companion animals. Recently, several studies described the emergence of S. aureus CC398 as etiologies of severe infections in humans living in an animal-free environment. Recent sequencing efforts showed that the mobile genetic elements found in CC398 isolates were specific for each population and enabled differentiation of strains responsible for asymptomatic colonization from strains involved in bloodstream infections. We mobilized prophages from a human CC398 isolate and introduced them into two naïve ancestral isolates devoid of prophages that exclusively colonize animals. These lysogenized ancestral CC398 isolates acquired features related to virulence, such as an increased capacity to adhere to human extracellular matrix proteins and the ability to invade and survive within non-phagocytic cells. Pathogenicity of several clinical isolates from the CC398 lineage as well as ancestral and in vitro lysogenized ancestral counterparts was assessed in a model of infectious endocarditis in rats. Natural and artificial lysogens were not only more invasive than their prophage-free parent but also showed an increased capacity to multiply within aortic vegetations. This study identified prophages as mediators of bacterial virulence in a model of infectious endocarditis, probably through promotion of interaction with extracellular matrix components. Further studies are needed to identify mechanisms leading to promotion of intrinsic virulence.
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Affiliation(s)
- Floriane Laumay
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
| | - Anna-Rita Corvaglia
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
| | - Seydina M Diene
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine et de Pharmacie, Aix-Marseille University, Marseille, France
| | - Myriam Girard
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - José Manuel Entenza
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
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Mancini S, Oechslin F, Menzi C, Que YA, Claes J, Heying R, Veloso TR, Vanassche T, Missiakas D, Schneewind O, Moreillon P, Entenza JM. Marginal role of von Willebrand factor-binding protein and coagulase in the initiation of endocarditis in rats with catheter-induced aortic vegetations. Virulence 2019; 9:1615-1624. [PMID: 30280967 PMCID: PMC7000203 DOI: 10.1080/21505594.2018.1528845] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Staphylococcus aureus is the leading cause of infective endocarditis (IE). While the role of S. aureus cell-wall associated protein clumping factor A (ClfA) in promoting IE has been already demonstrated, that of the secreted plasma-clotting factors staphylocoagulase (Coa) and von Willebrand factor-binding protein (vWbp) has not yet been elucidated. We investigated the role of Coa and vWbp in IE initiation in rats with catheter-induced aortic vegetations, using Lactococcus lactis expressing coa, vWbp, clfA or vWbp/clfA, and S. aureus Newman Δcoa, ΔvWbp, ΔclfA or Δcoa/ΔvWbp/ΔclfA mutants. vWbp-expression increased L. lactis valve infection compared to parent and coa-expressing strains (incidence: 62%, versus 0% and 13%, respectively; P < 0.01). Likewise, expression of clfA increased L. lactis infectivity (incidence: 80%), which was not further affected by co-expression of vWbp. In symmetry, deletion of the coa or vWbp genes in S. aureus did not decrease infectivity (incidence: 68 and 64%, respectively) whereas deletion of clfA did decrease valve infection (incidence: 45%; P = 0.03 versus parent), which was not further affected by the triple deletion Δcoa/ΔvWbp/ΔclfA (incidence: 36%; P > 0.05 versus ΔclfA mutant). Coa does not support the initial colonization of IE (in L. lactis) without other key virulence factors and vWbp contributes to initiation of IE (in L. lactis) but is marginal in the present of ClfA.
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Affiliation(s)
- Stefano Mancini
- a Department of Fundamental Microbiology , University of Lausanne , Lausanne , Switzerland
| | - Frank Oechslin
- a Department of Fundamental Microbiology , University of Lausanne , Lausanne , Switzerland
| | - Carmen Menzi
- a Department of Fundamental Microbiology , University of Lausanne , Lausanne , Switzerland
| | - Yok Ai Que
- b Department of Intensive Care Medicine , Bern University Hospital , Bern , Switzerland
| | - Jorien Claes
- c Cardiovascular Developmental Biology, Department of Cardiovascular Sciences , KU Leuven , Leuven , Belgium.,d Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences , KU Leuven , Leuven , Belgium
| | - Ruth Heying
- c Cardiovascular Developmental Biology, Department of Cardiovascular Sciences , KU Leuven , Leuven , Belgium
| | - Tiago Rafael Veloso
- a Department of Fundamental Microbiology , University of Lausanne , Lausanne , Switzerland
| | - Thomas Vanassche
- d Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences , KU Leuven , Leuven , Belgium
| | | | - Olaf Schneewind
- e Department of Microbiology , University of Chicago , Chicago , IL , USA
| | - Philippe Moreillon
- a Department of Fundamental Microbiology , University of Lausanne , Lausanne , Switzerland
| | - José Manuel Entenza
- a Department of Fundamental Microbiology , University of Lausanne , Lausanne , Switzerland
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10
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Leuenberger A, Sartori C, Boss R, Resch G, Oechslin F, Steiner A, Moreillon P, Graber H. Genotypes of Staphylococcus aureus: On-farm epidemiology and the consequences for prevention of intramammary infections. J Dairy Sci 2019; 102:3295-3309. [DOI: 10.3168/jds.2018-15181] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/09/2018] [Indexed: 12/22/2022]
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11
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McCallin S, Sarker SA, Sultana S, Oechslin F, Brüssow H. Metagenome analysis of Russian and Georgian Pyophage cocktails and a placebo-controlled safety trial of single phage versus phage cocktail in healthy Staphylococcus aureus carriers. Environ Microbiol 2018; 20:3278-3293. [PMID: 30051571 DOI: 10.1111/1462-2920.14310] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 06/11/2018] [Indexed: 01/30/2023]
Abstract
Bacteriophage therapy is a commonly used treatment for Staphylococcus aureus infections in countries of the former Soviet Union, using both single phages and phage cocktails. The scarce data available on Eastern phage cocktails prompted an investigation into commercially-available Pyophage cocktails from two different manufacturers used to treat skin and wound infections. Comparison of the metagenomic composition of two Pyophage products from Georgia and Russia revealed substantial differences in phage-types targeting Escherichia, Enterococcus, Salmonella, Pseudomonas aeruginosa and Proteus, therefore indicating multiple strategies for composing phage cocktails against these bacterial pathogens. Closely-related Kayvirus-like Myoviruses were, however, a shared component against S. aureus within all products, except for the inclusion of a secondary S. aureus Podovirus in one Microgen cocktail. Metagenomic analysis also revealed the presence of several probable prophage sequences but detected no genetic safety risks in terms of virulence factors or antibiotic resistance genes. The safety of broad-spectrum cocktails was tested by comparing the effects of nasal and oral exposure to Eliava Pyophage, a monospecies counterpart and placebo in healthy human carriers of S. aureus. The lack of adverse effects in any treatment groups supports the clinical safety of S. aureus phages administered as a single phage or as phage cocktail.
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Affiliation(s)
- Shawna McCallin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shafiqul A Sarker
- International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Shamima Sultana
- International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Harald Brüssow
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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12
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Abstract
Bacteriophage (phage) therapy, i.e., the use of viruses that infect bacteria as antimicrobial agents, is a promising alternative to conventional antibiotics. Indeed, resistance to antibiotics has become a major public health problem after decades of extensive usage. However, one of the main questions regarding phage therapy is the possible rapid emergence of phage-resistant bacterial variants, which could impede favourable treatment outcomes. Experimental data has shown that phage-resistant variants occurred in up to 80% of studies targeting the intestinal milieu and 50% of studies using sepsis models. Phage-resistant variants have also been observed in human studies, as described in three out of four clinical trials that recorded the emergence of phage resistance. On the other hand, recent animal studies suggest that bacterial mutations that confer phage-resistance may result in fitness costs in the resistant bacterium, which, in turn, could benefit the host. Thus, phage resistance should not be underestimated and efforts should be made to develop methodologies for monitoring and preventing it. Moreover, understanding and taking advantage of the resistance-induced fitness costs in bacterial pathogens is a potentially promising avenue.
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Affiliation(s)
- Frank Oechslin
- Department of Fundamental Microbiology (DMF), University of Lausanne, CH-1015 Lausanne, Switzerland.
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Larpin Y, Oechslin F, Moreillon P, Resch G, Entenza JM, Mancini S. In vitro characterization of PlyE146, a novel phage lysin that targets Gram-negative bacteria. PLoS One 2018; 13:e0192507. [PMID: 29408864 PMCID: PMC5800649 DOI: 10.1371/journal.pone.0192507] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/24/2018] [Indexed: 11/18/2022] Open
Abstract
The recent rise of multidrug-resistant Gram-negative bacteria represents a serious threat to public health and makes the search for novel effective alternatives to antibiotics a compelling need. Bacteriophage (Phage) lysins are enzymes that hydrolyze the cell wall of bacteria and represent a promising alternative to tackle this ever-increasing problem. Despite their use is believed to be restricted to Gram-positive bacteria, recent findings have shown that they can also be used against Gram-negative bacteria. By using a phage genome-based screening approach, we identified and characterized a novel lysin, PlyE146, encoded by an Escherichia coli prophage and with a predicted molecular mass of ca. 17 kDa. PlyE146 is composed of a C-terminal cationic peptide and a N-terminal N-acetylmuramidase domain. Histidine-tagged PlyE146 was overexpressed from a plasmid in Lactococcus lactis NZ9000 and purified by NI-NTA chromatography. PlyE146 exhibited in vitro optimal bactericidal activity against E. coli K12 (3.6 log10 CFU/mL decrease) after 2 h of incubation at 37°C at a concentration of 400 μg/mL in the absence of NaCl and at pH 6.0. Under these conditions, PlyE146 displayed antimicrobial activity towards several other E. coli, Pseudomonas aeruginosa (3 to 3.8-log10 CFU/mL decrease) and Acinetobacter baumannii (4.9 to >5-log10 CFU/mL decrease) strains. Therefore, PlyE146 represents a promising therapeutic agent against E. coli, P. aeruginosa and A. baumannii infections. However, further studies are required to improve the efficacy of PlyE146 under physiological conditions.
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Affiliation(s)
- Yu Larpin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Philippe Moreillon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Grégory Resch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - José Manuel Entenza
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- * E-mail:
| | - Stefano Mancini
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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14
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Oechslin F, Piccardi P, Mancini S, Gabard J, Moreillon P, Entenza JM, Resch G, Que YA. Synergistic Interaction Between Phage Therapy and Antibiotics Clears Pseudomonas Aeruginosa Infection in Endocarditis and Reduces Virulence. J Infect Dis 2017; 215:703-712. [PMID: 28007922 PMCID: PMC5388299 DOI: 10.1093/infdis/jiw632] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023] Open
Abstract
Background. Increasing antibiotic resistance warrants therapeutic alternatives. Here we investigated the efficacy of bacteriophage-therapy (phage) alone or combined with antibiotics against experimental endocarditis (EE) due to Pseudomonas aeruginosa, an archetype of difficult-to-treat infection. Methods. In vitro fibrin clots and rats with aortic EE were treated with an antipseudomonas phage cocktail alone or combined with ciprofloxacin. Phage pharmacology, therapeutic efficacy, and resistance were determined. Results. In vitro, single-dose phage therapy killed 7 log colony-forming units (CFUs)/g of fibrin clots in 6 hours. Phage-resistant mutants regrew after 24 hours but were prevented by combination with ciprofloxacin (2.5 × minimum inhibitory concentration). In vivo, single-dose phage therapy killed 2.5 log CFUs/g of vegetations in 6 hours (P < .001 vs untreated controls) and was comparable with ciprofloxacin monotherapy. Moreover, phage/ciprofloxacin combinations were highly synergistic, killing >6 log CFUs/g of vegetations in 6 hours and successfully treating 64% (n = 7/11) of rats. Phage-resistant mutants emerged in vitro but not in vivo, most likely because resistant mutations affected bacterial surface determinants important for infectivity (eg, the pilT and galU genes involved in pilus motility and LPS formation). Conclusions. Single-dose phage therapy was active against P. aeruginosa EE and highly synergistic with ciprofloxacin. Phage-resistant mutants had impaired infectivity. Phage-therapy alone or combined with antibiotics merits further clinical consideration.
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Affiliation(s)
- Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - Philippe Piccardi
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - Stefano Mancini
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | | | - Philippe Moreillon
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - José M Entenza
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - Gregory Resch
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - Yok-Ai Que
- Department of Intensive Care Medicine, Bern University Hospital, Switzerland
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15
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Veloso TR, Oechslin F, Que YA, Moreillon P, Entenza JM, Mancini S. Aspirin plus ticlopidine prevented experimental endocarditis due to Enterococcus faecalis and Streptococcus gallolyticus. Pathog Dis 2015; 73:ftv060. [PMID: 26310867 DOI: 10.1093/femspd/ftv060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2015] [Indexed: 01/01/2023] Open
Abstract
Enterococcus faecalis and Streptococcus gallolyticus cause infective endocarditis (IE), which can originate from the continuous release or translocation of low bacterial numbers into the bloodstream. In this context, IE cannot be prevented with antibiotics. We previously demonstrated that aspirin plus ticlopidine protected rats from IE due to S. gordonii and Staphylococcus aureus. Here we showed that aspirin plus ticlopidine significantly reduced vegetation weight and protected 73 and 64% rats (P < 0.005) from IE due to E. faecalis and S. gallolyticus, respectively. These results further support the potential use of aspirin plus ticlopidine for a global prevention of IE in high-risk patients.
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Affiliation(s)
- Tiago Rafael Veloso
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Yok-Ai Que
- Department of Intensive Care Medicine, Lausanne University Hospital Center (CHUV), CH-1011 Lausanne, Switzerland
| | - Philippe Moreillon
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - José Manuel Entenza
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Stefano Mancini
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
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