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Nakonieczna A, Topolska-Woś A, Łobocka M. New bacteriophage-derived lysins, LysJ and LysF, with the potential to control Bacillus anthracis. Appl Microbiol Biotechnol 2024; 108:76. [PMID: 38194144 PMCID: PMC10776502 DOI: 10.1007/s00253-023-12839-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/10/2024]
Abstract
Bacillus anthracis is an etiological agent of anthrax, a severe zoonotic disease that can be transmitted to people and cause high mortalities. Bacteriophages and their lytic enzymes, endolysins, have potential therapeutic value in treating infections caused by this bacterium as alternatives or complements to antibiotic therapy. They can also be used to identify and detect B. anthracis. Endolysins of two B. anthracis Wbetavirus phages, J5a and F16Ba which were described by us recently, differ significantly from the best-known B. anthracis phage endolysin PlyG from Wbetavirus genus bacteriophage Gamma and a few other Wbetavirus genus phages. They are larger than PlyG (351 vs. 233 amino acid residues), contain a signal peptide at their N-termini, and, by prediction, have a different fold of cell binding domain suggesting different structural basis of cell epitope recognition. We purified in a soluble form the modified versions of these endolysins, designated by us LysJ and LysF, respectively, and depleted of signal peptides. Both modified endolysins could lyse the B. anthracis cell wall in zymogram assays. Their activity against the living cells of B. anthracis and other species of Bacillus genus was tested by spotting on the layers of bacteria in soft agar and by assessing the reduction of optical density of bacterial suspensions. Both methods proved the effectiveness of LysJ and LysF in killing the anthrax bacilli, although the results obtained by each method differed. Additionally, the lytic efficiency of both proteins was different, which apparently correlates with differences in their amino acid sequence. KEY POINTS: • LysJ and LysF are B. anthracis-targeting lysins differing from lysins studied so far • LysJ and LysF could be overproduced in E. coli in soluble and active forms • LysJ and LysF are active in killing cells of B. anthracis virulent strains.
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Affiliation(s)
- Aleksandra Nakonieczna
- Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Center, 24-100, Puławy, Poland.
| | | | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
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2
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Costa P, Pereira C, Romalde JL, Almeida A. A game of resistance: War between bacteria and phages and how phage cocktails can be the solution. Virology 2024; 599:110209. [PMID: 39186863 DOI: 10.1016/j.virol.2024.110209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024]
Abstract
While phages hold promise as an antibiotic alternative, they encounter significant challenges in combating bacterial infections, primarily due to the emergence of phage-resistant bacteria. Bacterial defence mechanisms like superinfection exclusion, CRISPR, and restriction-modification systems can hinder phage effectiveness. Innovative strategies, such as combining different phages into cocktails, have been explored to address these challenges. This review delves into these defence mechanisms and their impact at each stage of the infection cycle, their challenges, and the strategies phages have developed to counteract them. Additionally, we examine the role of phage cocktails in the evolving landscape of antibacterial treatments and discuss recent studies that highlight the effectiveness of diverse phage cocktails in targeting essential bacterial receptors and combating resistant strains.
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Affiliation(s)
- Pedro Costa
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Carla Pereira
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CRETUS & CIBUS - Faculty of Biology, University of Santiago de Compostela, CP 15782 Santiago de Compostela, Spain.
| | - Adelaide Almeida
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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3
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Ghate MM, Gulati K, Poluri KM. Alginate binding enhances the structural stability and potentiates the lytic activity of bacteriophage endolysin's partially folded conformation. Arch Biochem Biophys 2024; 760:110129. [PMID: 39159898 DOI: 10.1016/j.abb.2024.110129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/15/2024] [Accepted: 08/16/2024] [Indexed: 08/21/2024]
Abstract
Polysaccharide polymers are increasingly being used as chaperon-like macromolecules in assisting protein folding of unfolded protein molecules. They interact with unfolded or partially folded proteins in a charge and conformation specific manner that results in the formation of stable protein-polysaccharide complexes. In most of the cases, the complex formation of protein-polysaccharide is driven via non-covalent interactions that have found to endorse the activity of proteins. T4L (18.7 kDa) and T7L (17 kDa) endolysins belong to the hydrolase and amidase class of peptidoglycan degrading enzymes. Both T4L and T7L exist in partially folded forms and are devoid of lytic activity at low pH conditions. In the current study, we assessed the binding of alginate with T4L and T7L at pH 7 and 3 using variety of biophysical and biochemical techniques. Spectroscopic studies revealed differential structural modulations of partially folded T4L and T7L upon their interaction with alginate. Further, the complex formation of alginate with partially folded T4L/T7L was confirmed by ITC and STEM. Additionally, the formed complexes of alginate with both T4L/T7L PF endolysins were found to be chemically and enzymatically stable. Moreover, such complexes were also marked with differential enhancement in their lytic activities at acidic pH conditions. This implied the potency of alginate as an excellent choice of matrix to preserve the structural and functional integrity of partially folded forms of T4L and T7L at highly acidic conditions.
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Affiliation(s)
- Mayur Mohan Ghate
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, Uttarakhand, India
| | - Khushboo Gulati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, Uttarakhand, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee-247667, Uttarakhand, India.
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Krone L, Mahankali S, Geiger T. Cytolysin A is an intracellularly induced and secreted cytotoxin of typhoidal Salmonella. Nat Commun 2024; 15:8414. [PMID: 39341826 PMCID: PMC11438861 DOI: 10.1038/s41467-024-52745-0] [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: 01/16/2024] [Accepted: 09/20/2024] [Indexed: 10/01/2024] Open
Abstract
Typhoidal Salmonella enterica serovars, such as Typhi and Paratyphi A, cause severe systemic infections, thereby posing a significant threat as human-adapted pathogens. This study focuses on cytolysin A (ClyA), a virulence factor essential for bacterial dissemination within the human body. We show that ClyA is exclusively expressed by intracellular S. Paratyphi A within the Salmonella-containing vacuole (SCV), regulated by the PhoP/Q system and SlyA. ClyA localizes in the bacterial periplasm, suggesting potential secretion. Deletion of TtsA, an essential Type 10 Secretion System component, completely abolishes intracellular ClyA detection and its presence in host cell supernatants. Host cells infected with wild-type S. Paratyphi A contain substantial ClyA, with supernatants capable of lysing neighboring cells. Notably, ClyA selectively lyses macrophages and erythrocytes while sparing epithelial cells. These findings identify ClyA as an intracellularly induced cytolysin, dependent on the SCV environment and secreted via a Type 10 Secretion System, with specific cytolytic activity.
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Affiliation(s)
- Lena Krone
- Max von Pettenkofer-Institute, Chair for Medical Microbiology and Hygiene, Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
| | - Srujita Mahankali
- Max von Pettenkofer-Institute, Chair for Medical Microbiology and Hygiene, Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
| | - Tobias Geiger
- Max von Pettenkofer-Institute, Chair for Medical Microbiology and Hygiene, Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany.
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5
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Gangakhedkar R, Jain V. Elucidating the molecular properties and anti-mycobacterial activity of cysteine peptidase domain of D29 mycobacteriophage endolysin. J Virol 2024:e0132824. [PMID: 39287392 DOI: 10.1128/jvi.01328-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
Emergence of antibiotic resistance in pathogenic Mycobacterium tuberculosis (Mtb) has elevated tuberculosis to a serious global threat, necessitating alternate solutions for its eradication. D29 mycobacteriophage can infect and kill several mycobacterial species including Mtb. It encodes an endolysin LysA to hydrolyze host bacteria peptidoglycan for progeny release. We previously showed that out of the two catalytically active domains of LysA [N-terminal domain (NTD) and lysozyme-like domain], NTD, when ectopically expressed in Mycobacterium smegmatis (Msm), is able to kill the bacterium nearly as efficiently as full-length LysA. Here, we dissected the functioning of NTD to develop it as a phage-derived small molecule anti-mycobacterial therapeutic. We performed a large-scale site-directed mutagenesis of the conserved residues in NTD and examined its structure, stability, and function using molecular dynamic simulations coupled with biophysical and biochemical experiments. Our data show that NTD functions as a putative cysteine peptidase with a catalytic triad composed of Cys41, His112, and Glu137, acting as nucleophile, base, and acid, respectively, and showing characteristics similar to the NlpC/P60 family of cysteine peptidases. Additionally, our peptidoglycan hydrolysis assays suggested that NTD hydrolyzes only mycobacterial peptidoglycan and does not act on Gram-positive and Gram-negative bacterial peptidoglycans. More importantly, the combined activity of exogenously added NTD and sub-lethal doses of anti-mycobacterial drugs kills Msm in vitro and exhibits disruption of pre-formed mycobacterial biofilm. We additionally show that NTD treatment increases the permeability of antibiotics in Msm, which reduces the minimum inhibitory concentration of the antibiotics. Collectively, we present NTD as a promising phage-derived therapeutic against mycobacteria.IMPORTANCEMycobacteriophages are the viruses that use mycobacteria as host for their progeny production and, in the process, kill them. Mycobacteriophages are, therefore, considered as promising alternatives to antibiotics for killing pathogenic Mycobacterium tuberculosis. The endolysin LysA produced by mycobacteriophage D29 plays an important role in host cell lysis and virion release. Our work presented here highlights the functioning of LysA's N-terminal catalytic domain (NTD) in order to develop it as phage-derived small molecule therapeutics. We show that combined treatment of exogenously added NTD and sub-lethal doses of anti-mycobacterial drugs kills M. smegmatis, shows synergism by reducing the minimum inhibitory concentration of these antibiotics, and exhibits disruption of pre-formed mature biofilm. These outcomes and our detailed biochemical and biophysical dissection of the protein further pave the way toward engineering and development of NTD as a promising therapeutic against mycobacterial infections such as tuberculosis.
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Affiliation(s)
- Rutuja Gangakhedkar
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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Mondal A, Teimouri H, Kolomeisky AB. Molecular mechanisms of precise timing in cell lysis. Biophys J 2024; 123:3090-3099. [PMID: 38971973 PMCID: PMC11427807 DOI: 10.1016/j.bpj.2024.07.008] [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: 02/07/2024] [Revised: 04/03/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024] Open
Abstract
Many biological systems exhibit precise timing of events, and one of the most known examples is cell lysis, which is a process of breaking bacterial host cells in the virus infection cycle. However, the underlying microscopic picture of precise timing remains not well understood. We present a novel theoretical approach to explain the molecular mechanisms of effectively deterministic dynamics in biological systems. Our hypothesis is based on the idea of stochastic coupling between relevant underlying biophysical and biochemical processes that lead to noise cancellation. To test this hypothesis, we introduced a minimal discrete-state stochastic model to investigate how holin proteins produced by bacteriophages break the inner membranes of gram-negative bacteria. By explicitly solving this model, the dynamic properties of cell lysis are fully evaluated, and theoretical predictions quantitatively agree with available experimental data for both wild-type and holin mutants. It is found that the observed threshold-like behavior is a result of the balance between holin proteins entering the membrane and leaving the membrane during the lysis. Theoretical analysis suggests that the cell lysis achieves precise timing for wild-type species by maximizing the number of holins in the membrane and narrowing their spatial distribution. In contrast, for mutated species, these conditions are not satisfied. Our theoretical approach presents a possible molecular picture of precise dynamic regulation in intrinsically random biological processes.
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Affiliation(s)
- Anupam Mondal
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemistry, Rice University, Houston, Texas
| | - Hamid Teimouri
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemistry, Rice University, Houston, Texas
| | - Anatoly B Kolomeisky
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemistry, Rice University, Houston, Texas; Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas.
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7
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German GJ, DeGiulio JV, Ramsey J, Kropinski AM, Misra R. The TolC and Lipopolysaccharide-Specific Escherichia coli Bacteriophage TLS-the Tlsvirus Archetype Virus. PHAGE (NEW ROCHELLE, N.Y.) 2024; 5:173-183. [PMID: 39372356 PMCID: PMC11447400 DOI: 10.1089/phage.2023.0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Introduction TLS is a virulent bacteriophage of Escherichia coli that utilizes TolC and lipopolysaccharide as its cell surface receptors. Methods The genome was reannotated using the latest online resources and compared to other T1-like phages. Results The TLS genome consists of 49,902 base pairs, encoding 86 coding sequences that display considerable sequence similarity with the T1 phage genome. It also contains 18 intergenic 21-base long repeats, each of them upstream of a predicted start codon and in the direction of transcription. Data revealed that DNA packaging occurs through the pac site-mediated headful mechanism. Conclusions Based on sequence analysis of its genome, TLS belongs to the Drexlerviridae family and represents the type member of the Tlsvirus genus.
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Affiliation(s)
- Gregory J. German
- St. Joseph’s Health Centre, Unity Health Toronto, Toronto, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Canada
| | | | - Jolene Ramsey
- Texas A&M University, Biology Department, College Station, TX USA
| | - Andrew M. Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Canada
| | - Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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8
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Zhydzetski A, Głowacka-Grzyb Z, Bukowski M, Żądło T, Bonar E, Władyka B. Agents Targeting the Bacterial Cell Wall as Tools to Combat Gram-Positive Pathogens. Molecules 2024; 29:4065. [PMID: 39274911 PMCID: PMC11396672 DOI: 10.3390/molecules29174065] [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: 07/28/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/16/2024] Open
Abstract
The cell wall is an indispensable element of bacterial cells and a long-known target of many antibiotics. Penicillin, the first discovered beta-lactam antibiotic inhibiting the synthesis of cell walls, was successfully used to cure many bacterial infections. Unfortunately, pathogens eventually developed resistance to it. This started an arms race, and while novel beta-lactams, either natural or (semi)synthetic, were discovered, soon upon their application, bacteria were developing resistance. Currently, we are facing the threat of losing the race since more and more multidrug-resistant (MDR) pathogens are emerging. Therefore, there is an urgent need for developing novel approaches to combat MDR bacteria. The cell wall is a reasonable candidate for a target as it differentiates not only bacterial and human cells but also has a specific composition unique to various groups of bacteria. This ensures the safety and specificity of novel antibacterial agents that target this structure. Due to the shortage of low-molecular-weight candidates for novel antibiotics, attention was focused on peptides and proteins that possess antibacterial activity. Here, we describe proteinaceous agents of various origins that target bacterial cell wall, including bacteriocins and phage and bacterial lysins, as alternatives to classic antibiotic candidates for antimicrobial drugs. Moreover, advancements in protein chemistry and engineering currently allow for the production of stable, specific, and effective drugs. Finally, we introduce the concept of selective targeting of dangerous pathogens, exemplified by staphylococci, by agents specifically disrupting their cell walls.
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Affiliation(s)
- Aliaksandr Zhydzetski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Zuzanna Głowacka-Grzyb
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicza St. 11, 30-348 Cracow, Poland
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Tomasz Żądło
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicza St. 11, 30-348 Cracow, Poland
| | - Emilia Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Benedykt Władyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
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van der Els S, Boekhorst J, Bron PA, Kleerebezem M. The lactococcal ICE-ome encodes a repertoire of exchangeable traits with potential industrial relevance. BMC Genomics 2024; 25:734. [PMID: 39080539 PMCID: PMC11288074 DOI: 10.1186/s12864-024-10646-y] [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: 05/29/2024] [Accepted: 07/22/2024] [Indexed: 08/03/2024] Open
Abstract
Dairy industries apply selected lactococcal strains and mixed cultures to produce diverse fermented products with distinctive flavor and texture properties. Innovation of the starter culture functionality in cheese applications embraces natural biodiversity of the Lactococcus species to identify novel strains with alternative flavor or texture forming capacities and/or increased processing robustness and phage resistance. Mobile genetic elements (MGE), like integrative conjugative elements (ICEs) play an important role in shaping the biodiversity of bacteria. Besides the genes involved in the conjugation of ICEs from donor to recipient strains, these elements also harbor cargo genes that encode a wide range of functions. The definition of such cargo genes can only be achieved by accurate identification of the ICE boundaries (delimiting). Here, we delimited 25 ICEs in lactococcal genome sequences with low contig numbers using insertion-sites flanking single-copy core-genome genes as markers for each of the distinct ICE-integrases we identified previously within the conserved ICE-core genes. For ICEs in strains for which genome information with large numbers of contigs is available, we exemplify that CRISPR-Cas9 driven ICE-curing, followed by resequencing, allows accurate delimitation and cargo definition of ICEs. Finally, we compare and contrast the cargo gene repertoire of the 26 delimited lactococcal ICEs, identifying high plasticity among the cargo of lactococccal ICEs and a range of encoded functions that is of apparent industrial interest, including restriction modification, abortive infection, and stress adaptation genes.
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Affiliation(s)
- Simon van der Els
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University & Research, De Elst 1, Wageningen, 6708 WD, The Netherlands
- NIZO B.V, Kernhemseweg 2, Ede, 6718 ZB, The Netherlands
- BE-Basic Foundation, Mijnbouwstraat 120, Delft, 2628 RX, The Netherlands
| | - Jos Boekhorst
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University & Research, De Elst 1, Wageningen, 6708 WD, The Netherlands
| | - Peter A Bron
- NIZO B.V, Kernhemseweg 2, Ede, 6718 ZB, The Netherlands
- BE-Basic Foundation, Mijnbouwstraat 120, Delft, 2628 RX, The Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University & Research, De Elst 1, Wageningen, 6708 WD, The Netherlands.
- BE-Basic Foundation, Mijnbouwstraat 120, Delft, 2628 RX, The Netherlands.
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Li H, Zhong W, Zhang X, Rui Z, Yang Y, Xu J, Gao J, Zhou X, Wu J, Xu J. Isolation and Characterization of a Novel Vibrio Phage vB_ValA_R15Z. Curr Microbiol 2024; 81:285. [PMID: 39073500 DOI: 10.1007/s00284-024-03736-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/08/2024] [Indexed: 07/30/2024]
Abstract
Vibrio phages have emerged as a potential alternative to antibiotic therapy for treating Vibrio infections. In this study, a lytic Vibrio phage, vB_ValA_R15Z against Vibrio alginolyticus ATCC 17749T, was isolated from an aquatic water sample collected in Xiamen, China. The phage had an icosahedral head (diameter 69 ± 2 nm) and a short, non-contractile tail measuring 16 ± 2 nm. The genome of vB_ValA_R15Z was found to be a double-stranded DNA consisting of 43, 552 bp, containing 54 coding sequences (CDSs) associated with phage packaging, structure, DNA metabolism, lysis and additional functions. The BLASTN results indicated that vB_ValA_R15Z shared less than 90.18% similarity with known phages recorded in the NCBI GenBank database, suggesting that vB_ValA_R15Z was a novel Vibrio phage. Furthermore, phylogenetic analysis revealed that vB_ValA_R15Z belongs to the genus Kaohsiungvirus. In addition, a typical lytic mechanism (holin-endolysim) was found in the genome of vB_ValA_R15Z, while no antibiotic resistance- or virulence factor-related gene was detected. Overall, the study provides valuable insights into the isolation and characterization of vB_ValA_R15Z, highlighting its potential as an effective phage therapy option for combating Vibrio alginolyticus infections.
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Affiliation(s)
- Huifang Li
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China.
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China.
| | - Wanxuan Zhong
- State Key Laboratory of Trophic Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xinyu Zhang
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Zhang Rui
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518061, Guangdong, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518061, Guangdong, China
| | - Juntian Xu
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jie Gao
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Xing Zhou
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jie Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China.
| | - Jie Xu
- Centre for Regional Oceans, Department of Ocean Science and Technology, Faculty of Science and Technology, University of Macau, Macau, 999078, China.
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11
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Mondal A, Teimouri H, Kolomeisky AB. Elucidating Physicochemical Features of Holin Proteins Responsible for Bacterial Cell Lysis. J Phys Chem B 2024; 128:7129-7140. [PMID: 38985954 DOI: 10.1021/acs.jpcb.4c03040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Bacterial resistance to conventional antibiotics stimulated the development of so-called "phage therapies" that rely on cell lysis, which is a process of destroying bacterial cells due to their infections by bacterial viruses. For λ bacteriophages, it is known that the critical role in this process is played by holin proteins that aggregate in cellular membranes before breaking them apart. While multiple experimental studies probed various aspects of cell lysis, the underlying molecular mechanisms remain not well understood. Here we investigate what physicochemical properties of holin proteins are the most relevant for these processes by employing statistical correlation analysis of cell lysis dynamics for different experimentally observed mutant species. Our findings reveal significant correlations between various physicochemical features and cell lysis dynamics. Notably, we uncover a strong inverse correlation between local hydrophobicity and cell lysis times, underscoring the crucial role of hydrophobic interactions in membrane disruption. Stimulated by these observations, a predictive model capable of explicitly estimating cell lysis times for any holin protein mutants based on their mean hydrophobicity values is developed. Our study not only provides important microscopic insights into cell lysis phenomena but also proposes specific routes to optimize medical and biotechnological applications of bacteriophages.
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Affiliation(s)
- Anupam Mondal
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Hamid Teimouri
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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12
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Das S, Kaledhonkar S. Physiochemical characterization of a potential Klebsiella phage MKP-1 and analysis of its application in reducing biofilm formation. Front Microbiol 2024; 15:1397447. [PMID: 39086652 PMCID: PMC11288805 DOI: 10.3389/fmicb.2024.1397447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/20/2024] [Indexed: 08/02/2024] Open
Abstract
The common intestinal pathogen Klebsiella pneumoniae (K. pneumoniae) is one of the leading causes of fatal superbug infections that can resist the effects of commonly prescribed medicines. The uncontrolled use or misuse of antibiotics has increased the prevalence of drug-resistant K. pneumoniae strains in the environment. In the quest to search for alternative therapeutics for treating these drug-resistant infections, bacteriophages (bacterial viruses) emerged as potential candidates for in phage therapy against Klebsiella. The effective formulation of phage therapy against drug-resistant Klebsiella infections demands thorough characterization and screening of many bacteriophages. To contribute effectively to the formulation of successful phage therapy against superbug infections by K. pneumoniae, this study includes the isolation and characterization of a novel lytic bacteriophage MKP-1 to consider its potential to be used as therapeutics in treating drug-resistant Klebsiella infections. Morphologically, having a capsid attached to a long non-contractile tail, it was found to be a siphovirus that belongs to the class Caudoviricetes and showed infectivity against different strains of the target host bacterium. Comparatively, this double-stranded DNA phage has a large burst size and is quite stable in various physiological conditions. More interestingly, it has the potential to degrade the tough biofilms formed by K. pneumoniae (Klebsiella pneumoniae subsp. pneumoniae (Schroeter) Trevisan [ATCC 15380]) significantly. Thus, the following study would contribute effectively to considering phage MKP-1 as a potential candidate for phage therapy against Klebsiella infection.
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Affiliation(s)
| | - Sandip Kaledhonkar
- Department of Bioscience and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
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13
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Wang Z, Peng X, Hülpüsch C, Khan Mirzaei M, Reiger M, Traidl-Hoffmann C, Deng L, Schloter M. Distinct prophage gene profiles of Staphylococcus aureus strains from atopic dermatitis patients and healthy individuals. Microbiol Spectr 2024; 12:e0091524. [PMID: 39012113 DOI: 10.1128/spectrum.00915-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/13/2024] [Indexed: 07/17/2024] Open
Abstract
Staphylococcus aureus strains exhibit varying associations with atopic dermatitis (AD), but the genetic determinants underpinning the pathogenicity are yet to be fully characterized. To reveal the genetic differences between S. aureus strains from AD patients and healthy individuals (HE), we developed and employed a random forest classifier to identify potential marker genes responsible for their phenotypic variations. The classifier was able to effectively distinguish strains from AD and HE. We also uncovered strong links between certain marker genes and phage functionalities, with phage holin emerging as the most pivotal differentiating factor. Further examination of S. aureus gene content highlighted the genetic diversity and functional implications of prophages in driving differentiation between strains from AD and HE. The HE group exhibited greater gene content diversity, largely influenced by their prophages. While strains from both AD and HE universally housed prophages, those in the HE group were distinctively higher at the strain level. Moreover, although prophages in the HE group exhibited variously higher enrichment of differential functions, the AD group displayed a notable enrichment of virulence factors within their prophages, underscoring the important contribution of prophages to the pathogenesis of AD-associated strains. Overall, prophages significantly shape the genetic and functional profiles of S. aureus strains, shedding light on their pathogenic potential and elucidating the mechanisms behind the phenotypic variations in AD and HE environments. IMPORTANCE Through a nuanced exploration of Staphylococcus aureus strains obtained from atopic dermatitis (AD) patients and healthy controls (HE), our research unveils pivotal genetic determinants influencing their pathogenic associations. Utilizing a random forest classifier, we illuminate distinct marker genes, with phage holin emerging as a critical differential factor, revealing the profound impact of prophages on genetic and pathogenic profiles. HE strains exhibited a diverse gene content, notably shaped by unique, heightened prophages. Conversely, AD strains emphasized a pronounced enrichment of virulence factors within prophages, signifying their key role in AD pathogenesis. This work crucially highlights prophages as central architects of the genetic and functional attributes of S. aureus strains, providing vital insights into pathogenic mechanisms and phenotypic variations, thereby paving the way for targeted AD therapeutic approaches and management strategies by demystifying specific genetic and pathogenic mechanisms.
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Affiliation(s)
- Zhongjie Wang
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Xue Peng
- Faculty of Biology, Biocenter, Ludwig Maximilian University of Munich, Munich, Germany
- Institute of Virology, Helmholtz Munich, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Claudia Hülpüsch
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
- Insitute of Environmental Medicine, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Christine Kühne Center for Allergy Research and Education, Davos, Switzerland
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Munich, German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Prevention of Microbial Infectious Diseases, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Matthias Reiger
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
- Insitute of Environmental Medicine, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Traidl-Hoffmann
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
- Insitute of Environmental Medicine, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Christine Kühne Center for Allergy Research and Education, Davos, Switzerland
| | - Li Deng
- Institute of Virology, Helmholtz Munich, German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Prevention of Microbial Infectious Diseases, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Environmental Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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14
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Hvid U, Mitarai N. Competitive advantages of T-even phage lysis inhibition in response to secondary infection. PLoS Comput Biol 2024; 20:e1012242. [PMID: 38976747 PMCID: PMC11257392 DOI: 10.1371/journal.pcbi.1012242] [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: 02/02/2024] [Revised: 07/18/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
T-even bacteriophages are known to employ lysis inhibition (LIN), where the lysis of an infected host is delayed in response to secondary adsorptions. Upon the eventual burst of the host, significantly more phage progenies are released. Here, we analysed the competitive advantage of LIN using a mathematical model. In batch culture, LIN provides a bigger phage yield at the end of the growth where all the hosts are infected due to an exceeding number of phage particles and, in addition, gives a competitive advantage against LIN mutants with rapid lysis by letting them adsorb to already infected hosts in the LIN state. By simulating plaque formation in a spatially structured environment, we show that, while LIN phages will produce a smaller zone of clearance, the area over which the phages spread is actually comparable to those without LIN. The analysis suggests that LIN induced by secondary adsorption is favourable in terms of competition, both in spatially homogeneous and inhomogeneous environments.
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Affiliation(s)
- Ulrik Hvid
- The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Namiko Mitarai
- The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
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15
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Xiang Y, Wang S, Huang H, Li X, Wei Y, Li H, Ji X. A novel endolysin from an Enterococcus faecalis phage and application. Microb Pathog 2024; 192:106689. [PMID: 38750777 DOI: 10.1016/j.micpath.2024.106689] [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: 12/27/2023] [Revised: 05/03/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024]
Abstract
Enterococcus faecalis is the primary species detected in cases of secondary persistent infection resulting from root canal therapy failure. Due to the overuse of antibacterial agents, E. faecalis has developed resistance to these drugs, making it challenging to treat clinical diseases caused by E. faecalis infection. Therefore, there is an urgent need to explore new alternative drugs for treating E. faecalis infections. We aimed to clone and express the genes of phage endolysins, purify the recombinant proteins, and analyze their antibacterial activity, lysis profile, and ability to remove biofilm. The crude enzyme of phage endolysin pEF51 (0.715 mg/mL), derived from phage PEf771 infecting E. faecalis, exhibited superior bacterial inhibitory activity and a broader bactericidal spectrum than its parental phage PEf771. Furthermore, pEF51 demonstrated high efficacy in eliminating E. faecalis biofilm. Therapeutic results of the infected Sprague-Dawley (SD) rat model indicated that among 10 SD rats, only one developed a thoracic peritoneal abscess and splenic peritoneal abscess after 72 h of treatment with pEF51. This suggests that pEF51 could provide protection against E. faecalis infection in SD rats. Based on the 16S rDNA metagenomic data of the intestinal microbial community of SD rats, endolysin pEF51 exerted a certain influence on the diversity of intestinal microorganisms at the genus level. Thus, pEF51 may serve as a promising alternative to antibiotics in the management of E. faecalis infection.
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Affiliation(s)
- Yingying Xiang
- -Department of Stomatology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650031, China
| | - Suping Wang
- -Life Science and Technology & Medical Faculty, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hao Huang
- -Department of Stomatology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650031, China
| | - Xuelin Li
- -Department of Stomatology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650031, China
| | - Yunlin Wei
- -Life Science and Technology & Medical Faculty, Kunming University of Science and Technology, Kunming, 650500, China
| | - Haiyan Li
- -Life Science and Technology & Medical Faculty, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xiuling Ji
- -Life Science and Technology & Medical Faculty, Kunming University of Science and Technology, Kunming, 650500, China.
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16
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González-Gómez JP, Rodríguez-Arellano SN, Gomez-Gil B, Vergara-Jiménez MDJ, Chaidez C. Genomic and biological characterization of bacteriophages against Enterobacter cloacae, a high-priority pathogen. Virology 2024; 595:110100. [PMID: 38714025 DOI: 10.1016/j.virol.2024.110100] [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: 11/08/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
Enterobacter cloacae is a clinically significant pathogen due to its multi-resistance to antibiotics, presenting a challenge in the treatment of infections. As concerns over antibiotic resistance escalate, novel therapeutic approaches have been explored. Bacteriophages, characterized by their remarkable specificity and ability to self-replicate within target bacteria, are emerging as a promising alternative therapy. In this study, we isolated and partially characterized nine lytic bacteriophages targeting E. cloacae, with two selected for comprehensive genomic analysis based on their host range and bacteriolytic activity. All identified phages exhibited a narrow host range, demonstrated stability within a temperature range of 30-60 °C, displayed pH tolerance from 3 to 10, and showed an excellent bacteriolytic capacity for up to 18 h. Notably, the fully characterized phage genomes revealed an absence of lysogenic, virulence, or antibiotic-resistance genes, positioning them as promising candidates for therapeutic intervention against E. cloacae-related diseases. Nonetheless, translating this knowledge into practical therapeutic applications mandates a deeper understanding of bacteriophage interactions within complex biological environments.
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Affiliation(s)
- Jean Pierre González-Gómez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico
| | | | - Bruno Gomez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Unidad Mazatlán en Acuicultura y Manejo Ambiental, AP 711, Mazatlan, Sinaloa, Mexico
| | | | - Cristobal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico.
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17
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Han NS, Harada M, Pham-Khanh NH, Kamei K. Isolation, Characterization, and Complete Genome Sequence of Escherichia Phage KIT06 Which Infects Nalidixic Acid-Resistant Escherichia coli. Antibiotics (Basel) 2024; 13:581. [PMID: 39061264 PMCID: PMC11274021 DOI: 10.3390/antibiotics13070581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Escherichia coli (E. coli) is one of the most common sources of infection in humans and animals. The emergence of E. coli which acquires resistance to various antibiotics has made treatment difficult. Bacteriophages can be considered promising agents to expand the options for the treatment of antibiotic-resistant bacteria. This study describes the isolation and characterization of Escherichia phage KIT06, which can infect E. coli resistant to the quinolone antibiotic nalidixic acid. Phage virions possess an icosahedral head that is 93 ± 8 nm in diameter and a contractile tail (116 ± 12 nm × 13 ± 5 nm). The phage was found to be stable under various thermal and pH conditions. A one-step growth curve showed that the latent time of the phage was 20 min, with a burst size of 28 particles per infected cell. Phage KIT06 infected 7 of 12 E. coli strains. It inhibited the growth of the host bacterium and nalidixic acid-resistant E. coli. The lipopolysaccharide and outer membrane proteins of E. coli, tsx and btuB, are phage receptors. Phage KIT06 is a new species of the genus Tequatrovirus with a genome of 167,059 bp consisting of 264 open reading frames (ORFs) that encode gene products related to morphogenesis, replication, regulation, and host lysis. The lack of genes encoding integrase or excisionase indicated that this phage was lytic. Thus, KIT06 could potentially be used to treat antibiotic-resistant E. coli using phage therapy. However, further studies are essential to understand its use in combination with other antimicrobial agents and its safe use in such applications.
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Affiliation(s)
- Nguyen Song Han
- Department of Functional Chemistry, Kyoto Institute of Technology, Kyoto 606-8585, Japan; (N.S.H.); (M.H.)
| | - Mana Harada
- Department of Functional Chemistry, Kyoto Institute of Technology, Kyoto 606-8585, Japan; (N.S.H.); (M.H.)
| | - Nguyen Huan Pham-Khanh
- Department of Biology, College of Natural Sciences, Can Tho University, Can Tho City 900000, Vietnam;
| | - Kaeko Kamei
- Department of Functional Chemistry, Kyoto Institute of Technology, Kyoto 606-8585, Japan; (N.S.H.); (M.H.)
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18
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Al-Faliti M, Wang P, Smith AL, Delgado Vela J. Phage phylogeny, molecular signaling, and auxiliary antimicrobial resistance in aerobic and anaerobic membrane bioreactors. WATER RESEARCH 2024; 256:121620. [PMID: 38677036 DOI: 10.1016/j.watres.2024.121620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/30/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024]
Abstract
Phage emit communication signals that inform their lytic and lysogenic life cycles. However, little is known regarding the abundance and diversity of the genes associated with phage communication systems in wastewater treatment microbial communities. This study focused on phage communities within two distinct biochemical wastewater environments, specifically aerobic membrane bioreactors (AeMBRs) and anaerobic membrane bioreactors (AnMBRs) exposed to varying antibiotic concentrations. Metagenomic data from the bench-scale systems were analyzed to explore phage phylogeny, life cycles, and genetic capacity for antimicrobial resistance and quorum sensing. Two dominant phage families, Schitoviridae and Peduoviridae, exhibited redox-dependent dynamics. Schitoviridae prevailed in anaerobic conditions, while Peduoviridae dominated in aerobic conditions. Notably, the abundance of lytic and lysogenic proteins varied across conditions, suggesting the coexistence of both life cycles. Furthermore, the presence of antibiotic resistance genes (ARGs) within viral contigs highlighted the potential for phage to transfer ARGs in AeMBRs. Finally, quorum sensing genes in the virome of AeMBRs indicated possible molecular signaling between phage and bacteria. Overall, this study provides insights into the dynamics of viral communities across varied redox conditions in MBRs. These findings shed light on phage life cycles, and auxiliary genetic capacity such as antibiotic resistance and bacterial quorum sensing within wastewater treatment microbial communities.
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Affiliation(s)
- Mitham Al-Faliti
- Department of Civil and Environmental Engineering, Howard University, Washington, D.C., USA
| | - Phillip Wang
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Jeseth Delgado Vela
- Department of Civil and Environmental Engineering, Howard University, Washington, D.C., USA.
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19
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Tyagi JL, Gupta P, Ghate MM, Kumar D, Poluri KM. Assessing the synergistic potential of bacteriophage endolysins and antimicrobial peptides for eradicating bacterial biofilms. Arch Microbiol 2024; 206:272. [PMID: 38772980 DOI: 10.1007/s00203-024-04003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/14/2024] [Indexed: 05/23/2024]
Abstract
Phage-encoded endolysins have emerged as a potential substitute to conventional antibiotics due to their exceptional benefits including host specificity, rapid host killing, least risk of resistance. In addition to their antibacterial potency and biofilm eradication properties, endolysins are reported to exhibit synergism with other antimicrobial agents. In this study, the synergistic potency of endolysins was dissected with antimicrobial peptides to enhance their therapeutic effectiveness. Recombinantly expressed and purified bacteriophage endolysin [T7 endolysin (T7L); and T4 endolysin (T4L)] proteins have been used to evaluate the broad-spectrum antibacterial efficacy using different bacterial strains. Antibacterial/biofilm eradication studies were performed in combination with different antimicrobial peptides (AMPs) such as colistin, nisin, and polymyxin B (PMB) to assess the endolysin's antimicrobial efficacy and their synergy with AMPs. In combination with T7L, polymyxin B and colistin effectively eradicated the biofilm of Pseudomonas aeruginosa and exhibited a synergistic effect. Further, a combination of T4L and nisin displayed a synergistic effect against Staphylococcus aureus biofilms. In summary, the obtained results endorse the theme of combinational therapy consisting of endolysins and AMPs as an effective remedy against the drug-resistant bacterial biofilms that are a serious concern in healthcare settings.
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Affiliation(s)
- Jaya Lakshmi Tyagi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Payal Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
- Department of Biotechnology, Graphic Era Deemed to be University, Dehradun, Uttarakhand, 248001, India
| | - Mayur Mohan Ghate
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Dinesh Kumar
- Centre of Bio-Medical Research, SGPGIMS, Lucknow, Uttar Pradesh, 226014, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
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20
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Turchi B, Campobasso C, Nardinocchi A, Wagemans J, Torracca B, Lood C, Di Giuseppe G, Nieri P, Bertelloni F, Turini L, Ruffo V, Lavigne R, Di Luca M. Isolation and characterization of novel Staphylococcus aureus bacteriophage Hesat from dairy origin. Appl Microbiol Biotechnol 2024; 108:299. [PMID: 38619619 PMCID: PMC11018700 DOI: 10.1007/s00253-024-13129-y] [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: 09/05/2023] [Revised: 03/05/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024]
Abstract
A novel temperate phage, named Hesat, was isolated by the incubation of a dairy strain of Staphylococcus aureus belonging to spa-type t127 with either bovine or ovine milk. Hesat represents a new species of temperate phage within the Phietavirus genus of the Azeredovirinae subfamily. Its genome has a length of 43,129 bp and a GC content of 35.11% and contains 75 predicted ORFs, some of which linked to virulence. This includes (i) a pathogenicity island (SaPln2), homologous to the type II toxin-antitoxin system PemK/MazF family toxin; (ii) a DUF3113 protein (gp30) that is putatively involved in the derepression of the global repressor Stl; and (iii) a cluster coding for a PVL. Genomic analysis of the host strain indicates Hesat is a resident prophage. Interestingly, its induction was obtained by exposing the bacterium to milk, while the conventional mitomycin C-based approach failed. The host range of phage Hesat appears to be broad, as it was able to lyse 24 out of 30 tested S. aureus isolates. Furthermore, when tested at high titer (108 PFU/ml), Hesat phage was also able to lyse a Staphylococcus muscae isolate, a coagulase-negative staphylococcal strain. KEY POINTS: • A new phage species was isolated from a Staphylococcus aureus bovine strain. • Pathogenicity island and PVL genes are encoded within phage genome. • The phage is active against most of S. aureus strains from both animal and human origins.
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Affiliation(s)
- Barbara Turchi
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Claudia Campobasso
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Arianna Nardinocchi
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Jeroen Wagemans
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Beatrice Torracca
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
- Department of Microbial and Molecular Systems, Centre for Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium
| | | | - Paola Nieri
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano 6, 56126, Pisa, Italy
| | - Fabrizio Bertelloni
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Luca Turini
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Valeria Ruffo
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Mariagrazia Di Luca
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy.
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21
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Quinones-Olvera N, Owen SV, McCully LM, Marin MG, Rand EA, Fan AC, Martins Dosumu OJ, Paul K, Sanchez Castaño CE, Petherbridge R, Paull JS, Baym M. Diverse and abundant phages exploit conjugative plasmids. Nat Commun 2024; 15:3197. [PMID: 38609370 PMCID: PMC11015023 DOI: 10.1038/s41467-024-47416-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 65 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the evolutionarily promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.
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Affiliation(s)
- Natalia Quinones-Olvera
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Siân V Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Lucy M McCully
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Maximillian G Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eleanor A Rand
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Alice C Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Boston University, Boston, MA, 02215, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Oluremi J Martins Dosumu
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Kay Paul
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Cleotilde E Sanchez Castaño
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Rachel Petherbridge
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jillian S Paull
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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22
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Dicks LMT, Vermeulen W. Bacteriophage-Host Interactions and the Therapeutic Potential of Bacteriophages. Viruses 2024; 16:478. [PMID: 38543843 PMCID: PMC10975011 DOI: 10.3390/v16030478] [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: 02/05/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 05/23/2024] Open
Abstract
Healthcare faces a major problem with the increased emergence of antimicrobial resistance due to over-prescribing antibiotics. Bacteriophages may provide a solution to the treatment of bacterial infections given their specificity. Enzymes such as endolysins, exolysins, endopeptidases, endosialidases, and depolymerases produced by phages interact with bacterial surfaces, cell wall components, and exopolysaccharides, and may even destroy biofilms. Enzymatic cleavage of the host cell envelope components exposes specific receptors required for phage adhesion. Gram-positive bacteria are susceptible to phage infiltration through their peptidoglycan, cell wall teichoic acid (WTA), lipoteichoic acids (LTAs), and flagella. In Gram-negative bacteria, lipopolysaccharides (LPSs), pili, and capsules serve as targets. Defense mechanisms used by bacteria differ and include physical barriers (e.g., capsules) or endogenous mechanisms such as clustered regularly interspaced palindromic repeat (CRISPR)-associated protein (Cas) systems. Phage proteins stimulate immune responses against specific pathogens and improve antibiotic susceptibility. This review discusses the attachment of phages to bacterial cells, the penetration of bacterial cells, the use of phages in the treatment of bacterial infections, and the limitations of phage therapy. The therapeutic potential of phage-derived proteins and the impact that genomically engineered phages may have in the treatment of infections are summarized.
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Affiliation(s)
- Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa;
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23
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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] [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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24
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Cahill J, Holt A, Theodore M, Moreland R, O'Leary C, Martin C, Bettridge K, Xiao J, Young R. Spatial and temporal control of lysis by the lambda holin. mBio 2024; 15:e0129023. [PMID: 38126784 PMCID: PMC10865782 DOI: 10.1128/mbio.01290-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
The infection cycle of phage λ terminates in lysis mediated by three types of lysis proteins, each disrupting a layer in the bacterial envelope: the S105 holin, the R endolysin, and the Rz/Rz1 spanin complex targeting the inner membrane, cell wall or peptidoglycan, and the outer membrane, respectively. Video microscopy has shown that in most infections, lysis occurs as a sudden, explosive event at a cell pole, such that the initial product is a less refractile ghost that retains rod-shaped morphology. Here, we investigate the molecular basis of polar lysis using time-lapse fluorescence microscopy. The results indicate that the holin determines the morphology of lysis by suddenly forming two-dimensional rafts at the poles about 100 s prior to lysis. Given the physiological and biochemical similarities between the lambda holin and other class I holins, dynamic redistribution and sudden concentration may be common features of holins, probably reflecting the fitness advantage of all-or-nothing lysis regulation.IMPORTANCEIn this study, we use fluorescent video microscopy to track -green fluorescent protein (GFP)-labeled holin in the minutes prior to phage lysis. Our work contextualizes prior genetic and biochemical data, showing when hole formation starts and where holin oligomers form in relation to the site of lytic rupture. Furthermore, prior work showed that the morphology of lambda-infected cells is characterized by an explosive event starting at the cell pole; however, the basis for this was not clear. This study shows that holin most often oligomerizes at cell poles and that the site of the oligomerization is spatially correlated with the site of lytic blowout. Therefore, the holin is the key contributor to polar lysis morphology for phage lambda.
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Affiliation(s)
- Jesse Cahill
- Sandia National Labs, Albuquerque, New Mexico, USA
| | - Ashley Holt
- Department of Biochemistry and Biophysics, Center of Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Matthew Theodore
- Department of Biochemistry and Biophysics, Center of Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Russell Moreland
- Department of Biochemistry and Biophysics, Center of Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Chandler O'Leary
- Department of Biochemistry and Biophysics, Center of Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Cody Martin
- Department of Biochemistry and Biophysics, Center of Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Kelsey Bettridge
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ry Young
- Sandia National Labs, Albuquerque, New Mexico, USA
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25
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Lucas-Elío P, ElAlami T, Martínez A, Sanchez-Amat A. Marinomonas mediterranea synthesizes an R-type bacteriocin. Appl Environ Microbiol 2024; 90:e0127323. [PMID: 38169292 PMCID: PMC10870725 DOI: 10.1128/aem.01273-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
Prophages integrated into bacterial genomes can become cryptic or defective prophages, which may evolve to provide various traits to bacterial cells. Previous research on Marinomonas mediterranea MMB-1 demonstrated the production of defective particles. In this study, an analysis of the genomes of three different strains (MMB-1, MMB-2, and MMB-3) revealed the presence of a region named MEDPRO1, spanning approximately 52 kb, coding for a defective prophage in strains MMB-1 and MMB-2. This prophage seems to have been lost in strain MMB-3, possibly due to the presence of spacers recognizing this region in an I-F CRISPR array in this strain. However, all three strains produce remarkably similar defective particles. Using strain MMB-1 as a model, mass spectrometry analyses indicated that the structural proteins of the defective particles are encoded by a second defective prophage situated within the MEDPRO2 region, spanning approximately 13 kb. This finding was further validated through the deletion of this second defective prophage. Genomic region analyses and the detection of antimicrobial activity of the defective prophage against other Marinomonas species suggest that it is an R-type bacteriocin. Marinomonas mediterranea synthesizes antimicrobial proteins with lysine oxidase activity, and the synthesis of an R-type bacteriocin constitutes an additional mechanism in microbial competition for the colonization of habitats such as the surface of marine plants.IMPORTANCEThe interactions between bacterial strains inhabiting the same environment determine the final composition of the microbiome. In this study, it is shown that some extracellular defective phage particles previously observed in Marinomonas mediterranea are in fact R-type bacteriocins showing antimicrobial activity against other Marinomonas strains. The operon coding for the R-type bacteriocin has been identified.
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Affiliation(s)
- Patricia Lucas-Elío
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | - Tarik ElAlami
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | - Alicia Martínez
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
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26
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Ye Y, Zhang L, Hong X, Chen M, Liu X, Zhou S. Interspecies ecological competition rejuvenates decayed Geobacter electroactive biofilm. THE ISME JOURNAL 2024; 18:wrae118. [PMID: 38916438 PMCID: PMC11227281 DOI: 10.1093/ismejo/wrae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 06/26/2024]
Abstract
Bioelectrochemical systems (BESs) exploit electroactive biofilms (EABs) for promising applications in biosensing, wastewater treatment, energy production, and chemical biosynthesis. However, during the operation of BESs, EABs inevitably decay. Seeking approaches to rejuvenate decayed EABs is critical for the sustainability and practical application of BESs. Prophage induction has been recognized as the primary reason for EAB decay. Herein, we report that introducing a competitive species of Geobacter uraniireducens suspended prophage induction in Geobacter sulfurreducens and thereby rejuvenated the decayed G. sulfurreducens EAB. The transcriptomic profile of G. sulfurreducens demonstrated that the addition of G. uraniireducens significantly affected the expression of metabolism- and stress response system-related genes and in particular suppressed the induction of phage-related genes. Mechanistic analyses revealed that interspecies ecological competition exerted by G. uraniireducens suppressed prophage induction. Our findings not only reveal a novel strategy to rejuvenate decayed EABs, which is significant for the sustainability of BESs, but also provide new knowledge for understanding phage-host interactions from an ecological perspective, with implications for developing therapies to defend against phage attack.
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Affiliation(s)
- Yin Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lu Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaohui Hong
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Man Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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27
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Ishii T, Tsuchida N, Hemelda NM, Saito K, Bao J, Watanabe M, Toyoda A, Matsubara T, Sato M, Toyooka K, Ishihama N, Shirasu K, Matsui H, Toyoda K, Ichinose Y, Hayashi T, Kawaguchi A, Noutoshi Y. Rhizoviticin is an alphaproteobacterial tailocin that mediates biocontrol of grapevine crown gall disease. THE ISME JOURNAL 2024; 18:wrad003. [PMID: 38365227 PMCID: PMC10811719 DOI: 10.1093/ismejo/wrad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 02/18/2024]
Abstract
Tailocins are headless phage tail structures that mediate interbacterial antagonism. Although the prototypical tailocins, R- and F-pyocins, in Pseudomonas aeruginosa, and other predominantly R-type tailocins have been studied, their presence in Alphaproteobacteria remains unexplored. Here, we report the first alphaproteobacterial F-type tailocin, named rhizoviticin, as a determinant of the biocontrol activity of Allorhizobium vitis VAR03-1 against crown gall. Rhizoviticin is encoded by a chimeric prophage genome, one providing transcriptional regulators and the other contributing to tail formation and cell lysis, but lacking head formation genes. The rhizoviticin genome retains a nearly intact early phage region containing an integrase remnant and replication-related genes critical for downstream gene transcription, suggesting an ongoing transition of this locus from a prophage to a tailocin-coding region. Rhizoviticin is responsible for the most antagonistic activity in VAR03-1 culture supernatant against pathogenic A. vitis strain, and rhizoviticin deficiency resulted in a significant reduction in the antitumorigenic activity in planta. We identified the rhizoviticin-coding locus in eight additional A. vitis strains from diverse geographical locations, highlighting a unique survival strategy of certain Rhizobiales bacteria in the rhizosphere. These findings advance our understanding of the evolutionary dynamics of tailocins and provide a scientific foundation for employing rhizoviticin-producing strains in plant disease control.
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Affiliation(s)
- Tomoya Ishii
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Natsuki Tsuchida
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
- Present address: Division of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Niarsi Merry Hemelda
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Department of Biology, University of Indonesia, Depok 16424, Indonesia
| | - Kirara Saito
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Present address: Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki 885-0091, Japan
| | - Jiyuan Bao
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Megumi Watanabe
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehiro Matsubara
- Okayama University Hospital Biobank, Okayama University Hospital, Okayama 700-8558, Japan
| | - Mayuko Sato
- Mass Spectrometry and Microscopy Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Kiminori Toyooka
- Mass Spectrometry and Microscopy Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Nobuaki Ishihama
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Graduate School of Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hidenori Matsui
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
| | - Yuki Ichinose
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akira Kawaguchi
- Western Region Agricultural Research Center (WARC), National Agricultural and Food Research Organization (NARO), Fukuyama, Hiroshima 721-8514, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Faculty of Agriculture, Okayama University, Okayama 700-8530, Japan
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28
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Samir S. Molecular Machinery of the Triad Holin, Endolysin, and Spanin: Key Players Orchestrating Bacteriophage-Induced Cell Lysis and their Therapeutic Applications. Protein Pept Lett 2024; 31:85-96. [PMID: 38258777 DOI: 10.2174/0109298665181166231212051621] [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: 09/06/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 01/24/2024]
Abstract
Phage therapy, a promising alternative to combat multidrug-resistant bacterial infections, harnesses the lytic cycle of bacteriophages to target and eliminate bacteria. Key players in this process are the phage lysis proteins, including holin, endolysin, and spanin, which work synergistically to disrupt the bacterial cell wall and induce lysis. Understanding the structure and function of these proteins is crucial for the development of effective therapies. Recombinant versions of these proteins have been engineered to enhance their stability and efficacy. Recent progress in the field has led to the approval of bacteriophage-based therapeutics as drugs, paving the way for their clinical use. These proteins can be combined in phage cocktails or combined with antibiotics to enhance their activity against bacterial biofilms, a common cause of treatment failure. Animal studies and clinical trials are being conducted to evaluate the safety and efficacy of phage therapy in humans. Overall, phage therapy holds great potential as a valuable tool in the fight against multidrug- resistant bacteria, offering hope for the future of infectious disease treatment.
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Affiliation(s)
- Safia Samir
- Department of Biochemistry and Molecular Biology, Theodor Bilharz Research Institute, Giza, Egypt
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29
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Kim D, Kim M. Sensitive detection of viable Cronobacter sakazakii by bioluminescent reporter phage emitting stable signals with truncated holin. Food Res Int 2023; 174:113665. [PMID: 37981373 DOI: 10.1016/j.foodres.2023.113665] [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: 07/28/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/21/2023]
Abstract
As outbreaks of foodborne illness caused by the opportunistic pathogen Cronobacter sakazakii (Cs) continue to occur, particularly in infants consuming powdered infant formula (PIF), the need for sensitive, rapid, and easy-to-use detection of Cs from food and food processing environments is increasing. Here, we developed bioluminescent reporter bacteriophages for viable Cs-specific, substrate-free, rapid detection by introducing luciferase and its corresponding substrate-providing enzyme complex into the virulent phage ΦC01. Although the reporter phage ΦC01_lux, constructed by replacing non-essential genes for phage infectivity with a luxCDABE reporter operon, produced bioluminescence upon Cs infection, the emitted signal was quickly decayed due to the superior bacteriolytic activity of ΦC01. By truncating the membrane pore-forming protein holin and thus limiting its function, the bacterial lysis was delayed and the resultant engineered reporter phage ΦC01_lux_Δhol could produce a more stable and reliable bioluminescent signal. Accordingly, ΦC01_lux_Δhol was able to detect at least an average of 2 CFU/ml of Cs artificially contaminated PIF and Sunsik and food contact surface models within a total of 7 h of assays, including 5 h of pre-enrichment for Cs amplification. The sensitive, easy-to-use, and specific detection of live Cs with the developed reporter phage could be applied as a novel complementary tool for monitoring Cs in food and food-related environments for food safety and public health.
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Affiliation(s)
- Doyeon Kim
- Laboratory of Molecular Food Microbiology, Department of Food and Nutrition, Brain Korea 21 FOUR, College of Human Ecology, Yonsei University, Seoul 03722, Republic of Korea
| | - Minsik Kim
- Laboratory of Molecular Food Microbiology, Department of Food and Nutrition, Brain Korea 21 FOUR, College of Human Ecology, Yonsei University, Seoul 03722, Republic of Korea.
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30
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Viglasky J, Piknova M, Pristas P. Gene and domain shuffling in lytic cassettes of Enterococcus spp. bacteriophages. 3 Biotech 2023; 13:388. [PMID: 38023582 PMCID: PMC10630273 DOI: 10.1007/s13205-023-03775-w] [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: 01/12/2023] [Accepted: 09/15/2023] [Indexed: 12/01/2023] Open
Abstract
The genomes of Enterococcus faecalis and Enterococcus faecium bacteriophages were analysed for gene shuffling in the lytic cassettes of bacteriophages infecting. It was found that enterococcal bacteriophages could be classified into well-defined groups based on the size of their genomes and each size group had its own conserved gene composition of lytic cassettes. Enterococcal bacteriophages use a relatively broad spectrum of holins and endolysins with variable cell-wall binding (CWB) and catalytic domains, and most of them utilise a lytic cassette with more than two genes. Enterococcal bacteriophages most commonly use endolysins with amidase catalytic domains and the CWB domain SH3_5. Some bacteriophages possess in their lytic cassette a holin-like gene with the XhlA domain protein, characteristic of hemolysin. Regardless of the shuffling of genes encoding holins and endolysins in lytic modules, a novel example of CWB domain shuffling within enterococcal endolysins was identified. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03775-w.
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Affiliation(s)
- Jakub Viglasky
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Srobarova 2, 041 54 Košice, Slovakia
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Košice, 041 81 Košice, Slovakia
| | - Maria Piknova
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Srobarova 2, 041 54 Košice, Slovakia
| | - Peter Pristas
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Srobarova 2, 041 54 Košice, Slovakia
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, Soltesovej 4-6, 040 01 Kosice, Slovakia
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31
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Niblock DJ, Winkler AR, Curtin CE, Kokinda JF, Danker WA, Llorente Fernandez I, Smith AR, Ali A, Cruz GG, Givvines LC, Lee-Soety JY. Isolating and characterizing cluster AB Mycobacteriophage NoShow, which encodes lysis proteins shared with cluster H2 phages. Microbiol Resour Announc 2023; 12:e0064923. [PMID: 37747255 PMCID: PMC10586156 DOI: 10.1128/mra.00649-23] [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: 07/18/2023] [Accepted: 08/09/2023] [Indexed: 09/26/2023] Open
Abstract
We present here Mycobacteriophage NoShow, isolated from a soil sample collected on the Maguire Campus of Saint Joseph's University in Merion Station, Pennsylvania. Even though NoShow's 52,825 bp genome is most similar to phages in cluster AB, its lysA and lysB genes are most similar to phages in cluster H2.
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Affiliation(s)
- Danielle J. Niblock
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Anne R. Winkler
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Caroline E. Curtin
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Jacqui F. Kokinda
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Walter A. Danker
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | | | - Ava R. Smith
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Asad Ali
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Gabrielle G. Cruz
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Leya C. Givvines
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Julia Y. Lee-Soety
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
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32
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Ge F, Guo R, Liang Y, Chen Y, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Wang M. Characterization and genomic analysis of Stutzerimonas stutzeri phage vB_PstS_ZQG1, representing a novel viral genus. Virus Res 2023; 336:199226. [PMID: 37739268 PMCID: PMC10520572 DOI: 10.1016/j.virusres.2023.199226] [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: 06/12/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.
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Affiliation(s)
- Fuyue Ge
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Centre for Marine Studies, Qingdao, China.
| | - Ying Chen
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Centre for Marine Studies, Qingdao, China; Haide College, Ocean University of China, Qingdao, China; The Affiliated Hospital of Qingdao University, Qingdao, China.
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Aframian N, Eldar A. Abortive infection antiphage defense systems: separating mechanism and phenotype. Trends Microbiol 2023; 31:1003-1012. [PMID: 37268559 DOI: 10.1016/j.tim.2023.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/04/2023]
Abstract
Bacteria have evolved a wide array of mechanisms that allow them to eliminate phage infection. 'Abortive infection' (abi) systems are an expanding category of such mechanisms, defined as those which induce programmed cell death (or dormancy) upon infection, and thus halt phage propagation within a bacterial population. This definition entails two requirements - a phenotypic observation (cell death upon infection), and a mechanistic determination of its sources (system-induced death). The phenotypic and mechanistic aspects of abi are often implicitly assumed to be tightly linked, and studies regularly tend to establish one and deduce the other. However, recent evidence points to a complicated relationship between the mechanism of defense and the phenotype observed upon infection. We argue that rather than viewing the abi phenotype as an inherent quality of a set of defense systems, it should be more appropriately thought of as an attribute of interactions between specific phages and bacteria under given conditions. Consequently, we also point to potential pitfalls in the prevailing methods for ascertaining the abi phenotype. Overall, we propose an alternative framework for parsing interactions between attacking phages and defending bacteria.
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Affiliation(s)
- Nitzan Aframian
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Avigdor Eldar
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel.
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Cai H, Zhou Y, Li X, Xu T, Ni Y, Wu S, Yu Y, Wang Y. Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake. Viruses 2023; 15:2038. [PMID: 37896815 PMCID: PMC10611076 DOI: 10.3390/v15102038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Viruses in aquatic ecosystems exhibit remarkable abundance and diversity. However, scattered studies have been conducted to mine uncultured viruses and identify them taxonomically in lake water. Here, whole genomes (29-173 kbp) of seven uncultured dsDNA bacteriophages were discovered in Dishui Lake, the largest artificial lake in Shanghai. We analyzed their genomic signatures and found a series of viral auxiliary metabolic genes closely associated with protein synthesis and host metabolism. Dishui Lake phages shared more genes with uncultivated environmental viruses than with reference viruses based on the gene-sharing network classification. Phylogeny of proteomes and comparative genomics delineated three new genera within two known viral families of Kyanoviridae and Autographiviridae, and four new families in Caudoviricetes for these seven novel phages. Their potential hosts appeared to be from the dominant bacterial phyla in Dishui Lake. Altogether, our study provides initial insights into the composition and diversity of bacteriophage communities in Dishui Lake, contributing valuable knowledge to the ongoing research on the roles played by viruses in freshwater ecosystems.
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Affiliation(s)
- Haoyun Cai
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yifan Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Xiefei Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Tianqi Xu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Shuang Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai 201306, China
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DiBenedetto NV, Oberkampf M, Cersosimo L, Yeliseyev V, Bry L, Peltier J, Dupuy B. The TcdE holin drives toxin secretion and virulence in Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.16.558055. [PMID: 37745472 PMCID: PMC10516005 DOI: 10.1101/2023.09.16.558055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Clostridioides difficile is the leading cause of healthcare associated infections. The Pathogenicity Locus (PaLoc) toxins TcdA and TcdB promote host disease. These toxins lack canonical N-terminal signal sequences for translocation across the bacterial membrane, suggesting alternate mechanisms of release, which have included targeted secretion and passive release from cell lysis. While the holin TcdE has been implicated in TcdA and TcdB release, its role in vivo remains unknown. Here, we show profound reductions in toxin secretion in ΔtcdE mutants in the highly virulent strains UK1 (epidemic ribotype 027, Clade 3) and VPI10463 (ribotype 087, Clade 1). Notably, tcdE deletion in either strain rescued highly susceptible gnotobiotic mice from lethal infection by reducing acute extracellular toxin to undetectable levels, limiting mucosal damage, and enabling long-term survival, in spite of continued toxin gene expression in ΔtcdE mutants. Our findings confirm TcdE's critical functions in vivo for toxin secretion and C. difficile virulence.
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Affiliation(s)
- N V DiBenedetto
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Oberkampf
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - L Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - V Yeliseyev
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - L Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - J Peltier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - B Dupuy
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
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Chen Y, Zhang T, Lai Q, Zhang M, Yu M, Zeng R, Jin M. Characterization and Comparative Genomic Analysis of a Deep-Sea Bacillus Phage Reveal a Novel Genus. Viruses 2023; 15:1919. [PMID: 37766325 PMCID: PMC10535572 DOI: 10.3390/v15091919] [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: 08/23/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
As the most abundant biological entities, viruses are the major players in marine ecosystems. However, our knowledge on virus diversity and virus-host interactions in the deep sea remains very limited. In this study, vB_BteM-A9Y, a novel bacteriophage infecting Bacillus tequilensis, was isolated from deep-sea sediments in the South China Sea. vB_BteM-A9Y has a hexametric head and a long, complex contractile tail, which are typical features of myophages. vB_BteM-A9Y initiated host lysis at 60 min post infection with a burst size of 75 PFU/cell. The phage genome comprises 38,634 base pairs and encodes 54 predicted open reading frames (ORFs), of which 27 ORFs can be functionally annotated by homology analysis. Interestingly, abundant ORFs involved in DNA damage repair were identified in the phage genome, suggesting that vB_BteM-A9Y encodes multiple pathways for DNA damage repair, which may help to maintain the stability of the host/phage genome. A BLASTn search of the whole genome sequence of vB_BteM-A9Y against the GenBank revealed no existing homolog. Consistently, a phylogenomic tree and proteome-based phylogenetic tree analysis showed that vB_BteM-A9Y formed a unique branch. Further comparative analysis of genomic nucleotide similarity and ORF homology of vB_BteM-A9Y with its mostly related phages showed that the intergenomic similarity between vB_BteM-A9Y and these phages was 0-33.2%. Collectively, based on the comprehensive morphological, phylogenetic, and comparative genomic analysis, we propose that vB_BteM-A9Y belongs to a novel genus under Caudoviricetes. Therefore, our study will increase our knowledge on deep-sea virus diversity and virus-host interactions, as well as expanding our knowledge on phage taxonomy.
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Affiliation(s)
- Yuan Chen
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
| | - Tianyou Zhang
- Fujian Provincial Center for Disease Control and Prevention, Fuzhou 350000, China;
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
| | - Menghui Zhang
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
| | - Meishun Yu
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China
| | - Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Y.C.); (Q.L.); (M.Z.); (M.Y.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China
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Braetz S, Schwerk P, Figueroa-Bossi N, Tedin K, Fulde M. Prophage Gifsy-1 Induction in Salmonella enterica Serovar Typhimurium Reduces Persister Cell Formation after Ciprofloxacin Exposure. Microbiol Spectr 2023; 11:e0187423. [PMID: 37306609 PMCID: PMC10433948 DOI: 10.1128/spectrum.01874-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/28/2023] [Indexed: 06/13/2023] Open
Abstract
Persister cells are drug-tolerant bacteria capable of surviving antibiotic treatment despite the absence of heritable resistance mechanisms. It is generally thought that persister cells survive antibiotic exposure through the implementation of stress responses and/or energy-sparing strategies. Exposure to DNA gyrase-targeting antibiotics could be particularly detrimental for bacteria that carry prophages integrated in their genomes. Gyrase inhibitors are known to induce prophages to switch from their dormant lysogenic state into the lytic cycle, causing the lysis of their bacterial host. However, the influence of resident prophages on the formation of persister cells has only been recently appreciated. Here, we evaluated the effect of endogenous prophage carriage on the generation of bacterial persistence during Salmonella enterica serovar Typhimurium exposure to both gyrase-targeting antibiotics and other classes of bactericidal antibiotics. Results from the analysis of strain variants harboring different prophage combinations revealed that prophages play a major role in limiting the formation of persister cells during exposure to DNA-damaging antibiotics. In particular, we present evidence that prophage Gifsy-1 (and its encoded lysis proteins) are major factors limiting persister cell formation upon ciprofloxacin exposure. Resident prophages also appear to have a significant impact on the initial drug susceptibility, resulting in an alteration of the characteristic biphasic killing curve of persister cells into a triphasic curve. In contrast, a prophage-free derivative of S. Typhimurium showed no difference in the killing kinetics for β-lactam or aminoglycoside antibiotics. Our study demonstrates that induction of prophages increased the susceptibility toward DNA gyrase inhibitors in S. Typhimurium, suggesting that prophages have the potential for enhancing antibiotic efficacy. IMPORTANCE Bacterial infections resulting from antibiotic treatment failure can often be traced to nonresistant persister cells. Moreover, intermittent or single treatment of persister cells with β-lactam antibiotics or fluoroquinolones can lead to the formation of drug-resistant bacteria and to the emergence of multiresistant strains. It is therefore important to have a better understanding of the mechanisms that impact persister formation. Our results indicate that prophage-associated bacterial killing significantly reduces persister cell formation in lysogenic cells exposed to DNA-gyrase-targeting drugs. This suggests that therapies based on gyrase inhibitors should be favored over alternative strategies when dealing with lysogenic pathogens.
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Affiliation(s)
- Sebastian Braetz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Peter Schwerk
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Karsten Tedin
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Marcus Fulde
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
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Lee W, Sung S, Ha J, Kim E, An ES, Kim SH, Kim SH, Kim HY. Molecular and Genomic Analysis of the Virulence Factors and Potential Transmission of Hybrid Enteropathogenic and Enterotoxigenic Escherichia coli (EPEC/ETEC) Strains Isolated in South Korea. Int J Mol Sci 2023; 24:12729. [PMID: 37628911 PMCID: PMC10454139 DOI: 10.3390/ijms241612729] [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: 07/19/2023] [Revised: 08/06/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Hybrid strains Escherichia coli acquires genetic characteristics from multiple pathotypes and is speculated to be more virulent; however, understanding their pathogenicity is elusive. Here, we performed genome-based characterization of the hybrid of enteropathogenic (EPEC) and enterotoxigenic E. coli (ETEC), the strains that cause diarrhea and mortality in children. The virulence genes in the strains isolated from different sources in the South Korea were identified, and their phylogenetic positions were analyzed. The EPEC/ETEC hybrid strains harbored eae and est encoding E. coli attaching and effacing lesions and heat-stable enterotoxins of EPEC and ETEC, respectively. Genome-wide phylogeny revealed that all hybrids (n = 6) were closely related to EPEC strains, implying the potential acquisition of ETEC virulence genes during ETEC/EPEC hybrid emergence. The hybrids represented diverse serotypes (O153:H19 (n = 3), O49:H10 (n = 2), and O71:H19 (n = 1)) and sequence types (ST546, n = 4; ST785, n = 2). Furthermore, heat-stable toxin-encoding plasmids possessing estA and various other virulence genes and transporters, including nleH2, hlyA, hlyB, hlyC, hlyD, espC, espP, phage endopeptidase Rz, and phage holin, were identified. These findings provide insights into understanding the pathogenicity of EPEC/ETEC hybrid strains and may aid in comparative studies, virulence characterization, and understanding evolutionary biology.
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Affiliation(s)
- Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea; (W.L.); (S.S.); (J.H.); (E.S.A.); (S.H.K.)
- Institute of Life Sciences & Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea;
| | - Soohyun Sung
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea; (W.L.); (S.S.); (J.H.); (E.S.A.); (S.H.K.)
| | - Jina Ha
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea; (W.L.); (S.S.); (J.H.); (E.S.A.); (S.H.K.)
| | - Eiseul Kim
- Institute of Life Sciences & Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea;
| | - Eun Sook An
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea; (W.L.); (S.S.); (J.H.); (E.S.A.); (S.H.K.)
| | - Seung Hwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea; (W.L.); (S.S.); (J.H.); (E.S.A.); (S.H.K.)
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea; (W.L.); (S.S.); (J.H.); (E.S.A.); (S.H.K.)
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea;
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Nale JY, McEwan NR. Bacteriophage Therapy to Control Bovine Mastitis: A Review. Antibiotics (Basel) 2023; 12:1307. [PMID: 37627727 PMCID: PMC10451327 DOI: 10.3390/antibiotics12081307] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Bovine mastitis is a polymicrobial disease characterised by inflammation of the udders of dairy and beef cattle. The infection has huge implications to health and welfare of animals, impacting milk and beef production and costing up to EUR 32 billion annually to the dairy industry, globally. Bacterial communities associated with the disease include representative species from Staphylococcus, Streptococcus, Enterococcus, Actinomyces, Aerococcus, Escherichia, Klebsiella and Proteus. Conventional treatment relies on antibiotics, but antimicrobial resistance, declining antibiotic innovations and biofilm production negatively impact therapeutic efficacy. Bacteriophages (phages) are viruses which effectively target and lyse bacteria with extreme specificity and can be a valuable supplement or replacement to antibiotics for bovine mastitis. In this review, we provide an overview of the etiology of bovine mastitis, the advantages of phage therapy over chemical antibiotics for the strains and research work conducted in the area in various model systems to support phage deployment in the dairy industry. We emphasise work on phage isolation procedures from samples obtained from mastitic and non-mastitic sources, characterisation and efficacy testing of single and multiple phages as standalone treatments or adjuncts to probiotics in various in vitro, ex vivo and in vivo bovine mastitis infection models. Furthermore, we highlight the areas where improvements can be made with focus on phage cocktail optimisation, formulation, and genetic engineering to improve delivery, stability, efficacy, and safety in cattle. Phage therapy is becoming more attractive in clinical medicine and agriculture and thus, could mitigate the impending catastrophe of antimicrobial resistance in the dairy sector.
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Affiliation(s)
- Janet Y. Nale
- Centre for Epidemiology and Planetary Health, Scotland’s Rural College (SRUC), Inverness IV2 5NA, Scotland, UK
| | - Neil R. McEwan
- School of Veterinary Medicine, Scotland’s Rural College (SRUC), Aberdeen AB21 9YA, Scotland, UK;
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40
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Loganathan K, Viswanathan B. Genome editing for phage design and uses for therapeutic applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:203-224. [PMID: 37770172 DOI: 10.1016/bs.pmbts.2023.03.012] [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: 10/03/2023]
Abstract
The over usage of antibiotics leads to antibiotic abuse which in turn eventually raises resistance mechanisms among wide range of pathogens. Due to lack of experimental data of efficacy of phages as potential antimicrobial and therapeutic agent and also more specific and cumbersome isolation process against specific pathogens makes it not so feasible technology to be looked as an alternative therapy. But, recent developments in genome editing techniques enables programmed nuclease enzymes that has effectively improvised our methodology to make accurate changes in the genomes of prokaryote as well as eukaryote cells. It is already strengthening our ability to improvise genetic engineering to disease identification by facilitating the creation of more precise models to identify the root cause. The present chapter discusses on improvisation of phage therapy using recent genome editing tools and also shares data on the methods of usage of phages and their derivatives like proteins and enzymes such as lysins and depolymerases, as a potential therapeutic or prophylaxis agent. Methods involved in recombinant based techniques were also discussed in this chapter. Combination of traditional approach with modern tools has led to a potential development of phage-based therapeutics in near future.
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41
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Chen K, Guan Y, Hu R, Cui X, Liu Q. Characterization of the LysP2110-HolP2110 Lysis System in Ralstonia solanacearum Phage P2110. Int J Mol Sci 2023; 24:10375. [PMID: 37373522 DOI: 10.3390/ijms241210375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
Ralstonia solanacearum, a pathogen causing widespread bacterial wilt disease in numerous crops, currently lacks an optimal control agent. Given the limitations of traditional chemical control methods, including the risk of engendering drug-resistant strains and environmental harm, there is a dire need for sustainable alternatives. One alternative is lysin proteins that selectively lyse bacteria without contributing to resistance development. This work explored the biocontrol potential of the LysP2110-HolP2110 system of Ralstonia solanacearum phage P2110. Bioinformatics analyses pinpointed this system as the primary phage-mediated host cell lysis mechanism. Our data suggest that LysP2110, a member of the Muraidase superfamily, requires HolP2110 for efficient bacterial lysis, presumably via translocation across the bacterial membrane. LysP2110 also exhibits broad-spectrum antibacterial activity in the presence of the outer membrane permeabilizer EDTA. Additionally, we identified HolP2110 as a distinct holin structure unique to the Ralstonia phages, underscoring its crucial role in controlling bacterial lysis through its effect on bacterial ATP levels. These findings provide valuable insights into the function of the LysP2110-HolP2110 lysis system and establish LysP2110 as a promising antimicrobial agent for biocontrol applications. This study underpins the potential of these findings in developing effective and environment-friendly biocontrol strategies against bacterial wilt and other crop diseases.
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Affiliation(s)
- Kaihong Chen
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yanhui Guan
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Ronghua Hu
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Xiaodong Cui
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Qiongguang Liu
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
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Lopez MES, Gontijo MTP, Cardoso RR, Batalha LS, Eller MR, Bazzolli DMS, Vidigal PMP, Mendonça RCS. Complete genome analysis of Tequatrovirus ufvareg1, a Tequatrovirus species inhibiting Escherichia coli O157:H7. Front Cell Infect Microbiol 2023; 13:1178248. [PMID: 37274318 PMCID: PMC10236363 DOI: 10.3389/fcimb.2023.1178248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/27/2023] [Indexed: 06/06/2023] Open
Abstract
Introduction Bacteriophages infecting human pathogens have been considered potential biocontrol agents, and studying their genetic content is essential to their safe use in the food industry. Tequatrovirus ufvareg1 is a bacteriophage named UFV-AREG1, isolated from cowshed wastewater and previously tested for its ability to inhibit Escherichia coli O157:H7. Methods T. ufvareg1 was previously isolated using E. coli O157:H7 (ATCC 43895) as a bacterial host. The same strain was used for bacteriophage propagation and the one-step growth curve. The genome of the T. ufvareg1 was sequenced using 305 Illumina HiSeq, and the genome comparison was calculated by VIRIDIC and VIPTree. Results Here, we characterize its genome and compare it to other Tequatrovirus. T. ufvareg1 virions have an icosahedral head (114 x 86 nm) and a contracted tail (117 x 23 nm), with a latent period of 25 min, and an average burst size was 18 phage particles per infected E. coli cell. The genome of the bacteriophage T. ufvareg1 contains 268 coding DNA sequences (CDS) and ten tRNA genes distributed in both negative and positive strains. T. ufvareg1 genome also contains 40 promoters on its regulatory regions and two rho-independent terminators. T. ufvareg1 shares an average intergenomic similarity (VIRIDC) of 88.77% and an average genomic similarity score (VipTree) of 88.91% with eight four reference genomes for Tequatrovirus available in the NCBI RefSeq database. The pan-genomic analysis confirmed the high conservation of Tequatrovirus genomes. Among all CDS annotated in the T. ufvareg1 genome, there are 123 core genes, 38 softcore genes, 94 shell genes, and 13 cloud genes. None of 268 CDS was classified as being exclusive of T. ufvareg1. Conclusion The results in this paper, combined with other previously published findings, indicate that T. ufvareg1 bacteriophage is a potential candidate for food protection against E. coli O157:H7 in foods.
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Affiliation(s)
- Maryoris Elisa Soto Lopez
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Departamento de Ingeniería de Alimentos, Universidad de Córdoba, Montería, Colombia
| | - Marco Tulio Pardini Gontijo
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Duke University, Durham, NC, United States
| | - Rodrigo Rezende Cardoso
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Laís Silva Batalha
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Monique Renon Eller
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Deng X, Yuan J, Chen L, Chen H, Wei C, Nielsen PH, Wuertz S, Qiu G. CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter. WATER RESEARCH 2023; 235:119906. [PMID: 37004306 DOI: 10.1016/j.watres.2023.119906] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/27/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.
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Affiliation(s)
- Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jing Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China
| | - Per H Nielsen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg DK-9220, Denmark
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China.
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Megat Mazhar Khair MH, Tee AN, Wahab NF, Othman SS, Goh YM, Masarudin MJ, Chong CM, In LLA, Gan HM, Song AAL. Comprehensive Characterization of a Streptococcus agalactiae Phage Isolated from a Tilapia Farm in Selangor, Malaysia, and Its Potential for Phage Therapy. Pharmaceuticals (Basel) 2023; 16:ph16050698. [PMID: 37242481 DOI: 10.3390/ph16050698] [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: 03/29/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
The Streptococcus agalactiae outbreak in tilapia has caused huge losses in the aquaculture industry worldwide. In Malaysia, several studies have reported the isolation of S. agalactiae, but no study has reported the isolation of S. agalactiae phages from tilapia or from the culture pond. Here, the isolation of the S. agalactiae phage from infected tilapia is reported and it is named as vB_Sags-UPM1. Transmission electron micrograph (TEM) revealed that this phage showed characteristics of a Siphoviridae and it was able to kill two local S. agalactiae isolates, which were S. agalactiae smyh01 and smyh02. Whole genome sequencing (WGS) of the phage DNA showed that it contained 42,999 base pairs with 36.80% GC content. Bioinformatics analysis predicted that this phage shared an identity with the S. agalactiae S73 chromosome as well as several other strains of S. agalactiae, presumably due to prophages carried by these hosts, and it encodes integrase, which suggests that it was a temperate phage. The endolysin of vB_Sags-UPM1 termed Lys60 showed killing activity on both S. agalactiae strains with varying efficacy. The discovery of the S. agalactiae temperate phage and its antimicrobial genes could open a new window for the development of antimicrobials to treat S. agalactiae infection.
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Affiliation(s)
- Megat Hamzah Megat Mazhar Khair
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - An Nie Tee
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nurul Fazlin Wahab
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Siti Sarah Othman
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Yong Meng Goh
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Mas Jaffri Masarudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Nanomaterials Synthesis and Characterisation Laboratory, Institute of Nanoscience and Nanotechnology, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Chou Min Chong
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Lionel Lian Aun In
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur 56000, Selangor, Malaysia
| | - Han Ming Gan
- Patriot Biotech, Sunway Geo Avenue, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
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Wang JM, Seok SH, Yoon WS, Kim JH, Seo MD. Crystal structure of the engineered endolysin mtEC340M. Acta Crystallogr F Struct Biol Commun 2023; 79:105-110. [PMID: 37132476 PMCID: PMC10167747 DOI: 10.1107/s2053230x23002583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/17/2023] [Indexed: 05/04/2023] Open
Abstract
Endolysins produced by bacteriophages play essential roles in the release of phage progeny by degrading the peptidoglycan layers of the bacterial cell wall. Bacteriophage-encoded endolysins have emerged as a new class of antibacterial agents to combat surging antibiotic resistance. The crystal structure of mtEC340M, an engineered endolysin EC340 from the PBEC131 phage that infects Escherichia coli, was determined. The crystal structure of mtEC340M at 2.4 Å resolution consists of eight α-helices and two loops. The three active residues of mtEC340M were predicted by structural comparison with peptidoglycan-degrading lysozyme.
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Affiliation(s)
- Jee-Min Wang
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Seung-Hyeon Seok
- College of Pharmacy and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju, Jeju 63243, Republic of Korea
| | - Won-Su Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk 28160, Republic of Korea
| | - Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
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46
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Liu H, Hu Z, Li M, Yang Y, Lu S, Rao X. Therapeutic potential of bacteriophage endolysins for infections caused by Gram-positive bacteria. J Biomed Sci 2023; 30:29. [PMID: 37101261 PMCID: PMC10131408 DOI: 10.1186/s12929-023-00919-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/14/2023] [Indexed: 04/28/2023] Open
Abstract
Gram-positive (G+) bacterial infection is a great burden to both healthcare and community medical resources. As a result of the increasing prevalence of multidrug-resistant G+ bacteria such as methicillin-resistant Staphylococcus aureus (MRSA), novel antimicrobial agents must urgently be developed for the treatment of infections caused by G+ bacteria. Endolysins are bacteriophage (phage)-encoded enzymes that can specifically hydrolyze the bacterial cell wall and quickly kill bacteria. Bacterial resistance to endolysins is low. Therefore, endolysins are considered promising alternatives for solving the mounting resistance problem. In this review, endolysins derived from phages targeting G+ bacteria were classified based on their structural characteristics. The active mechanisms, efficacy, and advantages of endolysins as antibacterial drug candidates were summarized. Moreover, the remarkable potential of phage endolysins in the treatment of G+ bacterial infections was described. In addition, the safety of endolysins, challenges, and possible solutions were addressed. Notwithstanding the limitations of endolysins, the trends in development indicate that endolysin-based drugs will be approved in the near future. Overall, this review presents crucial information of the current progress involving endolysins as potential therapeutic agents, and it provides a guideline for biomaterial researchers who are devoting themselves to fighting against bacterial infections.
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Affiliation(s)
- He Liu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China
| | - Zhen Hu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China
| | - Mengyang Li
- Department of Microbiology, School of Medicine, Chongqing University, Chongqing, 400044, China
| | - Yi Yang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China
| | - Shuguang Lu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China.
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, 400038, China.
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Lang J, Zhen J, Li G, Li B, Xie J. Characterization and genome analysis of G1 sub-cluster mycobacteriophage Lang. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 109:105417. [PMID: 36804468 DOI: 10.1016/j.meegid.2023.105417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Phage therapy is revitalized as an alternative to antibiotics therapy against antimicrobials resistant pathogens. Mycobacteriophages are genetically diverse viruses that can specifically infect Mycobacterium genus including Mycobacterium tuberculosis and Mycobacterium smegmatis. Here, we isolated and annotated the genome of a mycobacteriophage Lang, a temperate mycobacteriophage isolated from the soil of Hohhot, Inner Mongolia, China, by using Mycolicibacterium smegmatis mc2 155 as the host. It belongs to the Siphoviridae family of Caudovirales as determined by transmission electron microscopy. The morphological characteristics and certain biological properties of the phage were considered in detail. Phage Lang genomes is 41,487 bp in length with 66.85% GC content and encodes 60 putative open reading frames and belongs to the G1 sub-cluster. Genome annotation indicated that genes for structure proteins, assembly proteins, replications/transcription and lysis of the host are present in function clucters. The genome sequence of phage Lang is more than 95% similar to that of mycobacteriophage Grizzly and Sweets, differing in substitutions, insertions and deletions in Lang. One-step growth curve revealed that Lang has a latent period of 30 min and a outbreak period of 90 min. The short latent period and rapid outbreak mark the unique properties of phage Lang, which can be another potential source for combating M. tuberculosis.
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Affiliation(s)
- Junying Lang
- Tuberculosis Department of Hohhot Second Hospital, Inner Mongolia, 010020, China; Hohhot Tuberculosis Prevention and Control Institute, Inner Mongolia, 010020, China
| | - Junfeng Zhen
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Guimei Li
- Tuberculosis Department of Hohhot Second Hospital, Inner Mongolia, 010020, China
| | - Bin Li
- Intensive Care Medicine Department of Hohhot First Hospital, Inner Mongolia, 010020, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China.
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48
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Deng H, Li M, Zhang Q, Gao C, Song Z, Chen C, Wang Z, Feng X. The Broad-Spectrum Endolysin LySP2 Improves Chick Survival after Salmonella Pullorum Infection. Viruses 2023; 15:v15040836. [PMID: 37112818 PMCID: PMC10142873 DOI: 10.3390/v15040836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/19/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Salmonella pullorum causes typical “Bacillary White Diarrhea” and loss of appetite in chicks, which leads to the death of chicks in severe cases; thus, it is still a critical issue in China. Antibiotics are conventional medicines used for Salmonella infections; however, due to the extensive long-term use and even abuse of antibiotics, drug resistance becomes increasingly severe, making treating pullorum disease more difficult. Most of the endolysins are hydrolytic enzymes produced by bacteriophages to cleave the host’s cell wall during the final stage of the lytic cycle. A virulent bacteriophage, YSP2, of Salmonella was isolated in a previous study. A Pichia pastoris expression strain that can express the Salmonella bacteriophage endolysin was constructed efficiently, and the Gram-negative bacteriophage endolysin, LySP2, was obtained in this study. Compared with the parental phage YSP2, which can only lyse Salmonella, LySP2 can lyse Salmonella and Escherichia. The survival rate of Salmonella-infected chicks treated with LySP2 can reach up to 70% and reduce Salmonella abundance in the liver and intestine. The treatment group showed that LySP2 significantly improved the health of infected chicks and alleviated organ damage caused by Salmonella infection. In this study, the Salmonella bacteriophage endolysin was expressed efficiently by Pichia pastoris, and the endolysin LySP2 showed good potential for the treatment of pullorum disease caused by Salmonella pullorum.
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Affiliation(s)
- Hewen Deng
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Mengjiao Li
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Qiuyang Zhang
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Chencheng Gao
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Zhanyun Song
- Changchun Customs District, Changchun 130000, China
| | - Chunhua Chen
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Zhuo Wang
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Xin Feng
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
- Correspondence: ; Tel.: +86-135-0430-0193
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Teklemariam AD, Al-Hindi RR, Alharbi MG, Alotibi I, Azhari SA, Qadri I, Alamri T, Esmael A, Harakeh S. Isolation and Characterization of a Novel Lytic Phage, vB_PseuP-SA22, and Its Efficacy against Carbapenem-Resistant Pseudomonas aeruginosa. Antibiotics (Basel) 2023; 12:497. [PMID: 36978364 PMCID: PMC10044225 DOI: 10.3390/antibiotics12030497] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) poses a serious public health threat in multiple clinical settings. In this study, we detail the isolation of a lytic bacteriophage, vB_PseuP-SA22, from wastewater using a clinical strain of CRPA. Transmission electron microscopy (TEM) analysis identified that the phage had a podovirus morphology, which agreed with the results of whole genome sequencing. BLASTn search allowed us to classify vB_PseuP-SA22 into the genus Bruynoghevirus. The genome of vB_PseuP-SA22 consisted of 45,458 bp of double-stranded DNA, with a GC content of 52.5%. Of all the open reading frames (ORFs), only 26 (44.8%) were predicted to encode certain functional proteins, whereas the remaining 32 (55.2%) ORFs were annotated as sequences coding functionally uncharacterized hypothetical proteins. The genome lacked genes coding for toxins or markers of lysogenic phages, including integrases, repressors, recombinases, or excisionases. The phage produced round, halo plaques with a diameter of 1.5 ± 2.5 mm on the bacterial lawn. The TEM revealed that vB_PseuP-SA22 has an icosahedral head of 57.5 ± 4.5 nm in length and a short, non-contractile tail (19.5 ± 1.4 nm). The phage showed a latent period of 30 min, a burst size of 300 PFU/infected cells, and a broad host range. vB_PseuP-SA22 was found to be stable between 4-60 °C for 1 h, while the viability of the virus was reduced at temperatures above 60 °C. The phage showed stability at pH levels between 5 and 11. vB_PauP-SA22 reduced the number of live bacteria in P. aeruginosa biofilm by almost five logs. The overall results indicated that the isolated phage could be a candidate to control CRPA infections. However, experimental in vivo studies are essential to ensure the safety and efficacy of vB_PauP-SA22 before its use in humans.
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Affiliation(s)
- Addisu D. Teklemariam
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rashad R. Al-Hindi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mona G. Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ibrahim Alotibi
- Health Information Technology Department, Applied College, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sheren A. Azhari
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ishtiaq Qadri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Turki Alamri
- Family and Community Medicine Department, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed Esmael
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha 13518, Egypt
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Steve Harakeh
- King Fahd Medical Research Center, Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Wohlfarth JC, Feldmüller M, Schneller A, Kilcher S, Burkolter M, Meile S, Pilhofer M, Schuppler M, Loessner MJ. L-form conversion in Gram-positive bacteria enables escape from phage infection. Nat Microbiol 2023; 8:387-399. [PMID: 36717719 PMCID: PMC9981463 DOI: 10.1038/s41564-022-01317-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/22/2022] [Indexed: 02/01/2023]
Abstract
At the end of a lytic bacteriophage replication cycle in Gram-positive bacteria, peptidoglycan-degrading endolysins that cause explosive cell lysis of the host can also attack non-infected bystander cells. Here we show that in osmotically stabilized environments, Listeria monocytogenes can evade phage predation by transient conversion to a cell wall-deficient L-form state. This L-form escape is triggered by endolysins disintegrating the cell wall from without, leading to turgor-driven extrusion of wall-deficient, yet viable L-form cells. Remarkably, in the absence of phage predation, we show that L-forms can quickly revert to the walled state. These findings suggest that L-form conversion represents a population-level persistence mechanism to evade complete eradication by phage attack. Importantly, we also demonstrate phage-mediated L-form switching of the urinary tract pathogen Enterococcus faecalis in human urine, which underscores that this escape route may be widespread and has important implications for phage- and endolysin-based therapeutic interventions.
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Affiliation(s)
- Jan C Wohlfarth
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Miki Feldmüller
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Alissa Schneller
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Samuel Kilcher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Marco Burkolter
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Susanne Meile
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Markus Schuppler
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland.
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