Characterization and Genomic Analysis of a Novel Lytic Phage DCp1 against Clostridium perfringens Biofilms

Clostridium perfringens (C. perfringens) is one of the foremost pathogens responsible for diarrhea in foals. As antibiotic resistance increases, phages that specifically lyse bacteria are of great interest to us with regard to C. perfringens. In this study, a novel C. perfringens phage DCp1 was isolated from the sewage of a donkey farm. Phage DCp1 had a non-contractile short tail (40 nm in length) and a regular icosahedral head (46 nm in diameter). Whole-genome sequencing indicated that phage DCp1 had a linear double-stranded DNA genome with a total length of 18,555 bp and a G + C content of 28.2%. A total of 25 ORFs were identified in the genome, 6 of which had been assigned to functional genes, others were annotated to encode hypothetical proteins. The genome of phage DCp1 lacked any tRNA, virulence gene, drug resistance gene, or lysogenic gene. Phylogenetic analysis indicated that phage DCp1 belonged to the family Guelinviridae, Susfortunavirus. Biofilm assay showed that phage DCp1 was effective in inhibiting the formation of C. perfringens D22 biofilms. Phage DCp1 could completely degrade the biofilm after 5 h of interaction. The current study provides some basic information for further research on phage DCp1 and its application.

[1]  Huiying Ren,et al.  Complete genome sequencing of a Tequintavirus bacteriophage with a broad host range against Salmonella Abortus equi isolates from donkeys , 2022, Frontiers in Microbiology.

[2]  Yuan Tian,et al.  The Broad Host Range Phage vB_CpeS_BG3P Is Able to Inhibit Clostridium perfringens Growth , 2022, Viruses.

[3]  B. Grygorcewicz,et al.  Comparative Assessment of Bacteriophage and Antibiotic Activity against Multidrug-Resistant Staphylococcus aureus Biofilms , 2022, International journal of molecular sciences.

[4]  A. Węgrzyn,et al.  Bacteriophage-Encoded DNA Polymerases—Beyond the Traditional View of Polymerase Activities , 2022, International journal of molecular sciences.

[5]  Yuan Tian,et al.  Virulent phage vB_CpeP_HN02 inhibits Clostridium perfringens on the surface of the chicken meat , 2021, International Journal of Food Microbiology.

[6]  Hong Lin,et al.  Characterizations of the endolysin Lys84 and its domains from phage qdsa002 with high activities against Staphylococcus aureus and its biofilms. , 2021, Enzyme and microbial technology.

[7]  Jong-Hyun Park,et al.  Characterization and Food Application of the Novel Lytic Phage BECP10: Specifically Recognizes the O-polysaccharide of Escherichia coli O157:H7 , 2021, Viruses.

[8]  X. Qi,et al.  Characterization of a Novel Bacteriophage swi2 Harboring Two Lysins Can Naturally Lyse Escherichia coli , 2021, Frontiers in Microbiology.

[9]  V. Mlambo,et al.  Efficacy of novel phages for control of multi-drug resistant Escherichia coli O177 on artificially contaminated beef and their potential to disrupt biofilm formation. , 2021, Food microbiology.

[10]  Ling-Chun Lin,et al.  Phage φAB6-Borne Depolymerase Combats Acinetobacter baumannii Biofilm Formation and Infection , 2021, Antibiotics.

[11]  K. Seo,et al.  Characterization of a novel bacteriophage φCJ22 and its prophylactic and inhibitory effects on necrotic enteritis and Clostridium perfringens in broilers , 2020, Poultry science.

[12]  Hongye Li,et al.  Isolation and characterization of a novel Escherichia coli Kayfunavirus phage DY1. , 2020, Virus research.

[13]  J. J. Franceschelli,et al.  Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants , 2020, PloS one.

[14]  Xinchun Liu,et al.  Genomic characterization of a novel virulent phage infecting Shigella fiexneri and isolated from sewage. , 2020, Virus research.

[15]  J. Prescott,et al.  NetF-producing Clostridium perfringens and its associated diseases in dogs and foals , 2020, Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc.

[16]  F. Uzal,et al.  Clostridium sordellii–associated gas gangrene in 8 horses, 1998–2019 , 2020, Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc.

[17]  P. He,et al.  A Novel Polysaccharide Depolymerase Encoded by the Phage SH-KP152226 Confers Specific Activity Against Multidrug-Resistant Klebsiella pneumoniae via Biofilm Degradation , 2019, Front. Microbiol..

[18]  T. Kirn,et al.  Point-Counterpoint: Differences between the European Committee on Antimicrobial Susceptibility Testing and Clinical and Laboratory Standards Institute Recommendations for Reporting Antimicrobial Susceptibility Results , 2019, Journal of Clinical Microbiology.

[19]  W. Shen,et al.  Characterization and genome annotation of a newly detected bacteriophage infecting multidrug-resistant Acinetobacter baumannii , 2019, Archives of Virology.

[20]  P. Turner,et al.  Phage Therapy: A Renewed Approach to Combat Antibiotic-Resistant Bacteria. , 2019, Cell host & microbe.

[21]  Jeremy J. Barr,et al.  Phage Therapy in the Postantibiotic Era , 2019, Clinical Microbiology Reviews.

[22]  Xinchun Liu,et al.  Characterization of the Escherichia coli Virulent Myophage ST32 , 2018, Viruses.

[23]  M. Jamal,et al.  Isolation, characterization and efficacy of phage MJ2 against biofilm forming multi-drug resistant Enterobacter cloacae , 2018, Folia Microbiologica.

[24]  L. Hall,et al.  An update on the human and animal enteric pathogen Clostridium perfringens , 2018, Emerging Microbes & Infections.

[25]  S. Ryu,et al.  Clostridium perfringens Virulent Bacteriophage CPS2 and Its Thermostable Endolysin LysCPS2 , 2018, Viruses.

[26]  Z. Zong,et al.  Two New Lytic Bacteriophages of the Myoviridae Family Against Carbapenem-Resistant Acinetobacter baumannii , 2018, Front. Microbiol..

[27]  M. Clokie,et al.  Review of the nature, diversity and structure of bacteriophage receptor binding proteins that target Gram-positive bacteria , 2018, Biophysical Reviews.

[28]  V. Fischetti.  Lysin Therapy for Staphylococcus aureus and Other Bacterial Pathogens. , 2017, Current topics in microbiology and immunology.

[29]  Z. Abbas,et al.  The Lytic SA Phage Demonstrate Bactericidal Activity against Mastitis Causing Staphylococcus aureus , 2016 .

[30]  M. Rossmann,et al.  Structure and function of bacteriophage T4. , 2014, Future microbiology.

[31]  S. Reardon.  Phage therapy gets revitalized , 2014, Nature.

[32]  M. Jacques,et al.  Biofilm formation of Clostridium perfringens and its exposure to low-dose antimicrobials , 2014, Front. Microbiol..

[33]  J. Prescott,et al.  Characterization of Clostridium perfringens in the feces of adult horses and foals with acute enterocolitis. , 2014, Canadian journal of veterinary research = Revue canadienne de recherche veterinaire.

[34]  P. Mullany,et al.  Phage ϕC2 Mediates Transduction of Tn6215, Encoding Erythromycin Resistance, between Clostridium difficile Strains , 2013, mBio.

[35]  Robert J. Moore,et al.  Changes in the caecal microflora of chickens following Clostridium perfringens challenge to induce necrotic enteritis. , 2012, Veterinary microbiology.

[36]  E. Svetoch,et al.  Molecular Characterization of Podoviral Bacteriophages Virulent for Clostridium perfringens and Their Comparison with Members of the Picovirinae , 2012, PloS one.

[37]  D. Veesler,et al.  Structure of the phage TP901-1 1.8 MDa baseplate suggests an alternative host adhesion mechanism , 2012, Proceedings of the National Academy of Sciences.

[38]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[39]  B. Chopade,et al.  Novel lytic bacteriophage AB7-IBB1 of Acinetobacter baumannii: isolation, characterization and its effect on biofilm , 2012, Archives of Virology.

[40]  H. Kinde,et al.  Pathology of Clostridium perfringens Type C Enterotoxemia in Horses , 2012, Veterinary pathology.

[41]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[42]  S. Millet,et al.  The European ban on antibiotic growth promoters in animal feed: from challenges to opportunities. , 2011, Veterinary journal.

[43]  B. Seal,et al.  Recombinant expression of two bacteriophage proteins that lyse clostridium perfringens and share identical sequences in the C-terminal cell wall binding domain of the molecules but are dissimilar in their N-terminal active domains. , 2010, Journal of agricultural and food chemistry.

[44]  C. Hill,et al.  Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon , 2010, Proceedings of the National Academy of Sciences.

[45]  N. Perna,et al.  progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement , 2010, PloS one.

[46]  J. Rubinstein,et al.  The crystal structure of bacteriophage HK97 gp6: defining a large family of head-tail connector proteins. , 2010, Journal of molecular biology.

[47]  J. Gong,et al.  Identification of changes in the composition of ileal bacterial microbiota of broiler chickens infected with Clostridium perfringens. , 2010, Veterinary microbiology.

[48]  Paul Stoodley,et al.  Evolving concepts in biofilm infections , 2009, Cellular microbiology.

[49]  A. Kropinski,et al.  Bacteriophage enrichment from water and soil. , 2009, Methods in molecular biology.

[50]  H. Ackermann.  Basic phage electron microscopy. , 2009, Methods in molecular biology.

[51]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[52]  Thomas D. Schneider,et al.  Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases , 2005, Nucleic acids research.

[53]  Peter Schattner,et al.  The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs , 2005, Nucleic Acids Res..

[54]  Mark Borodovsky,et al.  GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses , 2005, Nucleic Acids Res..

[55]  Fumio Arisaka,et al.  The bacteriophage T4 DNA injection machine. , 2004, Current opinion in structural biology.

[56]  Deog-Yong Lee,et al.  Clostridium perfringens type A myonecrosis in a horse in Korea. , 2003, The Journal of veterinary medical science.

[57]  H. P. Fleming,et al.  Isolation and characterization of a Lactobacillus plantarum bacteriophage, phiJL-1, from a cucumber fermentation. , 2003, International journal of food microbiology.

[58]  D. Davies,et al.  Understanding biofilm resistance to antibacterial agents , 2003, Nature Reviews Drug Discovery.

[59]  T. Bernhardt,et al.  Breaking free: "protein antibiotics" and phage lysis. , 2002, Research in microbiology.

[60]  P. Forterre,et al.  Evolution of DNA Polymerase Families: Evidences for Multiple Gene Exchange Between Cellular and Viral Proteins , 2002, Journal of Molecular Evolution.

[61]  Vincent A. Fischetti,et al.  Rapid Killing of Streptococcus pneumoniae with a Bacteriophage Cell Wall Hydrolase , 2001, Science.

[62]  L. Petit,et al.  Clostridium perfringens: toxinotype and genotype. , 1999, Trends in microbiology.

[63]  U. Bläsi,et al.  Holins: form and function in bacteriophage lysis. , 1995, FEMS microbiology reviews.

[64]  D. E. Caldwell,et al.  Lytic infection of Escherichia coli biofilms by bacteriophage T4. , 1995, Canadian journal of microbiology.

[65]  E. Adelberg,et al.  Growth of Male-Specific Bacteriophage in Proteus mirabilis Harboring F-Genotes Derived from Escherichia coli , 1965, Journal of bacteriology.