Complete Genome Sequence of Proteus mirabilis Phage pPM_01 Isolated from Raw SewageWirjon I.A.a, b · Lau N.-S.b · Arip Y.M.a
aSchool of Biological Sciences and bCentre for Chemical Biology, University Sains Malaysia, Sains@USM, Bayan Lepas, Penang, Malaysia
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Objectives: Phage pPM_01 was previously isolated from a raw sewage treatment facility located in Batu Maung, Penang, Malaysia, and it was highly lytic against Proteus mirabilis, which causes urinary tract infections in humans. In this paper, we characterize the biology and complete genome sequence of the phage. Methods and Results: Transmission electron microscopy revealed phage pPM_01 to be a siphovirus (the first reported virus to infect P. mirabilis), with its complete genome sequence successfully determined. The genome was sequenced using Illumina technology and the reads obtained were assembled using CLC Genomic Workbench v.7.0.3. The whole genome contains a total of 58,546 bp of linear double-stranded DNA with a G+C content of 46.9%. Seventy putative genes were identified and annotated using various bioinformatics tools including RAST, Geneious v.R7, National Center for Biotechnology Information (NCBI) BLAST, and tRNAscan-SE-v1.3 Search. Functional clusters of related potential genes were defined (structural, lytic, packaging, replication, modification, and modulatory). The whole genome sequence showed a low similarity to known phages (i.e., Enterobacter phage Enc34 and Enterobacteria phage Chi). Host range determination and SDS-PAGE analysis were also performed. Conclusions: The inability to lysogenize a host, the absence of endotoxin genes in the annotated genome, and the lytic behavior suggest phage pPM_01 as a possible safe biological candidate to control P. mirabilis infection.
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- Kutateladze M, Adamia R: Bacteriophages as potential new therapeutics to replace or supplement antibiotics. Trends Biotechnol 2010;28:591-595.
- Dorval Courchesne NM, Parisien A, Lan CQ: Production and application of bacteriophage and bacteriophage-encoded lysins. Recent Pat Biotechnol 2009;3:37-45.
- Ahern SJ, Das M, Bhowmick TS, Young R, Gonzalez CF: Characterization of novel virulent broad-host-range phages of Xylella fastidiosa and Xanthomonas. J Bacteriol 2014;196:459-471.
- Breitbart M, Rohwer F: Here a virus, there a virus, everywhere the same virus? Trends Microbiol 2005;13:278-284.
- Matsuzaki S, Rashel M, Uchiyama J, Sakurai S, Ujihara T, Kuroda M, Ikeuchi M, Tani T, Fujieda M, Wakiguchi H, Imai S: Bacteriophage therapy: a revitalized therapy against bacterial infectious diseases. J Infect Chemother 2005;11:211-219.
- Kutter E, De Vos D, Gvasalia G, Alavidze Z, Gogokhia L, Kuhl S, Abedon ST: Phage therapy in clinical practice: treatment of human infections. Curr Pharm Biotechnol 2010;11:69-86.
- Clark JR, March JB: Bacteriophages and biotechnology: Vaccines, gene therapy and antibacterials. Trends Biotechnol 2006;24:212-218.
Ackermann HW: Bacteriophage taxonomy. Microbiol Aust 2011;32:90-94.
- Gill JJ, Hyman P: Phage choice, isolation, and preparation for phage therapy. Curr Pharm Biotechnol 2010;11:2-14.
- Motlagh AM, Bhattacharjee AS, Goel R: Biofilm control with natural and genetically-modified phages. World J Microbiol Biotechnol 2016;32:1-10.
Brovko LY, Anany H, Griffiths MW: Chapter six - bacteriophages for detection and control of bacterial pathogens in food and food-processing environment; in Jeyakumar H (ed): Advances in Food and Nutrition Research. Cambridge, Academic Press, 2012, vol 67, pp 241-288.
Madigan MT, Martinko JM, Dunlap PV, Clark DP: Brock Biology of Microorganisms, ed 12. London, Pearson, 2008, pp 65-73.
- Groisman EA, Casadesús J: The origin and evolution of human pathogens. Mol Microbiol 2005;56:1-7.
Goldman E, Green LH: Practical Handbook of Microbiology. Boca Raton, CRC Press, 2015.
Price P, Price P, Frey KB: Microbiology for Surgical Technologists. Albany, Thomson/Delmar Learning, 2003.
- Carson L, Gorman SP, Gilmore BF: The use of lytic bacteriophages in the prevention and eradication of biofilms of Proteus mirabilis and Escherichia coli. FEMS Immunol Med Microbiol 2010;59:447-455.
- Gravitz L: Turning a new phage. Nat Med 2012;18:1318-1320.
- Parasion S, Kwiatek M, Gryko R, Mizak L, Malm A: Bacteriophages as an alternative strategy for fighting biofilm development. Pol J Microbiol 2014;63:137-145.
Manos J, Belas R: The genera Proteus, Providencia, and Morganella; in Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds): The Prokaryotes. New York, Springer, 2006, pp 245-269.
- Chen C-Y, Chen Y-H, Lu P-L, Lin W-R, Chen T-C, Lin C-Y: Proteus mirabilis urinary tract infection and bacteremia: risk factors, clinical presentation, and outcomes. J Microbiol Immunol Infect 2012;45:228-236.
- Lee JBL, Neild GH: Urinary tract infection. Medicine 2007;35:423-428.
- Natarajan V: Urinary tract infection. Surgery 2008;26:193-196.
- Sheerin NS: Urinary tract infection. Medicine 2011;39:384-389.
- Srivastava R, Vasudev A: Urinary tract infections: current management. Apollo Med 2011;8:270-275.
- Nagano N, Shibata N, Saitou Y, Nagano Y, Arakawa Y: Nosocomial outbreak of infections by Proteus mirabilis that produces extended-spectrum CTX-M-2 type β-lactamase. J Clin Microbiol 2003;41:5530-5536.
- Torres-Barceló C, Hochberg ME: Evolutionary rationale for phages as complements of antibiotics. Trends Microbiol 2016;24:249-256.
- Domingo-Calap P, Georgel P, Bahram S: Back to the future: bacteriophages as promising therapeutic tools. HLA 2016;87:133-140.
Adams M: Bacteriophages. New York, Interscience, 1959.
- Carey-Smith GV, Billington C, Cornelius AJ, Hudson JA, Heinemann JA: Isolation and characterization of bacteriophages infecting Salmonella spp. FEMS Microbiol Lett 2006;258:182-186.
- Sillankorva S, Neubauer P, Azeredo J: Isolation and characterization of a T7-like lytic phage for Pseudomonas fluorescens. BMC Biotechnol 2008;8:80.
Sambrook JF, Russell DW: Molecular Cloning: a Laboratory Manual. New York, Cold Spring Harbor Laboratory Press, 2001, vol 3.
- Chekabab SM, Jubelin G, Dozois CM, Harel J: Phob activates Escherichia coli O157:H7 virulence factors in response to inorganic phosphate limitation. PLoS One 2014;9:e94285.
- Bradley D, Douglas C, Peschon J: Flagella-specific bacteriophages of Agrobacterium tumefaciens: demonstration of virulence of nonmotile mutants. Can J Microbiol 1984;30:676-681.
- Brenner S, Horne R: A negative staining method for high resolution electron microscopy of viruses. Biochim Biophys Acta 1959;34:103-110.
- Jun JW, Kim JH, Shin SP, Han JE, Chai JY, Park SC: Characterization and complete genome sequence of the Shigella bacteriophage pSf-1. Res Microbiol 2013;164:979-986.
Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Short Protocols in Molecular Biology, ed 4. Hoboken, Wiley, 1999.
- Denes T, Vongkamjan K, Ackermann H-W, Moreno Switt AI, Wiedmann M, den Bakker HC: Comparative genomic and morphological analyses of Listeria phages isolated from farm environments. Appl Environ Microbiol 2014;80:4616-4625.
- Sajben-Nagy E, Maróti G, Kredics L, Horváth B, Párducz Á, Vágvölgyi C, Manczinger L: Isolation of new Pseudomonas tolaasii bacteriophages and genomic investigation of the lytic phage BF7. FEMS Microbiol Lett 2012;332:162-169.
- Lowe T, Eddy S: tRNAscan-se: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997;25:955-964.
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990;215:403-410.
- Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R, Formsma K, Gerdes S, Glass E, Kubal M, Meyer F, Olsen G, Olson R, Osterman A, Overbeek R, McNeil L, Paarmann D, Paczian T, Parrello B, Pusch G, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O: The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75.
- Laemmli UK: Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970;227:680-686.
- Petrovski S, Dyson ZA, Seviour RJ, Tillett D: Small but sufficient: the Rhodococcus phage RRH1 has the smallest known Siphoviridae genome at 14.2 kilobases. J Virol 2012;86:358-363.
- Lu TK, Koeris MS: The next generation of bacteriophage therapy. Curr Opin Microbiol 2011;14:524-531.
- Kazaks A, Dislers A, Lipowsky G, Nikolajeva V, Tars K: Complete genome sequence of the Enterobacter cancerogenus bacteriophage Enc34. J Virol 2012;86:11403-11404.
- Duffy C, Feiss M: The large subunit of bacteriophage lambda's terminase plays a role in DNA translocation and packaging termination. J Mol Biol 2002;316:547-561.
Casjens SR, Gilcrease EB: Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions; in Clokie MRJ, Kropinski AM (eds): Bacteriophages: Methods and Protocols. Totowa, Humana Press, 2009, vol 2, pp 91-111.
- Kwiatek M, Parasion S, Mizak L, Gryko R, Bartoszcze M, Kocik J: Characterization of a bacteriophage, isolated from a cow with mastitis, that is lytic against Staphylococcus aureus strains. Arch Virol 2012;157:225-234.
- Moreno Switt A, Orsi R, den Bakker H, Vongkamjan K, Altier C, Wiedmann M: Genomic characterization provides new insight into Salmonella phage diversity. BMC Genom 2013;14:481.
- Dobbins AT, George M, Basham DA, Ford ME, Houtz JM, Pedulla ML, Lawrence JG, Hatfull GF, Hendrix RW: Complete genomic sequence of the virulent Salmonella bacteriophage SP6. J Bacteriol 2004;186:1933-1944.
- Roberts MD, Martin NL, Kropinski AM: The genome and proteome of coliphage T1. Virology 2004;318:245-266.
- Choi Y, Shin H, Lee J-H, Ryu S: Identification and characterization of a novel flagellum-dependent Salmonella-infecting bacteriophage, iEPS5. Appl Environ Microbiol 2013;79:4829-4837.
- Gan H, Sieo C, Tang S, Omar A, Ho Y: The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80. Virol J 2013;10:1-8.
- O'Flynn G, Ross RP, Fitzgerald GF, Coffey A: Evaluation of a cocktail of three bacteriophages for biocontrol of Escherichia coli O157:H7. Appl Environ Microbiol 2004;70:3417-3424.
- Skurnik M, Strauch E: Phage therapy: facts and fiction. Int J Med Microbiol 2006;296:5-14.
- Sulakvelidze A, Alavidze Z, Morris JG: Bacteriophage therapy. Antimicrob Agents Chemother 2001;45:649-659.
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