Characterising the biology of novel lytic bacteriophages infecting multidrug resistant Klebsiella pneumoniae

Virology Journal

Andrew M Kropinski⁴  Andrzej Górski³  Maciej Żaczek¹  Marzanna Łusiak-Szelachowska¹  Daria Augustyniak²  Grażyna Majkowska-Skrobek²  Jerzy Kassner²  Beata Weber-Dąbrowska¹  Zuzanna Drulis-Kawa²  Agata Kęsik-Szeloch² 

[1] L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Centre of Excellence, Weigla 12, Wroclaw, 53-114, Poland;Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, Wroclaw, 51-148, Poland;Department of Clinical Immunology, The Medical University of Warsaw, Nowogrodzka 59, Warszawa, 02-006, Poland;Department of Molecular & Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2 W1, Canada

关键词: Podoviridae;    Siphoviridae;    Myoviridae;    Restriction endonuclease patterns;    Multidrug resistance;    Klebsiella spp.;    Bacteriophage;   

Others  :  1151101
DOI  :  10.1186/1743-422X-10-100

 received in 2012-10-23, accepted in 2013-03-25,  发布年份 2013

【 摘 要 】

Background

Members of the genus Klebsiella are among the leading microbial pathogens associated with nosocomial infection. The increased incidence of antimicrobial resistance in these species has propelled the need for alternate/combination therapeutic regimens to aid clinical treatment. Bacteriophage therapy forms one of these alternate strategies.

Methods

Electron microscopy, burst size, host range, sensitivity of phage particles to temperature, chloroform, pH, and restriction digestion of phage DNA were used to characterize Klebsiella phages.

Results and conclusions

Of the 32 isolated phages eight belonged to the family Myoviridae, eight to the Siphoviridae whilst the remaining 16 belonged to the Podoviridae. The host range of these phages was characterised against 254 clinical Enterobacteriaceae strains including multidrug resistant Klebsiella isolates producing extended-spectrum beta-lactamases (ESBLs). Based on their lytic potential, six of the phages were further characterised for burst size, physicochemical properties and sensitivity to restriction endonuclease digestion. In addition, five were fully sequenced. Multiple phage-encoded host resistance mechanisms were identified. The Siphoviridae phage genomes (KP16 and KP36) contained low numbers of host restriction sites similar to the strategy found in T7-like phages (KP32). In addition, phage KP36 encoded its own DNA adenine methyltransferase. The φKMV-like KP34 phage was sensitive to all endonucleases used in this study. Dam methylation of KP34 DNA was detected although this was in the absence of an identifiable phage encoded methyltransferase. The Myoviridae phages KP15 and KP27 both carried Dam and Dcm methyltransferase genes and other anti-restriction mechanisms elucidated in previous studies. No other anti-restriction mechanisms were found, e.g. atypical nucleotides (hmC or glucosyl hmC), although Myoviridae phage KP27 encodes an unknown anti-restriction mechanism that needs further investigation.

【 授权许可】

   
2013 Kęsik-Szeloch et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Abedon ST: Bacteriophage ecology. In Population growth, evolution, and impact of bacterial viruses. 1st edition. Edited by Abedon ST. Cambridge, UK: Cambridge University Press; 2008.
• [2]Hemminga MA, Vos WL, Nazarov PV, Koehorst RB, Wolfs CJ, Spruijt RB, Stopar D: Viruses: incredible nanomachines. New advances with filamentous phages. Eur Biophys J 2010, 39:541-550.
• [3]Łusiak-Szelachowska M, Weber-Dąbrowska B, Górski A: The presence of bacteriophages in human feces and their potential importance. Pol Merkur Lekarski 2006, 21:381-383.
• [4]Clokie MR, Millard AD, Letarov AV, Heaphy S: Phages in nature. Bacteriophage 2011, 1:31-45.
• [5]Chibani-Chennoufi S, Bruttin A, Dillmann ML, Brüssow H: Phage-host interaction: an ecological perspective. J Bacteriol 2004, 186:3677-3686.
• [6]Shapiro OH, Kushmaro A: Bacteriophage ecology in environmental biotechnology processes. Curr Opin Biotechnol 2011, 22:449-455.
• [7]Zaleski P, Wojciechowski M, Piekarowicz A: The role of Dam methylation in phase variation of haemophilus influenzae genes involved in defence against phage infection. Microbiology 2005, 151:3361-3369.
• [8]Kropinski AM: Measurement of the bacteriophage inactivation kinetics with purified receptors. Methods Mol Biol 2009, 501:157-160.
• [9]Withey S, Cartmell E, Avery LM, Stephenson T: Bacteriophages – potential for application in wastewater treatment processes. Sci Total Environ 2005, 339:1-18.
• [10]Donlan RM: Preventing biofilms of clinically relevant organisms using bacteriophage. Trends Microbiol 2009, 17:66-72.
• [11]Weinbauer MG: Ecology of prokaryotic viruses. FEMS Microbiol Rev 2004, 28:127-181.
• [12]Stern A, Sorek R: The phage-host arms race: shaping the evolution of microbes. Bioessays 2011, 33:43-51.
• [13]Bickle TA, Krüger DH: Biology of DNA restriction. Microbiol Rev 1993, 57:434-450.
• [14]Labrie SJ, Samson JE, Moineau S: Bacteriophage Resistance mechanisms. Nat Rev Microbiol 2010, 8:317-327.
• [15]Warren RAJ: Modified bases in bacteriophage DNAs. Annu Rev Microbiol 1980, 34:137-158.
• [16]Kutateladze M, Adamia R: Bacteriophages as potential new therapeutics to replace or supplement antibiotics. Trends Biotechnol 2010, 28:591-595.
• [17]European antimicrobial Resistance surveillance network. http://ecdc.europa.eu/en/activities/surveillance/EARS-Net/database/Pages/database.aspx webcite
• [18]Pappas G: An animal farm called extended-spectrum beta-lactamase: antimicrobial resistance as a zoonosis. Clin Microbiol Infect 2011, 17:797-798.
• [19]Carattoli A: Animal reservoirs for extended spectrum beta-lactamase producers. Clin Microbiol Infect 2008, 14(Suppl 1):117-123. Erratum in: Clin Microbiol Infect 2008, 14 (Suppl 5):21–24
• [20]Warren RE, Ensor VM, O’Neill P, Butler V, Taylor J, Nye K, Harvey M, Livermore DM, Woodford N, Hawkey PM: Imported chicken meat as a potential source of quinolone-resistant Escherichia coli producing extended-spectrum beta-lactamases in the UK. J Antimicrob Chemother 2008, 61:504-508.
• [21]Leverstein-van Hall MA, Dierikx CM, Cohen Stuart J, Voets GM, van den Munckhof MP, van Essen-Zandbergen A, Platteel T, Fluit AC, van de Sande-Bruinsma N, Scharinga J, Bonten MJ, Mevius DJ, National ESBL surveillance group: Dutch patients, retail chicken meat and poultry share the same ESBL genes, plasmids and strains. Clin Microbiol Infect 2011, 17:873-880.
• [22]Kropinski AM, Prangishvili D, Lavigne R: Position paper: the creation of a rational scheme for the nomenclature of viruses of bacteria and archaea. Environ Microbiol 2009, 11:2775-2777.
• [23]Ackermann HW: Classification of bacteriophages. In The bacteriophages. 2nd edition. Edited by Calendar R. New York: Oxford University Press; 2006:8-16.
• [24]Mehling JS, Lavender H, Clegg S: A Dam methylation mutant of Klebsiella pneumoniae is partially attenuated. FEMS Microbiol Lett 2007, 268:187-193.
• [25]Römling U, Grothues D, Bautsch W, Tümmler B: A physical genome map of pseudomonas aeruginosa PAO. EMBO J 1989, 8:4081-4089.
• [26]Gu J, Liu X, Li Y, Han W, Lei L, Yang Y, Zhao H, Gao Y, Song J, Lu R, Sun C, Feng X: A method for generation phage cocktail with great therapeutic potential. PLoS One 2012, 7:e31698.
• [27]Kumari S, Harjai K, Chhibber S: Isolation and characterization of Klebsiella pneumoniae specific bacteriophages from sewage samples. Folia Microbiol (Praha) 2010, 55:221-227.
• [28]Šimoliūnas E, Kaliniene L, Truncaite L, Klausa V, Zajančkauskaite A, Meškys R: Genome of klebsiella sp.-infecting bacteriophage vB_KleM_RaK2. J Virol 2012, 86:5406.
• [29]Verma V, Harjai K, Chhibber S: Characterization of a T7-like lytic bacteriophage of Klebsiella pneumoniae B5055: a potential therapeutic agent. Curr Microbiol 2009, 59:274-281.
• [30]Wu LT, Chang SY, Yen MR, Yang TC, Tseng YH: Characterization of extended-host-range pseudo-T-even bacteriophage Kpp95 isolated on Klebsiella pneumoniae. Appl Environ Microbiol 2007, 73:2532-2540.
• [31]Hughes KA, Sutherland IW, Clark J, Jones MV: Bacteriophage and associated polysaccharide depolymerases – novel tools for study of bacterial biofilms. J Appl Microbiol 1998, 85:583-590. Erratum in: J Appl Microbiol 1999, 86(2):359
• [32]Hausmann R, Gold M: The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid. IX. Deoxyribonucleic acid methylase in bacteriophage-infected Escherichia coli. J Biol Chem 1966, 241:1985-1994.
• [33]Auer B, Schweiger M: Evidence that Escherichia coli virus T1 induces a DNA methyltransferase. J Virol 1984, 49:588-590.
• [34]Wagner EF, Auer B, Schweiger M: Development of Escherichia coli virus T1: escape from host restriction. J Virol 1979, 29:1229-1231.
• [35]Hung CH, Kuo CF, Wang CH, Wu CM, Tsao N: Experimental phage therapy in treating Klebsiella pneumoniae-mediated liver abscesses and bacteremia in mice. Antimicrob Agents Chemother 2011, 55:1358-1365.
• [36]Karamoddini MK, Fazli-Bazzaz BS, Emamipour F, Ghannad MS, Jahanshahi AR, Saed N, Sahebkar A: Antibacterial efficacy of lytic bacteriophages against antibiotic-resistant Klebsiella species. ScientificWorldJournal 2011, 11:1332-1340.
• [37]Kumari S, Harjai K, Chhibber S: Efficacy of bacteriophage treatment in murine burn wound infection induced by Klebsiella pneumoniae. J Microbiol Biotechnol 2009, 19:622-628.
• [38]Kumari S, Harjai K, Chhibber S: Evidence to support the therapeutic potential of bacteriophage Kpn5 in burn wound infection caused by Klebsiella pneumoniae in BALB/c mice. J Microbiol Biotechnol 2010, 20:935-941.
• [39]Kumari S, Harjai K, Chhibber S: Bacteriophage versus antimicrobial agents for the treatment of murine burn wound infection caused by Klebsiella pneumoniae B5055. J Med Microbiol 2011, 60:205-210.
• [40]Gill JJ, Hyman P: Phage choice, isolation, and preparation for phage therapy. Curr Pharm Biotechnol 2010, 11:2-14.
• [41]Jończyk E, Kłak M, Międzybrodzki R, Górski A: The influence of external factors on bacteriophages – review. Folia Microbiol (Praha) 2011, 56:191-200.
• [42]Ryan EM, Gorman SP, Donnelly RF, Gilmore BF: Recent advances in bacteriophage therapy: how delivery routes, formulation, concentration and timing influence the success of phage therapy. J Pharm Pharmacol 2011, 63:1253-1264.
• [43]Leclerc H, Edberg S, Pierzo V, Delattre JM: Bacteriophages as indicators of enteric viruses and public health risk in groundwaters. J Appl Microbiol 2000, 88:5-21.
• [44]Adams MH: Bacteriophages. New York: Interscience Publishers, Inc.; 1959.
• [45]Ślopek S, Durlakowa I, Kucharewicz-Krukowska A, Krzywy T, Ślopek A, Weber B: Phage typing of shigella flexneri. Arch Immunol Ther Exp (Warsz) 1972, 20:1-60.
• [46]Kutter E: Phage host range and efficiency of plating. In Bacteriophages: methods And protocols. Volume 1: isolation, characterization, and interactions. 1st edition. Edited by Clokie MRJ, Kropinski AM. New York: Humana Press; 2009:141-149.
• [47]Gallet R, Shao Y, Wang IN: High adsorption rate is detrimental to bacteriophage fitness in a Biofilm-like environment. BMC Evol Biol 2009, 9:241-253. BioMed Central Full Text
• [48]Pajunen M, Kiljunen S, Skurnik M: Bacteriophage φYeO3-12, specific for yersinia enterocolitica serotype O:3, is related to coliphages T3 and T7. J Bacteriol 2000, 182:5114-5120.