Pengjun Han, Mingfang Pu, Yahao Li, Huahao Fan and Yigang Tong. Characterization of bacteriophage BUCT631 lytic for K1 Klebsiella pneumoniae and its therapeutic efficacy in Galleria mellonella larvae[J]. Virologica Sinica, 2023, 38(5): 801-812. doi: 10.1016/j.virs.2023.07.002
Citation: Pengjun Han, Mingfang Pu, Yahao Li, Huahao Fan, Yigang Tong. Characterization of bacteriophage BUCT631 lytic for K1 Klebsiella pneumoniae and its therapeutic efficacy in Galleria mellonella larvae .VIROLOGICA SINICA, 2023, 38(5) : 801-812.  http://dx.doi.org/10.1016/j.virs.2023.07.002

K1型肺炎克雷伯菌噬菌体BUCT631的鉴定及其对大蜡螟幼虫的治疗效果评估

  • 由多重耐药性肺炎克雷伯菌(K. pneumoniae)引起的严重感染凸显了对这种病原体具有活性的新疗法的需求。噬菌体疗法是治疗多重耐药性肺炎克雷伯菌感染的一种替代治疗方法。在此,我们报告了一株新的噬菌体BUCT631,它能特异性地裂解K1荚膜类型的肺炎克雷伯菌。生理特征分析表明,噬菌体BUCT631能迅速吸附在肺炎克雷伯菌的表面并形成明显的晕环,它具有相对有利的热稳定性(4-50℃)和pH耐受性(pH=4-12)。此外,噬菌体BUCT631的最佳感染复数(MOI)为0.01,爆发量约为303 PFU/cell。基因组分析表明,噬菌体BUCT631具有双链DNA(总长度为44,812 bp),G+C含量为54.1%,基因组包含57个开放阅读框(ORFs),没有毒力或抗生素抗性相关基因。根据系统发育分析,噬菌体BUCT631可以被归入Slopekvirinae亚科Drulisvirus属中的一个新种。最重要的是,噬菌体BUCT631可以在体外2小时内迅速抑制肺炎克雷伯菌的生长,并在体内将感染肺炎克雷伯菌的大蜡螟幼虫的存活率从10%显著提高到90%。这些研究表明,噬菌体BUCT631具有很好的开发潜力,是控制和治疗多重耐药性K1肺炎克雷伯菌感染的安全替代品。

Characterization of bacteriophage BUCT631 lytic for K1 Klebsiella pneumoniae and its therapeutic efficacy in Galleria mellonella larvae

  • Severe infections caused by multidrug-resistant Klebsiella pneumoniae (K. pneumoniae) highlight the need for new therapeutics with activity against this pathogen. Phage therapy is an alternative treatment approach for multidrug-resistant K. pneumoniae infections. Here, we report a novel bacteriophage (phage) BUCT631 that can specifically lyse capsule-type K1 K. pneumoniae. Physiological characterization revealed that phage BUCT631 could rapidly adsorb to the surface of K. pneumoniae and form an obvious halo ring, and it had relatively favorable thermal stability (4-50 °C) and pH tolerance (pH=4-12). In addition, the optimal multiplicity of infection (MOI) of phage BUCT631 was 0.01, and the burst size was approximately 303 PFU/cell. Genomic analysis showed that phage BUCT631 has double-stranded DNA (total length of 44,812 bp) with a G + C content of 54.1%, and the genome contains 57 open reading frames (ORFs) and no virulence or antibiotic resistance related genes. Based on phylogenetic analysis, phage BUCT631 could be assigned to a new species in the genus Drulisvirus of the subfamily Slopekvirinae. In addition, phage BUCT631 could quickly inhibit the growth of K. pneumoniae within 2 h in vitro and significantly elevated the survival rate of K. pneumoniae infected Galleria mellonella larvae from 10% to 90% in vivo. These studies suggest that phage BUCT631 has promising potential for development as a safe alternative for control and treatment of multidrug-resistant K. pneumoniae infection.

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    1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST:a new generation of protein database search programs. Nucleic Acids Res, 25:3389-3402.

    2. Anderl JN, Franklin MJ, Stewart PS. 2000. Role of antibiotic penetration limitation in Klebsiella pneumoniae biofilm resistance to ampicillin and ciprofloxacin. Antimicrob Agents Chemother, 44:1818-1824.

    3. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes:a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol, 19:455-477.

    4. Bao J, Wu N, Zeng Y, Chen L, Li L, Yang L, Zhang Y, Guo M, Li L, Li J, Tan D, Cheng M, Gu J, Qin J, Liu J, Li S, Pan G, Jin X, Yao B, Guo X, Zhu T, Le S. 2020. Non-active antibiotic and bacteriophage synergism to successfully treat recurrent urinary tract infection caused by extensively drug-resistant Klebsiella pneumoniae. Emerg Microbes Infect, 9:771-774.

    5. Bengoechea JA, Sa Pessoa J. 2019. Klebsiella pneumoniae infection biology:living to counteract host defences. FEMS Microbiol Rev, 43:123-144.

    6. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic:a flexible trimmer for Illumina sequence data. Bioinformatics, 30:2114-2120.

    7. Cano EJ, Caflisch KM, Bollyky PL, Van Belleghem JD, Patel R, Fackler J, Brownstein MJ, Horne B, Biswas B, Henry M, Malagon F, Lewallen DG, Suh GA. 2021. Phage Therapy for Limb-threatening Prosthetic Knee Klebsiella pneumoniae Infection:Case Report and In Vitro Characterization of Anti-biofilm Activity. Clin Infect Dis, 73:e144-e151.

    8. Cantu VA, Salamon P, Seguritan V, Redfield J, Salamon D, Edwards RA, Segall AM. 2020. PhANNs, a fast and accurate tool and web server to classify phage structural proteins. PLoS Comput Biol, 16:e1007845.

    9. Chen X, Tang Q, Li X, Zheng X, Li P, Li M, Wu F, Xu Z, Lu R, Zhang W. 2022. Isolation, characterization, and genome analysis of bacteriophage P929 that could specifically lyase the KL19 capsular type of Klebsiella pneumoniae. Virus Res, 314:198750.

    10. Choby JE, Howard-Anderson J, Weiss DS. 2020. Hypervirulent Klebsiella pneumoniae-clinical and molecular perspectives. J Intern Med, 287:283-300.

    11. Chuang YP, Fang CT, Lai SY, Chang SC, Wang JT. 2006. Genetic determinants of capsular serotype K1 of Klebsiella pneumoniae causing primary pyogenic liver abscess. J Infect Dis, 193:645-654.

    12. Clausen P, Aarestrup FM, Lund O. 2018. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics, 19:307.

    13. Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O. 2013. PathogenFinder——distinguishing friend from foe using bacterial whole genome sequence data. PLoS One, 8:e77302.

    14. Domingo-Calap P, Beamud B, Mora-Quilis L, González-Candelas F, Sanjuán R. 2020. Isolation and Characterization of Two Klebsiella pneumoniae Phages Encoding Divergent Depolymerases. Int J Mol Sci, 21:3160.

    15. Fang CT, Lai SY, Yi WC, Hsueh PR, Liu KL, Chang SC. 2007. Klebsiella pneumoniae genotype K1:an emerging pathogen that causes septic ocular or central nervous system complications from pyogenic liver abscess. Clin Infect Dis, 45:284-293.

    16. Fang Q, Zong Z. 2022. Lytic Phages against ST11 K47 Carbapenem-Resistant Klebsiella pneumoniae and the Corresponding Phage Resistance Mechanisms. mSphere, 7:e0008022.

    17. Feng J, Li F, Sun L, Dong L, Gao L, Wang H, Yan L, Wu C. 2023. Characterization and genome analysis of phage vB_KpnS_SXFY507 against Klebsiella pneumoniae and efficacy assessment in Galleria mellonella larvae. Front Microbiol, 14:1081715.

    18. Gu J, Liu X, Li Y, Han W, Lei L, Yang Y, Zhao H, Gao Y, Song J, Lu R, Sun C, Feng X. 2012. A method for generation phage cocktail with great therapeutic potential. PLoS One, 7:e31698.

    19. Han P, Hu Y, An X, Song L, Fan H, Tong Y. 2021. Biochemical and genomic characterization of a novel bacteriophage BUCT555 lysing Stenotrophomonas maltophilia. Virus Res, 301:198465.

    20. Han P, Zhang W, Pu M, Li Y, Song L, An X, Li M, Li F, Zhang S, Fan H, Tong Y. 2022. Characterization of the Bacteriophage BUCT603 and Therapeutic Potential Evaluation Against Drug-Resistant Stenotrophomonas maltophilia in a Mouse Model. Front Microbiol, 13:906961.

    21. Harada S, Ishii Y, Saga T, Aoki K, Tateda K. 2018. Molecular epidemiology of Klebsiella pneumoniae K1 and K2 isolates in Japan. Diagn Microbiol Infect Dis, 91:354-359.

    22. Hatfull GF, Dedrick RM, Schooley RT. 2022. Phage Therapy for Antibiotic-Resistant Bacterial Infections. Annu Rev Med, 73:197-211.

    23. Herridge WP, Shibu P, O'Shea J, Brook TC, Hoyles L. 2020. Bacteriophages of Klebsiella spp., their diversity and potential therapeutic uses. J Med Microbiol, 69:176-194.

    24. Holst Sørensen MC, van Alphen LB, Fodor C, Crowley SM, Christensen BB, Szymanski CM, Brøndsted L. 2012. Phase variable expression of capsular polysaccharide modifications allows Campylobacter jejuni to avoid bacteriophage infection in chickens. Front Cell Infect Microbiol, 2:11.

    25. Hung CH, Kuo CF, Wang CH, Wu CM, Tsao N. 2011. Experimental phage therapy in treating Klebsiella pneumoniae-mediated liver abscesses and bacteremia in mice. Antimicrob Agents Chemother, 55:1358-1365.

    26. Kim SG, Lee SB, Giri SS, Kim HJ, Kim SW, Kwon J, Park J, Roh E, Park SC. 2020. Characterization of Novel Erwinia amylovora Jumbo Bacteriophages from Eneladusvirus Genus. Viruses, 12:1373.

    27. Kumar S, Stecher G, Tamura K. 2016. MEGA7:Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol, 33:1870-1874.

    28. Latka A, Maciejewska B, Majkowska-Skrobek G, Briers Y, Drulis-Kawa Z. 2017. Bacteriophage-encoded virion-associated enzymes to overcome the carbohydrate barriers during the infection process. Appl Microbiol Biotechnol, 101:3103-3119.

    29. Lee D, Im J, Na H, Ryu S, Yun CH, Han SH. 2019. The Novel Enterococcus Phage vB_EfaS_HEf13 Has Broad Lytic Activity Against Clinical Isolates of Enterococcus faecalis. Front Microbiol, 10:2877.

    30. Letarov AV, Kulikov EE. 2017. Adsorption of Bacteriophages on Bacterial Cells. Biochemistry (Mosc), 82:1632-1658.

    31. Li L, Zhang Z. 2014. Isolation and characterization of a virulent bacteriophage SPW specific for Staphylococcus aureus isolated from bovine mastitis of lactating dairy cattle. Mol Biol Rep, 41:5829-5838.

    32. Li M, Wang H, Chen L, Guo G, Li P, Ma J, Chen R, Du H, Liu Y, Zhang W. 2022. Identification of a phage-derived depolymerase specific for KL47 capsule of Klebsiella pneumoniae and its therapeutic potential in mice. Virol Sin, 37:538-546.

    33. Li P, Ma W, Shen J, Zhou X. 2022. Characterization of Novel Bacteriophage vB_KpnP_ZX1 and Its Depolymerases with Therapeutic Potential for K57 Klebsiella pneumoniae Infection. Pharmaceutics, 14:1916.

    34. Lin TL, Hsieh PF, Huang YT, Lee WC, Tsai YT, Su PA, Pan YJ, Hsu CR, Wu MC, Wang JT. 2014. Isolation of a bacteriophage and its depolymerase specific for K1 capsule of Klebsiella pneumoniae:implication in typing and treatment. J Infect Dis, 210:1734-1744.

    35. Lin YT, Cheng YH, Juan CH, Wu PF, Huang YW, Chou SH, Yang TC, Wang FD. 2018. High mortality among patients infected with hypervirulent antimicrobial-resistant capsular type K1 Klebsiella pneumoniae strains in Taiwan. Int J Antimicrob Agents, 52:251-257.

    36. Lowe TM, Eddy SR. 1997. tRNAscan-SE:a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res, 25:955-964.

    37. Luong T, Salabarria AC, Roach DR. 2020. Phage Therapy in the Resistance Era:Where Do We Stand and Where Are We Going. Clin Ther, 42:1659-1680.

    38. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH. 2011. CDD:a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res, 39:D225-229.

    39. McCallin S, Alam Sarker S, Barretto C, Sultana S, Berger B, Huq S, Krause L, Bibiloni R, Schmitt B, Reuteler G, Brüssow H. 2013. Safety analysis of a Russian phage cocktail:from metagenomic analysis to oral application in healthy human subjects. Virology, 443:187-196.

    40. McNair K, Zhou C, Dinsdale EA, Souza B, Edwards RA. 2019. PHANOTATE:a novel approach to gene identification in phage genomes. Bioinformatics, 35:4537-4542.

    41. Melo L, Oliveira H, Pires DP, Dabrowska K, Azeredo J. 2020. Phage therapy efficacy:a review of the last 10 years of preclinical studies. Crit Rev Microbiol, 46:78-99.

    42. Moraru C, Varsani A, Kropinski AM. 2020. VIRIDIC-A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses. Viruses, 12:1268.

    43. Ménard G, Rouillon A, Cattoir V, Donnio PY. 2021. Galleria mellonella as a Suitable Model of Bacterial Infection:Past, Present and Future. Front Cell Infect Microbiol, 11:782733.

    44. Pires DP, Oliveira H, Melo LD, Sillankorva S, Azeredo J. 2016. Bacteriophage-encoded depolymerases:their diversity and biotechnological applications. Appl Microbiol Biotechnol, 100:2141-2151.

    45. Podschun R, Ullmann U. 1998. Klebsiella spp. as nosocomial pathogens:epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev, 11:589-603.

    46. Pu M, Li Y, Han P, Lin W, Geng R, Qu F, An X, Song L, Tong Y, Zhang S, Cai Z, Fan H. 2022. Genomic characterization of a new phage BUCT541 against Klebsiella pneumoniae K1-ST23 and efficacy assessment in mouse and Galleria mellonella larvae. Front Microbiol, 13:950737.

    47. Ramirez MS, Traglia GM, Lin DL, Tran T, Tolmasky ME. 2014. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives:the Klebsiella pneumoniae Paradigm. Microbiol Spectr, 2:PLAS-0016-2013.

    48. Rohde C, Resch G, Pirnay JP, Blasdel BG, Debarbieux L, Gelman D, Górski A, Hazan R, Huys I, Kakabadze E, Łobocka M, Maestri A, Almeida G, Makalatia K, Malik DJ, Mašlaňová I, Merabishvili M, Pantucek R, Rose T, Štveráková D, Van Raemdonck H, Verbeken G, Chanishvili N. 2018. Expert Opinion on Three Phage Therapy Related Topics:Bacterial Phage Resistance, Phage Training and Prophages in Bacterial Production Strains. Viruses, 10:178.

    49. Saha D, Mukherjee R. 2019. Ameliorating the antimicrobial resistance crisis:phage therapy. IUBMB Life, 71:781-790.

    50. Sarker SA, McCallin S, Barretto C, Berger B, Pittet AC, Sultana S, Krause L, Huq S, Bibiloni R, Bruttin A, Reuteler G, Brüssow H. 2012. Oral T4-like phage cocktail application to healthy adult volunteers from Bangladesh. Virology, 434:222-232.

    51. Solovieva EV, Myakinina VP, Kislichkina AA, Krasilnikova VM, Verevkin VV, Mochalov VV, Lev AI, Fursova NK, Volozhantsev NV. 2018. Comparative genome analysis of novel Podoviruses lytic for hypermucoviscous Klebsiella pneumoniae of K1, K2, and K57 capsular types. Virus Res, 243:10-18.

    52. Storms ZJ, Sauvageau D. 2014. Evidence that the heterogeneity of a T4 population is the result of heritable traits. PLoS One, 9:e116235.

    53. Söding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res, 33:W244-248.

    54. Teng T, Li Q, Liu Z, Li X, Liu Z, Liu H, Liu F, Xie L, Wang H, Zhang L, Wu D, Chen M, Li Y, Ji A. 2019. Characterization and genome analysis of novel Klebsiella phage Henu1 with lytic activity against clinical strains of Klebsiella pneumoniae. Arch Virol, 164:2389-2393.

    55. Thapa S, Adhikari N, Shah AK, Lamichhane I, Dhungel B, Shrestha UT, Adhikari B, Banjara MR, Ghimire P, Rijal KR. 2021. Detection of NDM-1 and VIM Genes in Carbapenem-Resistant Klebsiella pneumoniae Isolates from a Tertiary Health-Care Center in Kathmandu, Nepal. Chemotherapy, 66:199-209.

    56. Thiry D, Passet V, Danis-Wlodarczyk K, Lood C, Wagemans J, De Sordi L, van Noort V, Dufour N, Debarbieux L, Mainil JG, Brisse S, Lavigne R. 2019. New Bacteriophages against Emerging Lineages ST23 and ST258 of Klebsiella pneumoniae and Efficacy Assessment in Galleria mellonella Larvae. Viruses, 11:411.

    57. Wilkins MR, Gasteiger E, Bairoch A, Sanchez JC, Williams KL, Appel RD, Hochstrasser DF. 1999. Protein identification and analysis tools in the ExPASy server. Methods Mol Biol, 112:531-552.

    58. Wittebole X, De Roock S, Opal SM. 2014. A historical overview of bacteriophage therapy as an alternative to antibiotics for the treatment of bacterial pathogens. Virulence, 5:226-235.

    59. Zhang R, Lin D, Chan EW, Gu D, Chen GX, Chen S. 2016. Emergence of Carbapenem-Resistant Serotype K1 Hypervirulent Klebsiella pneumoniae Strains in China. Antimicrob Agents Chemother, 60:709-711.

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    Characterization of bacteriophage BUCT631 lytic for K1 Klebsiella pneumoniae and its therapeutic efficacy in Galleria mellonella larvae

      Corresponding author: Huahao Fan, fanhuahao@mail.buct.edu.cn
      Corresponding author: Yigang Tong, tongyigang@mail.buct.edu.cn
    • a. College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China;
    • b. Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China

    Abstract: Severe infections caused by multidrug-resistant Klebsiella pneumoniae (K. pneumoniae) highlight the need for new therapeutics with activity against this pathogen. Phage therapy is an alternative treatment approach for multidrug-resistant K. pneumoniae infections. Here, we report a novel bacteriophage (phage) BUCT631 that can specifically lyse capsule-type K1 K. pneumoniae. Physiological characterization revealed that phage BUCT631 could rapidly adsorb to the surface of K. pneumoniae and form an obvious halo ring, and it had relatively favorable thermal stability (4-50 °C) and pH tolerance (pH=4-12). In addition, the optimal multiplicity of infection (MOI) of phage BUCT631 was 0.01, and the burst size was approximately 303 PFU/cell. Genomic analysis showed that phage BUCT631 has double-stranded DNA (total length of 44,812 bp) with a G + C content of 54.1%, and the genome contains 57 open reading frames (ORFs) and no virulence or antibiotic resistance related genes. Based on phylogenetic analysis, phage BUCT631 could be assigned to a new species in the genus Drulisvirus of the subfamily Slopekvirinae. In addition, phage BUCT631 could quickly inhibit the growth of K. pneumoniae within 2 h in vitro and significantly elevated the survival rate of K. pneumoniae infected Galleria mellonella larvae from 10% to 90% in vivo. These studies suggest that phage BUCT631 has promising potential for development as a safe alternative for control and treatment of multidrug-resistant K. pneumoniae infection.

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