Two new lytic bacteriophages of the Myoviridae family against carbapenem-resistant Acinetobacter baumannii

Frontiers in Microbiology

Volumn 9, Issue APR, 2018, Pages

  Zhou, Weilong ^a,b   Feng, Yu ^a,b   Zong, Zhiyong ^a,b  

^a SICHUAN UNIVERSITY   (China)

^b SICHUAN UNIVERSITY   (China)

Author keywords

Acinetobacter baumannii; Bacteriophage; Carbapenem resistance; Galleria mellonella; Phage therapy

Indexed keywords

POLYMYXIN B;

ACINETOBACTER BAUMANNII; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL GROWTH; BACTERIOPHAGE; BIOINFORMATICS; CARBAPENEM RESISTANT ACINETOBACTER BAUMANNII; CONTROLLED STUDY; CYTOLYSIS; DNA PACKAGING; GALLERIA MELLONELLA; GENE FUNCTION; HOST RANGE; MICROBIAL METABOLISM; MYOVIRIDAE; NONHUMAN; TAXONOMY; TRANSMISSION ELECTRON MICROSCOPY; VIROGENESIS; VIRUS ATTACHMENT; VIRUS ISOLATION; VIRUS TITRATION;

EID: 85046629973     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2018.00850     Document Type: Article

References (62)

1. Abubakar, S., Suleiman, B. H., Abbagana, B. A., Mustafa, I. A., and Musa, I. A. (2016). Novel uses of bacteriophages in the treatment of human infections and antibiotic resistance. Am. J. Biosci. 4, 34-40. doi: 10.11648/j.ajbio.20160403.13
2. Adams, M. J., Lefkowitz, E. J., King, A. M. Q., Harrach, B., Harrison, R. L., Knowles, N. J., et al. (2017). Changes to taxonomy and the international code of virus classification and nomenclature ratified by the international committee on taxonomy of viruses (2017). Arch. Virol. 162, 1-34. doi: 10.1007/s00705-017-3358-5
3. Alikhan, N. F., Petty, N. K., Ben Zakour, N. L., and Beatson, S. A. (2011). BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12:402. doi: 10.1186/1471-2164-12-402
4. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410. doi: 10.1016/S0022-2836(05)80360-2
5. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402. doi: 10.1093/nar/25.17.3389
6. Anisimova, M., and Gascuel, O. (2006). Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst. Biol. 55, 539-552. doi: 10.1080/10635150600755453
7. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. doi: 10.1089/cmb.2012.0021
8. Berlau, J., Aucken, H. M., Houang, E., and Pitt, T. L. (1999). Isolation of Acinetobacter spp. including A. baumannii from vegetables: implications for hospital-acquired infections. J. Hosp. Infect. 42, 201-204. doi: 10.1053/jhin.1999.0602
9. Bernhardt, T. G., Wang, I. N., Struck, D. K., and Young, R. (2001). A protein antibiotic in the phage Qβ virion: diversity in lysis targets. Science 292, 2326-2329. doi: 10.1126/science.1058289
10. Boulanger, P. (2009). Purification of bacteriophages and SDS-PAGE analysis of phage structural proteins from ghost particles. Methods Mol. Biol. 502, 227. doi: 10.1007/978-1-60327-565-1_13
11. Bruynoghe, R., and Maisin, J. (1921). Essais de thérapeutique au moyen du bacteriophage. CR Soc. Biol. 85, 1120-1121
12. Bryan, M. J., Burroughs, N. J., Spence, E. M., Clokie, M. R. J., Mann, N. H., and Bryan, S. J. (2008). Evidence for the intense exchange of mazG in marine cyanophages by horizontal gene transfer. PLoS ONE 3:e2048. doi: 10.1371/journal.pone.0002048
13. Casjens, S. R., and Gilcrease, E. B. (2009). Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions. Methods Mol. Biol. 502, 91-111. doi: 10.1007/978-1-60327-565-1_7
14. CLSI (2017). Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Third Informational Supplement. M100-S27. (Wayne, PA: Clinical and Laboratory Standards Institute)
15. d'herelle, F. (1917). Sur un microbe invisible antagoniste des bacilles dysentériques. CR Acad. Sci. Paris 165, 373-375
16. Di, P. A., Giannouli, M., Triassi, M., Brisse, S., and Zarrilli, R. (2011). Molecular epidemiological investigation of multidrug-resistant Acinetobacter baumannii strains in four Mediterranean countries with a multilocus sequence typing scheme. Clin. Microb. Infect. 17, 197-201. doi: 10.1111/j.1469-0691.2010.03254.x
17. Dijkshoorn, L., Nemec, A., and Seifert, H. (2007). An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii. Nat. Rev. Microbiol. 5, 939-951. doi: 10.1038/nrmicro1789
18. Duda, R. L. (2008). Icosahedral tailed dsDNA bacterial viruses. Encycl. Virol. 30-37. doi: 10.1016/B978-012374410-4.00754-8
19. Eijsink, V. G. H., Vaaje-Kolstad, G., Vårum, K. M., and Horn, S. J. (2008). Towards new enzymes for biofuels: lessons from chitinase research. Trends Biotechnol. 26, 228-235. doi: 10.1016/j.tibtech.2008.02.004
20. Feiss, M., and Rao, V. B. (2012). The bacteriophage DNA packaging machine. Adv. Exp. Med. Biol. 726, 489-509. doi: 10.1007/978-1-4614-0980-9_22
21. Ghajavand, H., Esfahani, B. N., Havaei, A., Fazeli, H., Jafari, R., and Moghim, S. (2017). Isolation of bacteriophages against multidrug resistant Acinetobacter baumannii. Res. Pharm. Sci. 12, 373-380. doi: 10.4103/1735-5362.213982
22. Harding, C. M., Hennon, S. W., and Feldman, M. F. (2018). Uncovering the mechanisms of Acinetobacter baumannii virulence. Nat. Rev. Microbiol. 16, 91-102. doi: 10.1038/nrmicro.2017.148
23. Helvoort, T. V. (2001). Felix d'Herelle and the origins of molecular biology. J. Hist. Med. Allied Sci. 56, 305-307. doi: 10.1093/jhmas/56.3.305
24. Hornsey, M., and Wareham, D. W. (2011). In vivo efficacy of glycopeptide-colistin combination therapies in a Galleria mellonella model of Acinetobacter baumannii infection. Antimicrob. Agents Chemother. 55, 3534-3537. doi: 10.1128/AAC.00230-11
25. Hornsey, M., Phee, L., Longshaw, C., and Wareham, D. W. (2013). In vivo efficacy of telavancin/colistin combination therapy in a Galleria mellonella model of Acinetobacter baumannii infection. Int. J. Antimicrob. Agents 41, 285-287. doi: 10.1016/j.ijantimicag.2012.11.013
26. Jin, J., Li, Z. J., Wang, S. W., Wang, S. M., Huang, D. H., Li, Y. H., et al. (2012). Isolation and characterization of ZZ1, a novel lytic phage that infects Acinetobacter baumannii clinical isolates. BMC Microbiol. 12:156. doi: 10.1186/1471-2180-12-156
27. Khan, M. M., and Nilsson, A. S. (2015). Isolation of phages for phage therapy: a comparison of spot tests and efficiency of plating analyses for determination of host range and efficacy. PLoS ONE 10:e0118557. doi: 10.1371/journal.pone.0118557
28. Krawczyk, B., Lewandowski, K., and Kur, J. (2002). Comparative studies of the Acinetobacter genus and the species identification method based on the recA sequences. Mol. Cell. Probes 16, 1-11. doi: 10.1006/mcpr.2001.0388
29. Krogh, A., Larsson, B., Von Heijne, G., and Sonnhammer, E. L. (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567-580. doi: 10.1006/jmbi.2000.4315
30. Kropinski, A. M., Mazzocco, A., Waddell, T. E., Lingohr, E., and Johnson, R. P. (2009). Enumeration of bacteriophages by double agar overlay plaque assay. Methods Mol. Biol. 501, 69-76. doi: 10.1007/978-1-60327-164-6_7
31. Kurtböke, I. (2012). Bacteriophages. Rijeka: InTech. doi: 10.5772/1065
32. Kutter, E. M., Kuhl, S. J., and Abedon, S. T. (2015). Re-establishing a place for phage therapy in western medicine. Future Microbiol. 10, 685-688. doi: 10.2217/fmb.15.28
33. Laslett, D., and Canback, B. (2004). ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32, 11-16. doi: 10.1093/nar/gkh152
34. Lee, C. N., Tseng, T. T., Lin, J. W., Fu, Y. C., Weng, S. F., and Tseng, Y. H. (2011). Lytic myophage Abp53 encodes several proteins similar to those encoded by host Acinetobacter baumannii and phage phiKO2. Appl. Environ. Microbiol. 77, 6755-6762. doi: 10.1128/AEM.05116-11
35. Li, J., Rayner, C. R., Nation, R. L., Owen, R. J., Spelman, D., Tan, K. E., et al. (2006). Heteroresistance to colistin in multidrug-resistant Acinetobacter baumannii. Antimicrob. Agents Chemother. 50, 2946-2950. doi: 10.1128/AAC.00103-06
36. Lowe, T. (1997). tRNAscan-SE: a program for improved transfer RNA detection in genomic sequence (release: 1.23). Nucleic Acids Res. 25, 955-964. doi: 10.1093/nar/25.5.0955
37. Mahadevan, P., King, J. F., and Seto, D. (2009a). CGUG: in silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb. BMC Res. Notes 2:168. doi: 10.1186/1756-0500-2-168
38. Mahadevan, P., King, J. F., and Seto, D. (2009b). Data mining pathogen genomes using geneorder and coregenes and CGUG: gene order, synteny and in silico proteomes. Int. J. Comput. Biol. Drug Des. 2, 100-114. doi: 10.1504/IJCBDD.2009.027586
39. Mandell, J. D., and Hershey, A. D. (1960). A fractionating column for analysis of nucleic acids. Anal. Biochem. 1, 66-77. doi: 10.1016/0003-2697(60)90020-8
40. Marchlerbauer, A., Lu, S., Anderson, J. B., Chitsaz, F., Derbyshire, M. K., Deweesescott, C., et al. (2011). CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 39, D225-D229. doi: 10.1093/nar/gkq1189
41. Merabishvili, M., Pirnay, J.-P., Verbeken, G., Chanishvili, N., Tediashvili, M., Lashkhi, N., et al. (2009). Quality-controlled small-scale production of a well-defined bacteriophage cocktail for use in human clinical trials. PLoS ONE 4:e4944. doi: 10.1371/journal.pone.0004944
42. Ohmetakagi, M., and Shinshi, H. (1995). Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7, 173-182. doi: 10.1105/tpc.7.2.173
43. Oliveira, L., Tavares, P., and Alonso, J. C. (2013). Headful DNA packaging: bacteriophage SPP1 as a model system. Virus Res. 173, 247-259. doi: 10.1016/j.virusres.2013.01.021
44. Peleg, A. Y., and Jara, S. D. (2009). Galleria mellonella as a model system to study Acinetobacter baumannii pathogenesis and therapeutics. Antimicrob. Agents Chemother. 53, 2605-2609. doi: 10.1128/AAC.01533-08
45. Peleg, A. Y., Seifert, H., and Paterson, D. L. (2008). Acinetobacter baumannii: emergence of a successful pathogen. Clin. Microbiol. Rev. 21, 538-582. doi: 10.1128/CMR.00058-07
46. Peng, F., Mi, Z., Huang, Y., Yuan, X., Niu, W., Wang, Y., et al. (2014). Characterization, sequencing and comparative genomic analysis of vB_AbaM-IME-AB2, a novel lytic bacteriophage that infects multidrug-resistant Acinetobacter baumannii clinical isolates. BMC Microbiol. 14:181. doi: 10.1186/1471-2180-14-181
47. Perez, F., Hujer, A. M., Hujer, K. M., Decker, B. K., Rather, P. N., and Bonomo, R. A. (2007). Global challenge of multidrug-resistant Acinetobacter baumannii. Antimicrob. Agents Chemother. 51, 3471-3484. doi: 10.1128/AAC.01464-06
48. Perez, F., Ponceterashima, R., Adams, M. D., and Bonomo, R. A. (2011). Are we closing in on an "elusive enemy"? The current status of our battle with Acinetobacter baumannii. Virulence 2, 86-90. doi: 10.4161/viru.2.2.15748
49. Petersen, T. N., Brunak, S., Von, H. G., and Nielsen, H. (2011). SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785-786. doi: 10.1038/nmeth.1701
50. Popova, A. V., Zhilenkov, E. L., Myakinina, V. P., Krasilnikova, V. M., and Volozhantsev, N. V. (2012). Isolation and characterization of wide host range lytic bacteriophage AP22 infecting Acinetobacter baumannii. FEMS Microbiol. Lett. 332, 40-46. doi: 10.1111/j.1574-6968.2012.02573.x
51. Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., et al. (2005). InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116-W120. doi: 10.1093/nar/gki442
52. Rakhuba, D. V., Kolomiets, E. I., Dey, E. S., and Novik, G. I. (2010). Bacteriophage receptors, mechanisms of phage adsorption and penetration into host cell. Pol. J. Microbiol. 59, 145-155. doi: 10.1016/j.micres.2015.01.008.1.94
53. Seemann, T. (2014). Prokka: rapid prokaryotic genome annotation. Bioinform 30, 2068-2069. doi: 10.1093/bioinformatics/btu153
54. Sitbon, E., and Pietrokovski, S. (2003). New types of conserved sequence domains in DNA-binding regions of homing endonucleases. Trends Biochem. Sci. 28, 473-477. doi: 10.1016/S0968-0004(03)00170-1
55. Smith, H. W., and Huggins, M. B. (1983). Effectiveness of phages in treating experimental Escherichia coli diarrhoea in calves, piglets and lambs. J. Gen. Microbiol. 129:2659. doi: 10.1099/00221287-129-8-2659
56. Soothill, J. S. (1992). Treatment of experimental infections of mice with bacteriophages. J. Med. Microbiol. 37, 258-261. doi: 10.1099/00222615-37-4-258
57. Stojkovic, E. A., and Rothman-Denes, L. B. (2007). Coliphage N4 N-acetylmuramidase defines a new family of murein hydrolases. J. Mol. Biol. 366, 406-419. doi: 10.1016/j.jmb.2006.11.028
58. Strynadka, N. C., and James, M. N. (1996). Lysozyme: a model enzyme in protein crystallography. EXS 75, 185-222. doi: 10.1007/978-3-0348-9225-4_11
59. World Health Organization (2017). Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics. Geneva: World Health Organization
60. Young, I., Wang, I., and Roof, W. D. (2000). Phages will out: strategies of host cell lysis. Trends Microbiol. 8, 120-128. doi: 10.1016/S0966-842X(00)01705-4
61. Young, R. F. III., and White, R. L. (2008). Lysis of the host by bacteriophage. Encycl. Virol. 248-258. doi: 10.1016/B978-012374410-4.00752-4
62. Zafar, N., Mazumder, R., and Seto, D. (2002). Coregenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. BMC Bioinform. 3:12. doi: 10.1186/1471-2105-3-12