Abstract
The increasing prevalence of antibiotic-resistant Shigella sp. emphasizes that alternatives to conventional antibiotics are needed. Siphoviridae bacteriophage (phage), pSf-2, infecting S. flexneri ATCC® 12022 was isolated from Geolpocheon stream in Korea. Morphological analysis by transmission electron microscopy revealed that pSf-2 has a head of about 57 ± 4 nm in diameter with a long tail of 136 ± 3 nm in length and 15 ± 2 nm in width. One-step growth analysis revealed that pSf-2 has latent period of 30 min and burst size of 16 PFU/infected cell. The DNA genome of pSf-2 is composed of 50,109 bp with a G+C content of 45.44 %. The genome encodes 83 putative ORFs, 19 putative promoters, and 23 transcriptional terminator regions. Genome sequence analysis of pSf-2 and comparative analysis with the homologous T1-like Shigella phages, Shfl1 and pSf-1, revealed that pSf-2 is a novel T1-like Shigella phage. These results showed that pSf-2 might have a high potential as a biocontrol agent to control shigellosis. Also, the genomic information may lead to further understanding of phage biodiversity, especially T1-like phages.
Similar content being viewed by others
References
Allison GE, Verma NK (2000) Serotype-converting bacteriophages and O-antigen modification in Shigella flexneri. Trends Microbiol 8:17–23
Ball LA (2005) The universal taxonomy of viruses in theory and practice. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy: eight report of the international committee on taxonomy of viruses. Elsevier Academic Press, Amsterdam, pp 3–8
Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618
Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J (2005) ACT: the artemis comparison tool. Bioinformatics 21:3422–3423
Casjens SR, Gilcrease EB, Winn-Stapley DA et al (2005) The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J Bacteriol 187:1091–1104
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641
Ellis EL, Delbrück M (1939) The growth of bacteriophage. J Gen Physiol 22:365–384
Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399:541–548
Grose JH, Casjens SR (2014) Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Virology 468–470:421–443
Hagens S, Loessner MJ (2010) Bacteriophage for biocontrol of foodborne pathogens: calculations and considerations. Curr Pharm Biotechnol 11:58–68
Housby JN, Mann NH (2009) Phage therapy. Drug Discov Today 14:536–540
Jun JW, Kim HJ, Yun SK, Chai JY, Park SC (2014) Eating oysters without risk of vibriosis: application of a bacteriophage against Vibrio parahaemolyticus in oysters. Int J Food Microbiol 188:31–35
Jun JW, Kim JH, Shin SP, Han JE, Chai JY, Park SC (2013) Characterization and complete genome sequence of the Shigella bacteriophage pSf-1. Res Microbiol 164:979–986
Jun JW, Shin TH, Kim JH, Shin SP, Han JE, Heo GJ, De Zoysa M, Shin GW, Chai JY, Park SC (2014) Bacteriophage therapy of a Vibrio parahaemolyticus infection caused by a multiple antibiotic resistant O3: K6 pandemic clinical strain. J Infect Dis 210:72–78
Jun JW, Yun SK, Kim HJ, Chai JY, Park SC (2014) Characterization and complete genome sequence of a novel N4-like bacteriophage, pSb-1 infecting Shigella boydii. Res Microbiol 165:671–678
Kim JO, Rho S, Kim SH, Kim H, Song HJ, Kim EJ, Kim RY, Kim EH, Sinha A, Dey A, Yang JS, Song MK, Nandy RK, Czerkinsky C, Kim DW (2015) Shigella outer membrane protein PSSP-1 broadly protective against Shigella infection. Clin Vaccine Immunol 22:381–388
Kim KH, Chang HW, Nam YD, Roh SW, Bae JW (2010) Phenotypic characterization and genomic analysis of the Shigella sonnei bacteriophage SP18. J Microbiol 48:213–222
Kingwell K (2015) Bacteriophage therapies re-enter clinical trials. Nat Rev Drug Discov 14:515–516
Kotloff KL, Winickoff JP, Ivanoff B, Clemens JD, Swerdlow DL, Sansonetti PJ, Adak GK, Levine MM (1999) Global burden of Shigella infections: implications for vaccine development and implementation of control strategies. Bull World Health Organ 77:651–666
Niu YD, McAllister TA, Nash JHE, Kropinski AM, Stanford K (2014) Four Escherichia coli O157: H7 phages: a new bacteriophage genus and taxonomic classification of T1-like phages. PLoS One 9:e100426
Niyogi SK (2005) Shigellosis. J Microbiol 43:133–143
Pichel M, Brengi SP, Cooper KLF et al (2012) Standardization and international multicenter validation of a PulseNet pulsed-field gel electrophoresis protocol for subtyping Shigella flexneri isolates. Foodborne Pathog Dis 9:418–424
Ranallo RT, Fonseka S, Boren TL, Bedford LA, Kaminski RW, Thakkar S, Venkatesan MM (2012) Two live attenuated Shigella Flexneri 2a strains WRSf2G12 and WRSf2G15: a new combination of gene deletions for 2nd generation live attenuated vaccine candidates. Vaccine 30:5159–5171
Schofield DA, Wray DJ, Molineux IJ (2015) Isolation and development of bioluminescent reporter phages for bacterial dysentery. Eur J Clin Microbiol Infect Dis 34:395–403
Skurnik M, Strauch E (2006) Phage therapy: facts and fiction. Int J Med Microbiol 296:5–14
Sulakvelidze A, Kutter E (2005) Bacteriophage therapy in humans. In: Kutter E, Sulakvelidze A (eds) Bacteriophages: biology and applications. CRC Press, Boca Raton, FL, pp 381–436
von Seidlein L, Kim DR, Ali M et al (2006) A multicentre study of Shigella diarrhoea in six Asian countries: disease burden, clinical manifestations, and microbiology. PLoS Med 3:e353
Wang IN (2006) Lysis timing and bacteriophage fitness. Genetics 172:17–26
[WHO] World Health Organization (2005) Guidelines for the control of shigellosis, including epidemics due to Shigella dysenteriae type 1. WHO Document Production Services, Geneva
Wilkins MR, Gasteiger E, Bairoch A et al (1999) Protein identification and analysis tools in the ExPASy server. In: Link AJ (ed) 2-D proteome analysis protocols. Humana Press, Totowa, NJ, pp 531–552
Zafar A, Sabir N, Bhutta ZA (2005) Frequency of isolation of Shigella serogroups/serotypes and their antimicrobial susceptibility pattern in children from slum areas in Karachi. J Pak Med Assoc 55:184–188
Zafar N, Mazumder R, Seto D (2002) CoreGenes: a computational tool for identifying and cataloging core genes in a set of small genomes. BMC Bioinform 3:12
Acknowledgments
We would like to thank Dr. Marina Tediashvi (Head of the Laboratory of Microbial Ecology) and Dr. George Tsertsvadze (Head of Electron Microscopy Unit) at G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, Georgia for their valuable advice during the manuscript preparation. This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2013R1A1A2006794 and 2014R1A2A1A11050093).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
None.
Ethics statement
This study was approved by the institutional review board of Seoul National University, Seoul, Republic of Korea.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Jun, J.W., Kim, H.J., Yun, S.K. et al. Isolation and Comparative Genomic Analysis of T1-Like Shigella Bacteriophage pSf-2. Curr Microbiol 72, 235–241 (2016). https://doi.org/10.1007/s00284-015-0935-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00284-015-0935-2