Complete genome sequence analysis of a lytic Shigella flexneri vB_SflS-ISF001 bacteriophage
Complete genome sequence analysis of a lytic Shigella flexneri vB_SflS-ISF001 bacteriophage
Shigellosis is one of the most important acute enteric infections caused by different species of Shigella, such asShigella flexneri. Despite the use of antibiotic therapy to reduce disease duration, this approach is becoming less effectivedue to the emergence of antibiotic resistance among Shigella spp. Bacteriophages have been introduced as an alternativefor controlling shigellosis. However, the bacteriophages must be without any lysogenic or virulence factors, toxin coding,or antibiotic-resistant genes. In this study, the whole genome sequence of vB_SflS-ISF001, a virulent Siphoviridaebacteriophage specific for Shigella flexneri, was obtained, and a comparative genomic analysis was carried out to identifyits properties and safety. vB_SflS-ISF001 genomic DNA was measured at 50,552 bp with 78 deduced open reading frames(ORFs), with 24 ORFs (30.77%) sharing similarities with proteins from the genomes of homologous phages that had beenreported earlier. Genetic analysis classifies it under the genus T1virus of the subfamily Tunavirinae. Moreover, comparativegenomic analysis revealed no undesirable genes in the genome of vB_SflS-ISF001, such as antibiotic resistance, virulence,lysogeny, or toxin-coding genes. The results of this investigation indicate that vB_SflS-ISF001 is a new species, and confirmits safety for the biocontrol of S. flexneri.Key words: Bacteriophage, Shigella flexneri,
___
- 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.
- Besemer J, Lomsadze A, Borodovsky M (2001). GeneMarkS: a selftraining method for prediction of gene starts in microbial
genomes. Implications for finding sequence motifs in
regulatory regions. Nucleic Acids Res 29: 2607-2618.
- Bhensdadia D, Bhimani H, Rawal C, Kothari V, Raval V, Kothari
C, Patel A, Bhatt V, Parmar N, Sajnani M (2013). Complete
genome sequence of Escherichia phage ADB-2 isolated from
a fecal sample of poultry. Genome Announc 1: e00043-00013.
- Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J (2009).
DNAPlotter: circular and linear interactive genome
visualization. Bioinformatics 25: 119-120.
- Darling AC, Mau B, Blattner FR, Perna NT (2004). Mauve:
multiple alignment of conserved genomic sequence with
rearrangements. Genome Res 14: 1394-1403.
- Fernandes S, São‐José C (2016). More than a hole: the holin lethal
function may be required to fully sensitize bacteria to the lytic
action of canonical endolysins. Mol Microbiol 102: 92-106.
- Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL,
Potter SC, Punta M, Qureshi M, Sangrador-Vegas A (2015).
- The Pfam protein families database: towards a more sustainable
future. Nucleic Acids Res 44: D279-D285.
- Gasteiger E, Hoogland C, Gattiker A, Duvaud Se, Wilkins MR, Appel
RD, Bairoch A (2005). Protein identification and analysis tools
on the ExPASy server. In: Walker JM, editor. The Proteomics
Protocols Handbook. Totowa, NJ, USA: Humana Press. pp.
571-607.
- Gemski P, Koeltzow D, Formal S (1975). Phage conversion of Shigella
flexneri group antigens. Infect Immun 11: 685-691.
- Ghasemi SM, Bouzari M, Baygloo NS, Chang H-I (2014). Insights
into new bacteriophages of Lactococcus garvieae belonging to
the family Podoviridae. Arch Virol 159: 2909-2915.
- Hamdi S, Rousseau GM, Labrie SJ, Tremblay DM, Kourda RS, Slama
KB, Moineau S (2017). Characterization of two polyvalent
phages infecting Enterobacteriaceae. Sci Rep 7: 40349.
- James CE, Stanley KN, Allison HE, Flint HJ, Stewart CS, Sharp
RJ, Saunders JR, McCarthy AJ (2001). Lytic and lysogenic
infection of diverse Escherichia coli and Shigella strains with a
verocytotoxigenic bacteriophage. Appl Environ Microbiol 67:
4335-4337.
- Jennison AV, Verma NK (2004). Shigella flexneri infection:
pathogenesis and vaccine development. FEMS Microbiol Rev
28: 43-58.
- Jun JW, Giri SS, Kim HJ, Yun SK, Chi C, Chai JY, Lee BC, Park SC
(2016). Bacteriophage application to control the contaminated
water with Shigella. Sci Rep 6: 22636.
- Kropinski AM, Mazzocco A, Waddell TE, Lingohr E, Johnson RP
(2009). Enumeration of bacteriophages by double agar overlay
plaque assay. Methods Mol Biol 501: 69-76.
- Kumar S, Stecher G, Tamura K (2016). MEGA7: Molecular
Evolutionary Genetics Analysis version 7.0 for bigger datasets.
Mol Biol Evol 33: 1870-1874.
- Niu C, Yang J, Liu H, Cui Y, Xu H, Wang R, Liu X, Feng E, Wang D,
Pan C (2017). Role of the virulence plasmid in acid resistance
of Shigella flexneri. Sci Rep 7: 46465.
- Olszak T, Latka A, Roszniowski B, Valvano M, Drulis-Kawa Z (2017).
Phage life cycles behind bacterial biodiversity. Curr Med Chem
24: 3987-4001.
- Roberts MD, Martin NL, Kropinski AM (2004). The genome and
proteome of coliphage T1. Virology 318: 245-266.
- Sambrook J, Russell DW (2001) Molecular Cloning: A Laboratory
Manual. 2nd ed. Cold Spring Harbor, NY, USA: Cold Spring
Harbor Laboratory Press.
- Schattner P, Brooks AN, Lowe TM (2005). The tRNAscan-SE,
snoscan and snoGPS web servers for the detection of tRNAs
and snoRNAs. Nucleic Acids Res 33: W686-W689.
- Shahin K, Bouzari M (2018). Bacteriophage application for
biocontrolling Shigella flexneri in contaminated foods. J Food
Sci Technol 55: 550-559.
- Shahin K, Bouzari M, Wang R (2018). Isolation, characterization
and genomic analysis of a novel lytic bacteriophage vB_SsoSISF002 infecting Shigella sonnei and Shigella flexneri. J Med
Microbiol 67: 376-386.
- Shen M, Zhu H, Lu S, Le S, Li G, Tan Y, Zhao X, Shen W, Hu F,
Wang J (2016). Complete genome sequences of T1-like phages
JMPW1 and JMPW2. Genome Announc 4: e00601-00616.
- Turner D, Reynolds D, Seto D, Mahadevan P (2013). CoreGenes3.5: a
webserver for the determination of core genes from sets of viral
and small bacterial genomes. BMC Res Notes 6: 140.
- Wagner PL, Waldor MK (2002). Bacteriophage control of bacterial
virulence. Infect Immun 70: 3985-3993.
- Walker JC, Verma NK (2002). Identification of a putative
pathogenicity island in Shigella flexneri using subtractive
hybridisation of the S. flexneri and Escherichia coli genomes.
FEMS Microbiol Lett 213: 257-264.
- Wommack KE, Colwell RR (2000). Virioplankton: viruses in aquatic
ecosystems. Microbiol Mol Biol Rev 64: 69-114.
- Ye C, Lan R, Xia S, Zhang J, Sun Q, Zhang S, Jing H, Wang L, Li
Z, Zhou Z (2010). Emergence of a new multidrug-resistant
serotype X variant in an epidemic clone of Shigella flexneri. J
Clin Microbiol 48: 419-426.
- Zhang H, Wang R, Bao H (2013). Phage inactivation of foodborne
Shigella on ready-to-eat spiced chicken. Poult Sci 92: 211-217.