Abstract
Bacteriophage TAC1 was isolated using a clinical isolate of Acinetobacter baumannii as the host. It showed stability over wide pH and temperature range and has exhibited in vitro antibacterial activity when applied at an MOI of 1. It demonstrated a broad intraspecies host range and infected 66% of the isolates tested. It has produced 454 virions from a single bacterium with a short latent period of 15 minutes. TAC1 has a linear dsDNA genome with a length of 101.77 kb and 37.5% GC content. The genome encodes 161 proteins and 13 putative tRNAs. Whole-genome sequence comparisons using BLASTn and phylogenetic analysis showed that TAC1 is related to unclassified bacteriophages of the family Myoviridae.
Data availability
The genome sequence has been submitted to the NCBI GenBank database (accession no. MK170160).
References
Frère J-M, Rigali S (2016) The alarming increase in antibiotic-resistant bacteria. Drug Target Rev 3:26–30
CLSI (2016) Performance standards for antimicrobial susceptibility testing: 25th informational supplement. In: CLSI document M100-S26 Clinical and Laboratory Standards Institute
Khawaja KA, Rauf M, Abbas Z (2016) A virulent phage JHP against Pseudomonas aeruginosa showed infectivity against multiple genera. J Basic Microbiol 56:1090–1097
Lin N-T, Chiou P-Y, Chang K-C, Chen L-K, Lai M-J (2010) Isolation and characterization of ϕAB2: a novel bacteriophage of Acinetobacter baumannii. Res Microbiol 161(4):308–314
Yang H, Liang L, Lin S, Jia S (2010) Isolation and characterization of a virulent bacteriophage AB1 of Acinetobacter baumannii. BMC Microbiol 10(1):1–10. https://doi.org/10.1186/1471-2180-10-131
Jin J, Li Z-J, Wang S-W, Wang S-M, Huang D-H, Li Y-H, Ma Y-Y, Wang J, Liu F, Chen X-D, Li G-X, Wang X-T, Wang Z-Q, Zhao G-Q (2012) Isolation and characterization of ZZ1, a novel lytic phage that infects Acinetobacter baumannii clinical isolates. BMC Microbiol 12:156. https://doi.org/10.1186/1471-2180-12-156
Abedon ST (2011) Lysis from without. Bacteriophage 1(1):46–49
Chaudhry WN, Haq IU, Andleeb S, Qadri I (2014) Characterization of a virulent bacteriophage LK1 specific for Citrobacter freundii isolated from sewage water. J Basic Microbiol 54(6):531–541
Roach DR, Leung CY, Henry M, Morello E, Singh D, Di Santo JP, Weitz JS, Debarbieux L (2017) Synergy between the host immune system and bacteriophage is essential for successful phage therapy against an acute respiratory pathogen. Cell Host Microbe 22(1):38–47.e34
Bibi Z, Abbas Z, Rehman Su (2016) The phage P. E1 isolated from hospital sewage reduces the growth of Escherichia coli. Biocontrol Sci Technol 26(2):181–188
Merabishvili M, Vandenheuvel D, Kropinski AM, Mast J, De Vos D, Verbeken G, Noben J-P, Lavigne R, Vaneechoutte M, Pirnay J-P (2014) Characterization of newly isolated lytic bacteriophages active against Acinetobacter baumannii. PLoS One 9(8):e104853. https://doi.org/10.1371/journal.pone.0104853
Tabassum R, Shafique M, Khawaja KA, Alvi IA, Rehman Y, Sheik CS, Abbas Z, Rehman Su (2018) Complete genome analysis of a Siphoviridae phage TSK1 showing biofilm removal potential against Klebsiella pneumoniae. Sci Rep 8(1):17904. https://doi.org/10.1038/s41598-018-36229-y
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. Nucl Acids Res 29(12):2607–2618
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9(1):75
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucl Acids Res 31(13):3784–3788
Stothard P (2000) The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28(6):1102–1104
Lowe TM, Chan PP (2016) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucl Acids Res 44(W1):W54–W57
Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucl Acids Res 32(1):11–16. https://doi.org/10.1093/nar/gkh152
Naville M, Ghuillot-Gaudeffroy A, Marchais A, Gautheret D (2011) ARNold: a web tool for the prediction of Rho-independent transcription terminators. RNA Biol 8(1):11–13
Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8(10):785
Krogh A, Larsson B, Von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305(3):567–580
Orfanoudaki G, Markaki M, Chatzi K, Tsamardinos I, Economou A (2017) MatureP: prediction of secreted proteins with exclusive information from their mature regions. Sci Rep 7(1):3263. https://doi.org/10.1038/s41598-017-03557-4
Lavigne R, Sun W, Volckaert G (2004) PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. Bioinformatics 20(5):629–635
Young R (2013) Phage lysis: do we have the hole story yet? Curr Opin Microbiol 16(6):790–797. https://doi.org/10.1016/j.mib.2013.08.008
Zhou W, Feng Y, Zong Z (2018) Two new lytic bacteriophages of the Myoviridae family against carbapenem-resistant Acinetobacter baumannii. Front Microbiol 9:850
Catalão MJ, Gil F, Moniz-Pereira J, São-José C, Pimentel M (2013) Diversity in bacterial lysis systems: bacteriophages show the way. FEMS Microbiol Rev 37(4):554–571. https://doi.org/10.1111/1574-6976.12006
Garneau JR, Depardieu F, Fortier L-C, Bikard D, Monot M (2017) PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data. Sci Rep 7(1):8292
Liu J, Mushegian A (2004) Displacements of prohead protease genes in the late operons of double-stranded-DNA bacteriophages. J Bacteriol 186(13):4369–4375. https://doi.org/10.1128/jb.186.13.4369-4375.2004
Turner D, Ackermann H-W, Kropinski AM, Lavigne R, Sutton JM, Reynolds DM (2017) Comparative analysis of 37 Acinetobacter bacteriophages. Viruses 10(1):5
Acknowledgements
We acknowledge Cody S. Sheik, Swenson College of Science and Engineering, University of Minnesota Duluth, USA, for helping us with genome sequencing. We are also very thankful to the Higher Education Commission (HEC) of Pakistan for providing funds (HEC-NRPU-4501) to conduct this research.
Author information
Authors and Affiliations
Contributions
M.A. conducted the majority of the experiments, and Dr. S.R. supervised all experiments and the manuscript write-up. I.A.A. performed the genome analysis, and R.T. helped in characterizing the TAC1 bacteriophage. All authors have reviewed the final version of the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no competing interests.
Additional information
Handling Editor: Chan-Shing Lin.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Asif, M., Alvi, I.A., Tabassum, R. et al. TAC1, an unclassified bacteriophage of the family Myoviridae infecting Acinetobacter baumannii with a large burst size and a short latent period. Arch Virol 165, 419–424 (2020). https://doi.org/10.1007/s00705-019-04483-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-019-04483-8