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Genomic characterization of Salmonella bacteriophages isolated from India

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Abstract

Salmonella are a medically important Gram-negative foodborne pathogen. Genomic diversity of Salmonella is increasingly studied but at the same time, we have limited knowledge of Salmonella phage diversity. In this study, we have isolated Salmonella phages from sewage and river water. Genomic characterization of 12 Salmonella phages was carried out using next-generation sequencing platform. Newly sequenced phages were classified based on amino acid sequence phylogenetic analysis. In newly sequenced phages, several virulence genes, DNA metabolism genes, tRNA genes, antibiotic resistance genes and genes not having known role in the life cycle of phages were identified. Annotations of newly sequenced phage genome showed the presence of polymyxin-b resistance gene and penicillin binding protein. Annotation identified number of genes which are involved in DNA metabolism. Results suggest that most of the phages having G + C content different than their host possess DNA metabolism genes. The presence of tRNAs in the genome of Salmonella_phage38-India was identified; however, we did not observe any correlation between tRNA genes and overall codon usage in the phage genome. It is suggested that the phage-encoded tRNAs may increase fitness of phages. In summary, we isolated novel Salmonella phages, determined full genome sequences and provided phylogenetic analysis-based classification.

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Acknowledgments

Authors are thankful to Dr. K. M. Paknikar, Director, MACS-ARI, Pune for all support. Authors are grateful to Dr. H. W. Ackermann and Dr. H. Gelderblom for electron microscopy analysis. Authors are thankful to Ms. Rupali Bambe for technical support, also authors are thankful to Ms. Priyanka Patel for carrying out phylogenetic analysis.

Authors contribution

Conceived and designed the experiments: YK, KB, VA; Performed the experiments: GK, KP, YK; Performed the phylogenetic analysis: VA; Analyzed the data: YK, GK, KP; Wrote the manuscript: YK, GK, KP, VA, KB.

Funding

This work is funded by the intramural Grant of Agharkar Research Institute, Pune (VIR001).

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Authors and Affiliations

  1. Nanobioscience Group, Agharkar Research Institute, G. G. Agarkar Road, Pune, 411004, India

    Yogesh A. Karpe, Gayatri D. Kanade, Kunal D. Pingale, Vidya A. Arankalle & Kalyan Banerjee

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  1. Yogesh A. Karpe
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  2. Gayatri D. Kanade
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  3. Kunal D. Pingale
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  4. Vidya A. Arankalle
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Correspondence to Yogesh A. Karpe.

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The authors have declared that he/she has no conflict of interest. This article does not contain any studies with human participants or animals performed by any of the authors.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Edited by Detlev H. Kruger.

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Karpe, Y.A., Kanade, G.D., Pingale, K.D. et al. Genomic characterization of Salmonella bacteriophages isolated from India. Virus Genes 52, 117–126 (2016). https://doi.org/10.1007/s11262-015-1269-7

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  • DOI: https://doi.org/10.1007/s11262-015-1269-7

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