Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage

Mukesh K. Meghvansi,D. V. Kamboj,Prince Kumar

doi:10.1038/s41598-021-01419-8

Mukesh K. Meghvansi, D. V. Kamboj + Show 1 more

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https://doi.org/10.1038/s41598-021-01419-8

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Abstract

Shigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controlling Shigella infections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity against Shigella dysenteriae, Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticus and Enterococcus faecium. The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genus Hanrivervirus of subfamily Tempevirinae under the family Drexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members of Drexlerviridae taking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genus Hanrivervirus. The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.

Highlights

Shigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis)
Shigella is the etiological agent of Shigellosis with clinical manifestations ranging from mild watery diarrhoea to severe dysentery and other systemic complications such as electrolyte imbalance and hemolytic uremic syndrome[1]
In 2002, another outbreak of S. dysenteriae type 1 occurred in West Bengal and tea gardens of Siliguri area with the overall attack rate, death rate among those admitted to hospital, and the overall case-fatality reported to be as high as 25.6%, 6.0% and 0.9% respectively[6]

Summary

Introduction

Shigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). Shigella is a Gram-negative, nonmotile, rod-shaped facultative anaerobic and non-spore-forming bacterium belonging to Enterobacteriaceae family This genus includes four species namely, Shigella boydii, Shigella dysenteriae, Shigella flexneri and Shigella sonnei. In 2003, studies from various parts of India reported that the newly emerged strains of S. dysenteriae type 1 exhibited resistance to fluoroquinolones[14,15]. Diverse resistance genes causing the emergence of antibiotic-resistant strains of S. dysenteriae have been reported from various parts of India (e.g. plasmid mediated gene bla-oxa[1] for β-lactam resistance[18], plasmid mediated gene aac (6′)-Ib-cr conferring quinolene resistance[19]). Similar reports of antibiotic resistance in S. dysenteriae have been reported w orldwide[20,21]

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