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Gene sequencing analysis of tailed phages identified diverse (Kayfunavirus and Berlinvirus) coliphages in aquatic niche against AMR Escherichia coli

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Abstract

Escherichia coli has been recognized as a pathogen of concern in the antimicrobial resistance (AMR) perspective. Globally initiatives were taken to control AMR. Bacteriophages are recognized as promising alternative to antibiotics. Harnessing broad-spectrum bacteriophages for augmenting phage repositories is being prioritized across continents for future health care needs. In this context, a study was conducted to isolate coliphages against a collection of AMR E. coli isolated from diverse aquatic niche. Thirty pooled water samples (5 each from rivers, aquaculture ponds, lake, sewage treatment plant, domestic waste and canals) were analysed, and fifty-four lytic coliphages were isolated against the wide range of E. coli host strains. Broad host-spectrum phages were isolated predominantly from sewage water samples. Enriched phages were quantified, and the concentrations ranged from 106 to 107 PFU/mL. Ten phages, viz. ФEC-S-18, ФEC-S-21, ФEC-S-22, ФEC-S-23, ФEC-S-24, ФEC-S-25, ФEC-S-28, ФEC-S-30, ФEC-S-39 and ФEC-S-49, exhibited lytic activity against more than ten AMR strains of E. coli. PCR analysis of the 54 phages using the major capsid protein (MCP) specific primers coupled with gene sequence analysis identified two phages related to Berlinvirus and 35 phages to Kayfunavirus of Autographiviridae. However, the remaining 17 phages did not show amplification using the MCP primers. The study has demonstrated that aquatic environment harboured phages with broad host spectrum that can potentially be used as agents for biological control of E. coli for infection control and food safety.

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Acknowledgements

The authors are highly indebted to Dr. C. N. Ravishankar, Director, ICAR-CIFT, Cochin, India, for providing necessary support to complete the research work. The authors are also thankful to the Department of Biotechnology (DBT), Govt. of India, for providing financial support for the project. The project is funded by Department of Biotechnology, Government of India (Grant no: BT/PR26949/AAQ/3/888/2017).

Funding

This work was funded by Department of Biotechnology, Ministry of Science and Technology (Grant no: BT/PR26949/AAQ/3/888/2017).

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Authors and Affiliations

  1. Microbiology Fermentation and Biotechnology Division of ICAR-Central Institute of Fisheries Technology (ICAR-CIFT), Matsyapuri Post, Willingdon Island, Cochin, Kerala, 682029, India

    Iris George, Karthika Raveendran, Murugadas Vaiyapuri, Anna Sherin, Devi Sanjeev, Suraji Kumar, Visnuvinayagam Sivam & Mukteswar Prasad Mothadaka

  2. Visakhapatnam Research Centre of ICAR-Central Institute of Fisheries Technology, Visakhapatnam, Andhra Pradesh, 530003, India

    Manikantha Benala & Madhusudana Rao Badireddy

  3. Agharkar Research Institute (DST), Gopal Ganesh, Agarkar Rd, Shivajinagar, , Pune, Maharashtra, 411004, India

    Iris George

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  1. Iris George
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Contributions

IG and KR involved in isolation of phages, characterization of phages, analysis of data, gene sequencing analysis, phylogenetic tree construction and drafting of manuscript; MV, MPM and MRB conceptualized the work and analysis of data and reviewed the manuscript; MB involved in standardization of phage isolation and enumeration process; AS and DS carried out PCR identification of the phages; and IG, KR, SK and VS collected the samples from various aquatic niche and determined the host range for all the AMR E. coli.

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Correspondence to Murugadas Vaiyapuri.

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George, I., Raveendran, K., Vaiyapuri, M. et al. Gene sequencing analysis of tailed phages identified diverse (Kayfunavirus and Berlinvirus) coliphages in aquatic niche against AMR Escherichia coli. Arch Microbiol 204, 429 (2022). https://doi.org/10.1007/s00203-022-03055-w

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