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Genome-Wide Identification and Analysis of Chromosomally Integrated Putative Prophages Associated with Clinical Klebsiella pneumoniae Strains

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Abstract

Klebsiella pneumoniae, an opportunistic pathogen found in the environment and human mucosal surfaces, is a leading cause of nosocomial infections. K. pneumoniae is now considered a global threat owing to the emergence of multidrug-resistant strains making its infections untreatable. In this study, 254 strains of K. pneumoniae were screened for the presence of prophages using the PHASTER tool. Very few strains lacked prophages (3.1%), while the remaining harboured both intact (811) and defective prophages (709). A subset of 42 unique strains of K. pneumoniae was chosen for further analysis. Our analysis revealed the presence of 110 complete prophages which were further classified as belonging to Myoviridae (67.3%), Siphoviridae (28.2%) and Podoviridae family (4.5%). An alignment of the 110 complete, prophage genome sequences clustered the prophages into 16 groups and 3 singletons. While none of the prophages encoded for virulence factors, 2 (1.8%) prophages were seen to encode for the antibiotic resistance-related genes. The CRISPR-Cas system was prevalent in 10 (23.8%) out of the 42 strains. Further analysis of the CRISPR spacers revealed 11.42% of the total spacers integrated in K. pneumoniae chromosome to match prophage protein sequences.

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Acknowledgements

The authors gratefully acknowledge the financial support received from the Department of Biotechnology, Government of India, under the Bioinformatics Centre programme (BT/BI/04/049/99).

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  1. Department of Aquatic Animal Health Mangement, Bioinformatics Centre, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002, India

    Pallavi Baliga, Malathi Shekar & Girisha Shivani Kallappa

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  1. Pallavi Baliga
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Contributions

MS, PB and GSK designed this study. PB carried out the analysis work and drafted the manuscript. MS was involved in data curation and supervision, reviewing and editing of the manuscript. GSK was involved in funding acquisition and supervision. All the authors read and approved the final manuscript.

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Correspondence to Malathi Shekar.

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Baliga, P., Shekar, M. & Kallappa, G.S. Genome-Wide Identification and Analysis of Chromosomally Integrated Putative Prophages Associated with Clinical Klebsiella pneumoniae Strains. Curr Microbiol 78, 2015–2024 (2021). https://doi.org/10.1007/s00284-021-02472-2

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