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Published on: August 20, 2021
Genome-Wide Identification and Analysis of Chromosomally Integrated Putative Prophages Associated with Clinical
Pallavi Baliga1, Malathi Shekar2, Girisha Shivani Kallappa1
1Department of Aquatic Animal Health Mangement, Bioinformatics Centre, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002, India.
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.
Insights
Klebsiella pneumoniae frequently harbors prophages, which are viral DNA integrated into bacterial genomes. A small fraction of these prophages carry antibiotic resistance genes, contributing to the threat of multidrug-resistant Klebsiella pneumoniae infections.
Area of Science:
- Microbiology
- Virology
- Genomics
Background:
- Klebsiella pneumoniae is a significant cause of hospital-acquired infections.
- The rise of multidrug-resistant (MDR) K. pneumoniae strains poses a global health challenge.
- Prophages, integrated viral DNA, are common in bacterial genomes and can influence host traits.
Purpose of the Study:
- To investigate the prevalence and characteristics of prophages in Klebsiella pneumoniae strains.
- To identify potential roles of prophages in antibiotic resistance and host defense mechanisms.
Main Methods:
- Screening of 254 K. pneumoniae strains for prophages using the PHASTER tool.
- Bioinformatic analysis of 110 complete prophage genomes.
- Investigation of CRISPR-Cas systems and their interaction with prophage sequences.
Main Results:
- The vast majority of K. pneumoniae strains harbored intact or defective prophages.
- Prophages belonged to Myoviridae, Siphoviridae, and Podoviridae families.
- Two prophages (1.8%) encoded antibiotic resistance genes; none encoded virulence factors.
- The CRISPR-Cas system was present in 23.8% of strains, with spacers matching prophage sequences.
Conclusions:
- Prophages are ubiquitous in K. pneumoniae and can carry antibiotic resistance genes.
- The CRISPR-Cas system in K. pneumoniae targets prophage DNA, suggesting a role in bacterial defense.
- Understanding prophage-host interactions is crucial for combating MDR K. pneumoniae infections.
