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

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,...

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Bibliographic Details
Published in:Current microbiology 2021-05, Vol.78 (5), p.2015-2024
Main Authors: Baliga, Pallavi, Shekar, Malathi, Kallappa, Girisha Shivani
Format: Article
Language:English
Subjects:
Antibiotic resistance
Antibiotics
Biomedical and Life Sciences
Biotechnology
Chromosomes
Clustered Regularly Interspaced Short Palindromic Repeats
CRISPR
CRISPR-Cas Systems
Gene sequencing
Genome, Bacterial
Genomes
Humans
Klebsiella
Klebsiella pneumoniae
Klebsiella pneumoniae - genetics
Life Sciences
Microbiology
Mucosa
Multidrug resistance
Nosocomial infection
Nosocomial infections
Opportunist infection
Prophages
Prophages - genetics
Spacers
Virulence
Virulence factors
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Summary: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.
ISSN:0343-8651
1432-0991
DOI:10.1007/s00284-021-02472-2