Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates.

Andreia T Marques,Luís Tanoeiro,Aida Duarte,Luisa Gonçalves,Jorge M B Vítor,Filipa F Vale

doi:10.3390/microorganisms9112252

Andreia T Marques, Luís Tanoeiro + Show 4 more

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https://doi.org/10.3390/microorganisms9112252

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Abstract

Klebsiella pneumoniae is an increasing threat to public health and represents one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic elements which can easily spread between bacteria populations and co-evolve with its genomic host. In this study, we present the full genomic sequences, insertion sites and phylogenetic analysis of 150 prophages found in 40 K. pneumoniae clinical isolates obtained from an outbreak in a Portuguese hospital. All strains harbored at least one prophage and we identified 104 intact prophages (69.3%). The prophage size ranges from 29.7 to 50.6 kbp, coding between 32 and 78 putative genes. The prophage GC content is 51.2%, lower than the average GC content of 57.1% in K. pneumoniae. Complete prophages were classified into three families in the order Caudolovirales: Myoviridae (59.6%), Siphoviridae (38.5%) and Podoviridae (1.9%). In addition, an alignment and phylogenetic analysis revealed nine distinct clusters. Evidence of recombination was detected within the genome of some prophages but, in most cases, proteins involved in viral structure, transcription, replication and regulation (lysogenic/lysis) were maintained. These results support the knowledge that prophages are diverse and widely disseminated in K. pneumoniae genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified K. pneumoniae prophages in a set of endolysin genes, which were found to code for proteins with lysozyme activity, cleaving the β-1,4 linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in the peptidoglycan network and thus representing genes with the potential for lysin phage therapy.

Highlights

IntroductionKlebsiella pneumoniae is an opportunistic and commensal gram-negative human pathogen prevalent in the hospital environment
The genome sequences of 40 K. pneumoniae clinical isolates from 23 patients were analysed with a web server tool for identification and annotation of prophage sequences within bacterial genomes, PHASTER, with default arguments [36]
Prophages of Klebsiella pneumoniae. (B) Bars graph showing the distribution of total prophages in K. pneumoniae strains

Summary

Introduction

Klebsiella pneumoniae is an opportunistic and commensal gram-negative human pathogen prevalent in the hospital environment. This bacterium is mainly found in gastrointestinal and respiratory tracts and on the skin of healthy individuals, but in recent years it has become one of the world’s leading causes of community and hospital-acquired infections, such as urinary tract infections (UTIs), pneumonia, septicaemia, and wound/soft tissue infections, with an increasing mortality rate, in immunocompromised individuals, neonates, and the elderly [1,2,3,4,5]. K. pneumoniae strains are recurrently resistant to antibiotics available in therapy to treat serious human diseases, such as fluoroquinolones, aminoglycosides, and beta-lactams. Given the reduction in the effectiveness of antimicrobial therapeutics to treat K. pneumoniae-associated infections, alternative strategies must be developed in response

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