Genomic Analysis of Prophages from <i>Klebsiella pneumoniae</i> Clinical Isolates

<i>Klebsiella pneumoniae</i> 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 popula...

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Autores principales:	Andreia T. Marques, Luís Tanoeiro, Aida Duarte, Luisa Gonçalves, Jorge M. B. Vítor, Filipa F. Vale
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>K. pneumoniae</i> genomes prophages bacteriophage bioinformatics genomic analysis comparative genomics Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/6724e1816c874d1d8886eede536585b2
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spelling	oai:doaj.org-article:6724e1816c874d1d8886eede536585b22021-11-25T18:24:36ZGenomic Analysis of Prophages from <i>Klebsiella pneumoniae</i> Clinical Isolates10.3390/microorganisms91122522076-2607https://doaj.org/article/6724e1816c874d1d8886eede536585b22021-10-01T00:00:00Zhttps://www.mdpi.com/2076-2607/9/11/2252https://doaj.org/toc/2076-2607<i>Klebsiella pneumoniae</i> 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 <i>K. pneumoniae</i> 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 <i>K. pneumoniae</i>. Complete prophages were classified into three families in the order <i>Caudolovirales</i>: <i>Myoviridae</i> (59.6%), <i>Siphoviridae</i> (38.5%) and <i>Podoviridae</i> (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 <i>K. pneumoniae</i> genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified <i>K. pneumoniae</i> 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.Andreia T. MarquesLuís TanoeiroAida DuarteLuisa GonçalvesJorge M. B. VítorFilipa F. ValeMDPI AGarticle<i>K. pneumoniae</i> genomesprophagesbacteriophagebioinformaticsgenomic analysiscomparative genomicsBiology (General)QH301-705.5ENMicroorganisms, Vol 9, Iss 2252, p 2252 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>K. pneumoniae</i> genomes prophages bacteriophage bioinformatics genomic analysis comparative genomics Biology (General) QH301-705.5
spellingShingle	<i>K. pneumoniae</i> genomes prophages bacteriophage bioinformatics genomic analysis comparative genomics Biology (General) QH301-705.5 Andreia T. Marques Luís Tanoeiro Aida Duarte Luisa Gonçalves Jorge M. B. Vítor Filipa F. Vale Genomic Analysis of Prophages from <i>Klebsiella pneumoniae</i> Clinical Isolates
description	<i>Klebsiella pneumoniae</i> 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 <i>K. pneumoniae</i> 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 <i>K. pneumoniae</i>. Complete prophages were classified into three families in the order <i>Caudolovirales</i>: <i>Myoviridae</i> (59.6%), <i>Siphoviridae</i> (38.5%) and <i>Podoviridae</i> (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 <i>K. pneumoniae</i> genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified <i>K. pneumoniae</i> 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.
format	article
author	Andreia T. Marques Luís Tanoeiro Aida Duarte Luisa Gonçalves Jorge M. B. Vítor Filipa F. Vale
author_facet	Andreia T. Marques Luís Tanoeiro Aida Duarte Luisa Gonçalves Jorge M. B. Vítor Filipa F. Vale
author_sort	Andreia T. Marques
title	Genomic Analysis of Prophages from <i>Klebsiella pneumoniae</i> Clinical Isolates
title_short	Genomic Analysis of Prophages from <i>Klebsiella pneumoniae</i> Clinical Isolates
title_full	Genomic Analysis of Prophages from <i>Klebsiella pneumoniae</i> Clinical Isolates
title_fullStr	Genomic Analysis of Prophages from <i>Klebsiella pneumoniae</i> Clinical Isolates
title_full_unstemmed	Genomic Analysis of Prophages from <i>Klebsiella pneumoniae</i> Clinical Isolates
title_sort	genomic analysis of prophages from <i>klebsiella pneumoniae</i> clinical isolates
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/6724e1816c874d1d8886eede536585b2
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Genomic Analysis of Prophages from <i>Klebsiella pneumoniae</i> Clinical Isolates

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