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Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates

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...

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Autores principales: Marques, Andreia T., Tanoeiro, Luís, Duarte, Aida, Gonçalves, Luisa, Vítor, Jorge M. B., Vale, Filipa F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8617712/
https://www.ncbi.nlm.nih.gov/pubmed/34835377
http://dx.doi.org/10.3390/microorganisms9112252
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author Marques, Andreia T.
Tanoeiro, Luís
Duarte, Aida
Gonçalves, Luisa
Vítor, Jorge M. B.
Vale, Filipa F.
author_facet Marques, Andreia T.
Tanoeiro, Luís
Duarte, Aida
Gonçalves, Luisa
Vítor, Jorge M. B.
Vale, Filipa F.
author_sort Marques, Andreia T.
collection PubMed
description 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.
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spelling pubmed-86177122021-11-27 Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates Marques, Andreia T. Tanoeiro, Luís Duarte, Aida Gonçalves, Luisa Vítor, Jorge M. B. Vale, Filipa F. Microorganisms Article 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. MDPI 2021-10-28 /pmc/articles/PMC8617712/ /pubmed/34835377 http://dx.doi.org/10.3390/microorganisms9112252 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Marques, Andreia T.
Tanoeiro, Luís
Duarte, Aida
Gonçalves, Luisa
Vítor, Jorge M. B.
Vale, Filipa F.
Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
title Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
title_full Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
title_fullStr Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
title_full_unstemmed Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
title_short Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
title_sort genomic analysis of prophages from klebsiella pneumoniae clinical isolates
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8617712/
https://www.ncbi.nlm.nih.gov/pubmed/34835377
http://dx.doi.org/10.3390/microorganisms9112252
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