Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates

Detalhes bibliográficos
Autor(a) principal: Marques, Andreia T.
Data de Publicação: 2021
Outros Autores: Tanoeiro, Luis, Duarte, Aida, Gonçalves, Luisa, Vítor, Jorge M. B., Vale, Filipa F.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10451/58867
Resumo: 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.
id RCAP_1ca2bec1793db508e553b361168c81ac
oai_identifier_str oai:repositorio.ul.pt:10451/58867
network_acronym_str RCAP
network_name_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository_id_str 7160
spelling Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical IsolatesK. pneumoniae genomesProphagesBacteriophageBioinformaticsGenomic analysisComparative genomicsPhylogenySequence annotation and comparisonPhage endolysinsKlebsiella 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.F.F.V. is funded by Fundação para a Ciência e a Tecnologia (FCT) through an Assistant Researcher grant CEECIND/03023/2017, and a project grant (PTDC/BTM-SAL/28978/2017) that supported this work. The work is partially supported by National funds from FCT, projects UIDB/04138/2020 and UIDP/04138/2020.MDPIRepositório da Universidade de LisboaMarques, Andreia T.Tanoeiro, LuisDuarte, AidaGonçalves, LuisaVítor, Jorge M. B.Vale, Filipa F.2023-08-14T12:14:20Z2021-10-282022-10-19T21:32:02Z2021-10-28T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/58867engMarques AT, Tanoeiro L, Duarte A, Gonçalves L, Vítor JMB, Vale FF. Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates. Microorganisms [Internet]. 2021 Oct 28;9(11):2252. Available from: http://dx.doi.org/10.3390/microorganisms9112252cv-prod-260633810.3390/microorganisms9112252info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T17:01:29Zoai:repositorio.ul.pt:10451/58867Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:05:36.440775Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
title Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
spellingShingle Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
Marques, Andreia T.
K. pneumoniae genomes
Prophages
Bacteriophage
Bioinformatics
Genomic analysis
Comparative genomics
Phylogeny
Sequence annotation and comparison
Phage endolysins
title_short 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_sort Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
author Marques, Andreia T.
author_facet Marques, Andreia T.
Tanoeiro, Luis
Duarte, Aida
Gonçalves, Luisa
Vítor, Jorge M. B.
Vale, Filipa F.
author_role author
author2 Tanoeiro, Luis
Duarte, Aida
Gonçalves, Luisa
Vítor, Jorge M. B.
Vale, Filipa F.
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Marques, Andreia T.
Tanoeiro, Luis
Duarte, Aida
Gonçalves, Luisa
Vítor, Jorge M. B.
Vale, Filipa F.
dc.subject.por.fl_str_mv K. pneumoniae genomes
Prophages
Bacteriophage
Bioinformatics
Genomic analysis
Comparative genomics
Phylogeny
Sequence annotation and comparison
Phage endolysins
topic K. pneumoniae genomes
Prophages
Bacteriophage
Bioinformatics
Genomic analysis
Comparative genomics
Phylogeny
Sequence annotation and comparison
Phage endolysins
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.
publishDate 2021
dc.date.none.fl_str_mv 2021-10-28
2021-10-28T00:00:00Z
2022-10-19T21:32:02Z
2023-08-14T12:14:20Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/58867
url http://hdl.handle.net/10451/58867
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Marques AT, Tanoeiro L, Duarte A, Gonçalves L, Vítor JMB, Vale FF. Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates. Microorganisms [Internet]. 2021 Oct 28;9(11):2252. Available from: http://dx.doi.org/10.3390/microorganisms9112252
cv-prod-2606338
10.3390/microorganisms9112252
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
_version_ 1799134608153903104