Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals

Abstract Klebsiella pneumoniae is an important nosocomial infectious agent with a high antimicrobial resistance (AMR) burden. The application of long read sequencing technologies is providing insights into bacterial chromosomal and putative extra-chromosomal genetic elements (PEGEs) associated with...

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Autores principales:	Anton Spadar, João Perdigão, Jody Phelan, James Charleston, Ana Modesto, Rita Elias, Paola Florez de Sessions, Martin L. Hibberd, Susana Campino, Aida Duarte, Taane G. Clark
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d2702d05b8e7434cb941442c05a2aea7
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spelling	oai:doaj.org-article:d2702d05b8e7434cb941442c05a2aea72021-12-02T17:04:07ZMethylation analysis of Klebsiella pneumoniae from Portuguese hospitals10.1038/s41598-021-85724-22045-2322https://doaj.org/article/d2702d05b8e7434cb941442c05a2aea72021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85724-2https://doaj.org/toc/2045-2322Abstract Klebsiella pneumoniae is an important nosocomial infectious agent with a high antimicrobial resistance (AMR) burden. The application of long read sequencing technologies is providing insights into bacterial chromosomal and putative extra-chromosomal genetic elements (PEGEs) associated with AMR, but also epigenetic DNA methylation, which is thought to play a role in cleavage of foreign DNA and expression regulation. Here, we apply the PacBio sequencing platform to eight Portuguese hospital isolates, including one carbapenemase producing isolate, to identify methylation motifs. The resulting assembled chromosomes were between 5.2 and 5.5Mbp in length, and twenty-six PEGEs were found. Four of our eight samples carry bla CTX-M-15, a dominant Extended Spectrum Beta Lactamase in Europe. We identified methylation motifs that control Restriction–Modification systems, including GATC of the DNA adenine methylase (Dam), which methylates N6-methyladenine (m6A) across all our K. pneumoniae assemblies. There was a consistent lack of methylation by Dam of the GATC motif downstream of two genes: fosA, a locus associated with low level fosfomycin resistance, and tnpB transposase on IncFIB(K) plasmids. Overall, we have constructed eight high quality reference genomes of K. pneumoniae, with insights into horizontal gene transfer and methylation m6A motifs.Anton SpadarJoão PerdigãoJody PhelanJames CharlestonAna ModestoRita EliasPaola Florez de SessionsMartin L. HibberdSusana CampinoAida DuarteTaane G. ClarkNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Anton Spadar João Perdigão Jody Phelan James Charleston Ana Modesto Rita Elias Paola Florez de Sessions Martin L. Hibberd Susana Campino Aida Duarte Taane G. Clark Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals
description	Abstract Klebsiella pneumoniae is an important nosocomial infectious agent with a high antimicrobial resistance (AMR) burden. The application of long read sequencing technologies is providing insights into bacterial chromosomal and putative extra-chromosomal genetic elements (PEGEs) associated with AMR, but also epigenetic DNA methylation, which is thought to play a role in cleavage of foreign DNA and expression regulation. Here, we apply the PacBio sequencing platform to eight Portuguese hospital isolates, including one carbapenemase producing isolate, to identify methylation motifs. The resulting assembled chromosomes were between 5.2 and 5.5Mbp in length, and twenty-six PEGEs were found. Four of our eight samples carry bla CTX-M-15, a dominant Extended Spectrum Beta Lactamase in Europe. We identified methylation motifs that control Restriction–Modification systems, including GATC of the DNA adenine methylase (Dam), which methylates N6-methyladenine (m6A) across all our K. pneumoniae assemblies. There was a consistent lack of methylation by Dam of the GATC motif downstream of two genes: fosA, a locus associated with low level fosfomycin resistance, and tnpB transposase on IncFIB(K) plasmids. Overall, we have constructed eight high quality reference genomes of K. pneumoniae, with insights into horizontal gene transfer and methylation m6A motifs.
format	article
author	Anton Spadar João Perdigão Jody Phelan James Charleston Ana Modesto Rita Elias Paola Florez de Sessions Martin L. Hibberd Susana Campino Aida Duarte Taane G. Clark
author_facet	Anton Spadar João Perdigão Jody Phelan James Charleston Ana Modesto Rita Elias Paola Florez de Sessions Martin L. Hibberd Susana Campino Aida Duarte Taane G. Clark
author_sort	Anton Spadar
title	Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals
title_short	Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals
title_full	Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals
title_fullStr	Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals
title_full_unstemmed	Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals
title_sort	methylation analysis of klebsiella pneumoniae from portuguese hospitals
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/d2702d05b8e7434cb941442c05a2aea7
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Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals

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