Plasmidome-analysis of ESBL-producing escherichia coli using conventional typing and high-throughput sequencing.

Infections caused by Extended spectrum β-lactamase (ESBL)-producing E. coli are an emerging global problem, threatening the effectiveness of the extensively used β-lactam antibiotics. ESBL dissemination is facilitated by plasmids, transposons, and other mobile elements. We have characterized the pla...

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Autores principales:	Alma Brolund, Oscar Franzén, Ojar Melefors, Karin Tegmark-Wisell, Linus Sandegren
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7dfa7800b19d4e488ccc20c32b7882d2
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spelling	oai:doaj.org-article:7dfa7800b19d4e488ccc20c32b7882d22021-11-18T07:41:54ZPlasmidome-analysis of ESBL-producing escherichia coli using conventional typing and high-throughput sequencing.1932-620310.1371/journal.pone.0065793https://doaj.org/article/7dfa7800b19d4e488ccc20c32b7882d22013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23785449/?tool=EBIhttps://doaj.org/toc/1932-6203Infections caused by Extended spectrum β-lactamase (ESBL)-producing E. coli are an emerging global problem, threatening the effectiveness of the extensively used β-lactam antibiotics. ESBL dissemination is facilitated by plasmids, transposons, and other mobile elements. We have characterized the plasmid content of ESBL-producing E. coli from human urinary tract infections. Ten diverse isolates were selected; they had unrelated pulsed-field gel electrophoresis (PFGE) types (<90% similarity), were from geographically dispersed locations and had diverging antibiotic resistance profiles. Three isolates belonged to the globally disseminated sequence type ST131. ESBL-genes of the CTX-M-1 and CTX-M-9 phylogroups were identified in all ten isolates. The plasmid content (plasmidome) of each strain was analyzed using a combination of molecular methods and high-throughput sequencing. Hidden Markov Model-based analysis of unassembled sequencing reads was used to analyze the genetic diversity of the plasmid samples and to detect resistance genes. Each isolate contained between two and eight distinct plasmids, and at least 22 large plasmids were identified overall. The plasmids were variants of pUTI89, pKF3-70, pEK499, pKF3-140, pKF3-70, p1ESCUM, pEK204, pHK17a, p083CORR, R64, pLF82, pSFO157, and R721. In addition, small cryptic high copy-number plasmids were frequent, containing one to seven open reading frames per plasmid. Three clustered groups of such small cryptic plasmids could be distinguished based on sequence similarity. Extrachromosomal prophages were found in three isolates. Two of them resembled the E. coli P1 phage and one was previously unknown. The present study confirms plasmid multiplicity in multi-resistant E. coli. We conclude that high-throughput sequencing successfully provides information on the extrachromosomal gene content and can be used to generate a genetic fingerprint of possible use in epidemiology. This could be a valuable tool for tracing plasmids in outbreaks.Alma BrolundOscar FranzénOjar MeleforsKarin Tegmark-WisellLinus SandegrenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 6, p e65793 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Alma Brolund Oscar Franzén Ojar Melefors Karin Tegmark-Wisell Linus Sandegren Plasmidome-analysis of ESBL-producing escherichia coli using conventional typing and high-throughput sequencing.
description	Infections caused by Extended spectrum β-lactamase (ESBL)-producing E. coli are an emerging global problem, threatening the effectiveness of the extensively used β-lactam antibiotics. ESBL dissemination is facilitated by plasmids, transposons, and other mobile elements. We have characterized the plasmid content of ESBL-producing E. coli from human urinary tract infections. Ten diverse isolates were selected; they had unrelated pulsed-field gel electrophoresis (PFGE) types (<90% similarity), were from geographically dispersed locations and had diverging antibiotic resistance profiles. Three isolates belonged to the globally disseminated sequence type ST131. ESBL-genes of the CTX-M-1 and CTX-M-9 phylogroups were identified in all ten isolates. The plasmid content (plasmidome) of each strain was analyzed using a combination of molecular methods and high-throughput sequencing. Hidden Markov Model-based analysis of unassembled sequencing reads was used to analyze the genetic diversity of the plasmid samples and to detect resistance genes. Each isolate contained between two and eight distinct plasmids, and at least 22 large plasmids were identified overall. The plasmids were variants of pUTI89, pKF3-70, pEK499, pKF3-140, pKF3-70, p1ESCUM, pEK204, pHK17a, p083CORR, R64, pLF82, pSFO157, and R721. In addition, small cryptic high copy-number plasmids were frequent, containing one to seven open reading frames per plasmid. Three clustered groups of such small cryptic plasmids could be distinguished based on sequence similarity. Extrachromosomal prophages were found in three isolates. Two of them resembled the E. coli P1 phage and one was previously unknown. The present study confirms plasmid multiplicity in multi-resistant E. coli. We conclude that high-throughput sequencing successfully provides information on the extrachromosomal gene content and can be used to generate a genetic fingerprint of possible use in epidemiology. This could be a valuable tool for tracing plasmids in outbreaks.
format	article
author	Alma Brolund Oscar Franzén Ojar Melefors Karin Tegmark-Wisell Linus Sandegren
author_facet	Alma Brolund Oscar Franzén Ojar Melefors Karin Tegmark-Wisell Linus Sandegren
author_sort	Alma Brolund
title	Plasmidome-analysis of ESBL-producing escherichia coli using conventional typing and high-throughput sequencing.
title_short	Plasmidome-analysis of ESBL-producing escherichia coli using conventional typing and high-throughput sequencing.
title_full	Plasmidome-analysis of ESBL-producing escherichia coli using conventional typing and high-throughput sequencing.
title_fullStr	Plasmidome-analysis of ESBL-producing escherichia coli using conventional typing and high-throughput sequencing.
title_full_unstemmed	Plasmidome-analysis of ESBL-producing escherichia coli using conventional typing and high-throughput sequencing.
title_sort	plasmidome-analysis of esbl-producing escherichia coli using conventional typing and high-throughput sequencing.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/7dfa7800b19d4e488ccc20c32b7882d2
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Plasmidome-analysis of ESBL-producing escherichia coli using conventional typing and high-throughput sequencing.

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