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Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing

Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto...

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Autores principales: Paramita, Rafika Indah, Nelwan, Erni Juwita, Fadilah, Fadilah, Renesteen, Editha, Puspandari, Nelly, Erlina, Linda
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7757869/
https://www.ncbi.nlm.nih.gov/pubmed/33362261
http://dx.doi.org/10.1371/journal.pone.0244358
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author Paramita, Rafika Indah
Nelwan, Erni Juwita
Fadilah, Fadilah
Renesteen, Editha
Puspandari, Nelly
Erlina, Linda
author_facet Paramita, Rafika Indah
Nelwan, Erni Juwita
Fadilah, Fadilah
Renesteen, Editha
Puspandari, Nelly
Erlina, Linda
author_sort Paramita, Rafika Indah
collection PubMed
description Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms.
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spelling pubmed-77578692021-01-06 Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing Paramita, Rafika Indah Nelwan, Erni Juwita Fadilah, Fadilah Renesteen, Editha Puspandari, Nelly Erlina, Linda PLoS One Research Article Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms. Public Library of Science 2020-12-23 /pmc/articles/PMC7757869/ /pubmed/33362261 http://dx.doi.org/10.1371/journal.pone.0244358 Text en © 2020 Paramita et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Paramita, Rafika Indah
Nelwan, Erni Juwita
Fadilah, Fadilah
Renesteen, Editha
Puspandari, Nelly
Erlina, Linda
Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing
title Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing
title_full Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing
title_fullStr Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing
title_full_unstemmed Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing
title_short Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing
title_sort genome-based characterization of escherichia coli causing bloodstream infection through next-generation sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7757869/
https://www.ncbi.nlm.nih.gov/pubmed/33362261
http://dx.doi.org/10.1371/journal.pone.0244358
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