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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2020
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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. |
format | Online Article Text |
id | pubmed-7757869 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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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