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Advances in Molecular Serotyping and Subtyping of Escherichia coli()

Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract. E. coli have traditionally been serotyped using an...

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Autores principales: Fratamico, Pina M., DebRoy, Chitrita, Liu, Yanhong, Needleman, David S., Baranzoni, Gian Marco, Feng, Peter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4853403/
https://www.ncbi.nlm.nih.gov/pubmed/27199968
http://dx.doi.org/10.3389/fmicb.2016.00644
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author Fratamico, Pina M.
DebRoy, Chitrita
Liu, Yanhong
Needleman, David S.
Baranzoni, Gian Marco
Feng, Peter
author_facet Fratamico, Pina M.
DebRoy, Chitrita
Liu, Yanhong
Needleman, David S.
Baranzoni, Gian Marco
Feng, Peter
author_sort Fratamico, Pina M.
collection PubMed
description Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract. E. coli have traditionally been serotyped using antisera against the ca. 186 O-antigens and 53 H-flagellar antigens. Phenotypic methods, including bacteriophage typing and O- and H- serotyping for differentiating and characterizing E. coli have been used for many years; however, these methods are generally time consuming and not always accurate. Advances in next generation sequencing technologies have made it possible to develop genetic-based subtyping and molecular serotyping methods for E. coli, which are more discriminatory compared to phenotypic typing methods. Furthermore, whole genome sequencing (WGS) of E. coli is replacing established subtyping methods such as pulsed-field gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. A variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers.
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spelling pubmed-48534032016-05-19 Advances in Molecular Serotyping and Subtyping of Escherichia coli() Fratamico, Pina M. DebRoy, Chitrita Liu, Yanhong Needleman, David S. Baranzoni, Gian Marco Feng, Peter Front Microbiol Microbiology Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract. E. coli have traditionally been serotyped using antisera against the ca. 186 O-antigens and 53 H-flagellar antigens. Phenotypic methods, including bacteriophage typing and O- and H- serotyping for differentiating and characterizing E. coli have been used for many years; however, these methods are generally time consuming and not always accurate. Advances in next generation sequencing technologies have made it possible to develop genetic-based subtyping and molecular serotyping methods for E. coli, which are more discriminatory compared to phenotypic typing methods. Furthermore, whole genome sequencing (WGS) of E. coli is replacing established subtyping methods such as pulsed-field gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. A variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers. Frontiers Media S.A. 2016-05-03 /pmc/articles/PMC4853403/ /pubmed/27199968 http://dx.doi.org/10.3389/fmicb.2016.00644 Text en Copyright © 2016 Fratamico, DebRoy, Liu, Needleman, Baranzoni and Feng. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Fratamico, Pina M.
DebRoy, Chitrita
Liu, Yanhong
Needleman, David S.
Baranzoni, Gian Marco
Feng, Peter
Advances in Molecular Serotyping and Subtyping of Escherichia coli()
title Advances in Molecular Serotyping and Subtyping of Escherichia coli()
title_full Advances in Molecular Serotyping and Subtyping of Escherichia coli()
title_fullStr Advances in Molecular Serotyping and Subtyping of Escherichia coli()
title_full_unstemmed Advances in Molecular Serotyping and Subtyping of Escherichia coli()
title_short Advances in Molecular Serotyping and Subtyping of Escherichia coli()
title_sort advances in molecular serotyping and subtyping of escherichia coli()
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4853403/
https://www.ncbi.nlm.nih.gov/pubmed/27199968
http://dx.doi.org/10.3389/fmicb.2016.00644
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