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Title: Advances in molecular serotyping and subtyping of Escherichia coli

Abstract

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 pulsedfield gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. Furthermore, 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.

Authors:
 [1];  [2];  [1];  [1];  [1];  [3]
  1. U.S. Dept. of Agriculture, Wyndmoor, PA (United States)
  2. Pennsylvania State Univ., University Park, PA (United States)
  3. U.S. Food and Drug Administration, College Park, MD (United States)
Publication Date:
Research Org.:
Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1257610
Grant/Contract Number:  
AC05-06OR23100
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Escherichia coli; molecular serotyping; subtyping; detection; identification; whole genome sequencing; O-group; H-type

Citation Formats

Fratamico, Pina M., DebRoy, Chitrita, Liu, Yanhong, Needleman, David S., Baranzoni, Gian Marco, and Feng, Peter. Advances in molecular serotyping and subtyping of Escherichia coli. United States: N. p., 2016. Web. doi:10.3389/fmicb.2016.00644.
Fratamico, Pina M., DebRoy, Chitrita, Liu, Yanhong, Needleman, David S., Baranzoni, Gian Marco, & Feng, Peter. Advances in molecular serotyping and subtyping of Escherichia coli. United States. doi:10.3389/fmicb.2016.00644.
Fratamico, Pina M., DebRoy, Chitrita, Liu, Yanhong, Needleman, David S., Baranzoni, Gian Marco, and Feng, Peter. Tue . "Advances in molecular serotyping and subtyping of Escherichia coli". United States. doi:10.3389/fmicb.2016.00644. https://www.osti.gov/servlets/purl/1257610.
@article{osti_1257610,
title = {Advances in molecular serotyping and subtyping of Escherichia coli},
author = {Fratamico, Pina M. and DebRoy, Chitrita and Liu, Yanhong and Needleman, David S. and Baranzoni, Gian Marco and Feng, Peter},
abstractNote = {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 pulsedfield gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. Furthermore, 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.},
doi = {10.3389/fmicb.2016.00644},
journal = {Frontiers in Microbiology},
number = ,
volume = 7,
place = {United States},
year = {2016},
month = {5}
}

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Cited by: 8 works
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