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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 Institute for Science and Education (ORISE), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1257610
Grant/Contract Number:  
AC05-06OR23100
Resource Type:
Journal Article: 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. https://doi.org/10.3389/fmicb.2016.00644
Fratamico, Pina M., DebRoy, Chitrita, Liu, Yanhong, Needleman, David S., Baranzoni, Gian Marco, and Feng, Peter. 2016. "Advances in molecular serotyping and subtyping of Escherichia coli". United States. https://doi.org/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},
url = {https://www.osti.gov/biblio/1257610}, journal = {Frontiers in Microbiology},
issn = {1664-302X},
number = ,
volume = 7,
place = {United States},
year = {Tue May 03 00:00:00 EDT 2016},
month = {Tue May 03 00:00:00 EDT 2016}
}

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Cited by: 69 works
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Works referenced in this record:

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Whole-genome mapping: A new paradigm in strain-typing technology
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Improved traceability of Shiga-toxin-producing Escherichia coli using CRISPRs for detection and typing
journal, October 2015


Synthesis of lipopolysaccharide O-antigens by ABC transporter-dependent pathways
journal, July 2012


Extraintestinal pathogenic Escherichia coli (ExPEC) of human and avian origin belonging to sequence type complex 95 (STC95) portray indistinguishable virulence features
journal, October 2014


Escherichia coli O antigen typing using DNA microarrays
journal, June 2006


Rapid O serogroup identification of the ten most clinically relevant STECs by Luminex microbead-based suspension array
journal, October 2011


Rapid O serogroup identification of the six clinically relevant Shiga toxin-producing Escherichia coli by antibody microarray
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Pathogenic Escherichia coli
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Escherichia coliO104:H4 Outbreak in Germany
journal, February 2012


Extraintestinal Pathogenic Escherichia coli
journal, June 2007


Comparison of Multiplex Immunochemical and Molecular Serotyping Methods for Shiga Toxin–Producing Escherichia coli
journal, February 2015


Multilocus Sequence Typing and Virulence Gene Profiles Associated with Escherichia coli from Human and Animal Sources
journal, April 2015


Food-Borne Origins of Escherichia coli Causing Extraintestinal Infections
journal, May 2012


A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster
journal, November 2014


Phage-Typing Scheme for Escherichia coli O157:H7
journal, April 1987


Optical maps distinguish individual strains of Escherichia coli O157 : H7
journal, June 2007


A group of Escherichia coli and Salmonella enterica O antigens sharing a common backbone structure
journal, July 2007


Optical mapping and 454 sequencing of Escherichia coli O157 : H7 isolates linked to the US 2006 spinach-associated outbreak
journal, November 2008


Rapid microarray-based DNA genoserotyping of Escherichia coli: Genoserotyping of E. coli
journal, February 2014


Structural diversity in Salmonella O antigens and its genetic basis
journal, January 2014


The JUMPstart sequence: a 39 bp element common to several polysaccharide gene clusters
journal, June 1994


Structure and genetics of Shigella O antigens
journal, July 2008


Zur Serologie Der Coli-Gruppe
journal, March 1944


Diverse Virulence Gene Content of Shiga Toxin-Producing Escherichia coli from Finishing Swine
journal, August 2014


Highly Virulent Non-O157 Enterohemorrhagic Escherichia coli (EHEC) Serotypes Reflect Similar Phylogenetic Lineages, Providing New Insights into the Evolution of EHEC
journal, July 2015


Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics.
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Identification of Fecal Escherichia colifrom Humans and Animals by Ribotyping
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Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation
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Role of Capsule and O Antigen in the Virulence of Uropathogenic Escherichia coli
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journal, June 2010


Development of a Multiplex PCR Assay for Detection of Shiga Toxin-Producing Escherichia coli, Enterohemorrhagic E. coli, and Enteropathogenic E. coli Strains
journal, January 2012


Foodborne urinary tract infections: a new paradigm for antimicrobial-resistant foodborne illness
journal, January 2013


Works referencing / citing this record:

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing
journal, August 2016


Complete Genome Sequence of Escherichia coli Phage Paul
journal, October 2019


The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters
journal, February 2017


New Approaches for Escherichia coli Genotyping
journal, January 2020


Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing
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Escherichia coli Bloodstream Infections in Patients at a University Hospital: Virulence Factors and Clinical Characteristics
journal, June 2019


Variability in Characterizing Escherichia coli from Cattle Feces: A Cautionary Tale
journal, July 2018


Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure
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Complete Genome Sequence of Escherichia coli Phage Paul
journal, October 2019


The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters
journal, February 2017


Escherichia coli Bloodstream Infections in Patients at a University Hospital: Virulence Factors and Clinical Characteristics
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Imaging Inflammation and Infection in the Gastrointestinal Tract
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