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:
-
- U.S. Dept. of Agriculture, Wyndmoor, PA (United States)
- Pennsylvania State Univ., University Park, PA (United States)
- 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:
- 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. Tue .
"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},
journal = {Frontiers in Microbiology},
number = ,
volume = 7,
place = {United States},
year = {Tue May 03 00:00:00 EDT 2016},
month = {Tue May 03 00:00:00 EDT 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 69 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Foodborne urinary tract infections: a new paradigm for antimicrobial-resistant foodborne illness
journal, January 2013
- Nordstrom, Lora; Liu, Cindy M.; Price, Lance B.
- Frontiers in Microbiology, Vol. 4
Sequence Variations in the Flagellar Antigen Genes fliCH25 and fliCH28 of Escherichia coli and Their Use in Identification and Characterization of Enterohemorrhagic E. coli (EHEC) O145:H25 and O145:H28
journal, May 2015
- Beutin, Lothar; Delannoy, Sabine; Fach, Patrick
- PLOS ONE, Vol. 10, Issue 5
DNA Sequencing and Identification of Serogroup-Specific Genes in the Escherichia coli O118 O Antigen Gene Cluster and Demonstration of Antigenic Diversity But Only Minor Variation in DNA Sequence of the O Antigen Clusters of E. coli O118 and O151
journal, August 2008
- Liu, Yanhong; Fratamico, Pina; Debroy, Chitrita
- Foodborne Pathogens and Disease, Vol. 5, Issue 4
Structural diversity in Salmonella O antigens and its genetic basis
journal, January 2014
- Liu, Bin; Knirel, Yuriy A.; Feng, Lu
- FEMS Microbiology Reviews, Vol. 38, Issue 1
Virulence gene profiling of enterohemorrhagic (EHEC) and enteropathogenic (EPEC) Escherichia coli strains: a basis for molecular risk assessment of typical and atypical EPEC strains
journal, January 2011
- Bugarel, Marie; Martin, Annett; Fach, Patrick
- BMC Microbiology, Vol. 11, Issue 1
Extraintestinal Pathogenic Escherichia coli
journal, June 2007
- Smith, James L.; Fratamico, Pina M.; Gunther, Nereus W.
- Foodborne Pathogens and Disease, Vol. 4, Issue 2
Association of Nucleotide Polymorphisms within the O-Antigen Gene Cluster of Escherichia coli O26, O45, O103, O111, O121, and O145 with Serogroups and Genetic Subtypes
journal, July 2012
- Norman, Keri N.; Strockbine, Nancy A.; Bono, James L.
- Applied and Environmental Microbiology, Vol. 78, Issue 18
A group of Escherichia coli and Salmonella enterica O antigens sharing a common backbone structure
journal, July 2007
- Wang, Wei; Perepelov, Andrei V.; Feng, Lu
- Microbiology, Vol. 153, Issue 7
Escherichia coli O antigen typing using DNA microarrays
journal, June 2006
- Liu, Yanhong; Fratamico, Pina
- Molecular and Cellular Probes, Vol. 20, Issue 3-4
Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation
journal, July 2014
- Cheng, Keding; Sloan, Angela; McCorrister, Stuart
- BMC Research Notes, Vol. 7, Issue 1
Genetic Analysis and Detection of fliCH1 and fliCH12 Genes Coding for Serologically Closely Related Flagellar Antigens in Human and Animal Pathogenic Escherichia coli
journal, February 2016
- Beutin, Lothar; Delannoy, Sabine; Fach, Patrick
- Frontiers in Microbiology, Vol. 7
Diverse Virulence Gene Content of Shiga Toxin-Producing Escherichia coli from Finishing Swine
journal, August 2014
- Tseng, Marion; Fratamico, Pina M.; Bagi, Lori
- Applied and Environmental Microbiology, Vol. 80, Issue 20
Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
journal, June 2006
- Zhang, W.
- Genome Research, Vol. 16, Issue 6
Biosynthesis of O-antigens: genes and pathways involved in nucleotide sugar precursor synthesis and O-antigen assembly
journal, November 2003
- Samuel, Gabrielle; Reeves, Peter
- Carbohydrate Research, Vol. 338, Issue 23
Phage-Typing Scheme for Escherichia coli O157:H7
journal, April 1987
- Ahmed, R.; Bopp, C.; Borczyk, A.
- Journal of Infectious Diseases, Vol. 155, Issue 4
Synthesis of lipopolysaccharide O-antigens by ABC transporter-dependent pathways
journal, July 2012
- Greenfield, Laura K.; Whitfield, Chris
- Carbohydrate Research, Vol. 356
Canonical Single Nucleotide Polymorphisms (SNPs) for High-Resolution Subtyping of Shiga-Toxin Producing Escherichia coli (STEC) O157:H7
journal, July 2015
- Griffing, Sean M.; MacCannell, Duncan R.; Schmidtke, Amber J.
- PLOS ONE, Vol. 10, Issue 7
Escherichia coli serogroup O111 includes several clones of diarrheagenic strains with different virulence properties.
journal, January 1994
- Campos, L. C.; Whittam, T. S.; Gomes, T. A.
- Infection and Immunity, Vol. 62, Issue 8
Pathogenic Escherichia coli
journal, February 2004
- Kaper, James B.; Nataro, James P.; Mobley, Harry L. T.
- Nature Reviews Microbiology, Vol. 2, Issue 2
Micro-array for the identification of Shiga toxin-producing Escherichia coli (STEC) seropathotypes associated with Hemorrhagic Colitis and Hemolytic Uremic Syndrome in humans
journal, September 2010
- Bugarel, Marie; Beutin, Lothar; Martin, Annett
- International Journal of Food Microbiology, Vol. 142, Issue 3
Highly Virulent Non-O157 Enterohemorrhagic Escherichia coli (EHEC) Serotypes Reflect Similar Phylogenetic Lineages, Providing New Insights into the Evolution of EHEC
journal, July 2015
- Eichhorn, Inga; Heidemanns, Katrin; Semmler, Torsten
- Applied and Environmental Microbiology, Vol. 81, Issue 20
Zur Serologie Der Coli-Gruppe
journal, March 1944
- Kauffmann, F.
- Acta Pathologica Microbiologica Scandinavica, Vol. 21, Issue 1
Discrimination of Enterohemorrhagic Escherichia coli (EHEC) from Non-EHEC Strains Based on Detection of Various Combinations of Type III Effector Genes
journal, July 2013
- Delannoy, S.; Beutin, L.; Fach, P.
- Journal of Clinical Microbiology, Vol. 51, Issue 10
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
- Botkin, Douglas J.; Galli, Lucía; Sankarapani, Vinoth
- Frontiers in Cellular and Infection Microbiology, Vol. 2
Detection of Escherichia coli O157:H7 in Food Using Real-Time Multiplex PCR Assays Targeting the stx 1, stx 2, wzy O157, and the fliC h7 or eae Genes
journal, April 2010
- Fratamico, Pina M.; DebRoy, Chitrita
- Food Analytical Methods, Vol. 3, Issue 4, p. 330-337
Prevalence of Enterohemorrhagic Escherichia coli O26, O45, O103, O111, O121, O145, and O157 on Hides and Preintervention Carcass Surfaces of Feedlot Cattle at Harvest
journal, July 2015
- Stromberg, Zachary R.; Baumann, Nicholas W.; Lewis, Gentry L.
- Foodborne Pathogens and Disease, Vol. 12, Issue 7
Structure and genetics of Shigella O antigens
journal, July 2008
- Liu, Bin; Knirel, Yuriy A.; Feng, Lu
- FEMS Microbiology Reviews, Vol. 32, Issue 4
Molecular epidemiology of Escherichia coli O157:H7 by pulsed-field gel electrophoresis and comparison with that by bacteriophage typing.
journal, January 1996
- Krause, U.; Thomson-Carter, F. M.; Pennington, T. H.
- Journal of clinical microbiology, Vol. 34, Issue 4
Genomic anatomy of Escherichia coli O157:H7 outbreaks
journal, November 2011
- Eppinger, M.; Mammel, M. K.; Leclerc, J. E.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 50
Improved traceability of Shiga-toxin-producing Escherichia coli using CRISPRs for detection and typing
journal, October 2015
- Delannoy, Sabine; Beutin, Lothar; Fach, Patrick
- Environmental Science and Pollution Research, Vol. 23, Issue 9
Comparison of Multiplex Immunochemical and Molecular Serotyping Methods for Shiga Toxin–Producing Escherichia coli
journal, February 2015
- Clotilde, Laurie M.; Salvador, Alexandra; Bernard, Clay
- Foodborne Pathogens and Disease, Vol. 12, Issue 2
Food-Borne Origins of Escherichia coli Causing Extraintestinal Infections
journal, May 2012
- Manges, A. R.; Johnson, J. R.
- Clinical Infectious Diseases, Vol. 55, Issue 5
Optical mapping and 454 sequencing of Escherichia coli O157 : H7 isolates linked to the US 2006 spinach-associated outbreak
journal, November 2008
- Kotewicz, Michael L.; Mammel, Mark K.; LeClerc, J. Eugene
- Microbiology, Vol. 154, Issue 11
Multilocus Sequence Typing and Virulence Gene Profiles Associated with Escherichia coli from Human and Animal Sources
journal, April 2015
- Manges, Amee R.; Harel, Josée; Masson, Luke
- Foodborne Pathogens and Disease, Vol. 12, Issue 4
Urinary tract infections attributed to diverse ExPEC strains in food animals: evidence and data gaps
journal, February 2015
- Singer, Randall S.
- Frontiers in Microbiology, Vol. 6
Comparison of whole genome sequences from human and non-human Escherichia coli O26 strains
journal, March 2015
- Norman, Keri N.; Clawson, Michael L.; Strockbine, Nancy A.
- Frontiers in Cellular and Infection Microbiology, Vol. 5
Food Reservoir for Escherichia coli Causing Urinary Tract Infections
journal, January 2010
- Vincent, Caroline; Boerlin, Patrick; Daignault, Danielle
- Emerging Infectious Diseases, Vol. 16, Issue 1
Detection of O antigens in Escherichia coli
journal, December 2011
- DebRoy, Chitrita; Roberts, Elisabeth; Fratamico, Pina M.
- Animal Health Research Reviews, Vol. 12, Issue 2
Extraintestinal pathogenic Escherichia coli (ExPEC) of human and avian origin belonging to sequence type complex 95 (STC95) portray indistinguishable virulence features
journal, October 2014
- Nandanwar, Nishant; Janssen, Traute; Kühl, Michael
- International Journal of Medical Microbiology, Vol. 304, Issue 7
Rapid microarray-based DNA genoserotyping of Escherichia coli: Genoserotyping of E. coli
journal, February 2014
- Geue, Lutz; Monecke, Stefan; Engelmann, Ines
- Microbiology and Immunology, Vol. 58, Issue 2
Comparison of O-Antigen Gene Clusters of All O-Serogroups of Escherichia coli and Proposal for Adopting a New Nomenclature for O-Typing
journal, January 2016
- DebRoy, Chitrita; Fratamico, Pina M.; Yan, Xianghe
- PLOS ONE, Vol. 11, Issue 1
Novel Microarray Design for Molecular Serotyping of Shiga Toxin-Producing Escherichia coli Strains Isolated from Fresh Produce
journal, May 2014
- Lacher, David W.; Gangiredla, Jayanthi; Jackson, Scott A.
- Applied and Environmental Microbiology, Vol. 80, Issue 15
The JUMPstart sequence: a 39 bp element common to several polysaccharide gene clusters
journal, June 1994
- Hobbs, Matthew; Reeves, Peter R.
- Molecular Microbiology, Vol. 12, Issue 5
Rapid O serogroup identification of the six clinically relevant Shiga toxin-producing Escherichia coli by antibody microarray
journal, June 2013
- Hegde, Narasimha V.; Praul, Craig; Gehring, Andrew
- Journal of Microbiological Methods, Vol. 93, Issue 3
Serology, chemistry, and genetics of O and K antigens of Escherichia coli.
journal, January 1977
- Orskov, I.; Orskov, F.; Jann, B.
- Bacteriological Reviews, Vol. 41, Issue 3
Second Generation Subtyping: A Proposed PulseNet Protocol for Multiple-Locus Variable-Number Tandem Repeat Analysis of Shiga Toxin–Producing Escherichia coli O157 (STEC O157)
journal, March 2006
- Hyytiä-Trees, Eija; Smole, Sandra C.; Fields, Patricia A.
- Foodborne Pathogens and Disease, Vol. 3, Issue 1
A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster
journal, November 2014
- Iguchi, A.; Iyoda, S.; Kikuchi, T.
- DNA Research, Vol. 22, Issue 1
Escherichia coli O-Antigen Gene Clusters of Serogroups O62, O68, O131, O140, O142, and O163: DNA Sequences and Similarity between O62 and O68, and PCR-Based Serogrouping
journal, February 2015
- Liu, Yanhong; Yan, Xianghe; DebRoy, Chitrita
- Biosensors, Vol. 5, Issue 1
Designation of O174 and O175 to temporary O groups OX3 and OX7, and six new E. coli O groups that include Verocytotoxin-producing E. coli (VTEC): O176, O177, O178, O179, O180 and O181
journal, September 2004
- Scheutz, Flemming; Cheasty, Thomas; Woodward, David
- APMIS, Vol. 112, Issue 9
A High-Throughput Antibody-Based Microarray Typing Platform
journal, May 2013
- Gehring, Andrew; Barnett, Charles; Chu, Ted
- Sensors, Vol. 13, Issue 5
Evaluating the Use of Multilocus Variable Number Tandem Repeat Analysis of Shiga Toxin-Producing Escherichia coli O157 as a Routine Public Health Tool in England
journal, January 2014
- Byrne, Lisa; Elson, Richard; Dallman, Timothy J.
- PLoS ONE, Vol. 9, Issue 1
Low-Density Macroarray Targeting Non-Locus of Enterocyte Effacement Effectors (nle Genes) and Major Virulence Factors of Shiga Toxin-Producing Escherichia coli (STEC): a New Approach for Molecular Risk Assessment of STEC Isolates
journal, October 2009
- Bugarel, Marie; Beutin, Lothar; Fach, Patrick
- Applied and Environmental Microbiology, Vol. 76, Issue 1
Identification of Genetic Markers for Differentiation of Shiga Toxin-Producing, Enteropathogenic, and Avirulent Strains of Escherichia coli O26
journal, February 2011
- Bugarel, Marie; Beutin, Lothar; Scheutz, Flemming
- Applied and Environmental Microbiology, Vol. 77, Issue 7
Rapid, Sensitive, and Specific Escherichia coli H Antigen Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight-Based Peptide Mass Fingerprinting
journal, May 2015
- Chui, Huixia; Chan, Michael; Hernandez, Drexler
- Journal of Clinical Microbiology, Vol. 53, Issue 8
Rapid and Simple Determination of theEscherichia coli Phylogenetic Group
journal, October 2000
- Clermont, Olivier; Bonacorsi, Stéphane; Bingen, Edouard
- Applied and Environmental Microbiology, Vol. 66, Issue 10
Identification of Escherichia coli O-serogroups by restrictionof the amplified O-antigen gene cluster (rfb-RFLP)
journal, October 2000
- Coimbra, Roney S.; Grimont, Francine; Lenormand, Pascal
- Research in Microbiology, Vol. 151, Issue 8
Use of Clustered Regularly Interspaced Short Palindromic Repeat Sequence Polymorphisms for Specific Detection of Enterohemorrhagic Escherichia coli Strains of Serotypes O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 by Real-Time PCR
journal, October 2012
- Delannoy, S.; Beutin, L.; Fach, P.
- Journal of Clinical Microbiology, Vol. 50, Issue 12
Improved Multiplex PCR Strategy for Rapid Assignment of the Four Major Escherichia coli Phylogenetic Groups
journal, July 2012
- Doumith, M.; Day, M. J.; Hope, R.
- Journal of Clinical Microbiology, Vol. 50, Issue 9
Epidemic Profile of Shiga-Toxin–Producing Escherichia coli O104:H4 Outbreak in Germany
journal, November 2011
- Frank, Christina; Werber, Dirk; Cramer, Jakob P.
- New England Journal of Medicine, Vol. 365, Issue 19
Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems
journal, September 2014
- Franz, Eelco; Delaquis, Pascal; Morabito, Stefano
- International Journal of Food Microbiology, Vol. 187
Evaluation of a Multiplex Real-Time PCR Method for Detecting Shiga Toxin–Producing Escherichia coli in Beef and Comparison to the U.S. Department of Agriculture Food Safety and Inspection Service Microbiology Laboratory Guidebook Method
journal, February 2014
- Fratamico, Pina M.; Wasilenko, Jamie L.; Garman, Bradley
- Journal of Food Protection, Vol. 77, Issue 2
Escherichia coli O-Genotyping PCR: a Comprehensive and Practical Platform for Molecular O Serogrouping
journal, April 2015
- Iguchi, Atsushi; Iyoda, Sunao; Seto, Kazuko
- Journal of Clinical Microbiology, Vol. 53, Issue 8
Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli
journal, February 2014
- Joensen, K. G.; Scheutz, F.; Lund, O.
- Journal of Clinical Microbiology, Vol. 52, Issue 5
Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data
journal, May 2015
- Joensen, Katrine G.; Tetzschner, Anna M. M.; Iguchi, Atsushi
- Journal of Clinical Microbiology, Vol. 53, Issue 8
Optical maps distinguish individual strains of Escherichia coli O157 : H7
journal, June 2007
- Kotewicz, Michael L.; Jackson, Scott A.; LeClerc, J. Eugene.
- Microbiology, Vol. 153, Issue 6
Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
journal, January 2012
- Larsen, M. V.; Cosentino, S.; Rasmussen, S.
- Journal of Clinical Microbiology, Vol. 50, Issue 4
A comparison of AFLP and ERIC-PCR analyses for discriminating Escherichia coli from cattle, pig and human sources
journal, January 2004
- Leung, Kam Tin; Mackereth, Rob; Tien, Yuan-Ching
- FEMS Microbiology Ecology, Vol. 47, Issue 1
Rapid O serogroup identification of the ten most clinically relevant STECs by Luminex microbead-based suspension array
journal, October 2011
- Lin, Andrew; Nguyen, Lam; Lee, Teresa
- Journal of Microbiological Methods, Vol. 87, Issue 1
Identification of Escherichia coli flagellar types by restrictionof the amplified fliC gene
journal, September 2000
- Machado, Jorge; Grimont, Francine; Grimont, Patrick A. D.
- Research in Microbiology, Vol. 151, Issue 7
Whole-Genome Mapping: a New Paradigm in Strain-Typing Technology
journal, January 2013
- Miller, J. M.
- Journal of Clinical Microbiology, Vol. 51, Issue 4
Zoonotic Potential of Escherichia coli Isolates from Retail Chicken Meat Products and Eggs
journal, December 2014
- Mitchell, Natalie M.; Johnson, James R.; Johnston, Brian
- Applied and Environmental Microbiology, Vol. 81, Issue 3
Can the fliC PCR-Restriction Fragment Length Polymorphism Technique Replace Classic Serotyping Methods for Characterizing the H Antigen of Enterotoxigenic Escherichia coli Strains?
journal, April 2006
- Ramos Moreno, A. C.; Cabilio Guth, B. E.; Baquerizo Martinez, M.
- Journal of Clinical Microbiology, Vol. 44, Issue 4
Structure of the core and central channel of bacterial flagella
journal, December 1989
- Namba, Keiichi; Yamashita, Ichiro; Vonderviszt, Ferenc
- Nature, Vol. 342, Issue 6250
Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies
journal, January 2015
- Oulas, Anastasis; Pavloudi, Christina; Polymenakou, Paraskevi
- Bioinformatics and Biology Insights, Vol. 9
Standardization of Pulsed-Field Gel Electrophoresis Protocols for the Subtyping of Escherichia coli O157:H7, Salmonella , and Shigella for PulseNet
journal, March 2006
- Ribot, Efrain M.; Fair, M. A.; Gautom, R.
- Foodborne Pathogens and Disease, Vol. 3, Issue 1
Role of Capsule and O Antigen in the Virulence of Uropathogenic Escherichia coli
journal, April 2014
- Sarkar, Sohinee; Ulett, Glen C.; Totsika, Makrina
- PLoS ONE, Vol. 9, Issue 4
CRISPRs: Molecular Signatures Used for Pathogen Subtyping
journal, October 2013
- Shariat, Nikki; Dudley, Edward G.
- Applied and Environmental Microbiology, Vol. 80, Issue 2
Species-Wide Variation in the Escherichia coli Flagellin (H-Antigen) Gene
journal, May 2003
- Wang, Lei; Rothemund, Deborah; Curd, Heather
- Journal of Bacteriology, Vol. 185, Issue 9
Pathogenic Escherichia coli
journal, January 1996
- ,
- Nippon Shokuhin Kagaku Kogaku Kaishi, Vol. 43, Issue 9, p. 1077-1077
Pathogenic Escherichia coli
book, January 2001
- Puemte, Jose L.; Finlay, B. Brett
- Principles of Bacterial Pathogenesis
Whole-genome mapping: A new paradigm in strain-typing technology
journal, April 2015
- Lee, Yangsoon
- Journal of Microbiology, Immunology and Infection, Vol. 48, Issue 2
Pathogenic Escherichia coli
book, January 2001
- Meng, Jianghong; Feng, Peter; Doyle, Michael P.
- Compendium of Methods for The Microbiological Examination of Foods
Improved traceability of Shiga-toxin-producing Escherichia coli using CRISPRs for detection and typing
journal, October 2015
- Delannoy, Sabine; Beutin, Lothar; Fach, Patrick
- Environmental Science and Pollution Research, Vol. 23, Issue 9
Detection of Escherichia coli O157:H7 in Food Using Real-Time Multiplex PCR Assays Targeting the stx 1, stx 2, wzy O157, and the fliC h7 or eae Genes
journal, April 2010
- Fratamico, Pina M.; DebRoy, Chitrita
- Food Analytical Methods, Vol. 3, Issue 4, p. 330-337
Biosynthesis of O-antigens: genes and pathways involved in nucleotide sugar precursor synthesis and O-antigen assembly
journal, November 2003
- Samuel, Gabrielle; Reeves, Peter
- Carbohydrate Research, Vol. 338, Issue 23
Synthesis of lipopolysaccharide O-antigens by ABC transporter-dependent pathways
journal, July 2012
- Greenfield, Laura K.; Whitfield, Chris
- Carbohydrate Research, Vol. 356
Micro-array for the identification of Shiga toxin-producing Escherichia coli (STEC) seropathotypes associated with Hemorrhagic Colitis and Hemolytic Uremic Syndrome in humans
journal, September 2010
- Bugarel, Marie; Beutin, Lothar; Martin, Annett
- International Journal of Food Microbiology, Vol. 142, Issue 3
Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems
journal, September 2014
- Franz, Eelco; Delaquis, Pascal; Morabito, Stefano
- International Journal of Food Microbiology, Vol. 187
Extraintestinal pathogenic Escherichia coli (ExPEC) of human and avian origin belonging to sequence type complex 95 (STC95) portray indistinguishable virulence features
journal, October 2014
- Nandanwar, Nishant; Janssen, Traute; Kühl, Michael
- International Journal of Medical Microbiology, Vol. 304, Issue 7
Escherichia coli O antigen typing using DNA microarrays
journal, June 2006
- Liu, Yanhong; Fratamico, Pina
- Molecular and Cellular Probes, Vol. 20, Issue 3-4
Rapid O serogroup identification of the ten most clinically relevant STECs by Luminex microbead-based suspension array
journal, October 2011
- Lin, Andrew; Nguyen, Lam; Lee, Teresa
- Journal of Microbiological Methods, Vol. 87, Issue 1
Rapid O serogroup identification of the six clinically relevant Shiga toxin-producing Escherichia coli by antibody microarray
journal, June 2013
- Hegde, Narasimha V.; Praul, Craig; Gehring, Andrew
- Journal of Microbiological Methods, Vol. 93, Issue 3
Subtyping of foodborne and environmental isolates of Escherichia coli by multiplex-PCR, rep-PCR, PFGE, ribotyping and AFLP
journal, June 2003
- Hahm, Byoung-Kwon; Maldonado, Yadilka; Schreiber, Edgar
- Journal of Microbiological Methods, Vol. 53, Issue 3
Medical and economic impact of extraintestinal infections due to Escherichia coli: focus on an increasingly important endemic problem
journal, April 2003
- Russo, T.
- Microbes and Infection, Vol. 5, Issue 5
Pathogenic Escherichia coli
journal, February 2004
- Kaper, James B.; Nataro, James P.; Mobley, Harry L. T.
- Nature Reviews Microbiology, Vol. 2, Issue 2
Escherichia coliO104:H4 Outbreak in Germany
journal, February 2012
- Burger, R.
- New England Journal of Medicine, Vol. 366, Issue 8, p. 766-767
Second Generation Subtyping: A Proposed PulseNet Protocol for Multiple-Locus Variable-Number Tandem Repeat Analysis of Shiga Toxin–Producing Escherichia coli O157 (STEC O157)
journal, March 2006
- Hyytiä-Trees, Eija; Smole, Sandra C.; Fields, Patricia A.
- Foodborne Pathogens and Disease, Vol. 3, Issue 1
Extraintestinal Pathogenic Escherichia coli
journal, June 2007
- Smith, James L.; Fratamico, Pina M.; Gunther, Nereus W.
- Foodborne Pathogens and Disease, Vol. 4, Issue 2
Comparison of Multiplex Immunochemical and Molecular Serotyping Methods for Shiga Toxin–Producing Escherichia coli
journal, February 2015
- Clotilde, Laurie M.; Salvador, Alexandra; Bernard, Clay
- Foodborne Pathogens and Disease, Vol. 12, Issue 2
Multilocus Sequence Typing and Virulence Gene Profiles Associated with Escherichia coli from Human and Animal Sources
journal, April 2015
- Manges, Amee R.; Harel, Josée; Masson, Luke
- Foodborne Pathogens and Disease, Vol. 12, Issue 4
Prevalence of Enterohemorrhagic Escherichia coli O26, O45, O103, O111, O121, O145, and O157 on Hides and Preintervention Carcass Surfaces of Feedlot Cattle at Harvest
journal, July 2015
- Stromberg, Zachary R.; Baumann, Nicholas W.; Lewis, Gentry L.
- Foodborne Pathogens and Disease, Vol. 12, Issue 7
Food-Borne Origins of Escherichia coli Causing Extraintestinal Infections
journal, May 2012
- Manges, A. R.; Johnson, J. R.
- Clinical Infectious Diseases, Vol. 55, Issue 5
A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster
journal, November 2014
- Iguchi, A.; Iyoda, S.; Kikuchi, T.
- DNA Research, Vol. 22, Issue 1
Phage-Typing Scheme for Escherichia coli O157:H7
journal, April 1987
- Ahmed, R.; Bopp, C.; Borczyk, A.
- Journal of Infectious Diseases, Vol. 155, Issue 4
Optical maps distinguish individual strains of Escherichia coli O157 : H7
journal, June 2007
- Kotewicz, Michael L.; Jackson, Scott A.; LeClerc, J. Eugene.
- Microbiology, Vol. 153, Issue 6
A group of Escherichia coli and Salmonella enterica O antigens sharing a common backbone structure
journal, July 2007
- Wang, Wei; Perepelov, Andrei V.; Feng, Lu
- Microbiology, Vol. 153, Issue 7
Optical mapping and 454 sequencing of Escherichia coli O157 : H7 isolates linked to the US 2006 spinach-associated outbreak
journal, November 2008
- Kotewicz, Michael L.; Mammel, Mark K.; LeClerc, J. Eugene
- Microbiology, Vol. 154, Issue 11
Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
journal, June 2006
- Zhang, W.
- Genome Research, Vol. 16, Issue 6
Rapid microarray-based DNA genoserotyping of Escherichia coli: Genoserotyping of E. coli
journal, February 2014
- Geue, Lutz; Monecke, Stefan; Engelmann, Ines
- Microbiology and Immunology, Vol. 58, Issue 2
Structural diversity in Salmonella O antigens and its genetic basis
journal, January 2014
- Liu, Bin; Knirel, Yuriy A.; Feng, Lu
- FEMS Microbiology Reviews, Vol. 38, Issue 1
The JUMPstart sequence: a 39 bp element common to several polysaccharide gene clusters
journal, June 1994
- Hobbs, Matthew; Reeves, Peter R.
- Molecular Microbiology, Vol. 12, Issue 5
Structure and genetics of Shigella O antigens
journal, July 2008
- Liu, Bin; Knirel, Yuriy A.; Feng, Lu
- FEMS Microbiology Reviews, Vol. 32, Issue 4
Designation of O174 and O175 to temporary O groups OX3 and OX7, and six new E. coli O groups that include Verocytotoxin-producing E. coli (VTEC): O176, O177, O178, O179, O180 and O181
journal, September 2004
- Scheutz, Flemming; Cheasty, Thomas; Woodward, David
- APMIS, Vol. 112, Issue 9
Zur Serologie Der Coli-Gruppe
journal, March 1944
- Kauffmann, F.
- Acta Pathologica Microbiologica Scandinavica, Vol. 21, Issue 1
Association of Nucleotide Polymorphisms within the O-Antigen Gene Cluster of Escherichia coli O26, O45, O103, O111, O121, and O145 with Serogroups and Genetic Subtypes
journal, July 2012
- Norman, Keri N.; Strockbine, Nancy A.; Bono, James L.
- Applied and Environmental Microbiology, Vol. 78, Issue 18
Diverse Virulence Gene Content of Shiga Toxin-Producing Escherichia coli from Finishing Swine
journal, August 2014
- Tseng, Marion; Fratamico, Pina M.; Bagi, Lori
- Applied and Environmental Microbiology, Vol. 80, Issue 20
Highly Virulent Non-O157 Enterohemorrhagic Escherichia coli (EHEC) Serotypes Reflect Similar Phylogenetic Lineages, Providing New Insights into the Evolution of EHEC
journal, July 2015
- Eichhorn, Inga; Heidemanns, Katrin; Semmler, Torsten
- Applied and Environmental Microbiology, Vol. 81, Issue 20
Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique
journal, January 2016
- Ison, Sarah A.; Delannoy, Sabine; Bugarel, Marie
- Applied and Environmental Microbiology, Vol. 82, Issue 2
Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics.
journal, January 1986
- Selander, R. K.; Caugant, D. A.; Ochman, H.
- Applied and Environmental Microbiology, Vol. 51, Issue 5
Identification of Fecal Escherichia colifrom Humans and Animals by Ribotyping
journal, April 2001
- Carson, C. Andrew; Shear, Brian L.; Ellersieck, Mark R.
- Applied and Environmental Microbiology, Vol. 67, Issue 4
Serology, chemistry, and genetics of O and K antigens of Escherichia coli.
journal, January 1977
- Orskov, I.; Orskov, F.; Jann, B.
- Bacteriological Reviews, Vol. 41, Issue 3
Standard reference strains of Escherichia coli from natural populations.
journal, January 1984
- Ochman, H.; Selander, R. K.
- Journal of Bacteriology, Vol. 157, Issue 2
Fast DNA Serotyping of Escherichia coli by Use of an Oligonucleotide Microarray
journal, November 2006
- Ballmer, K.; Korczak, B. M.; Kuhnert, P.
- Journal of Clinical Microbiology, Vol. 45, Issue 2
Discrimination of Enterohemorrhagic Escherichia coli (EHEC) from Non-EHEC Strains Based on Detection of Various Combinations of Type III Effector Genes
journal, July 2013
- Delannoy, S.; Beutin, L.; Fach, P.
- Journal of Clinical Microbiology, Vol. 51, Issue 10
Evaluation of ribotyping as epidemiologic tool for typing Escherichia coli serogroup O157 isolates.
journal, January 1996
- Martin, I. E.; Tyler, S. D.; Tyler, K. D.
- Journal of clinical microbiology, Vol. 34, Issue 3
Virulence gene profiling of enterohemorrhagic (EHEC) and enteropathogenic (EPEC) Escherichia coli strains: a basis for molecular risk assessment of typical and atypical EPEC strains
journal, January 2011
- Bugarel, Marie; Martin, Annett; Fach, Patrick
- BMC Microbiology, Vol. 11, Issue 1
Genetical and functional investigation of fliC genes encoding flagellar serotype H4 in wildtype strains of Escherichia coli and in a laboratory E. coli K-12 strain expressing flagellar antigen type H48
journal, January 2005
- Beutin, Lothar; Strauch, Eckhard; Zimmermann, Sonja
- BMC Microbiology, Vol. 5, Issue 1, p. 4
Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation
journal, July 2014
- Cheng, Keding; Sloan, Angela; McCorrister, Stuart
- BMC Research Notes, Vol. 7, Issue 1
Evaluating the Use of Multilocus Variable Number Tandem Repeat Analysis of Shiga Toxin-Producing Escherichia coli O157 as a Routine Public Health Tool in England
journal, January 2014
- Byrne, Lisa; Elson, Richard; Dallman, Timothy J.
- PLoS ONE, Vol. 9, Issue 1
Role of Capsule and O Antigen in the Virulence of Uropathogenic Escherichia coli
journal, April 2014
- Sarkar, Sohinee; Ulett, Glen C.; Totsika, Makrina
- PLoS ONE, Vol. 9, Issue 4
Sequence Variations in the Flagellar Antigen Genes fliCH25 and fliCH28 of Escherichia coli and Their Use in Identification and Characterization of Enterohemorrhagic E. coli (EHEC) O145:H25 and O145:H28
journal, May 2015
- Beutin, Lothar; Delannoy, Sabine; Fach, Patrick
- PLOS ONE, Vol. 10, Issue 5
Canonical Single Nucleotide Polymorphisms (SNPs) for High-Resolution Subtyping of Shiga-Toxin Producing Escherichia coli (STEC) O157:H7
journal, July 2015
- Griffing, Sean M.; MacCannell, Duncan R.; Schmidtke, Amber J.
- PLOS ONE, Vol. 10, Issue 7
Comparison of O-Antigen Gene Clusters of All O-Serogroups of Escherichia coli and Proposal for Adopting a New Nomenclature for O-Typing
journal, January 2016
- DebRoy, Chitrita; Fratamico, Pina M.; Yan, Xianghe
- PLOS ONE, Vol. 11, Issue 1
Food Reservoir forEscherichia coliCausing Urinary Tract Infections
journal, June 2010
- Giufrè, Maria; Graziani, Caterina; Accogli, Marisa
- Emerging Infectious Diseases, Vol. 16, Issue 6
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
- Botkin, Douglas J.; Galli, Lucía; Sankarapani, Vinoth
- Frontiers in Cellular and Infection Microbiology, Vol. 2
Foodborne urinary tract infections: a new paradigm for antimicrobial-resistant foodborne illness
journal, January 2013
- Nordstrom, Lora; Liu, Cindy M.; Price, Lance B.
- Frontiers in Microbiology, Vol. 4
Genetic Analysis and Detection of fliCH1 and fliCH12 Genes Coding for Serologically Closely Related Flagellar Antigens in Human and Animal Pathogenic Escherichia coli
journal, February 2016
- Beutin, Lothar; Delannoy, Sabine; Fach, Patrick
- Frontiers in Microbiology, Vol. 7
Escherichia coli O-Antigen Gene Clusters of Serogroups O62, O68, O131, O140, O142, and O163: DNA Sequences and Similarity between O62 and O68, and PCR-Based Serogrouping
journal, February 2015
- Liu, Yanhong; Yan, Xianghe; DebRoy, Chitrita
- Biosensors, Vol. 5, Issue 1
Works referencing / citing this record:
Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing
journal, August 2016
- Ronholm, J.; Nasheri, Neda; Petronella, Nicholas
- Clinical Microbiology Reviews, Vol. 29, Issue 4
Complete Genome Sequence of Escherichia coli Phage Paul
journal, October 2019
- Holt, Ashley; Saldana, Robert; Moreland, Russell
- Microbiology Resource Announcements, Vol. 8, Issue 41
The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters
journal, February 2017
- Delannoy, Sabine; Beutin, Lothar; Mariani-Kurkdjian, Patricia
- Frontiers in Cellular and Infection Microbiology, Vol. 7
Multiplex polymerase chain reaction detection of Shiga toxin genes and antibiotic sensitivity of Escherichia coli O157:H7 isolated from beef meat in Quetta, Pakistan
journal, September 2018
- Samad, Abdul; Abbas, Ferhat; Ahmad, Zafar
- Journal of Food Safety, Vol. 38, Issue 6
New Approaches for Escherichia coli Genotyping
journal, January 2020
- Kotłowski, Roman; Grecka, Katarzyna; Kot, Barbara
- Pathogens, Vol. 9, Issue 2
Antimicrobial resistance and integron gene cassette arrays in commensal Escherichia coli from human and animal sources in IRI
journal, August 2016
- Kheiri, Roohollah; Akhtari, Leili
- Gut Pathogens, Vol. 8, Issue 1
Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing
journal, November 2018
- Novais, Ângela; Freitas, Ana R.; Rodrigues, Carla
- European Journal of Clinical Microbiology & Infectious Diseases, Vol. 38, Issue 3
Multiplex real-time PCR assay for detection of Escherichia coli O157:H7 and screening for non-O157 Shiga toxin-producing E. coli
journal, November 2017
- Li, Baoguang; Liu, Huanli; Wang, Weimin
- BMC Microbiology, Vol. 17, Issue 1
The relationship between phylogenetic classification, virulence and antibiotic resistance of extraintestinal pathogenic Escherichia coli in İzmir province, Turkey
journal, January 2018
- Bozcal, Elif; Eldem, Vahap; Aydemir, Sohret
- PeerJ, Vol. 6
Construction of a Pan-Genome Allele Database of Salmonella enterica Serovar Enteritidis for Molecular Subtyping and Disease Cluster Identification
journal, December 2016
- Liu, Yen-Yi; Chen, Chih-Chieh; Chiou, Chien-Shun
- Frontiers in Microbiology, Vol. 7
Escherichia coli Bloodstream Infections in Patients at a University Hospital: Virulence Factors and Clinical Characteristics
journal, June 2019
- Daga, Ana Paula; Koga, Vanessa Lumi; Soncini, João Gabriel Material
- Frontiers in Cellular and Infection Microbiology, Vol. 9
Variability in Characterizing Escherichia coli from Cattle Feces: A Cautionary Tale
journal, July 2018
- Stanford, Kim; Reuter, Tim; Hallewell, Jennyka
- Microorganisms, Vol. 6, Issue 3
Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure
journal, April 2017
- Cookson, Adrian L.; Biggs, Patrick J.; Marshall, Jonathan C.
- Scientific Reports, Vol. 7, Issue 1
Complete Genome Sequence of Escherichia coli Phage Paul
journal, October 2019
- Holt, Ashley; Saldana, Robert; Moreland, Russell
- Microbiology Resource Announcements, Vol. 8, Issue 41
Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective
journal, December 2018
- Rumore, Jillian; Tschetter, Lorelee; Kearney, Ashley
- BMC Genomics, Vol. 19, Issue 1
O-serogroups, virulence genes, antimicrobial susceptibility, and MLST genotypes of Shiga toxin-producing Escherichia coli from swine and cattle in Central China
journal, November 2019
- Peng, Zhong; Liang, Wan; Hu, Zizhe
- BMC Veterinary Research, Vol. 15, Issue 1
Antimicrobial resistance and integron gene cassette arrays in commensal Escherichia coli from human and animal sources in IRI
journal, August 2016
- Kheiri, Roohollah; Akhtari, Leili
- Gut Pathogens, Vol. 8, Issue 1
The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters
journal, February 2017
- Delannoy, Sabine; Beutin, Lothar; Mariani-Kurkdjian, Patricia
- Frontiers in Cellular and Infection Microbiology, Vol. 7
Escherichia coli Bloodstream Infections in Patients at a University Hospital: Virulence Factors and Clinical Characteristics
journal, June 2019
- Daga, Ana Paula; Koga, Vanessa Lumi; Soncini, João Gabriel Material
- Frontiers in Cellular and Infection Microbiology, Vol. 9
Imaging Inflammation and Infection in the Gastrointestinal Tract
journal, December 2019
- Frickenstein, Alex N.; Jones, Meredith A.; Behkam, Bahareh
- International Journal of Molecular Sciences, Vol. 21, Issue 1
Optical Temperature Control Unit and Convolutional Neural Network for Colorimetric Detection of Loop-Mediated Isothermal Amplification on a Lab-On-A-Disc Platform
journal, July 2019
- Lim, Da Ye Seul; Seo, Moo-Jung; Yoo, Jae Chern
- Sensors, Vol. 19, Issue 14
The relationship between phylogenetic classification, virulence and antibiotic resistance of extraintestinal pathogenic Escherichia coli in İzmir province, Turkey
journal, January 2018
- Bozcal, Elif; Eldem, Vahap; Aydemir, Sohret
- PeerJ, Vol. 6