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ARS Home » Northeast Area » Wyndmoor, Pennsylvania » Eastern Regional Research Center » Characterization and Interventions for Foodborne Pathogens » Research » Publications at this Location » Publication #326912

Research Project: Molecular Characterization of Foodborne Pathogen Responses to Stress

Location: Characterization and Interventions for Foodborne Pathogens

Title: Advances in genoserotyping and subtyping of Escherichia coli

item Fratamico, Pina
item DEBROY, CHITRITA - Pennsylvania State University
item Liu, Yanhong
item Needleman, David
item BARANZONI, GIAN MARCO - University Of Bologna, Italy
item FENG, PETER - Us Food & Drug Administration (FDA)

Submitted to: Frontiers in Microbiology
Publication Type: Review Article
Publication Acceptance Date: 4/18/2016
Publication Date: 5/3/2016
Citation: Fratamico, P.M., Debroy, C., Liu, Y., Needleman, D.S., Baranzoni, G., Feng, P. 2016. Advances in genoserotyping and subtyping of Escherichia coli. Frontiers in Microbiology. 7:644.

Interpretive Summary:

Technical Abstract: E. 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 genoserotyping 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 (PFGE), 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.