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 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.
authors.affiliation: Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor PA, USA.
authors.forename: Pina M
authors.initials: PM
authors.lastname: Fratamico
authors.affiliation: Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park PA, USA.
authors.forename: Chitrita
authors.initials: C
authors.lastname: DebRoy
authors.affiliation: Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor PA, USA.
authors.forename: Yanhong
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor PA, USA.
authors.forename: David S
authors.initials: DS
authors.lastname: Needleman
authors.affiliation: Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor PA, USA.
authors.forename: Gian Marco
authors.initials: GM
authors.lastname: Baranzoni
authors.affiliation: Division of Microbiology, U.S. Food and Drug Administration, College Park MD, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Feng
keywords: Escherichia coli; H-type; O-group; detection; identification; molecular serotyping; subtyping; whole genome sequencing