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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMIC AND PROTEOMIC ANALYSIS OF FOODBORNE PATHOGENS

Location: Molecular Characterization of Foodborne Pathogens

Title: Molecular serotyping of Escherichia coli: A verification and reclassification

Authors
item Yan, Xianghe
item Fratamico, Pina
item Tebbs, Robert -
item O'Connell, Catherine -
item Baranzoni, Gianmarco -
item Allred, Adam -
item Swimley, Michelle -
item Debroy, Chobi -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: February 25, 2014
Publication Date: May 18, 2014
Citation: Yan, X., Fratamico, P.M., Tebbs, R., O'Connell, C., Baranzoni, G., Allred, A., Swimley, M., Debroy, C. 2014. Molecular serotyping of Escherichia coli: A verification and reclassification. Meeting Abstract. MA.

Technical Abstract: Background: Serotyping of E. coli, based on the O- (polysaccharide side chain) and H- (flagellar) antigens using antisera is a common practice for diagnostics, outbreak investigations, and epidemiological surveillance. The full set of E. coli serogroups comprises O-groups O1 to O181, with several O-groups removed. One problem with conventional serotyping is that cross-reactions are observed among different E. coli serogroups, as well as with other bacterial genera. In this study, next generation sequencing technologies were applied to analyze all E. coli O-groups at the genomic level. This work provides information on all of the E. coli O-antigen gene clusters for further investigations and development of molecular serotyping systems, as well as for possible reclassification of E. coli serogroups. Materials and Method: Genomic DNA was isolated from over 75 different E. coli O-group reference strains and subjected to sequencing using the Ion Torrent PGMâ„¢. Other O-group sequences were obtained from GenBank. De novo genome assembly of these sequenced strains was performed using CLC Genomics Workbench v 6.5. The entire O-antigen gene cluster was pulled out by alignment with primers that targeted conserved regions in the neighboring JUMPstart region and gnd gene. Nucleotide diversities and species divergence calculations were performed using MEGA 6.0 and clustalW. Results and Conclusion: This is the first comprehensive study of the O-antigen gene clusters from the type strains of all of the known E. coli O-serogroups. Unique sequences within each cluster were identified that will allow for the development of high-throughput molecular serotyping methods and will overcome problems associated with traditional serotyping. The sequence data revealed that some O-groups have very similar O-antigen gene cluster sequences, thus there may be a need to reclassify some E. coli serogroups. This research will enhance the ability of clinical and public health laboratories to serogroup E. coli and may assist in furthering the understanding of the evolution of E. coli.

Last Modified: 11/25/2014
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