Basic Info

Serotype prediction based on their surface antigens, such as O, H, and K antigens.

More Details

The serotype represents the genetic markers displayed by proteins in blood plasma. Due to the genetic polymorphism of some serum proteins, phenotypic differences arise among individuals. Therefore, serotyping has become an important classification method, especially for many foodborne microorganisms such as Salmonella and Listeria monocytogenes. This method is also widely used in epidemiological investigations. By determining the serotype of bacteria, we can provide a solid basis for antimicrobial therapy. Specifically, through in-depth analysis of the characteristics of bacterial somatic cells, such as the O antigen, cell surface proteins, H antigen, and K antigen, we can accurately classify bacteria based on their serotypes.

What's New

The O-antigens of Escherichia Coli are components of the lipopolysaccharides (LPS) structure found on the surface of Gram-negative bacteria. Structurally, the LPS is composed of oligosaccharide repeats, which consist of 3 to 5 sugars residues. The chromosomal O-antigen gene cluster contains multiple genes and is crucial for the synthesis, transport, assembly, and maturation of the precursors that ultimately form part of the LPS. Notably, four genes have been identified that serve as ideal biomarkers for predicting the O-antigen type, due to their pivotal roles in determining the O-antigen structure. These genes include a flippase (wzx), a polymerase (wzy), and ABC-dependent transporters (wzm/wzt).

ECTyper is a standalone versatile serotyping module for Escherichia coli. The tool provides convenient species identification coupled to quality control module giving a complete, transparent and reference laboratories suitable report on E.coli in silico serotyping covering O and H antigens, Shiga toxin typing and DEC pathotyping.

Additional Information

Related links:

https://github.com/phac-nml/ecoli_serotyping

Literature

Bessonov K, Laing C, Robertson J, et al. ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data. Microb Genom. 2021;7(12):000728. doi:10.1099/mgen.0.000728