ena-STUDY-ROBERT KOCH INSTITUT-30-04-2019-14:17:29:133-343
Whole genome-based public health surveillance of STEC
Shiga toxin-producing E. coli (STEC) and the subgroup of enterohemorrhagic E. coli cause intestinal infections with symptoms ranging from watery diarrhea to hemolytic uremic syndrome (HUS). A key tool for epidemiological differentiation of STEC is serotyping. The serotype in combination with the main virulence determinants gives an important insight into the virulence potential of a strain. However a larger fraction of STEC found in human disease, including strains causing HUS, belong to less frequently detected STEC serovars or their O/H antigens are unknown or even untypable. It has been shown that whole genome sequence (WGS) analysis provides advances for deduction of serovar and virulence gene information. Here we focused on not frequently detected STEC serovars and non typable strains and compared classical serovar analysis and PCR-based virulence marker detection with WGS-based methods for 232 selected STEC strains. As a conclusion, WGS-based extraction showed a very high degree of overlap with the more classical methods. Specifically, concordance was 97% for O antigens (OAGs) or 100% for H antigens (HAGs) of typable strains and > 99% concerning stx1/2 or eaeA for all strains. 94% of non typable OAGs and 100% of nontypable Hags were defined by WGS analysis. Most importantly, we describe four novel STEC OAG loci. Phylogenetic analysis revealed that many isolates clustered according to their serotypes. WGS analysis is therefore a promising tool with respect to acquisition of serovar, virulence gene, and phylogenetic information for routine use from a public health perspective.
Shiga toxin-producing E. coli (STEC) and the subgroup of enterohemorrhagic E. coli cause intestinal infections with symptoms ranging from watery diarrhea to hemolytic uremic syndrome (HUS). A key tool for epidemiological differentiation of STEC is serotyping. The serotype in combination with the main virulence determinants gives an important insight into the virulence potential of a strain. However a larger fraction of STEC found in human disease, including strains causing HUS, belong to less frequently detected STEC serovars or their O/H antigens are unknown or even untypable. It has been shown that whole genome sequence (WGS) analysis provides advances for deduction of serovar and virulence gene information. Here we focused on not frequently detected STEC serovars and non typable strains and compared classical serovar analysis and PCR-based virulence marker detection with WGS-based methods for 232 selected STEC strains. As a conclusion, WGS-based extraction showed a very high degree of overlap with the more classical methods. Specifically, concordance was 97% for O antigens (OAGs) or 100% for H antigens (HAGs) of typable strains and > 99% concerning stx1/2 or eaeA for all strains. 94% of non typable OAGs and 100% of nontypable Hags were defined by WGS analysis. Most importantly, we describe four novel STEC OAG loci. Phylogenetic analysis revealed that many isolates clustered according to their serotypes. WGS analysis is therefore a promising tool with respect to acquisition of serovar, virulence gene, and phylogenetic information for routine use from a public health perspective.