Sequence-based typing of genetic targets encoded outside of the O-antigen gene cluster is indicative of Shiga toxin-producing Escherichia coli serogroup lineages

Abstract

Serogroup classifications based upon the O-somatic antigen of Shiga toxin-producing Escherichia coli (STEC) provide significant epidemiological information on clinical isolates. Each O-antigen determinant is encoded by a unique cluster of genes present between the gnd and galF chromosomal genes. Alternatively, serogroup-specific polymorphisms might be encoded in loci that are encoded outside of the O-antigen gene cluster. Segments of the core bacterial loci mdh, gnd, gcl, ppk, metA, ftsZ, relA and metG for 30 O26 STEC strains have previously been sequenced, and comparative analyses to O157 distinguished these two serogroups. To screen these loci for serogroup-specific traits within a broader range of clinically significant serogroups, DNA sequences were obtained for 19 strains of 10 additional STEC serogroups. Unique alleles were observed at the gnd locus for each examined STEC serogroup, and this correlation persisted when comparative analyses were extended to 144 gnd sequences from 26 O-serogroups (comprising 42 O : H-serotypes). These included O157, O121, O103, O26, O5 : non-motile (NM), O145 : NM, O113 : H21, O111 : NM and O117 : H7 STEC; and furthermore, non-toxin encoding O157, O26, O55, O6 and O117 strains encoded distinct gnd alleles compared to STEC strains of the same serogroup. DNA sequencing of a 643 bp region of gnd was, therefore, sufficient to minimally determine the O-antigen of STEC through molecular means, and the location of gnd next to the O-antigen gene cluster offered additional support for the co-inheritance of these determinants. The gnd DNA sequence-based serogrouping method could improve the typing capabilities for STEC in clinical laboratories, and was used successfully to characterize O121 : H19, O26 : H11 and O177 : NM clinical isolates prior to serological confirmation during outbreak investigations.

Real-Time Multiplex PCR for Detecting Shiga Toxin 2-Producing Escherichia coli O104:H4 in Human Stools

“…In addition, strain HUSEC038, which belongs to serotype Ont (nontypeable O antigen):H21 and to the same multilocus sequence type (ST672) as HUSEC037, also produced the wzy O104 but not the fliC H4 amplicon (see Table S1 in the supplemental material). The specificity of the wzy O104 amplification in HUSEC038 was confirmed by partial (627-bp) sequencing of the gnd locus, which is adjacent to the O104 antigen-encoding cluster and is serogroup specific (7). The partial gnd sequences of HUSEC038 and HUSEC037 were 100% identical to that of HUSEC041, demonstrating that HUSEC038 indeed belongs to serogroup O104.…”

Association between β-Lactamase-Encoding bla OXA-51 Variants and DiversiLab Rep-PCR-Based Typing of Acinetobacter baumannii Isolates

“…The major advantage of bla OXA-51-like gene typing is that sequencing is based on a single gene; therefore, this method appears to be an easier, faster, and cheaper way of A. baumannii typing. Single-locus sequencing has proved useful with typing of other species, for example, Shiga toxin-producing Escherichia coli (STEC) (5) and Staphylococcus aureus (spa typing) (12,22). However, some S. aureus single-locus methods, such as SCCmec and agr typing, while useful, are not as discriminatory as spa typing (22).…”

Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study

“…24 The alleles and sequence type (ST) were assigned in accordance with the E coliMLST databases at the Environmental Research Institute, University College Cork, Ireland. In addition to MLST, all strains were subjected to partial gnd sequencing (627 bp internal gnd gene fragment, positions 397-1023 in strain W3110, GenBank accession number AP009048) in accordance to the protocol of Gilmour and colleagues 25 Three reference E coli O104 strains including HUSEC041 (O104:H4), HUSEC037 (O104:H21), and enteroaggregative E coli strain 55989 (O104:H4; GenBank accession number NC_011748) were included as controls. The partial gnd sequence enables prediction of the O-phase of E coli.…”