An investigation of the diversity of strains of enteroaggregative Escherichia coli isolated from cases associated with a large multi-pathogen foodborne outbreak in the UK

Abstract

Following a large outbreak of foodborne gastrointestinal (GI) disease, a multiplex PCR approach was used retrospectively to investigate faecal specimens from 88 of the 413 reported cases. Gene targets from a range of bacterial GI pathogens were detected, including Salmonella species, Shigella species and Shiga toxin-producing Escherichia coli, with the majority (75%) of faecal specimens being PCR positive for aggR associated with the Enteroaggregative E. coli (EAEC) group. The 20 isolates of EAEC recovered from the outbreak specimens exhibited a range of serotypes, the most frequent being O104:H4 and O131:H27. None of the EAEC isolates had the Shiga toxin (stx) genes. Multilocus sequence typing and single nucleotide polymorphism analysis of the core genome confirmed the diverse phylogeny of the strains. The analysis also revealed a close phylogenetic relationship between the EAEC O104:H4 strains in this outbreak and the strain of E. coli O104:H4 associated with a large outbreak of haemolytic ureamic syndrome in Germany in 2011. Further analysis of the EAEC plasmids, encoding the key enteroaggregative virulence genes, showed diversity with respect to FIB/FII type, gene content and genomic architecture. Known EAEC virulence genes, such as aggR, aat and aap, were present in all but one of the strains. A variety of fimbrial genes were observed, including genes encoding all five known fimbrial types, AAF/1 to AAF/V. The AAI operon was present in its entirety in 15 of the EAEC strains, absent in three and present, but incomplete, in two isolates. EAEC is known to be a diverse pathotype and this study demonstrates that a high level of diversity in strains recovered from cases associated with a single outbreak. Although the EAEC in this study did not carry the stx genes, this outbreak provides further evidence of the pathogenic potential of the EAEC O104:H4 serotype.

Figure 1. Whole genome chromosomal phylogeny of strains of E. coli and Shigella spp using previously published sequences and showing the 20 strains of EAEC isolates during this outbreak (highlighted in red).

EAEC Enteroaggregative E. coli; EHEC Enterohaemorrhagic E. coli; ExPEC Extraintestinal Pathogenic E. Coli; EPEC Enteropathogenic E. coli; ETEC Enterotoxigenic E. coli.

Figure 2. Chromosomal phylogeny of sequenced EAEC ST687 (strains including five strains isolated during this study marked *) represented as a maximum-likelihood tree.

Previously published genome sequences included 280/11 isolated from a case linked to the outbreak in Germany in 2011 and 55989 isolated in the late 1990s in the Central African Republic. Other strains were previously described in Grad at al. 2013.

Figure 3. Assembled genomes displayed as concentric rings using BRIG and BLASTed against pAA genbank file as a reference.

Coloured bars represent regions of homology. The darker shades represent a high percentage similarity, lighter shades represent lower levels of similarity and the absence of colour signifies absence of the gene.