Simultaneous Presence of Insertion Sequence Excision Enhancer and Insertion Sequence IS 629 Correlates with Increased Diversity and Virulence in Shiga Toxin-Producing Escherichia coli

Abstract

cAlthough new serotypes of enterohemorrhagic Escherichia coli (EHEC) emerge constantly, the mechanisms by which these new pathogens arise and the reasons emerging serotypes tend to carry more virulence genes than other E. coli are not understood. An insertion sequence (IS) excision enhancer (IEE) was discovered in EHEC O157:H7 that promoted the excision of IS3 family members and generating various genomic deletions. One IS3 family member, IS629, actively transposes and proliferates in EHEC O157:H7 and enterotoxigenic E. coli (ETEC) O139 and O149. The simultaneous presence of the IEE and IS629 (and other IS3 family members) may be part of a system promoting not only adaptation and genome diversification in E. coli O157:H7 but also contributing to the development of pathogenicity among predominant serotypes. Prevalence comparisons of these elements in 461 strains, representing 72 different serotypes and 5 preassigned seropathotypes (SPT) A to E, showed that the presence of these two elements simultaneously was serotype specific and associated with highly pathogenic serotypes (O157 and top non-O157 Shiga toxin-producing Escherichia coli [STEC]) implicated in outbreaks and sporadic cases of human illness (SPT A and B). Serotypes lacking one or both elements were less likely to have been isolated from clinical cases. Our comparisons of IEE sequences showed sequence variations that could be divided into at least three clusters. Interestingly, the IEE sequences from O157 and the top 10 non-O157 STEC serotypes fell into clusters I and II, while less commonly isolated serotypes O5 and O174 fell into cluster III. These results suggest that IS629 and IEE elements may be acting synergistically to promote genome plasticity and genetic diversity among STEC strains, enhancing their abilities to adapt to hostile environments and rapidly take up virulence factors. Shiga toxin-producing Escherichia coli (STEC) strains are important food pathogens responsible for serious human disease worldwide (1-3). Although new STEC serotypes constantly emerge (4), the mechanisms by which these strains acquire virulence are not entirely understood. Elements such as phages, pathogenicity islands (PAIs), and plasmids can introduce new virulence genes (such as those for producing Shiga toxin) that contribute to the pathogenic potential of strains, but the existence of horizontal transfer is not sufficient to explain the subsequent evolution of these strains or why some strains carry more virulence genes than others.Karmali et al. (5) classified STEC into seropathotypes (SPT) from A to E in descending order of virulence. Serotypes that are frequently linked to outbreaks and severe disease, for example, hemolytic-uremic syndrome (HUS), are classified as SPT A. Serotypes in SPT B are also associated with outbreaks and severe disease, but these associations occur less frequently in SPT B serotypes than those in SPT A serotypes. Serotypes associated with sporadic cases of HUS, but not known to be responsible for outbreaks, are classified as SPT C, and ...

Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes

“…Pathogenome Architecture and Virulence Profiles of Stx (−) NSF O157:H7 and SF O157:NM Alterations in genome size and architecture in EHEC O157:H7/NM are driven by the individual prophage complement, particularly Stx-phages Eppinger et al, 2011b;Shaaban et al, 2016) and dynamics of other MGEs (Eppinger et al, 2011b;Yokoyama et al, 2011;Stanton et al, 2014;Toro et al, 2015). We compared the chromosomes of the Stx (−) NSF O157:H7 and SF O157:NM strains with BRIG (Alikhan et al, 2011) using Stx (+) strain EC4115 (stx1−, stx2a+, stx2c+) as reference (Eppinger et al, 2011b).…”

“…When compared to the 3072/96 pSFO157 reference plasmid (Brunder et al, 2006), we identified two InDel regions that account for the plasmid size difference of 2,078 bp, both of which are associated with IS elements (Supplementary Figure S7). Similar to the role of phages in microevolution and emergence of sublineages Eppinger et al, 2011b;Yokoyama et al, 2011;Stanton et al, 2014;Sanjar et al, 2015;Toro et al, 2015;Yin et al, 2015;, mobile elements are also major drivers of plasmid diversification and are responsible for the observed differences in pSFO157 plasmid size. InDel-1 is located within the boundaries of transposable element Tn2501 (Michiels et al, 1987) present in the LSU-61 and 3072/96 plasmids, though the LSU-61 variant is 400 bp larger (Supplementary Figure S7A).…”

“…SNP deserts correlated with the identified and excluded mobilome and repeat regions. subtyping in O157:H7 (Eppinger et al, 2011b;Yokoyama et al, 2011;Stanton et al, 2014;Toro et al, 2015). The mosaic-like composition of the large pO157 virulence plasmid types, as reflected by carriage of a number of replication-associated genes and mobile genetic elements driving plasmid diversification, clearly suggests complex evolutionary origins resulting in distinct coding capacity and architectures.…”

“…Our profiling of phage insertion loci in closed genomes of Stx (−) strains allowed us to identify different and mechanistically unrelated scenarios, from complete absence of Stx-phages to a more confined loss or disruption of the stx locus by IS629 (Eppinger et al, 2011b). This element plays a major role in shaping the STEC population structure Yokoyama et al, 2011;Stanton et al, 2014;Toro et al, 2015) including Stx-phage diversification (Eppinger et al, 2011b;Sanjar et al, 2015;Yin et al, 2015;.…”

Virulence Gene Profiles and Clonal Relationships of Escherichia coli O26:H11 Isolates from Feedlot Cattle as Determined by Whole-Genome Sequencing

“…Recently, an IS excision enhancer (IEE) element was discovered in EHEC O157 promoting the excision and deletion of IS3 family members, resulting in genomic rearrangements and strain diversification (44,45). In the strains analyzed, the IEE element (IEE cluster I) was present solely in O26 lineage 1, suggesting that these strains have a higher potential to increase their diversity and virulence than those of lineage 2 (46). IEE cluster I has been found in different pathogenic strains from diverse serotypes (O157:H7, O26:H11, O111:H11, O118:NM, O145:H28, and O139:NM/H38) that are frequently involved in serious outbreaks (2,47).…”