Association of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Elements with Specific Serotypes and Virulence Potential of Shiga Toxin-Producing Escherichia coli

Abstract

e Shiga toxin-producing Escherichia coli (STEC) strains (n ‫؍‬ 194) representing 43 serotypes and E. coli K-12 were examined for clustered regularly interspaced short palindromic repeat (CRISPR) arrays to study genetic relatedness among STEC serotypes. A subset of the strains (n ‫؍‬ 81) was further analyzed for subtype I-E cas and virulence genes to determine a possible association of CRISPR elements with potential virulence. Four types of CRISPR arrays were identified. CRISPR1 and CRISPR2 were present in all strains tested; 1 strain also had both CRISPR3 and CRISPR4, whereas 193 strains displayed a short, combined array, CRISPR3-4. A total of 3,353 spacers were identified, representing 528 distinct spacers. The average length of a spacer was 32 bp. Approximately one-half of the spacers (54%) were unique and found mostly in strains of less common serotypes. Overall, CRISPR spacer contents correlated well with STEC serotypes, and identical arrays were shared between strains with the same H type (O26:H11, O103:H11, and O111:H11). There was no association identified between the presence of subtype I-E cas and virulence genes, but the total number of spacers had a negative correlation with potential pathogenicity (P < 0.05). Fewer spacers were found in strains that had a greater probability of causing outbreaks and disease than in those with lower virulence potential (P < 0.05). The relationship between the CRISPR-cas system and potential virulence needs to be determined on a broader scale, and the biological link will need to be established.

Genetic Diversity and Pathogenic Potential of Attaching and Effacing Escherichia coli O26:H11 Strains Recovered from Bovine Feces in the United States

“…Many spacers in the CRISPR1 locus were shared among strains. Similar to previously reported findings, the CRISPR2a locus contributes to a greater diversity between alleles than does CRISPR1 (34,35,43). Indicative of this are the six direct repeats, 40 unique spacers, and six untypeable allele sequences that made up 15 unique CRISPR2a alleles in the O26:H11 bovine strains (8.4% allele diversity; 15 alleles/178 strains) (see Table S2 in the supplemental material).…”

Improved traceability of Shiga-toxin-producing Escherichia coli using CRISPRs for detection and typing

“…This is not unexpected, providing that most virulence genes are carried by mobile genetic elements which should be targets of a functional CRISPR-mediated adaptive immunity (Toro et al 2014;Garcia-Gutierrez et al 2015).…”

“…1). These two loci are both present in most E. coli strains, except for strains from the B2 group and Shigella (Touchon and Rocha 2010;Toro et al 2014). A smaller array, CRISPR2b (CRISPR2.2 in Diez-Villasenor et al 2010), containing only two spacers, can be found in the same region (Fig.…”

“…1). As a result, only three CRISPR arrays are generally found simultaneously in the same genome, two of which (CRISPR1 and CRISPR2a in STEC) can be epidemiologically informative (Touchon et al 2011;DiezVillasenor et al 2010;Yin et al 2013;Toro et al 2014). …”

Genomic Diversity and Virulence Profiles of Historical Escherichia coli O157 Strains Isolated from Clinical and Environmental Sources

“…As stated above, this H type is more closely related to O157:H7/H than other H types, which usually carry an EHEC plasmid that is partially responsible for its high pathogenicity. Other flagellar H2 STEC isolates (O103:H2 and O45:H2) also were shown to carry EHEC virulence plasmids and, due to previous findings of a close phylogenetic relationship of H types to O types, the presence of plasmids in this serotype could be a further indicator of a close relatedness to other H2 types (39,46,47). Therefore, the O157:H2 serogroup should be investigated further for its pathogenic potential and the possible emergence of another important serotype.…”