CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) as a Potential Molecular Subtyping Marker for High-risk Shiga Toxin-producing Escherichia coli (STEC) Isolates

Introduction: Shiga toxin-producing Escherichia coli (STEC) are a subgroup of E. colistrains that causes serious public health concerns due to their ability to cause disease of varying severity from mild diarrhea to bloody diarrhea to hemolytic uremic syndrome (HUS). For prevention and control purpose, it is important to be able to rapidly detect and track high-risk STEC strains. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is an immune system which confers to bacteria resistance to phages and plasmids by the acquisition of short DNA sequences (spacers) that target the invading DNA. 

Purpose: Previously, we have shown that CRISPR sequences are effective subtyping markers for Salmonella enterica subsp. enterica. Here, we hypothesize that the CRISPR loci of STECs can be potential markers for high-risk STEC isolate detection.

Methods: The CRISPR1 locus (cas to iap) was amplified and sequenced from a collection of 53 STEC isolates including 6 high-risk O serogroups (O26, O103, O111, O121, O145 and O157) from both human and non-human sources. Sequences were analyzed using a self-developed R script and each unique spacer was assigned a number. The spacer array of each isolate was represented by the spacer numbers.

Results: There were 5, 9 and 5 unique spacer arrays observed in O26, O103 and O111. Despite overlap in spacer content, only 3 complete spacer arrays were shared between O26 and O103 and 2 were shared between O103 and O111. No spacer array was common to all three serogroups. For the O serogroups that are less frequently observed clinically, the spacer found were distinct from those seen in O26, O103, and O111 isolates.

Significance: Therefore, CRISPR may be an effective molecular subtyping marker for certain STEC serogroups.