CRISPR Diversity in E. coli Isolates from Australian Animals, Humans and Environmental Waters

Abstract

Seventy four SNP genotypes and 54 E. coli genomes from kangaroo, Tasmanian devil, reptile, cattle, dog, horse, duck, bird, fish, rodent, human and environmental water sources were screened for the presence of the CRISPR 2.1 loci flanked by cas2 and iap genes. CRISPR 2.1 regions were found in 49% of the strains analysed. The majority of human E. coli isolates lacked the CRISPR 2.1 locus. We described 76 CRISPR 2.1 positive isolates originating from Australian animals and humans, which contained a total of 764 spacer sequences. CRISPR arrays demonstrated a long history of phage attacks especially in isolates from birds (up to 40 spacers). The most prevalent spacer (1.6%) was an ancient spacer found mainly in human, horse, duck, rodent, reptile and environmental water sources. The sequence of this spacer matched the intestinal P7 phage and the pO111 plasmid of E. coli.

Dynamics of Escherichia coli type I‐E CRISPR spacers over 42 000 years

“…; Sheludchenko et al . ), suggesting that the CRISPR‐Cas system is active in natural E. coli populations. However, compared to some other bacteria, very few E. coli spacers match known bacteriophages and plasmids, a surprising result considering the number of known E. coli mobile genetic elements (Diez‐Villasenor et al .…”

Cytolethal distending toxin producing Escherichia coli O157:H43 strain T22 represents a novel evolutionary lineage within the O157 serogroup

“…The spacers in the CRISPR1 array of T22 are identical to those carried by strain hu24 and k8, isolated from human source (GenBank KF707537.1 and KF707515.1; (Sheludchenko et al, 2015). However, when compared to the repeat regions of typical O157 EHEC strains (Delannoy et al, 2012), no common spacers can be observed.…”

Advances in Industrial Biotechnology Using CRISPR-Cas Systems

“…Since the CRISPR array serves as a genetic record of immunization events in response to exposure to invasive DNA, much like a genetic vaccination card, arrays provide insight into strain origin and divergence within a distinct bacterial species based on the collection of shared or unique spacer sequences within an array [42][43][44] (Figure 2). This method of spacer oligonucleotide typing ('spoligotyping') [45] has been used to detect, track, and type food pathogens [43], human pathogens [46], and industrial starter cultures [19].…”