Discovery of an identical CRISPR spacerome in a subset of global E. coli strains spanning decades

CRISPR is an immune system in bacteria composed of repeats and spacers. Motivated by the hypothesis that spacer identification can trace circulation routes, we analyzed CRISPR arrays of E. coli from environmental, animal, and clinical sources. CRISPR I-E type was predominant, with partial sharing of spacers in environmental isolates. Unexpectedly, we identified identical spaceromes across some clinical E. coli strains, first in carbapenemase-producing E. coli (CPE) of sequence type (ST) 167 (part of the ST10 clonal complex) from Iowa patients and subsequently in a broader subset of strains belonging to the ST10 clonal complex that often, but not always, carried carbapenemase enzymes. Notably, this broader subset of strains from the ST10 clonal complex shared an identical spacerome despite strains being isolated across 25 countries over two decades. Moreover, the identical spacerome was linked to specific STs and phylogroups, despite single nucleotide polymorphism (SNP) variation, demonstrating its potential as a complementary fine-scale strain-typing tool. Although additional validation with a larger and more diverse collection of isolates is needed, this work provides proof-of-concept that CRISPR spacerome identity can serve as a novel genomic marker for higher-resolution tracking of E. coli lineages across time and geography.