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bioRxiv · 10.64898/2026.01.12.698643

New paradigm of CRISPR spacerome for classification of global Escherichia coli lineages

Shin, H.·Rajaram, S. V.·Singh, P.·Zeng, E.·Cwiertny, D.·Mattes, T.·Pentella, M.·Nelson, M.·Jepson, R.·Thompson, D.
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Abstract

Our research team has recently identified a proof-of-concept for a previously unrecognized spacerome signature in a subset of globally distributed E. coli. Motivated by our initial observation, we pursued a more in-depth CRISPR spacerome analysis, which revealed a novel insight in discrimination of global E. coli sequence type (ST) lineages. We systematically retrieved publicly available E. coli complete genomes, analyzed and compared CRISPR spacerome of globally distributed strains. We found that global strains harbored spacerome that has remained conserved spaceromes for decades across multiple continents. Strains with the conserved spacerome belong to specific ST lineages of clinical importance. In addition, most protospacers were assigned to Gammaproteobacteria and Caudoviricetes. Our findings reveal unexpected long-term conservation of CRISPR spaceromes and their potential as high-resolution markers for E. coli epidemiological tracking.

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Shin, H., Rajaram, S. V., Singh, P., Zeng, E., Cwiertny, D., Mattes, T., Pentella, M., Nelson, M., Jepson, R., Thompson, D.. 2026-01-12. New paradigm of CRISPR spacerome for classification of global Escherichia coli lineages. https://doi.org/10.64898/2026.01.12.698643

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