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Genome Med. 2014 Nov 28;6(11):112. doi: 10.1186/s13073-014-0112-4. eCollection 2014.

Systematic identification and quantification of phase variation in commensal and pathogenic Escherichia coli.

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Racah Institute of Physics and the Sudarsky Center for Computational Biology, The Hebrew University, Edmond J. Safra Campus, Jerusalem, 91904 Israel.


Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting genotypes mediated by genomic inversions in bacterial cultures. We tested our method on widely used strains of Escherichia coli, and detected stable and reproducible phase variation in several invertible loci. These are shown here to be responsible for maintaining constant variation in populations grown from a single colony. Applying this tool on other bacterial strains can shed light on how pathogens adjust to hostile environments by diversifying their genomes.

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