Escherichia coli clonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing

While microbiomestudies have focused on diversity on the species or higher level, bacterial species in microbiomesare represented by different, often multiple strains. These strains could be clonally and phenotypically very different, making assessment of strain content vital to a full understanding of microbiomefunction. This is especially important with respect to antibiotic resistant strains, the clonal spread of which may be dependent on competition between them and susceptible strains from the same species. The pandemic, multi-drug resistant, and highly pathogenic E. coli subcloneST131-H30 (H30) is of special interest, as it has already been found persisting in the gut and bladder of healthy people. In order to rapidly assess E. coli clonal diversity, we developed a novel method based on deep sequencingof two loci used for sequence typing, along with an algorithm for analysis of resulting data. Using this method, we assessed fecal and urinary samples from healthy women carrying H30, and were able to uncover considerable diversity, including strains with frequencies at