Amplicon PacBio sequencing for quantification of SSR number at the bacterial population level to assess phase-variation driven heterogeneity.

Expression of the Haemophilus influenzae HMW adhesin is regulated by phase variation due to the variable number of a heptanucleotide simple sequence repeat (SSR) located in its promoter-regulatory region, transcribed as part of a long 5'-UTR. The SSR number is variable and such variation plays a regulatory role, as there is an inverse correlation between SSR and hmw gene expression. This project has developed a method for deep amplicon sequencing for quantification of SSR distribution in H. influenzae bacterial clonal populations of interest. Comparative analysis of such distribution among strains is key to gather mechanistic information taking place in this regulatory process.