Bacterially-displayed peptide libraries have been widely used as an alternative to phage-displayed peptide libraries in screening epitopes or mimotopes of antibodies. Using a protective monoclonal antibody (mAb) 3B9 against hepatitis B virus (HBV) preS protein as target, mimotopes were successfully screened from a FliTrx random peptide library. To monitor the enrichment ratios of each round and to isolate higher affinity clones from the library, a modified procedure was performed in which the titer of eluted bacteria from an antibody-coated well (P value) was compared with that from a non-coated well (N value). After sufficient enrichment of the library, bacterial colonies were randomly picked and identified further by the monoclonal bacterial P/N value assay and Western blotting analysis. Immunization of mice with the selected bacterially-displayed mimotopes, including the enriched populations without clone identification, elicited strong specific immune responses against the recombinant preS protein. The present study provides a potentially rapid and effective strategy for the development of engineered live bacterial vaccines without the need for information about the aetiological agents or their antigens.