There is a growing interest in development of novel vaccines against respiratory tract infections, due to COVID-19 pandemic. Here, we examined mucosal adjuvanticity and the mucosal booster effect of membrane vesicles (MVs) of a novel probiotic
E. coli
derivative lacking both flagella and potentially carcinogenic colibactin (Δ
flhD
Δ
clbP
). Δ
flhD
Δ
clbP
-derived MVs showed rather strong mucosal adjuvanticity as compared to those of a single flagellar mutant strain (Δ
flhD
-MVs). In addition, glycoengineered Δ
flhD
Δ
clbP
-MVs displaying serotype-14 pneumococcal capsular polysaccharide (CPS14
+
MVs) were well-characterized based on biological and physicochemical parameters. Subcutaneous (SC) and intranasal (IN) booster effects of CPS14
+
MVs on systemic and mucosal immunity were evaluated in mice that have already been subcutaneously prime-immunized with the same MVs. With a two-dose regimen, an IN boost (SC-IN) elicited stronger IgA responses than homologous prime-boost immunization (SC-SC). With a three-dose regimen, serum IgG levels were comparable among all tested regimens. Homologous immunization (SC-SC-SC) elicited the highest IgM responses among all regimens tested, whereas SC-SC-SC failed to elicit IgA responses in blood and saliva. Furthermore, serum IgA and salivary SIgA levels were increased with an increased number of IN doses administrated. Notably, SC-IN-IN induced not only robust IgG response, but also the highest IgA response in both serum and saliva among the groups. The present findings suggest the potential of a heterologous three-dose administration for building both systemic and mucosal immunity,
e.g
. an SC-IN-IN vaccine regimen could be beneficial. Another important observation was abundant packaging of colibactin in MVs, suggesting increased applicability of Δ
flhD
Δ
clbP
-MVs in the context of vaccine safety.