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The majority of deaths due to <i>Streptococcus pneumoniae</i> infections are in developing countries. Although polysaccharide-based pneumococcal vaccines are available, newer types of vaccines are needed to increase vaccine affordability, particularly in developing countries, and to provide broader protection across all pneumococcal serotypes. To attenuate pneumococcal virulence with the aim of engineering candidate live attenuated vaccines (LAVs), we constructed knockouts in <i>S. pneumoniae</i> D39 of one of the capsular biosynthetic genes, <i>cpsE</i> that encodes glycosyltransferase, and the endonuclease gene, <i>endA</i>, that had been implicated in the uptake of DNA from the environment as well as bacterial escape from neutrophil-mediated killing. The <i>cpsE</i> gene knockout significantly lowered peak bacterial density, BALB/c mice nasopharyngeal (NP) colonisation but increased biofilm formation when compared to the wild-type D39 strain as well as the <i>endA</i> gene knockout mutant. All constructed mutant strains were able to induce significantly high serum and mucosal antibody response in BALB/c mice. However, the <i>cpsE-endA</i> double mutant strain, designated SPEC, was able to protect mice from high dose mucosal challenge of the D39 wild-type. Furthermore, SPEC showed 23-fold attenuation of virulence compared to the wild-type. Thus, the <i>cpsE</i>-<i>endA</i> double-mutant strain could be a promising candidate for further development of a LAV for <i>S. pneumoniae</i>.