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Background  The polysaccharide capsule is a major virulence factor of the important human pathogen  Streptococcus pneumoniae . However,  S. pneumoniae  strains lacking capsule do occur.    Results  Here, we report a nasopharyngeal isolate of  Streptococcus pneumoniae  composed of a mixture of two phenotypes; one encapsulated (serotype 18C) and the other nonencapsulated, determined by serotyping, electron microscopy and fluorescence isothiocyanate dextran exclusion assay.  By whole genome sequencing, we demonstrated that the phenotypes differ by a single nucleotide base pair in capsular gene  cpsE  (C to G change at gene position 1135) predicted to result in amino acid change from arginine to glycine at position 379, located in the cytoplasmic, enzymatically active, region of this transmembrane protein. This SNP is responsible for loss of capsule production as the phenotype is transferred with the capsule operon. The nonencapsulated variant is superior in growth  in vitro  and is also 117-fold more adherent to and more invasive into Detroit 562 human epithelial cells than the encapsulated variant.  Expression of six competence pathway genes and one competence-associated gene was 11 to 34-fold higher in the nonencapsulated variant than the encapsulated and transformation frequency was 3.7-fold greater.    Conclusions  We identified a new single point mutation in capsule gene  cpsE  of a clinical  S. pneumoniae  serotype 18C isolate sufficient to cause loss of capsule expression resulting in the co-existence of the encapsulated and nonencapsulated phenotype. The mutation caused phenotypic changes in growth, adherence to epithelial cells and transformability. Mutation in capsule gene  cpsE  may be a way for  S. pneumoniae  to lose its capsule and increase its colonization potential.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-014-0210-x) contains supplementary material, which is available to authorized users.

A point mutation in cpsE renders Streptococcus pneumoniae nonencapsulated and enhances its growth, adherence and competence