ABSTRACTAlthough virulence ofStreptococcus pneumoniaeis associated with its capsule, some pathogenicS. pneumoniaeisolates lack capsules and are serologically nontypeable (NT). We obtained 64 isolates that were identified as NT “pneumococci” (i.e., bacteria satisfying the conventional definition but without the multilocus sequence typing [MLST]-based definition ofS. pneumoniae) by the traditional criteria. All 64 were optochin sensitive and hadlytA, and 63 hadply. Twelve isolates hadcpsA, suggesting the presence of a conventional but defective capsular polysaccharide synthesis (cps) locus. The 52cpsA-negative isolates could be divided into three null capsule clades (NCC) based onaliC(aliB-like ORF1),aliD(aliB-like ORF2), and our newly discovered gene,pspK, in theircpsloci.pspKencodes a protein with a long alpha-helical region containing an LPxTG motif and a YPT motif known to bind human pIgR. There were nine isolates in NCC1 (pspK+but negative foraliCandaliD), 32 isolates in NCC2 (aliC+aliD+but negative forpspK), and 11 in NCC3 (aliD+but negative foraliCandpspK). Among 52cpsA-negative isolates, 41 were identified asS. pneumoniaeby MLST analysis. All NCC1 and most NCC2 isolates wereS. pneumoniae, whereas all nine NCC3 and two NCC2 isolates were notS. pneumoniae. Several NCC1 and NCC2 isolates from multiple individuals had identical MLST andcpsregions, showing that unencapsulatedS. pneumoniaecan be infectious among humans. Furthermore, NCC1 and NCC2S. pneumoniaeisolates could colonize mice as well as encapsulatedS. pneumoniae, althoughS. pneumoniaewith an artificially disruptedcpslocus did not. Moreover, an NCC1 isolate withpspKdeletion did not colonize mice, suggesting thatpspKis critical for colonization. Thus, PspK may provide pneumococci a means of surviving in the nasopharynx without capsule.IMPORTANCEThe presence of a capsule is critical for many pathogenic bacteria, including pneumococci. Reflecting the pathogenic importance of the pneumococcal capsule, pneumococcal vaccines are designed to elicit anticapsule antibodies. Additional evidence for the pathogenic importance of the pneumococcal capsule is the fact that in pneumococci all the genes necessary for capsule production are together in one genetic locus, which is called thecpslocus. However, there are occasional pathogenic pneumococci without capsules, and how they survive in the host without the capsule is unknown. Here, we show that in these acapsular pneumococci, thecpsloci have been replaced with various novel genes and they can colonize mouse nasopharynges as well as capsulated pneumococci. Since the genes that replace thecpsloci are likely to be important in host survival, they may show new and/or alternative capsule-independent survival mechanisms used by pneumococci.