For evaluation of PCV7 and increased-valency conjugate vaccines projected to become licensed in the near future, it is vital to determine if disease cases caused by CS6As are true serotype 6A vaccine failures or are actually caused by serotype 6C strains. per 100,000 and 0.22 cases per 100,000, respectively; 164% increase from 1999 to 2007 [95% confidence interval, 87 to 270%]), while rates of IPD due to types 6A and 6B markedly decreased. In 2007, 31.2% of 6C isolates were not susceptible to penicillin. Serotype 6C is now the predominant serotype associated with serogroup 6 IPD in the United States and is often penicillin nonsusceptible. We performed multilocus sequence typing (MLST) on a limited sampling of Microtubule inhibitor 1 6C isolates with different antimicrobial susceptibility profiles. MLST of 42 6C isolates revealed 12 genotypes distributed among six distinct genetic groups. Fifteen 6C isolates shared one of four different Microtubule inhibitor 1 MLST types with 6C-negative CS6As. MLST results suggest 6C strains arose from independent recombination events involving only serotype 6A and 6C parental strains. A new pneumococcal serotype within serogroup 6, 6C, was recently discovered during the development of a monoclonal antibody (MAb)-based typing scheme (7,14), when a subset of conventionally serotyped 6A isolates (CS6As) did not bind to one of the two 6A-specific MAbs used. Subsequent analysis of this CS6A subset revealed a different capsular structure, which was designated 6C (14). The serotype 6C capsular biosynthetic locus (cps) appears to be derived from replacement of thewciNgene at the 6Acpslocus with a divergent 6C-specific counterpart that encodes a different glycosyl transferase, resulting in a sugar substitution in the polysaccharide repeating unit (13). The MAb typing system was used to resolve serotype 6C isolates among CS6As recovered during the pre-pneumococcal 7-valent conjugate vaccine (PCV7) year 1999 and post-PCV7 years 2003 to 2006 from areas under continuous surveillance in Active Bacterial Core surveillance (ABCs) in ADIPOQ the United States (10). This investigation revealed a marked decrease in the rate of serotype 6A invasive pneumococcal disease (IPD) in the post-PCV7 period that was apparently due to cross-protection mediated by the serotype 6B component included in PCV7. The investigation also revealed a small, yet significant, increase in the rate of serotype 6C IPD. Here, we describe an expedient PCR assay for resolution of serotype 6C and true serotype 6A from CS6As. We extend our recent observations (10) through testing all available CS6As recovered from expanded ABCs areas during 1999, 2006, and 2007. Our results show that the proportion of type 6C to true 6A IPD isolates continued to increase during 2006 and 2007. The incidence of IPD caused by serotype 6C remained stable during 2006 and 2007, while the incidence of serotype 6A and 6B IPD continued to decline. We also show that serotype 6C is genetically diverse, with four of six distinct clonal backgrounds shared with recently recovered serotype 6A strains. == MATERIALS AND METHODS == == CS6As and conventionally serotyped 6B isolates. == Cases of IPD were identified through the Centers for Disease Control and Prevention’s (CDC’s) ABCs system and were defined as being the isolation of pneumococci from normally sterile sites in residents of surveillance areas (http://www.cdc.gov/ncidod/dbmd/abcs/index.htm). The population under surveillance during 1999 increased considerably from the previous report (12), with approximately 18.6 million persons (compared to almost 16 million during 1999), including residents of California (San Francisco County), Connecticut, Georgia (20 counties in the Atlanta area), Maryland (six counties in the Baltimore area), Minnesota (seven counties in the Twin Cities area), New York (seven counties in the Rochester area and eight in the Albany area), Oregon (three counties in the Portland area), Microtubule inhibitor 1 and Tennessee (five urban counties). Populations of New Mexico and additional counties in California, Minnesota, and Tennessee were added during subsequent years such that the total population under surveillance during 2006 and 2007 was approximately 28.2 million according to 2006 postcensus population estimates (and therefore increased by more than 10 million individuals compared to the previous report [12]). All isolates described in this study were conventionally serotyped using latex agglutination and.