Using two monoclonal antibodies, we found subtypes among pneumococcal isolates that are typed as serotype 6A by the quellung reaction. The prevalent subtype bound to both monoclonal antibodies and was labeled here 6A␣, whereas the minor subtype bound to only one monoclonal antibody and was labeled 6A. To determine the biochemical nature of the two serologically defined subtypes, we purified capsular polysaccharides (PSs) from the two subtypes and examined their chemical structures with gas-liquid chromatography and mass spectrometry. The study results for 6A␣ PS are consistent with the previously published structure of 6A PS, which is 32) galactose (133) glucose (133) rhamnose (133) Streptococcus pneumoniae is a major human pathogen that is responsible for a large percentage of cases of pneumonia, meningitis, otitis media, and sepsis (6). All pathogenic pneumococci are known to display one of many structurally diverse carbohydrate capsules, which shield pneumococci from host phagocytes and increase their pathogenicity (2). Antisera to a capsule type can be used to treat patients infected with the pneumococci expressing that capsule type (4). Consequently, for the past century, the serological types of pneumococcal capsules have been extensively investigated with quellung reactions. These studies have culminated in identifying 90 different pneumococcal capsules with distinct serological patterns (9) and chemical structures (10).Not all 90 serotypes are equally pathogenic. For instance, serotypes 6A and 6B account for 4.7% and 7%, respectively, of cases of invasive pneumococcal disease in the U.S. population (19,20). Because of their medical importance, the molecular natures of serotype 6A and its related serotype, serotype 6B, have been studied extensively. Biochemical studies found that the capsular polysaccharides (PSs) of serotypes 6A and 6B are linear polymers with a repeating unit containing four monosaccharides/alditols: rhamnose, ribitol-phosphate (P), galactose, and glucose (10). The two PSs are identical except for a difference in the linkage between rhamnose and ribitol (see Fig. 6).Currently available pneumococcal vaccines are designed to elicit antibodies to the capsular PSs of the most common pneumococcal serotypes. Since vaccine-induced immunoprotection is serotype specific, serotyping pneumococcal isolates from patients is an important tool for monitoring the effectiveness of pneumococcal vaccines (3). Because the classical quellung reaction with rabbit antisera is tedious to perform (13), we have developed a new serotyping system based on mouse monoclonal antibodies (mAbs) and a multiplexed immunoassay (27). While validating the new system, we found that a minor fraction of the isolates determined to be serotype 6A by quellung reaction bound to one 6A-specific mAb (Hyp6AG1) but not to the other (Hyp6AM3), whereas the majority of the serotype 6A isolates bound to both mAbs (12). To distinguish between the isolates, we have labeled the isolates reacting with both mAbs as 6A␣ and those reacting wit...