Among 40 S. pneumoniae isolates recovered from middle ear fluid of children with AOM, 16 (40%) were serotype 19A. Serotype 19A was the most common serotype isolated in the study during 2004–2006.

Antimicrobial drug susceptibility testing was performed on the serotype 19A isolates. Eight (50%) of the 16 isolates of 19A were highly penicillin resistant (MIC >2.0 µg/mL), and all 8 were also multidrug resistant.

MLST of these16 S. pneumoniae isolates with serotype 19A showed that 6 (38%) were ST-320; 3 (19%) were ST-199; 2 (13%) were unreported STs now assigned ST- 2722 and ST-2704; 2 (13%) were ST-1673; and 1 (6%) each of the remaining 3 was ST-1451, ST-2265, and ST-63. Among the 8 multidrug-resistant isolates, 5 (63%) were ST-320, 1 (13%) was ST-1451, and 1 (13%) was the newly assigned ST-2722 (Table 1, Figure 1). The genetic distance of the Legacy strain is closest to 7 other multidrug-resistant strains with ST-320 and ST-1451 in our group of 40 recent isolates.

To determine the evolutionary relationship of the Legacy strain (ST-2722) to other strains, we constructed a neighbor-joining tree. ST-2722 is assumed to have genetic relatedness to another ST in the database when an ST has >5 of the same loci as ST-2722 (Figure 2). ST-2722 belonged to a cluster in which all strains have 6 of 7 same loci. This cluster consisted of 59 (88%) strains with molecular type ST-156 and 1 strain each with ST-2722, ST-2128, ST-1227, ST-2616, ST-1893, ST-334, ST-1556, ST-2684, and ST-1697. The major dissimilarity of strains in this cluster was on loci recP (Table 2, Figure 3). The recP gene had 3 major variable sites at the 10th, 121st, and 368th bp among strains. For instance, the DNA at the 10th, 121st, and 368th bp are T, C, T, respectively, in ST-2722; C, T, T in ST-156; and C, T, C in ST-2128 (Figure 3).

Forty-three (64%) of the 67 strains related to ST-2722 were penicillin resistant, and 28 (42%) of these strains were resistant to at least 1 other antimicrobial drug. Thirty-four (51%) of the 67 strains related to ST-2722 serotype 19A strains were serotype 9V; 18 (27%) were serotype 14; and 5 (7%) were serotype 11A. Among the 43 antimicrobial drug–resistant strains in this cluster, 24 (56%) were serotype 9V, and 14 (33%) were serotype 14; others were serotype 11, 15C, and 19F.

We described the molecular and capsular types of pneumococci causing AOM in children tested in Rochester, New York, during 2004–2006. Serotype 19A, a relatively new molecular type, accounted for 40% of the isolates and has emerged as the major serotype causing ear infections in children. Eight different molecular STs expressed the 19A capsule; most of the strains were multidrug resistant. Among the 40 strains studied, 5% were new molecular STs. In addition, we analyzed the genetic relatedness of the strains to other previously described strains of serotype 19A. We traced the genetic origin of ST-2722 to a strain first identified in 1988 in Spain as ST-156, which expressed capsular serotype 9V (16). Over nearly 20 years before ST-2722 emerged, variants of this original ST-156 strain were identified in 18 countries, with 8 different STs and 13 different sequence/capsular type combinations (according to records in S. pneumoniae database).

ST-2722 (Legacy strain) appears to have resulted from a mutation identified in the recP gene that coincided with acquisition of multidrug resistance, including a ceftriaxone MIC of 6.0 µg/mL, and acquisition of capsular DNA associated with the 19A serotype. Because of genetic plasticity, different capsular genes of S. pneumoniae may transfer through DNA-mediated genetic recombination (17–19). The multidrug-resistant epidemic type 23F Spanish/USA clone has expressed capsular types 3, 9N, 14, and 19F. Capsular transformation may equip multidrug-resistant strains with highly virulent blood invasive phenotypes (18).

Many studies have documented the impact of the PCV7 on pneumococcal diseases. Introduction of PCV7 containing serotype 4, 6B, 9V, 14, 18C, 19F, and 23F has dramatically decreased the rate of carriage and disease caused by these vaccine serotypes. However, the proportion of invasive pneumococcal diseases caused by nonvaccine serotypes has increased substantially in recent years, and multiresistant strains have rapidly emerged (16,20–23). In addition, PCV7 offers moderate protection against AOM (24). The lowest level of protective activity provided by PCV7 was against serotype 19F, and 19F polysaccharide antigen provided less cross-protection for disease caused by related serotypes such as 19A (24,25). An increase in the rate of middle ear infections with 19A strains and other strains expressing capsular types not contained in PCV7 also has been reported (11). These developments encourage further ongoing epidemiologic surveillance. Emergence of new 19A strains may represent a successful vaccine escape mechanism used by PCV7-targeted clones, and antimicrobial drug nonsusceptibility provides an additional survival advantage that could help these organisms spread further.

By MLST analysis and capsular typing, we found that multiple STs expressing capsular type 19A have emerged as the most important otopathogens of children. We also found a new strain of S. pneumoniae (ST-2722), expressing a 19A capsule that is resistant to all FDA-approved antimicrobial drugs. ST-2722 has a genetic relatedness close to ST-156 reported to the S. pneumoniae MLST database from 18 countries. ST-2722 was multiresistant to antimicrobial drugs but had an MIC to ceftriaxone of 6.0 µg/mL. A study by Pelton et al. showed that multidrug-resistant 19A strains with ST-320 had an MIC to ceftriaxone of 8.0 µg/mL (10). The clinical importance of such strains is potentially high because empiric treatment of suspected and even proven pneumococcal infections typically relies on the efficacy of ceftriaxone.