Streptococcus pneumoniae

Typing Services
Spn-cps1 + Spn-cps2
Spn-MLST ($250 per sample)

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$70/60/55/50 for 1/2/3/4 or more samples

Streptococcus pneumoniae is a common commensal of the nasopharynx, but also a major pathogen responsible for infections ranging in severity from otitis media and sinusitis to pneumonia, septicemia, and meningitis. Infants, the elderly, and the immunocompromised are at highest risk for pneumoccal disease. The antiphagocytic polysaccharide capsule is the major virulence factor, and is antigenically variable, with over 90 currently identified serotypes. Antibodies targeting the capsular polysaccharides are protective, which forms the basis for the pneumococcal conjugate vaccines (e.g., PCV7 and PCV13) introduced in recent years that confer protection to the more pathogenic serotypes. Since the PCVs were introduced, S. pneumoniae invasive infections due to vaccine serotypes have decreased, as expected, but other serotypes have increased such as multidrug-resistant serotype 19A. Capsular biosynthesis is mediated by multiple genes at the cps locus, and each serotype possesses a unique set of cps genes and/or alleles of these genes.

Surveillance of S. pneumoniae serotypes plays an important role in monitoring vaccine efficacy and strain replacement in a given geographical region. Unfortunately, conventional serotyping by the Quellung (Neufeld) reaction is costly in terms of antisera and labor, error prone, and limited by cross-reactions and non-typeable isolates. Consequently, DNA-based methods targeting a polymorphic region of the cps locus have been developed and validated. These include a sequential, multiplex PCR method which resolves up to 40 serotypes ( More promising in terms of resolution and portability is partial cps sequencing: analysis of 500 or 732 base pair regions resolved up to 46 serotypes, with many of the remaining strains partially resolved into serogroups (1,2).


As shown in the Spn-cps dendrogram, extending cps sequence analysis to 1510 base pairs resolves 75 out of 89 serotypes (highly divergent serotypes 25A, 25F, and 38 are not shown due to space limitations but are also resolved, for a total of 78 out of 92).

In addition, genotyping based on non-cps targets can play an important role in S. pneumoniae epidemiology in the vaccine era, since serotype/cps can vary in otherwise identical strains through capsular switching mediated by horizontal gene transfer. The gold standard for S. pneumoniae genotyping is MLST (multilocus sequence typing), which provides high resolution. For example, 594 serotype 19A isolates were resolved into 84 MLST types (3); however, MLST requires costly sequence analysis of 7 housekeeping genes.

In response to the need for affordable DNA-based typing, MicrobiType services for S. pneumonia include Spn-cps and Spn-MLST, our genomics-optimized versions of conventional cps and multilocus sequence typing, respectively. Note that Spn-cps has two parts in order to encompass the full 1510 base pairs: Spn-cps1 and Spn-cps2, resolving 65 and 71 serotypes, respectively. Each can be ordered individually, or together (at discounted price) to provide enhanced resolution.

(1) Elberse et al., 2011, PLoS One 6:e20390
(2) Leung et al., 2012, J. Clin. Microbiol. 50:2419
(3) Hulten et al., 2013, J. Clin. Microbiol. 51:1294

(MicrobiType services are for research/investigational use only.)