Non-pneumococcal mitis-group streptococci confound detection of pneumococcal capsular serotype-specific loci in upper respiratory tract

• Published in: PeerJ (San Francisco, CA) CA), 2013-06, Vol.1, p.e97-e97
• Main Authors: Carvalho, Maria da Gloria, Pimenta, Fabiana C, Moura, Iaci, Roundtree, Alexis, Gertz, Jr, Robert E, Li, Zhongya, Jagero, Geofrey, Bigogo, Godfrey, Junghae, Muthoni, Conklin, Laura, Feikin, Daniel R, Breiman, Robert F, Whitney, Cynthia G, Beall, Bernard W
• Format: Article
• Language: English
• Subjects: Biodiversity; Children; Conserved sequence; Disease control; HIV; Human immunodeficiency virus; Infectious Diseases; Medical research; Meningitis; Microbiology; Microbiota (Symbiotic organisms); Mitis group streptococci; Morphology; Oropharyngeal and nasopharyngeal flora; PCR for serotype deduction; Pneumococcal serotype-specific loci; Polysaccharides; Respiratory tract; Serotypes; Serotyping; Streptococcus infections; Streptococcus oralis; Streptococcus pneumoniae; Studies; Vaccines
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.97

We performed culture-based and PCR-based tests for pneumococcal identification and serotyping from carriage specimens collected in rural and urban Kenya. Nasopharyngeal specimens from 237 healthy children 98.7%) with the reference cmPCR amplicon for the st, while cmPCR amplicons from lytA-negative specimens were generally more divergent. Separate testing of 56 A-OPs and 56 A-NPs revealed that ∼94% of the positive cmPCR results from A-NP/OPs were from OP microbiota. In contrast, A-NPs yielded >2-fold more pneumococcal isolates than A-OPs. Verified and suspected non-pneumococcal cmPCR serotypes/serogroups appeared to be relatively rare in C-NPs and A-NPs compared to A-OPs. Our findings indicate that non-pneumococcal species can confound serotype-specific PCR and other sequence-based assays due to evolutionarily conserved genes most likely involved in biosyn