title: Non-pneumococcal mitis-group streptococci confound detection of pneumococcal capsular serotype-specific loci in upper respiratory tract.
abstract: 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 <5 years old (C-NPs) and combined nasopharyngeal/oropharyngeal specimens from 158 adults (A-NP/OPs, 118 HIV-positive) were assessed using pneumococcal isolation (following broth culture enrichment) with Quellung-based serotyping, real-time lytA-PCR, and conventional multiplexed PCR-serotyping (cmPCR). Culture-based testing from C-NPs, HIV-positive A-NP/OPs, and HIV-negative A-NP/OPs revealed 85.2%, 40.7%, and 12.5% pneumococcal carriage, respectively. In contrast, cmPCR serotypes were found in 93.2%, 98.3%, and 95.0% of these sets, respectively. Two of 16 lytA-negative C-NPs and 26 of 28 lytA-negative A-NP/OPs were cmPCR-positive for 1-10 serotypes (sts) or serogroups (sgs). A-NP/OPs averaged 5.5 cmPCR serotypes/serogroups (5.2 in HIV-positive, 7.1 in HIV-negative) and C-NPs averaged 1.5 cmPCR serotypes/serogroups. cmPCR serotypes/serogroups from lytA-negative A-NP/OPs included st2, st4, sg7F/7A, sg9N/9L, st10A, sg10F/10C/33C, st13, st17F, sg18C/18A/18B/18F, sg22F/22A, and st39. Nine strains of three non-pneumococcal species (S. oralis, S. mitis, and S. parasanguinis) (7 from A-OP, 1 from both A-NP and A-OP, and 1 from C-NP) were each cmPCR-positive for one of 7 serotypes/serogroups (st5, st13, sg15A/15F, sg10F/10C/33C, sg33F/33A/37, sg18C/18A/18B/18F, sg12F/12A/12B/ 44/46) with amplicons revealing 83.6-99.7% sequence identity to pneumococcal references. In total, 150 cmPCR amplicons from carriage specimens were sequenced, including 25 from lytA-negative specimens. Amplicon sequences derived from specimens yielding a pneumococcal isolate with the corresponding serotype were identical or highly conserved (>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 biosynthesis of surface polysaccharide structures.
authors.affiliation: National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention , Atlanta , USA.
authors.forename: Maria da Gloria
authors.initials: Mda G
authors.lastname: Carvalho
authors.forename: Fabiana C
authors.initials: FC
authors.lastname: Pimenta
authors.forename: Iaci
authors.initials: I
authors.lastname: Moura
authors.forename: Alexis
authors.initials: A
authors.lastname: Roundtree
authors.forename: Robert E
authors.initials: RE
authors.lastname: Gertz
authors.forename: Zhongya
authors.initials: Z
authors.lastname: Li
authors.forename: Geofrey
authors.initials: G
authors.lastname: Jagero
authors.forename: Godfrey
authors.initials: G
authors.lastname: Bigogo
authors.forename: Muthoni
authors.initials: M
authors.lastname: Junghae
authors.forename: Laura
authors.initials: L
authors.lastname: Conklin
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Feikin
authors.forename: Robert F
authors.initials: RF
authors.lastname: Breiman
authors.forename: Cynthia G
authors.initials: CG
authors.lastname: Whitney
authors.forename: Bernard W
authors.initials: BW
authors.lastname: Beall
keywords: Mitis group streptococci; Oropharyngeal and nasopharyngeal flora; PCR for serotype deduction; Pneumococcal serotype-specific loci