The isolate 7236-07 <i>cps</i> locus does not contain capsular biosynthetic or novel surface protein genes.

<p>Schematic of the <i>cps</i> locus between primers 5419 and 3419 from isolate 7236-07 (deposited to GenBank, accession no. KJ363164). Genes and spacing are to scale. <i>dexB</i> and <i>aliA</i> are truncated at their 5′ and 3′ ends, respectively, in the sequence coverage. Annotations of <i>tnp</i> pseudogenes were assigned corresponding to the serotype 5 <i>cps</i> locus (GenBank no. CR931637).</p

Population-Based Analysis of Invasive Nontypeable Pneumococci Reveals That Most Have Defective Capsule Synthesis Genes

<div><p>Since nasopharyngeal carriage of pneumococcus precedes invasive pneumococcal disease, characteristics of carriage isolates could be incorrectly assumed to reflect those of invasive isolates. While most pneumococci express a capsular polysaccharide, nontypeable pneumococci are sometimes isolated. Carriage nontypeables tend to encode novel surface proteins in place of a capsular polysaccharide synthetic locus, the <i>cps</i> locus. In contrast, capsular polysaccharide is believed to be indispensable for invasive pneumococcal disease, and nontypeables from population-based invasive pneumococcal disease surveillance have not been extensively characterized. We received 14,328 invasive pneumococcal isolates through the Active Bacterial Core surveillance program during 2006–2009. Isolates that were nontypeable by Quellung serotyping were characterized by PCR serotyping, sequence analyses of the <i>cps</i> locus, and multilocus sequence typing. Eighty-eight isolates were Quellung-nontypeable (0.61%). Of these, 79 (89.8%) contained <i>cps</i> loci. Twenty-two nontypeables exhibited serotype 8 <i>cps</i> loci with defects, primarily within <i>wchA</i>. Six of the remaining nine isolates contained previously-described <i>aliB</i> homologs in place of <i>cps</i> loci. Multilocus sequence typing revealed that most nontypeables that lacked capsular biosynthetic genes were related to established non-encapsulated lineages. Thus, invasive pneumococcal disease caused by nontypeable pneumococcus remains rare in the United States, and while carriage nontypeables lacking <i>cps</i> loci are frequently isolated, such nontypeable are extremely rare in invasive pneumococcal disease. Most invasive nontypeable pneumococci possess defective <i>cps</i> locus genes, with an over-representation of defective serotype 8 <i>cps</i> variants.</p></div

Mutations in PCR-serotype 8 Isolates.

a<p>Sequence numbers correspond to GenBank accession No. AJ239004.</p>b<p>Polymorphisms present in an alternative serotype 8 sequence (accession No. CR931644) were ignored.</p>c<p>Residue numbers correspond to amino acid sequence deduced from <i>cap8C</i> (Wzd), <i>cap8D</i> (Wze), or <i>cap8E</i> (WchA) in GenBank accession No. AJ239004.</p>d<p>FS, frameshift;</p><p>*, stop.</p>e<p>Residue previously identified as a site of inactivating mutation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097825#pone.0097825-Xayarath1" target="_blank">[29]</a>.</p

Multi-locus sequence types of Group II Nontypeable Isolates, 2006–2009.

1<p>Data obtained from MLST.net, accessed January 26, 2014.</p

PCR-8 nontypeable isolates contain inactivating mutations in <i>wchA</i>.

<p>A. Schematic of the serotype 8 <i>cps</i> locus (GenBank accession No. AJ239004). Alternative nomenclature is shown for regulatory genes. B. Molecular model of WchA as predicted by TMPRED (<a href="http://www.ch.embnet.org/software/TMPRED_form.html" target="_blank">http://www.ch.embnet.org/software/TMPRED_form.html</a>). Black arrows indicate nonsense (*) and frameshift (**) mutations; gray arrows indicate missense mutations. Residue numbers correspond to the predicted primary amino acid sequence for WchA.</p

PCR-serotype Distribution of Nontypeable Pneumococci, 2006–2009.

<p>PCR-serotype Distribution of Nontypeable Pneumococci, 2006–2009.</p