Microarray summary

Summary of microarray detection of pneumococcal serotypes present in nasopharyngeal specimen

Serotype-specific ranking of multiple pneumococcal carriage.

<p>Nasopharyngeal swabs collected from all children aged 6 weeks to 24 months from the Kathmandu Valley, Nepal were analysed by microarray, with each <i>Streptococcus</i> isolate from pneumococcus positive swabs ranked according to its relative abundance to other isolates present on the swab.</p

Serotype-specific propensity for isolation as a primary or non-primary isolate.

<p>Pneumococcal serotypes identified from nasopharyngeal swabs of Nepalese children aged 6 weeks to 24 months from the Kathmandu Valley, Nepal, were classified as to whether they occurred as a primary or non-primary isolate (*p<0·05). Specifically for each serotype: 15B, 10A, 35A, 34, 35F, 16F, 20, NT4b, 13, and NT4a p<0.0001; 6A p = 0.0005; 6B, 19A and 6C p = 0.0012; 23A and 33B p = 0.0016; NT2 p = 0.0257; 23F p = 0.0035; 4 p = 0.0101. The serotypes, 9V, 14, 19F, 3, 11D, 17F, 35B, 35C, 39, 7C, 45, 15, 7B, 8, 9N, 18C, 15A, 23B, 29, 22A, 28F, 31, 33C, 6D, 19B, 10F, 24A, 38, 48, 9L, 11A, 11B, 12F, 17A, 18A, 24B, 32F, 33A, 33F, 36, 1, 5, 7F, NT3b, 25F, 28A, 37, 40, 19C, and NT were not labelled and/or had non-significant p-values and/or were isolated on less than five occasions. MGS = Mitis-group Streptococcus.</p

Presence of Antibiotic Resistance Genes in Pneumococcal Positive Array Samples.

<p><i>cat</i>—chloramphenicol acetyltransferase, <i>ermB</i>—rRNA adenine N-6-methyltransferase (resistance to erythromycin), <i>tetM</i>—Ribosomal protection protein (conferring resistance to tetracycline), <i>aphA3</i>—kanamycin resistance, <i>sat4</i>—streptothricin, <i>mefA</i>—Macrolide-Lincosamide-Streptogramin B efflux pump, <i>ermC</i>—rRNA adenine N-6-methyltransferase (conferring resistance to erythromycin), <i>tetK</i>—tetracycline efflux pump, <i>tetO</i>—Ribosomal protection protein (conferring resistance to tetracycline).</p><p>Presence of Antibiotic Resistance Genes in Pneumococcal Positive Array Samples.</p

Heat map representation of nasopharyngeal swab isolates from children aged 6 weeks to 24 months from the Kathmandu Valley, Nepal.

<p>Isolates are ordered according to participant number and presence of pneumococcus. The depth of colour is representative of the relative abundance of the isolate identified by microarray. Each isolate was divided into three categories: S—Typeable pneumococci, N– Non-typeable pneumococci and, M—Mitis-group Streptococcus. Subsequent isolates within these categories were then ranked 1–4 according to relative abundance.</p

Directional node plot of nasopharyngeal swab pneumococcal serotypes identified by microarray from children aged 6 weeks to 24 months from the Kathmandu Valley, Nepal.

<p>The size of each node is representative of the number of primary isolates identified for each serotype. The width of the connecting line is representative of the number of times the connected serotype was found in conjunction with the primary isolate. Green coloured nodes are those serotypes covered by PCV13. Unfilled circles are serotypes that were only found as non-primary isolates.</p

Characteristics of Nepal Pneumococcal Carriage Study Subjects, n (%).

<p>Characteristics of Nepal Pneumococcal Carriage Study Subjects, n (%).</p

Multiple pneumococcal carriage by age group.

<p>The proportion of nasopharyngeal swabs from children from the Kathmandu Valley, Nepal, positive for pneumococcal serotype/s by microarray analysis categorised by age group. Error bars indicate 95% confidence interval upper limits.</p

Leader sequence upstream of <i>patAB</i>.

<p>The graph represents the free energy of the most stable folded form of the 5′ region of the <i>patAB</i> transcript, as it extends from the promoter, in 4038 (black line) and 4039 (red line). The positions of the C1855761A polymorphism (PUS) distinguishing the two isolates and translation initiation site are indicated by the dashed lines, while the Shine-Dalgarno sequence is represented by the shaded region. The terminator-like hairpin structures formed by both transcripts as the RNA reaches the point at which the Shine-Dalgarno sequence is transcribed are displayed; it is evident that the mutation in 4039 is predicted to greatly weaken the hairpin loop of this secondary structure.</p

Phylogenetic analysis of the clonal complex 180 isolates.

<p>(A) A simplified representation of the 2,036,867 bp genome of <i>S. pneumoniae</i> OXC141 with tick marks every 0.5 Mb. The loci encoding the proteinaceous antigens PspA and PspC, as well as the capsule biosynthesis locus, are labelled, as are the prophage φOXC141, a putative ICE-related sequence, the ∼22 kb bacteriocin island and Pneumococcal Pathogenicity Island 1 (PPI-1). (B) A maximum likelihood phylogeny of the serotype 3 isolates based on the vertically inherited substitutions not introduced through recombination events. The tree and taxa are coloured according to their geographical location. (C) The panel surrounded by the dotted line contains one row for each isolate in the tree, with a column for each base in the reference genome. Red blocks indicate recombination events reconstructed as occurring on an internal branch, hence are shared by more than one isolate through common descent, while blue blocks indicate recombinations unique to one particular isolate.</p