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

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

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