data file_micro results and vaccine status_17aug16

Excel file for Streptococcus pneumoniae carriage isolates showing serotypes, molecular types, antimicrobial susceptibility, and date of collection. Information on the age, ethnicity, and pneumococcal conjugate vaccine status of study participants from whom the isolates were obtained is provided

Silica Desiccant Packets for Storage and Transport of <i>Streptococcus pneumoniae</i> and Other Clinically Relevant Species

<div><p>Bacterial isolates are often transported between laboratories for research and diagnostic purposes. Silica desiccant packets (SDPs), which are inexpensive and do not require freezing, were evaluated for storage and recovery of bacterial isolates. Conditions such as inoculum size, swab type and temperature of storage were investigated using ten <i>Streptococcus pneumoniae</i> isolates. The optimized protocol was then tested using 49 additional <i>S. pneumoniae</i> isolates representing 40 serogroups. Overall, <i>S. pneumoniae</i> growth was considered satisfactory (>100 colony forming units) for 98/109 (89.9%) and 20/20 (100%) swabs after 14 days at room temperature or 28 days at 4° C, respectively. Storage in SDPs did not impact on the ability of <i>S. pneumoniae</i> isolates to be subsequently serotyped. When the survival of nine other clinically relevant bacterial species was tested, seven were viable after 28 days at room temperature, the exceptions being <i>Neisseria gonorrhoeae</i> and <i>Haemophilus influenzae</i>. SDPs are suitable for transport and short-term storage of bacterial species including <i>S. pneumoniae</i>.</p> </div

Performance of microarray in determining percent abundance of serotypes in spiked and field samples.

<p>The percent relative abundance reported by method 4 (culture microarray) compared with the inocula for 174 serotypeable pneumococci within 70 spiked samples with multiple serotypes (filled circles) and compared with results obtained by conventional serotyping according to the reference method for 61 serotypeable pneumococci within 27 field samples with multiple serotypes (open circles). For the spiked samples, the correlation of relative abundance results between the inocula and microarray was significant (<i>p <</i> 0.001): Spearman’s <i>r</i> = 0.863 (95% CI: 0.818, 0.897). Similarly, the correlation between actual relative abundance and microarray results was significant for the field samples (<i>p <</i> 0.001): Spearman’s <i>r</i> = 0.907 (95% CI: 0.847, 0.944).</p

Isolates used to create spiked samples.

<p>¹Isolates were kindly provided by Prof. Samir Saha (Bangladesh), Assoc. Prof Fiona Russell (Fiji), Dr. Peter Adrian and Prof. Shabir Madhi (South Africa), and Prof. Kate O’Brien (United States).</p><p>²Site of isolation not known.</p><p>Isolates used to create spiked samples.</p

Serotype distribution in field samples.

<p>A total of 307 serotypeable pneumococci (representing 49 serotypes) were identified in 260 nasopharyngeal swab samples collected from children in six countries. The 26 most common serotypes are shown here, with the remaining 23 serotypes identified combined as “other”.</p

Sensitivity and PPV of the five methods testing the 260 field samples.

<p>The point estimates and 95% CIs for sensitivity (A) and PPV (B) are depicted. The sensitivity of method 4 is higher than those of the other methods.</p

Spiked sample testing results.

<p>For each method (labelled m1–m22), the sensitivity of detection of the major serotypes (<i>x-</i>axis) and minor serotypes (<i>y-</i>axis) is plotted on the graph, with the PPV shown in colour according to the colour bar on the right. Methods that directly tested the sample or included a culture amplification step are represented by triangles and circles, respectively.</p

Agreement between serotypes obtained by culture and those obtained by qPCR.

<p>* NT = non-typeable pneumococci</p><p>Agreement between serotypes obtained by culture and those obtained by qPCR.</p

Algorithm for the identification and quantification of serotype 6 types directly from NP samples by S6-q(PCR)².

<p>DNA purified from NP samples is utilized as template in qPCR and PCR reactions. Arrows indicate reactions to be performed, qPCR in dark gray boxes or PCR in light gray boxes, and continuous lines indicate reaction results. The final serotype obtained is indicated in the black boxes.</p

Quantification and subtyping, by exclusion, of serotypes 6A, 6B, 6C, and 6D by S6-q(PCR)².

<p>DNA from NP samples was utilized as template in qPCR and PCR reactions. (I) The first set of qPCR reactions quantified serogroup 6, including serotype 6A, 6B, 6C and 6D (top panel), whereas the second specifically quantified serotypes 6C and 6D (bottom panel). Serotype 6A and 6B or serotype 6C or 6D are differentiated by one single nucleotide polymorphisms (SNPs) in the <i>wci</i>P gene. To type individual serotypes, PCR reactions were performed targeting subtype SNPs within the <i>wci</i>P gene to identify (II) serotypes 6A and 6C or (III) serotypes 6B and 6D strain. A PCR targeting (IV) serotypes 6C and 6D specifically by amplifying the <i>wci</i>Nβ gene was performed as an additional control.</p