Multilocus allele and 16S rRNA gene sequence designation depicting comparison of <i>S. salivarius</i> strain from meningitis patient to oral carriage isolates recovered from radiology physician assistant and technician.^a

a<p>The 8 housekeeping gene targets <i>glcK</i>, <i>ddlA</i>, <i>pepO</i>, <i>ilvC</i>, <i>thrS</i>, <i>pyrE</i>, <i>dnaE</i>, and <i>sodA</i> refer to the <i>S. salivarius</i>group MLST scheme described in reference 5 and the alleles correspond to the same ones listed in reference 5 except where in bold and italicized. The 7 remaining housekeeping gene targets (<i>rpoB</i>, <i>sodA2</i>, <i>pyk</i>, <i>ppaC</i>, <i>tuf</i>, <i>pfl</i>, <i>map</i>) refer to the viridans streptococcal MLST/speciating scheme available at <a href="http://viridans.emlsa.net/" target="_blank">http://viridans.emlsa.net/</a> (5). All bold/italicized designations correspond to sequences not found in the GenBank that were found in these isolates. GenBank accessions for the sequences corresponding to all of the underlined numbers are supplied in the Methods. The 8 following <i>S. salivarius</i> sequences have been previously documented by other investigators and are listed along with their GenBank accession numbers: <i>rpoB1</i>/GU556187, <i>sodA2-1</i>/AB200166, <i>ppaC1</i>/GU556189, <i>pyk2</i>/CP002888, <i>tuf1</i>/GU556190, <i>tuf2</i>/CP002888, 16S <i>rrnA2</i>/CP002888, and 16S <i>rrnA1</i>/GU175444.</p>b<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032169#s3" target="_blank">Results</a> shared between two isolates from case CSF.</p>c<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032169#s3" target="_blank">Results</a> shared between three carriage isolates (dorsal tongue and saliva).</p>d<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032169#s3" target="_blank">Results</a> shared between two carriage isolates (dorsal tongue and saliva).</p

Cases reported through national meningitis surveillance by age group and etiology, Burkina Faso, 2011–2013.

<p>Cases reported through national meningitis surveillance by age group and etiology, Burkina Faso, 2011–2013.</p

Effect of lytic enzyme treatment on extraction of nucleic acid from blood specimens.

<p>Average Ct value of individual real-time PCR reactions (<i>n</i> = 4) containing TNA extracted from healthy donor blood spiked with serial dilutions of <i>S. pyogenes</i> (A), <i>S. aureus</i> (B), or <i>K. pneumoniae</i> (C) without treatment or after incubation with TE buffer alone or TE buffer with lytic enzymes (lysozyme, lysostaphin, and mutanolysin) at 37°C for 30 min. (D) Ct values of serial dilutions of <i>K. pneumoniae</i> spiked into saline (to mimic NP/OP swab) or blood. Error bars display standard deviation. *<i>p</i><0.0001 compared to no treatment. ^#<i>p</i><0.05 compared to same concentration of organisms in saline.</p

Cumulative improvement of pathogen detection with optimization of experimental parameters.

<p>Potential improvement in Ct value (number of cycles) achieved by optimizing each experimental parameter. *Number of cycles gained varies based on organism, target, and specimen type. ^#Theoretical improvement calculated based on assumption of 3.3 cycle difference with 10-fold change in nucleic acid concentration.</p

National meningitis data quality and completeness indicators, Burkina Faso, 2011–2013.

<p>National meningitis data quality and completeness indicators, Burkina Faso, 2011–2013.</p

Epidemic curve of all suspected, probable, and confirmed meningitis cases by month, Burkina Faso, 2011–2013.

<p>Epidemic curve of all suspected, probable, and confirmed meningitis cases by month, Burkina Faso, 2011–2013.</p

Annual incidence (cases per 100,000 persons) of suspected, probable, and confirmed meningitis, Burkina Faso, 2011–2013.

<p>Annual incidence (cases per 100,000 persons) of suspected, probable, and confirmed meningitis, Burkina Faso, 2011–2013.</p

Flow diagram of the national case-based meningitis surveillance system, Burkina Faso, 2011–2013.

<p>Abbreviation: rt-PCR, real-time polymerase chain reaction. *Specimens can be tested by multiple methods.</p

Effect of enzyme system on detection of pathogen targets in primary clinical specimens.

<p>Data shown are difference in Ct value between reactions using Quanta One-step RT-PCR ToughMix and AgPath-ID One-step RT-PCR kit when testing TNA extracted from NP/OP swabs (A) or blood (B). Each data point represents the difference in Ct value between the two reactions for an individual clinical specimen. Median difference is indicated (<b>―</b>) for assays with ≥2 positive results. *Targets that were only detected using AgPath always occurred when Ct values were >33.</p

Epidemic curve of confirmed* pneumococcal meningitis cases, serotyped pneumococcal meningitis cases, PCV13-associated pneumococcal meningitis cases, and serotype 1 pneumococcal meningitis cases among children aged <5 years, by month, Burkina Faso, 2011–2013.

<p>*<i>S</i>. <i>pneumoniae</i> isolated from cerebrospinal fluid (CSF) by culture or detected in CSF by real-time polymerase chain reaction or latex.</p