To investigate the potential herd immunity effect of MenAfriVac, a new conjugate vaccine against serogroup A Neisseria meningitidis, a multiple cross-sectional carriage study was conducted in three districts in Burkina Faso in 2009, yielding a total of 20 326 oropharyngeal samples. A major challenge was the harmonisation of operational procedures and ensuring the reliability of results. Here we describe the laboratory quality control (QC) system that was implemented. Laboratory analysis performed by three local laboratories included colony morphology assessment, oxidase test, Gram stain, beta-galactosidase activity using o-nitrophenyl-beta-galactopyranoside (ONPG), gamma-glutamyl transferase (GGT) activity and slide agglutination serogrouping. Internal QC was performed on media, reagents, laboratory equipment and field conditions. Confirmation of results and molecular characterisation was performed at the Norwegian Institute of Public Health (Oslo, Norway). External QC was performed on 3% of specimens where no colonies morphologically resembling N. meningitidis had been identified and on 10% of non-ONPG-/GGT+ isolates. The QC system was a critical element: it identified logistical and operational problems in real time and ensured accuracy of the final data. The overall N. meningitidis carriage prevalence (3.98%) was probably slightly underestimated and the calculated true prevalence was 4.48%. The components of the presented QC system can easily be implemented in any other laboratory study.

Real-time PCR (rt-PCR) is a widely used molecular method for detection of Neisseria meningitidis (Nm). Several rt-PCR assays for Nm target the capsule transport gene, ctrA. However, over 16% of meningococcal carriage isolates lack ctrA, rendering this target gene ineffective at identification of this sub-population of meningococcal isolates. The Cu-Zn superoxide dismutase gene, sodC, is found in Nm but not in other Neisseria species. To better identify Nm, regardless of capsule genotype or expression status, a sodC-based TaqMan rt-PCR assay was developed and validated. Standard curves revealed an average lower limit of detection of 73 genomes per reaction at cycle threshold (C(t)) value of 35, with 100% average reaction efficiency and an average R(2) of 0.9925. 99.7% (624/626) of Nm isolates tested were sodC-positive, with a range of average C(t) values from 13.0 to 29.5. The mean sodC C(t) value of these Nm isolates was 17.6+/-2.2 (+/-SD). Of the 626 Nm tested, 178 were nongroupable (NG) ctrA-negative Nm isolates, and 98.9% (176/178) of these were detected by sodC rt-PCR. The assay was 100% specific, with all 244 non-Nm isolates testing negative. Of 157 clinical specimens tested, sodC detected 25/157 Nm or 4 additional specimens compared to ctrA and 24 more than culture. Among 582 carriage specimens, sodC detected Nm in 1 more than ctrA and in 4 more than culture. This sodC rt-PCR assay is a highly sensitive and specific method for detection of Nm, especially in carriage studies where many meningococcal isolates lack capsule genes.