Polymerase Chain Reaction (PCR) provides a superior tool for the diagnosis of Pneumococcal Infection in Burkina Faso

Purpose of study: The aim of this study was to determine the value of real-time Polymerase Chain Reaction (rt-PCR) in the routine surveillance of pneumococcal meningitis in Burkina Faso, compared to standard methods of culture, Gram stain and latex agglutination assay.Materiel and methods: A total of 385 specimens of cerebrospinal fluid were analyzed by the three standard bacteriological methods (Gram stain, latex agglutination assay, and culture) and real-time Polymerase Chain Reaction.Results: Of 385 specimens analyzed by these methods, 204 S. pneumoniae were detected by one or more  methods. Gram stain detected 36.4% (140/385) Gram positive encapsulated diplococci; 37.7% (145/385) and 20.8% (80/385) of the specimens were positive for pneumococci by latex agglutination assay and culture. These specimens were tested with rt-PCR, which confirmed 51.2% (197/385) S. pneumoniae positive. The sensitivity and specificity of culture were 54.4% and 31.5%, respectively, and the sensitivity and specificity of rt-PCR were 96.6% and 100%, respectively. These results showed that rt-PCR was more sensitive than Gram stain (p=0.0235), latex agglutination assay (p=0.0442)and culture (p=0.0006).The culture is the gold standard method; however, the result showed that rt-PCR had specificity and was as specific as Gram stain (p=0.3405) and latex agglutination assay (p=0.7745).Conclusion: rt-PCR was highly sensitive and specific. It could be used as a complementary diagnostic tool to  mprove case confirmation of bacterial meningitis. However,its high cost, the qualification of the technical staff and infrastructures required for its implementation, constitute obstacles to its widened use in countries with limited resources.Keywords: Streptococcus pneumoniae, meningitis, rt-PCR, standard bacteriological methods Objectif: Le but de cette étude était de déterminer la place de la rt-PCR dans la surveillance de routine deméningitespneumococciquesau Burkina Faso et la comparée avec les méthodes de la bactériologie classique: Culture, coloration de Gram et l’agglutination au latex.Matériel etméthodes: Au total, 385 échantillons deliquides céphalorachidiens (LCR)étaient analysés par les trois méthodes de la bactériologie classique (coloration de Gram, agglutination au latex, culture) et la PCR en temps réel.RESULTATS: Parmi 385 échantillons analysés, 204 cas de Streptococcuspneumoniae étaient détectés par une ou plusieurs méthodes. La coloration de Gram adétecté 36,4% (140/385) diplocoques encapsulés à Gram positif (DGP); 37,7% (145/385) et 20,8% (80/385) d’échantillons étaient positifs aux pneumocoques par l’agglutination au latex et la culture. Ces échantillons étaient aussi testés par rt-PCR qui a confirmé 51,2% (197/385) cas positifs de S. pneumoniae. La sensibilité et la spécificité de la culture étaient respectivement de 54,4% et 31,5%, et la sensibilité et la spécificité de rt-PCR étaient respectivement de 96,6% et 100%. Ces résultats ont montré que la rt-PCR était plus sensible que la coloration de Gram (p=0,0235), l’agglutination au latex (p=0,0442) et la  culture(p=0,0006).La culture est une méthode de référence; cependant, le résultat a montré que rt-PCR était plus sensibleet aussi spécifique que la coloration de Gram ((p=0,3405)et l’agglutination au latex (p=0,7745).Conclusion : :rt-PCR était plus sensible et plus spécifique. Elle pourrait être utilisée comme un outil de diagnosticcomplémentaire pour améliorer les cas de confirmation de méningites bactériennes. Cependant, ces coûts de réalisation, la qualification de techniciens et les matériels pour son application constituent des obstacles pour sa vulgarisation dans les pays à ressources limités.Keywords: Streptococcus pneumoniae, méningites, rt-PCR, méthodes de la bactériologie classique Article in English

Genetic diversity of bambara groundnut accessions from Burkina Faso using random amplified polymorphic DNA markers

Bambara groundnut (Vigna subterranea (L.) Verdc.) originated from Africa where it is an important grain legume. The knowledge of genetic variability level within a crop species is an important step towards improving it. The objective of this study was to determine the level and structure of genetic diversity of bambara groundnut from Burkina Faso. In this study, 92 bambara groundnut accessions from three climatic zones of Burkina Faso were characterized with 17 random amplified polymorphic DNA markers. The results revealed a high level of polymorphism 100%) for all loci tested and a total of 161 alleles counted with an average allelic richness of 9.471 alleles per locus. The average expected heterozygosity (0.270) reflected a moderate genetic diversity within the collection. A dendrogram established by the “neighbour joining” method classified the 92 accessions into three mixed clusters. A weak genetic diversity between the clusters was also observed. These results could lead to the development of conservation strategies and the implementation of varietal breeding in Burkina Faso.Keywords: Bambara groundnut, genetic diversity, RAPD markers, Burkina Fas

Profil de sensibilité des souches de pneumocoques aux antibiotiques avant l’introduction du vaccin anti pneumococcique conjugué à treize valences (PCV-13) au Burkina Faso

Introduction: Streptococcus pneumoniae constitue un pathogène important des méningites bactériennes aiguës au Burkina Faso. Cela a justifié l’introduction du vaccin pneumococcique conjugué en Octobre 2013 dans le programme élargi de vaccination chez les enfants de moins d’un an. L’objectif de ce travail consiste à établir le profil de sensibilité aux antibiotiques des souches de S. pneumoniae isolées du liquide cérébro-spinal. Méthodologie: Du 1er Janvier 2010 au 30 Décembre 2012, 37 souches de pneumocoques ont été collectées du réseau national de surveillance de la méningite du pays. Ces souches, repiquées sur de la gélose au sang frais, ont été confirmées par le test de sensibilité à l’optochine. Le test de Quellung a déterminé les sérotypes de pneumocoques et l’antibiogramme a été réalisé selon la méthode de diffusion et interprété selon le standard « European Committee of antibiotics susceptibility testing. Résultats: Sur 37 isolats sérotypés, 77% appartenaient aux sérotypes vaccinaux. L’antibiogramme a révélé que 92% des souches sensibles à l’oxacilline, 97% à l’érythromycine et 73% à la clindamycine. Le cotrimoxazole a été actif dans 14% et la tétracycline seulement 5% des souches. Conclusion: La majorité des souches de pneumocoques isolée des méningites au Burkina Faso appartiennent aux sérotypes vaccinaux. Mots clés: Sensibilité; Antibiotiques; Pneumocoques; PCV-13 English Title: Profile of antibiotics susceptibility testing of pneumococcal strains before the introduction of the thirteen-valent conjugate pneumococcal vaccine (PCV-13) in Burkina Faso English Abstract  Introduction: Streptococcus pneumoniae is an important pathogen of acute bacterial meningitis in Burkina Faso. This justify the introduction of the thirteen-valent pneumococcal vaccine in October 2013 in the expanded program of immunization in children under one year old. The aim of this work is to establish the antibiotics susceptibility testing profile of strains of S. pneumoniae isolated from cerebrospinal fluid. Methods: From January 1st, 2010 to December 30th, 2012, 37 strains of pneumococci were collected from the country's national meningitis surveillance network. These strains, subcultured on fresh blood agar, were confirmed by the optochin susceptibility testing. The Quellung test made it possible by determining the pneumococcal serotypes and the antibiogram carried out according to the diffusion method and interpreted according to the standard "European Committee of antibiotics susceptibility testing”. Results: Of the thirty-seven typed isolates, 77% belonged to the vaccine serotypes. Susceptibility to antibiotics reports 92% of strains susceptible to oxacillin, 97% to erythromycin and 73% to clindamycin. Cotrimoxazole was active in 14% and tetracycline only 5% of the strains. Conclusion: The majority of pneumococcal strains isolated from meningitis in Burkina Faso belong to vaccine serotypes. Keywords: Antibiotics; susceptibility testing; Pneumococci; PCV-1

: Lancet HIV

International audienceBACKGROUND: The decision about whether to switch to third-line antiretroviral therapy (ART) in patients with treatment failure on second-line therapy is difficult in settings with little access to genotypic resistance testing. In this study, we used a standardised algorithm including a wide range of adherence-enhancing interventions followed by a new viral load measurement to decide whether to switch to third-line therapy in this situation. The decision, made on the basis of effectiveness of the adherence reinforcement to drive viral resuppression, did not use genotypic resistance testing. METHODS: In this prospective cohort study, adults in four west African countries with treatment failure of a boosted protease inhibitor ART regimen were offered nine adherence reinforcement interventions, and followed up for 64 weeks. We measured viral load at week 12 and used the results to decide ART treatment at week 16: if successful resuppression (plasma HIV-1 RNA /=2 log10 copies per mL compared with baseline), patients continued the same second-line regimen; otherwise they switched to a third-line regimen based on ritonavir-boosted darunavir and raltegravir. The primary endpoint was virological success at week 64 (plasma HIV-1 RNA <50 copies per mL). After study termination we did genotypic resistance testing on frozen plasma samples collected at baseline, and retrospectively determined the appropriateness of the week 16 decision on the basis of the baseline genotypic susceptibility score. FINDINGS: Between March 28, 2013, and May 11, 2015, of the 198 eligible participants, five died before week 16. Of the 193 remaining, 130 (67%) reached viral resuppression and continued with second-line ART, and 63 (33%) switched to third-line ART at week 16. Post-study genotypic resistance testing showed that the baseline genotypic susceptibility score was calculable in 166 patients, of whom 57 (34%) had a score less than 2. We retrospectively concluded that the week 16 decision was appropriate in 145 (75%) patients. At week 64, four patients (2%) were lost to follow-up, ten (5%) had died, and 101 (52%) had a viral load less than 50 copies per mL. INTERPRETATION: Poor adherence is the first problem to tackle in patients for whom second-line ART is failing when resistance tests are not routinely available and is effectively a manageable problem. Lack of access to genotypic resistance testing should not be an obstacle to the prescription of third-line ART in patients who do not achieve viral resuppression after adherence reinforcement. FUNDING: French Agency for Research on AIDS and Viral Hepatitis