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Martin A.,Ghent University | Imperiale B.,Laboratorio Of Referencia Del Programa Of Control Of Tuberculosis | Ravolonandriana P.,Institute Pasteur Of Madagascar | Coban A.Y.,Ondokuz Mayis University | And 12 more authors.
Journal of Antimicrobial Chemotherapy | Year: 2014

Objectives: To perform a multicentre study evaluating the performance of the direct nitrate reductase assay (NRA) for the detection of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis in sputum samples. Methods: The study was conducted in six laboratories performing tuberculosis diagnosis that were located in six different countries. The NRA was performed directly on sputum samples in parallel with the reference method used at each site. Detection of resistance was performed for rifampicin, isoniazid, ofloxacin and kanamycin. Results: Excellent agreement was obtained for all drugs tested at the majority of sites. The accuracy was 93.7%-100% for rifampicin, 88.2%-100% for isoniazid, 94.6%-100% for ofloxacin and 100% for kanamycin. The majority of NRA results were available at day 21 for sites 1, 2 and 5. Site 3 had a turnaround time of 13.9 days, at site 4 it was 18.4 days and at site 6 it was 16.2 days. The contamination rate ranged between 2.5% and 12%. Conclusions: Rapid detection of drug resistance by the direct NRA on sputum smear-positive samples was accurate and easy to implement in clinical diagnostic laboratories, making it a good alternative for rapid screening for MDR and XDR tuberculosis. © The Author 2013. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. Source

Vandelannoote K.,Institute of Tropical Medicine | Vandelannoote K.,University of Antwerp | Jordaens K.,University of Antwerp | Jordaens K.,Royal Museum for Central Africa | And 16 more authors.
Applied and Environmental Microbiology | Year: 2014

Buruli ulcer is an indolent, slowly progressing necrotizing disease of the skin caused by infection with Mycobacterium ulcerans. In the present study, we applied a redesigned technique to a vast panel of M. ulcerans disease isolates and clinical samples originating from multiple African disease foci in order to (i) gain fundamental insights into the population structure and evolutionary history of the pathogen and (ii) disentangle the phylogeographic relationships within the genetically conserved cluster of African M. ulcerans. Our analyses identified 23 different African insertion sequence element single nucleotide polymorphism (ISE-SNP) types that dominate in different areas where Buruli ulcer is endemic. These ISE-SNP types appear to be the initial stages of clonal diversification from a common, possibly ancestral ISE-SNP type. ISE-SNP types were found unevenly distributed over the greater West African hydrological drainage basins. Our findings suggest that geographical barriers bordering the basins to some extent prevented bacterial gene flow between basins and that this resulted in independent focal transmission clusters associated with the hydrological drainage areas. Different phylogenetic methods yielded two well-supported sister clades within the African ISE-SNP types. The ISE-SNP types from the "pan-African clade" were found to be widespread throughout Africa, while the ISE-SNP types of the "Gabonese/Cameroonian clade" were much rarer and found in a more restricted area, which suggested that the latter clade evolved more recently. Additionally, the Gabonese/Cameroonian clade was found to form a strongly supported monophyletic group with Papua New Guinean ISE-SNP type 8, which is unrelated to other Southeast Asian ISE-SNP types. © 2014, American Society for Microbiology. Source

Gehre F.,Medical Research Council MRC Unit | Gehre F.,Institute of Tropical Medicine | Antonio M.,Medical Research Council MRC Unit | Faihun F.,Laboratoire Of Reference Des Mycobacteries | And 7 more authors.
PLoS ONE | Year: 2013

Mycobacterium africanum is an important cause of tuberculosis (TB) in West Africa. So far, two lineages called M. africanum West African 1 (MAF1) and M. africanum West African 2 (MAF2) have been defined. Although several molecular studies on MAF2 have been conducted to date, little is known about MAF1. As MAF1 is mainly present in countries around the Gulf of Guinea we aimed to estimate its prevalence in Cotonou, the biggest city in Benin. Between 2005-06 we collected strains in Cotonou/Benin and genotyped them using spoligo- and 12-loci-MIRU-VNTR-typing. Analyzing 194 isolates, we found that 31% and 6% were MAF1 and MAF2, respectively. Therefore Benin is one of the countries with the highest prevalence (37%) of M. africanum in general and MAF1 in particular. Moreover, we combined our data from Benin with publicly available genotyping information from Nigeria and Sierra Leone, and determined the phylogeographic population structure and genotypic clustering of MAF1. Within the MAF1 lineage, we identified an unexpected great genetic variability with the presence of at least 10 sub-lineages. Interestingly, 8 out of 10 of the discovered sub-lineages not only clustered genetically but also geographically. Besides showing a remarkable local restriction to certain regions in Benin and Nigeria, the sub-lineages differed dramatically in their capacity to transmit within the human host population. While identifying Benin as one of the countries with the highest overall prevalence of M. africanum, this study also contains the first detailed description of the transmission dynamics and phylogenetic composition of the MAF1 lineage. © 2013 Gehre et al. Source

Affolabi D.,Laboratoire Of Reference Des Mycobacteries | Torrea G.,Institute of Tropical Medicine | Odoun M.,Laboratoire Of Reference Des Mycobacteries | Senou N.,Laboratoire Of Reference Des Mycobacteries | And 3 more authors.
International Journal of Tuberculosis and Lung Disease | Year: 2010

SETTING: National Reference Laboratory, Benin. OBJECTIVES: To compare the performance of Fraen FluoLED™ and LW Lumin™ light-emitting diode (LED) fluorescence microscopy modules. DESIGN: Acid-fast bacilli (AFB) smears, routinely examined with a classical fluorescence microscope, were blindly re-read with both LED systems at 200x magnification. Smears with discordant results were rechecked on all systems at 200x, and 100 randomly chosen smears were read again at 400x. Confirmed presence of AFB with any system was accepted as a true positive. RESULTS: A total of 1937 smears were examined by all systems. The Fraen and LW detected 895 (46.2%) and 817 (42.2%) positive and scanty positive smears. After rechecking 201 smears, 15 false-positive and 61 false-negative results were declared for Fraen, against 11 and 135 for LW. The systems had similar false-positive rates (1.7% for Fraen and 1.4% for LW), but differed significantly regarding detection of confirmed microscopy positives (93.5% and 85.6% respectively, P < 0.00001). A high correlation between both LED systems was found at 400x magnification. CONCLUSIONS: The Fraen LED fluorescence microscopy module performed significantly better than the LW LED at the most efficient 200x magnification. It was also more appreciated by all users. The LW module may perform equally well at higher magnification. © 2010 The Union. Source

Affolabi D.,Laboratoire Of Reference Des Mycobacteries | Sanoussi N.,Laboratoire Of Reference Des Mycobacteries | Vandelannoote K.,Institute of Tropical Medicine | Odoun M.,Laboratoire Of Reference Des Mycobacteries | And 4 more authors.
Journal of Clinical Microbiology | Year: 2012

We compared two DNA extraction methods (a semiautomated method using a Maxwell kit and a modified Boom method) and three amplification procedures (a single-step PCR, a nested PCR, and a real-time quantitative PCR) on 74 surgical tissue specimens from patients with clinically suspected Buruli ulcer. All of these procedures were compared before and after decontamination. We observed that, among the procedures tested, real-time PCR after the modified Boom extraction method or a single-run PCR assay after the Maxwell 16 extraction method, performed on nondecontaminated suspensions, are the best for the molecular diagnosis of Mycobacterium ulcerans disease. Copyright © 2012, American Society for Microbiology. All Rights Reserved. Source

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