Application of PCR-DGGE to the study of dynamics and biodiversity of microbial contaminants during the processing of Hibiscus sabdariffa drinks and concentrates

Introduction. Bissap (Hibiscus sabdariffa L.) is a common plant in the tropics. In Senegal, the calyces are used to make a popular juice. In the food industry, small and medium-sized enterprises (SMEs) are responsible for the transformation of bissap calyces into drinks, concentrates, jam, etc. In spite of the very low pH of the juice (pH < 3), problems of contamination and fermentation are often observed in the final products post-pasteurization. They are mainly due to Pseudomonas spp., E. coli, Klebsiella spp. and Pichia opuntiae. To solve this issue, monitoring of the microbial ecology was performed during the full process of bissap products. Methods and results. Fresh calyces and dried mixed calyces of the two varieties of Hibiscus sabdariffa ('Koor' and 'Vimto'), as well as juice samples, were collected at every stage of the processing of a bissap drink and syrup in a Senegalese SME. The monitoring of microbial flora was performed by using molecular fingerprinting. The molecular technique PCR-DGGE was employed to evaluate the microbial dynamics using bacterial 16S rDNA, yeast 26S rDNA and 28S rDNA mold profiles at each critical stage of the process. Results and discussion. The genetic profiles generated contributed to identifying the critical points in the manufacturing processes. A multivariate analysis based on the presence or absence of spots in the denaturing gradient electrophoresis gels (DGGE) showed that the microbial flora (bacteria, yeasts, molds) of bissap evolved during the following phases: harvest (fresh flower), drying (dried calyces) and processing (before filtration, after pasteurization and before packaging). Conclusion. Our work contributed to determining the microorganisms responsible for the microbial contamination of the final products, and highlighted the origin of these contaminants. The most important critical point was identified as the pasteurization step. (Résumé d'auteur

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Mother-to-child transmission of hepatitis B in sub-Saharan Africa

Comment on : Global elimination of mother-to-child transmission of hepatitis B: revisiting the current strategy./Thio CL, Guo N, Xie C, Nelson KE, Ehrhardt S. Lancet Infect Dis. 2015 Aug;15(8):981-5. doi: 10.1016/S1473-3099(15)00158-9. Epub 2015 Jul 2. PMID: 26145195International audienceCorrespondenc

Desulfovibrio senegalensis sp. nov., a mesophilic sulfate reducer isolated from marine sediment

International audienc

Short Communication: High Viral Load and Multidrug Resistance Due to Late Switch to Second-Line Regimens Could Be a Major Obstacle to Reach the 90-90-90 UNAIDS Objectives in Sub-Saharan Africa

International audienceIn the context of lifelong antiretroviral treatment (ART) as early as possible and to end the HIV/AIDS epidemic as a public health treat by 2030, it is important to evaluate the potential risk of transmission of HIV-1 drug resistance (HIVDR) in resource-limited countries (RLCs). Since HIV transmission is driven by HIV-1 RNA viral load (VL), we studied the association between plasma VL and HIVDR profiles in 451 adults failing first-line ART from the 2LADY-ANRS12169/EDCTP trial in Burkina Faso, Cameroon, and Senegal. Median duration on first-line ART was 49 months (IQR: 33-69) and 91% patients were asymptomatic. Genotypic drug resistance testing was successful for 446 patients and 98.7% of them were resistant to at least one of the first-line drugs; 40.6% and 55.8% were resistant to two or three drugs of their ongoing first-line ART, respectively. The median VL was higher in patients with HIVDR to all ongoing first-line drugs than in those still susceptible to at least one drug; 4.7 log10 copies/ml (IQR: 4.3-5.2) versus 4.2 log10 copies/ml (IQR: 3.7-4.7), respectively (p 5.0 log10 copies/ml. High rates of cross-resistance to other nucleoside reverse-transcriptase inhibitors were observed and were also highest in patients with high VL. Without improvement of patient monitoring to avoid late switch to second-line regimens, a potential new epidemic caused by HIVDR strains could emerge in sub-Saharan Africa and compromise all efforts to reach 90-90-90 UNAIDS objective by 2020

Ending AIDS as a public health threat by 2030: Scientific Developments from the 2016 INTEREST Conference in Yaoundé, Cameroon.

The underpinning theme of the 2016 INTEREST Conference held in Yaoundé, Cameroon, 3-6 May 2016 was ending AIDS as a public health threat by 2030. Focused primarily on HIV treatment, pathogenesis and prevention research in resource-limited settings, the conference attracted 369 active delegates from 34 countries, of which 22 were in Africa. Presentations on treatment optimization, acquired drug resistance, care of children and adolescents, laboratory monitoring and diagnostics, implementation challenges, HIV prevention, key populations, vaccine and cure, hepatitis C, mHealth, financing the HIV response and emerging pathogens, were accompanied by oral, mini-oral and poster presentations. Spirited plenary debates on the UNAIDS 90-90-90 treatment cascade goal and on antiretroviral pre-exposure prophylaxis took place. Joep Lange career guidance sessions and grantspersonship sessions attracted early career researchers. At the closing ceremony, the Yaoundé Declaration called on African governments; UNAIDS; development, bilateral, and multilateral partners; and civil society to adopt urgent and sustained approaches to end HIV by 2030

Field evaluation of dried blood spots for routine HIV-1 viral load and drug resistance monitoring in patients receiving antiretroviral therapy in Africa and Asia.

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Effectiveness of the prevention of HIV mother -to-child transmission (PMTCT) program via early infant diagnosis (EID) data in Senegal.

BACKGROUND:To improve the care and treatment of HIV-exposed children, early infant diagnosis (EID) using dried blood spot (DBS) sampling has been performed in Senegal since 2007, making molecular diagnosis accessible for patients living in decentralized settings. This study aimed to determine the evolution of the HIV transmission rate in children from 2008 to 2015 and to analyze associated factors, particularly the mother's treatment status and/or child's prophylaxis status and the feeding mode. METHODS:The data were analyzed using EID reports from the reference laboratory. Information related to sociodemographic characteristics, HIV profiles, the mother's treatment status, the child's prophylaxis status, and the feeding mode was included. Descriptive statistics were calculated, and bivariate and multivariate logistic regression analyses were performed. RESULTS:During the study period, a total of 5418 samples (5020 DBS and 398 buffy coat) from 168 primary prevention of HIV mother-to-child transmission (PMTCT) intervention sites in Senegal were tested. The samples were collected from 4443 children with a median age of 8 weeks (1-140 weeks) and a sex ratio (M/F) of 1.1 (2309/2095). One-third (35.2%; N = 1564) of the children were tested before 6 weeks of age. Twenty percent (N = 885) underwent molecular diagnostic testing more than once. An increased number of mothers receiving treatment (57.4%; N = 2550) and children receiving prophylaxis (52.1%; N = 2315) for protection against HIV infection during breastfeeding was found over the study period. The transmission rate decreased from 14.8% (95% confidence interval (CI): 11.4-18.3) in 2008 to 4.1% (95% CI: 2.5-7.5) in 2015 (p < 0.001). However, multivariate logistic regression analysis revealed that independent predictors of HIV mother-to-child transmission included lack of mother's treatment (adjusted odd ratio (aOR) = 3.8, 95% CI: 1.9-7.7; p˂0.001), lack of child's prophylaxis (aOR = 7.8, 95% CI: 1.7-35.7; p = 0.009), infant age at diagnosis (aOR = 2.2, 95% CI: 1.1-4.3 for ≤6 weeks versus 12-24 weeks; p = 0.025) and protective effect of breastfeeding on ART against formula feeding (aOR = 0.4, 95% CI: 0.2, 0.7; p = 0.005). CONCLUSION:This study demonstrates the effectiveness of PMTCT interventions in Senegal but indicates also that increased efforts should be continued to reduce the MTCT rate to less than 2%