Phenotypic detection of Metallo-β-Lactamase in imipenem-resistant Pseudomonas aeruginosa and Stenotrophomonas maltophilia at Schiphra Hospital of Ouagadougou in Burkina Faso

Background: Epidemic of carbapenemase-producing bacteria has become worldwide. Thus, during the last decade, the prevalence of carbapenem-resistant Enterobacteriaceae and non fermentative Gram-negative bacteria in human patients have increased. Carbapenemase-producing bacteria are usually multidrug resistant. Therefore, early recognition of carbapenemase producers is critical to prevent their spread. Objectives: The aim of this study was to contribute establishing the prevalence of isolates producing Metallo-β-Lactamase isolated from patients admitted to Schiphra Hospital of Ouagadougou. Methods: Susceptibility of bacteria to antimicrobial agents was evaluated by disc diffusion method using imipenem as screening antibiotic. The combination of imipenem-EDTA was used after detection the resistance to imipenem. Results: A total of 52 isolates resisting one of the third generation cephalosporins were collected. Five isolates showed an intermediary resistance to imipenem (9.61%). Two isolates were resistant to imipenem-EDTA (3.85%). The test of imipenem-EDTA was done to confirm to production of Metallo-β-Lactamase. The hydrolysis of bacterial extract by meropenem was confirmed by production with a kinetic activity at spectrophotometer V0=4.77x10–5µM/min for Pseudomonas aeruginosa and V0=1.183x10-4 µM/min for Stenotrophomonas maltophilia. Conclusion: This study showed that bacterial resistances by production to metallo-β-lactamases are a reality in Burkina Faso

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

Wood fuel supply basin in Bakel (Senegal) : the spatial transcription of a cross-border supply chain to feed a small town

Au Sénégal, les combustibles ligneux sont source de revenus pour des milliers de personnes et l’énergie de cuisson principale pour près de 70 % de la population. A Bakel et dans les villes secondaires similaires, la dépendance peut atteindre 90 % de la population et les prélèvements s’effectuent sur des distances relativement longues. Dans ce contexte, se pose la question des limites et de l’organisation des bassins d’approvisionnement. Cette thèse se propose d’examiner le bassin d’approvisionnement de Bakel dans une perspective multiséculaire susceptible de rendre compte de sa structure originale. L’analyse des différents éléments structurants du bassin met en évidence la primauté des différentiels juridiques accentués par la décentralisation et des jeux d’acteurs de la filière sur des critères de localisation de la ressource. D’un point de vue spatial, la distance au centre urbain ne paraît pas constituer la seule logique d’explication des zones de prélèvement : celles-ci sont davantage situées en fonction des critères culturels et sociaux, ainsi que des règlementations locales.L’étude examine tout particulièrement le rôle joué par la triple frontière entre Mali, Mauritanie et Sénégal dans les flux de bois-énergie destinés à Bakel et ses conséquences en termes de coopération quant à la gestion des ressources ligneuses. Dans un dernier temps, sont examinées les pratiques de consommation du bois-énergie et la structuration de la filière d’approvisionnement au cœur de la ville de Bakel. Une quantification de l’approvisionnement et des pratiques de consommation permet de mettre en évidence le maintien du bois-énergie dans les pratiques des habitants, mais aussi le poids des acteurs informels dans le fonctionnement de la filière au sein de la ville. Ces éléments plaident pour une forme de planification de la filière, mais aussi des espaces qui y participent, qu’il s’agisse de la ville comme lieu de consommation privilégié ou de l’ensemble du bassin, en développant notamment des coopérations transfrontalières officielles sur cette question.In Senegal, wood fuels are a source of income for thousands of people and the main cooking energy for nearly 70% of the population. In Bakel and similar secondary towns, dependency can be as high as 90% of the population, and harvesting takes place over relatively long distances. In this context, the question of the limits and organisation of supply basins arises. This thesis proposes to examine the Bakel supply basin from a multi-secular perspective that can account for its original structure. The analysis of the various structuring elements of the basin highlights the primacy of legal differentials accentuated by decentralization and the interplay of actors in the sector over resource localization criteria. From a spatial point of view, the distance from the urban centre does not seem to be the only logical explanation for the withdrawal zones: these are more located according to cultural and social criteria, as well as local regulations.The study examines in particular the role played by the triple border between Mali, Mauritania and Senegal in the flow of fuelwood to Bakel and its consequences in terms of cooperation in the management of wood resources. Finally, the study examines woodfuel consumption practices and the structuring of the supply chain in the heart of Bakel city. A quantification of supply and consumption practices makes it possible to highlight the maintenance of wood energy in the practices of the inhabitants, but also the weight of informal actors in the functioning of the sector within the city. These elements plead in favour of a form of planning for the sector, but also for the spaces that participate in it, whether the city as a privileged place of consumption or the whole basin, notably by developing official cross-border cooperation on this issue

Diagnostic, entraves et importance des corridors de transport routier dans le processus d’intégration régionale en Afrique de l’Ouest : le cas du Sénégal et ses pays voisins

Abstract: African integration is a concept that has gained new momentum in the world since the mid-1990s. This new trend also concerns West African States. The first attempts at regional integration had a first phase, during the 1960s and 1970s, and produced mixed results, often disappointing in terms of trade creation and acceleration of economic growth. The renewed interest in regional integration now raises the question of its influence on the economies of the countries concerned. New attempts made with regard to regional integration raise the question of its influence on the economies of the countries concerned, with the establishment of basic infrastructures. Among which, there are the road transport corridors, because they constitute the main means of communication in the region or the sub-region. Thus, based on a large literary review, qualitative and quantitative surveys near the Senegalese border control services, the Ministry of Transport and that of the economy and the budget, this present study sets as its main objective, to analyze the obstacles to the road transit of goods, services and people between Senegal and neighboring countries with a view to strengthening regional integration in the West African space. Thus the results first reveal that regional integration in West Africa in general and in particular between Senegal and its neighboring countries is strongly hampered by abnormal practices such as: road harassment, illicit perceptions on road transport corridors, the innumerable number of checkpoints, etc. ; then, they show that the road transport corridors that connect Senegal and neighboring countries mostly need to be rehabilitated or renovated and must be strengthened to; and finally, they show that the application of ECOWAS and UEMOA Decisions and Conventions would allow road transport corridors to be vectors and carriers of regional integration between Senegal and its neighboring countries

Estuaire inverse de basse Casamance : Impacts sur la qualité de l'eau et des agrosystèmes en milieu insulaire

International audienceThe mouth of the Casamance River, that works as a ria is not without impacts on the estuarine environment of the islands of the lower Casamance. In these islands where the altitude is extremely low (2 to 3 m), silty deposits are almost flush. However, the small tributaries (locally called "bolongs") that crisscross the islands are connected to the main reach of the Casamance River. They therefore have a salinity increasing upstream except at the end the rainy season when cumulated rainfall is important. Therefore, this contribution aims to be an analysis of the impacts of the inverse functioning of the Casamance estuary on the quality of the water and the agrosystems. To do this, the approach relies on a literature review, the collection of field data (observations, surveys, interviews, etc.) in the islands of Diogue, Carabane and Niomoune, and on GIS analysis. At the same time, surveys of GPS points and the measures in situ of salinity were conducted (wells and sources of water supply, estuary, and mouth). The results showed that the salinity directly affects the wells which here are usually the main sources of water supply. Shallow aquifers are affected by saline intrusion. Besides, the hydrologic conditions of the Casamance River, not allowing an exchange of fresh water permanent, leave a risk of consumption of water from the well which so far is intended for secondary purposesRésumé L'embouchure du fleuve Casamance qui fonctionne en réalité comme une ria n'est pas sans effet sur l'environnement estuarien des îles de la basse Casamance. Dans ces îles où l'altitude est extrêmement basse (2 à 3m), les dépôts vaseux sont quasi affleurants. Or, les petits affluents « bolongs » qui sillonnent les îles sont Thior & al 2 connectés au bras principal du fleuve Casamance. Ces derniers ont donc une salinité croissant vers l'amont due aux faibles apports en eau douce, sauf en fin de saison des pluies lorsque la pluviométrie cumulée est importante. Ainsi, cette contribution se veut d'être une analyse des impacts du fonctionnement inverse de l'estuaire de la Casamance sur la qualité de l'eau et sur les agrosystèmes. Pour ce faire, la démarche utilisée s'appuie sur une revue documentaire, l'exploitation de données de terrain (observations, enquêtes, entretiens, etc.) collectées dans les îles de Diogué Carabane, Niomoune et de l'imagerie spatiale et la géomatique. Parallèlement, des relevés de points GPS et des mesures in situ de taux de salinité ont été réalisés (puits et sources d'approvisionnement en eau, estuaire, et embouchure). Les résultats ont montré que la présence de l'eau de mer affecte directement les puits qui ici sont généralement les principales sources d'approvisionnement en eau. Les nappes phréatiques peu profondes sont affectées par l'intrusion saline. En plus, les conditions hydrologiques du fleuve Casamance ne permettant pas un échange permanent d'eau douce, laissent un risque de consommation d'eau des puits qui jusque-là est destiné à des fins secondaires

Estuaire inverse de basse Casamance : Impacts sur la qualité de l'eau et des agrosystèmes en milieu insulaire

International audienceThe mouth of the Casamance River, that works as a ria is not without impacts on the estuarine environment of the islands of the lower Casamance. In these islands where the altitude is extremely low (2 to 3 m), silty deposits are almost flush. However, the small tributaries (locally called "bolongs") that crisscross the islands are connected to the main reach of the Casamance River. They therefore have a salinity increasing upstream except at the end the rainy season when cumulated rainfall is important. Therefore, this contribution aims to be an analysis of the impacts of the inverse functioning of the Casamance estuary on the quality of the water and the agrosystems. To do this, the approach relies on a literature review, the collection of field data (observations, surveys, interviews, etc.) in the islands of Diogue, Carabane and Niomoune, and on GIS analysis. At the same time, surveys of GPS points and the measures in situ of salinity were conducted (wells and sources of water supply, estuary, and mouth). The results showed that the salinity directly affects the wells which here are usually the main sources of water supply. Shallow aquifers are affected by saline intrusion. Besides, the hydrologic conditions of the Casamance River, not allowing an exchange of fresh water permanent, leave a risk of consumption of water from the well which so far is intended for secondary purposesRésumé L'embouchure du fleuve Casamance qui fonctionne en réalité comme une ria n'est pas sans effet sur l'environnement estuarien des îles de la basse Casamance. Dans ces îles où l'altitude est extrêmement basse (2 à 3m), les dépôts vaseux sont quasi affleurants. Or, les petits affluents « bolongs » qui sillonnent les îles sont Thior & al 2 connectés au bras principal du fleuve Casamance. Ces derniers ont donc une salinité croissant vers l'amont due aux faibles apports en eau douce, sauf en fin de saison des pluies lorsque la pluviométrie cumulée est importante. Ainsi, cette contribution se veut d'être une analyse des impacts du fonctionnement inverse de l'estuaire de la Casamance sur la qualité de l'eau et sur les agrosystèmes. Pour ce faire, la démarche utilisée s'appuie sur une revue documentaire, l'exploitation de données de terrain (observations, enquêtes, entretiens, etc.) collectées dans les îles de Diogué Carabane, Niomoune et de l'imagerie spatiale et la géomatique. Parallèlement, des relevés de points GPS et des mesures in situ de taux de salinité ont été réalisés (puits et sources d'approvisionnement en eau, estuaire, et embouchure). Les résultats ont montré que la présence de l'eau de mer affecte directement les puits qui ici sont généralement les principales sources d'approvisionnement en eau. Les nappes phréatiques peu profondes sont affectées par l'intrusion saline. En plus, les conditions hydrologiques du fleuve Casamance ne permettant pas un échange permanent d'eau douce, laissent un risque de consommation d'eau des puits qui jusque-là est destiné à des fins secondaires

Analysis of contact tracing data showed contribution of asymptomatic and non-severe infections to the maintenance of SARS-CoV-2 transmission in Senegal

Abstract During the COVID-19 pandemic in Senegal, contact tracing was done to identify transmission clusters, their analysis allowed to understand their dynamics and evolution. In this study, we used information from the surveillance data and phone interviews to construct, represent and analyze COVID-19 transmission clusters from March 2, 2020, to May 31, 2021. In total, 114,040 samples were tested and 2153 transmission clusters identified. A maximum of 7 generations of secondary infections were noted. Clusters had an average of 29.58 members and 7.63 infected among them; their average duration was 27.95 days. Most of the clusters (77.3%) are concentrated in Dakar, capital city of Senegal. The 29 cases identified as super-spreaders, i.e., the indexes that had the most positive contacts, showed few symptoms or were asymptomatic. Deepest transmission clusters are those with the highest percentage of asymptomatic members. The correlation between proportion of asymptomatic and degree of transmission clusters showed that asymptomatic strongly contributed to the continuity of transmission within clusters. During this pandemic, all the efforts towards epidemiological investigations, active case-contact detection, allowed to identify in a short delay growing clusters and help response teams to mitigate the spread of the disease

The West Africa ICEMR Partnerships for Guiding Policy to Improve the Malaria Prevention and Control

The Mali National Malaria Control Program (NMCP) recently established a phased set of goals for eliminat-ing malaria in Mali by 2030. Over the past decade, the scale-up of NMCP-led malaria control interventions has led to con-siderable progress, as evidenced by multiple malariometric indicators. The West Africa International Center of Excellence in Malaria Research (WA-ICEMR) is a multidisciplinary research program that works closely with the NMCP and its part-ners to address critical research needs for malaria control. This coordinated effort includes assessing the effectiveness of control interventions based on key malaria research topics, including immune status, parasite genetic diversity, insecti-cide and drug resistance, diagnostic accuracy, malaria vector populations and biting behaviors, and vectorial capacity. Several signature accomplishments of the WA-ICEMR include identifying changing malaria age demographic profiles, testing innovative approaches to improve control strategies, and providing regular reporting on drug and insecticide resistance status. The NMCP and WA-ICEMR partnership between the WA-ICEMR and the NMCP offers a comprehen-sive research platform that informs the design and implementation of malaria prevention and control research programs. These efforts build local expertise and capacity for the next generation of malaria researchers and guide local policy, which is crucial in sustaining efforts toward eliminating malaria in West Africa