Participatory varietal selection with improved pearl millet in West Africa

A reconnaissance survey and participatory varietal selection trials (PVS) were conducted in four major pearl millet-growing countries of the Sahel between 2001 and 2003. The studies aimed to identify farmers' preferences in improved pearl millet varieties, increase awareness, test new varieties and enhance farmers' access to the improved varieties. Farmers selected five out of 10 tested varieties, with preferred characteristics, namely, maturity cycles of 80-90 d in the Sahel and 90-100 d in the Sudanian agro-ecozones, acceptable grain yield, compact and long (30-100 cm) panicles, a large number of tillers with panicles, adaptation and an acceptable taste. Farmers indicated that their local varieties were of superior adaptation and taste. They mentioned that hindrances to uptake and sustained use of improved varieties were due to lack of awareness, traditional values, seed unavailability, early maturity, bird damage and lack of fertilizer. The strong genotype × environment interactions in the Sahel suggests that breeding should be directed towards producing varieties adapted to specific zones rather than for wide adaptation. Notably, since farmers often cultivate pearl millet without any soil amendments, it may be advisable to disseminate varieties as a package (with fertilizer and agronomic instructions) rather than as varieties alone in a PVS programme, in order to achieve the full potential of improved varieties. The PVS trials are synergistic to plant breeding in identifying varieties suitable for harsh environments, which are difficult to duplicate in the research station. However, in the absence of formal distribution seed systems in the trial countries, village- or community-based seed production of varieties selected by farmers appears critical to the sustainable adoption of selected varieties

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

Methanogens as emerging pathogens in anaerobic abscesses

AbstractMethanogens are strictly anaerobic archaea metabolising by-products of bacterial fermentation into methane by using threeknown metabolic pathways, i.e. the reduction of carbon dioxide, the fermentation of acetate or the dismutation of methanol ormethylamines. Methanogens described in human microbiota include only Euryarchaeota, i.e. Methanobrevibacter smithii,Methanobrevibacter oralis, Methanobrevibacter arbophilus, Methanobrevibacter massiliensis, Methanomassiliicoccusluminyensis, Methanosphaera stadtmanae and Ca. Methanomethylophilus alvus and Ca. Methanomassiliicoccus intestinalis.Methanogens are emerging pathogens associated with brain and muscular abscesses. They have been implicated in dysbiosis ofthe oral microbiota, periodontitis and peri-implantitis. They have also been associated with dysbiosis of the digestive tractmicrobiota linked to metabolic disorders (anorexia, malnutrition and obesity) and with lesions of the digestive tract (coloncancer). Their detection in anaerobic pus specimens and oral and digestive tract specimens relies on microscopic examinationby fluorescence in situ hybridisation, specific DNA extraction followed by polymerase chain reaction (PCR)-based amplificationof the 16S rRNA and mcrA gene fragments and isolation and culture in the supporting presence of hydrogen-producing bacteria.Diagnostic identification can be performed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry(MALDI-TOF MS) and can be further completed by genotyping through multi-spacer sequencing and, ultimately, whole genomesequencing (WGS). Ornidazole derivatives, fusidic acid and rifampicin are the compounds to be included in in vitro susceptibilitytesting to complete the clinical workflow. Clinical microbiology laboratories should work toward developing cheap and easyprotocols for the routine detection and identification of methanogens in selected specimens in order to refine the diagnosis ofinfections, as well as to expand the knowledge about this group of intriguing microorganisms

Methanogens as emerging pathogens in anaerobic abscesses

International audienc

Microbial biodiversity of natural toothbrushes in Mali

International audienceDifferent oral hygiene practices are used to overcome endemic diseases such as dental caries and oral infections. In Mali (Africa), natural plant-based toothbrushes are used for eliminating bacterial biofilm. The repertoire of microorganisms associated with natural toothbrushes is unknown. The aim of our study is to study microbial flora in particular the methanogenic archaea associated with natural toothbrushes recently recognized as responsible for periodontitis and peri-implantitis. We investigated the methanogens and bacteria associated with 15 different natural plant toothbrushes collected in Bamako local market (Mali). Microbiological investigations consisted in culturing the bacteria on agar plates and searching archaea using molecular techniques. No archaea were demonstrated by molecular biology but 50 bacterial species, including 33 aero-anaerobic and 17 aerobic species, were isolated from natural toothbrushes. We isolated Pseudomonas sp., Staphylococcus sp. and Klebsiella pneumoniae, which are acknowledged as opportunistic human pathogens. This study has highlighted the likely impact of the use of natural toothbrushes in the spread of potentially pathogenic bacteria in the human oral cavity

Case report: a rare case of NOMA (cancrum oris) in a Malian woman

Noma or cancrum oris is a multi-bacterial and opportunistic infection that destroys soft tissue, as well as muscle and bone, and can be fatal. We present a rare case of Noma in a 32-year-old Malian woman, from whom we isolated an Escherichia coli extended-spectrum beta-lactamase