Baobab Index

The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the disparity between developed and developing countries for infectious disease surveillance and the sequencing of pathogen genomes. The majority of SARS-CoV-2 sequences published are from Europe, North America, and Asia. Between April 2020 and January 2022, 795 SARS-CoV-2-positive nares swabs from individuals in the U.S. Navy installation Camp Lemonnier, Djibouti, were collected, sequenced, and analyzed. In this study, we described the results of genomic sequencing and analysis for 589 samples, the first published viral sequences for Djibouti, including 196 cases of vaccine breakthrough infections. This study contributes to the knowledge base of circulating SARS-CoV-2 lineages in the under-sampled country of Djibouti, where only 716 total genome sequences are available at time of publication. Our analysis resulted in the detection of circulating variants of concern, mutations of interest in lineages in which those mutations are not common, and emerging spike mutations.

The emergence of carbapenem resistance is a major public health threat in sub-Saharan Africa but remains poorly understood, particularly at the human-animal-environment interface. This study provides the first One Health-based study on the epidemiology of Carbapenemase-Producing Gram-Negative Bacteria (CP-GNB) in Djibouti City, Djibouti, East Africa. In total, 800 community urine samples and 500 hospital specimens from humans, 270 livestock fecal samples, 60 fish samples, and 20 water samples were collected and tested for carbapenem resistance. The overall estimated CP-GNB prevalence was 1.9 % (32/1650 samples) and specifically concerned 0.3 % of community urine samples, 2.8 % of clinical specimens, 2.6 % of livestock fecal samples, 11.7 % of fish samples, and 10 % of water samples. The 32 CP-GNB included 19 Escherichia coli, seven Acinetobacter baumannii, five Klebsiella pneumoniae, and one Proteus mirabilis isolate. Short-read (Illumina) and long-read (Nanopore) genome sequencing revealed that carbapenem resistance was mainly associated with chromosomal carriage of bla

This study provides an in-depth analysis of mpox, encompassing its history, characteristics, epidemiology, diagnostics, treatment options, and the ongoing evolution of the virus and its transmission dynamics. Mpox, though once successfully eradicated, has re-emerged with new modes of transmission and a broader host range. Genomic analyses have revealed the virus's adaptability, posing challenges for diagnostics and vaccine efficacy. The epidemiology has shifted from sporadic zoonotic transmission in rural Africa to a significant presence in urban areas, particularly impacting high-risk populations. Advancements in diagnostics and therapeutics offer hope, but challenges persist. This work underscores the critical need for enhanced surveillance, vaccination strategies, and continued research to bolster global health systems and preparedness for future outbreaks.

The invasion of Africa by the Asian urban malaria vector,

This work focuses on the extraction of cynthichlorine from the ascidian

This study provides a comprehensive investigation of Gonyaulax hyalina, integrating morphological, phylogenetic, and toxicological approaches. Strains were re-isolated from its type locality in the Gulf of Aden (western Indian Ocean) 124 years after its original description by Ostenfeld and Schmidt (1901, p. 141), along with additional Pacific strains collected from Korea and Viet Nam. The primary objective was to clarify the taxonomy of G. hyalina, which has frequently been confused with the morphologically similar G. fragilis. Morphological and molecular data confirmed that the Indo-Pacific strains examined belong to G. hyalina. Diagnostic morphological features supporting this identification included the presence of a characteristic surface ornamentation, a distinct anterior intercalary plate 1a, and comparatively smaller cell dimensions. Phylogenetic analyses based on LSU and SSU rRNA gene sequences revealed that these strains formed a distinct clade, separate from existing G. hyalina sequences in GenBank. This phylogenetic analyses indicated the presence of two ribotypes (A and B) within the species, although morphological characters do not reflect this, providing evidence of cryptic speciation in G. hyalina. Ribotype B corresponded to strains previously associated with gelatinous mucilage aggregates, known from the Mediterranean and New Zealand coastal waters. Toxicological assays conducted on strain DJ_I3 from the Gulf of Aden showed no detectable toxin production. Lastly, analysis of seasonal dynamics in the Gulf of Aden demonstrated that G. hyalina is present throughout the year, with abundance peaking in summer and declining markedly during winter months.

The invasive urban malaria vector

The World Health Organization African region has the greatest infectious disease burden in the world. However, many African countries have limited capacity to rapidly detect, report, and respond to public health events. The Centre for Epidemic Response and Innovation (CERI), KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) in South Africa, and global Climate Amplified Diseases and Epidemics (CLIMADE) consortium are investing in building the capacity of African scientists in pathogen genomics and bioinformatics. A two-week long (11-21 April 2023) intensive training in wet-laboratory genomic data production, bioinformatics, and phylogenetic analyses of viral and bacterial pathogens was held in Cape Town, South Africa. Training was provided to 36 fellows with diverse backgrounds from 16 countries, 14 of which were low- and middle-income African countries. In this report, we, the fellows, share our collective experiences and describe how the learnt skills have been integrated into the operations of our home institutions to advance genomic surveillance capabilities. We identified the in-person and hands-on learning format of the training, taught by genomics experts and field application specialists, as the most impactful elements of this training event. Adaptation and miniaturisation of protocols to detect other pathogens is a great enhancement over the traditional method of using a single protocol for a pathogen. We note the duration of the training as the largest limiting factor, particularly for the computationally intensive bioinformatics sessions. We recommend this programme continue to build pathogen genomics capacity in Africa.

Pearl millet (Pennisetum glaucum) thrives in arid and nutrient-poor environments, establishing its role as a crucial cereal crop for food security in sub-Saharan Africa. Despite its remarkable adaptability, its yields remain below genetic potential, primarily due to limited water and nutrient availability. In this study, we conducted ionomic profiling and genome-wide association studies (GWAS) in field conditions across two growing seasons to unravel the genetic basis of nutrient acquisition in pearl millet. Soil ion content analyses revealed significant differences in nutrient distribution between field sites, while certain ions, such as phosphorus (P) and zinc (Zn), consistently displayed stratified accumulation patterns across years, suggesting stable depth-dependent trends. Evaluation of a genetically diverse panel of inbred lines revealed substantial variation in leaf ion concentrations, with high heritability estimates. Correlations between leaf ion content and root anatomical or agromorphological traits highlighted the intricate interplay between genetic and environmental factors shaping leaf ion accumulation. These analyses also uncovered potential trade-offs in nutrient acquisition strategies. GWAS identified genomic regions associated with leaf ion concentrations, and the integration of genetic and gene expression data facilitated the identification of candidate genes implicated in ion transport and homeostasis. Our findings provide valuable insights into the genetic regulation of nutrient acquisition in pearl millet, offering potential targets for breeding nutrient-efficient and climate-resilient varieties. This study underscores the importance of integrating genetic, physiological, and root architectural traits to enhance agricultural productivity and sustainability in resource-constrained environments.