Baobab Index

Hypersaline environments are dynamic ecosystems, the chemistry of which is significantly influenced by climate change, which in turn impacts the microbiota and biogeochemical processes. This study investigates the microbiome of Lake Karum, a hypersaline lake in the Danakil Depression, Ethiopia, with a particular focus on genome-based potential of climate-relevant biogeochemical processes. The microbiomes of Lake Karum sediments and waters were dominated by halophilic Archaea (Halobacteriota) and Bacteria (Bacteroidota, Pseudomonadota, and Cyanobacteriota), with significant variation in community composition among sites, reflecting geochemical heterogeneity. Despite these taxonomic differences, sediment and water metagenomes exhibited broadly overlapping functional gene profiles. Genes involved in denitrification, carbon monoxide oxidation, osmotic stress tolerance, and utilisation of osmolytes were widespread and predominantly affiliated with Halobacteriales, indicating their pivotal role in nitrogen and carbon cycling. Genome‑resolved analyses revealed substantial intrageneric variation in metabolic potential within dominant halobacterial lineages as well as bacterial candidate phyla, including Candidatus Bipolaricaulota and Candidatus Salsurabacteriota, which encode genes linked to trace-gas metabolism and nitrogen cycling. Notably, a high‑quality metagenome‑assembled genome assigned to the Candidatus Salsurabacteriota was recovered that possesses novel combinations of functional genes not previously reported for this lineage. This study provides a comprehensive genome‑resolved assessment of the taxonomic and functional diversity of the Lake Karum microbiome and identifies microbial taxa with the potential to drive key carbon, nitrogen, and sulfur cycling processes in a hypersaline lake. By revealing previously unrecognised metabolic capabilities within bacterial candidate phyla and highlighting intrageneric functional heterogeneity among dominant halophilic Archaea, this work advances understanding of how hypersaline microbial communities contribute to biogeochemical cycling in extreme environments.

Ethiopian veterinary services encounter several difficulties, including inadequate infrastructure, difficult accessibility, and financial restrictions. Inadequate veterinary clinics, diagnostic laboratories, and cold chain facilities, particularly in rural and pastoralist settings, negatively affect livestock health and production. The objective of this review is to identify and analyze major challenges hindering effective veterinary service delivery in Ethiopia. This review was conducted by systematically searching electronic databases including PubMed, Google Scholar, Scopus, and the Web of Science for articles published between 2000 and 2025. Search keywords included 'Ethiopia', 'veterinary service delivery', 'animal health', 'infrastructure', 'diagnostic laboratories', 'veterinary workforce', 'financial constraints', and 'disease surveillance'. Additional sources were identified from the reference lists of relevant articles and from grey literature. The nation's access to and use of veterinary services are restricted by a severe shortage of qualified veterinary professionals (veterinarian-to-livestock ratio far below WOAH recommendations) as well as budgetary limitations. The underutilization of cutting-edge diagnostic technologies, such as genomic and molecular tools, impairs the ability to monitor and respond to illnesses, especially zoonotic ones. This is compounded by a tiered laboratory system where only the national reference lab has routine molecular diagnostic capacity, and inadequate quality control and standardization in laboratories lead to unreliable results. Inadequate data exchange and management hamper coordination of responses to epidemics. The economy and animal health services in Ethiopia are impacted by a scarcity of veterinary specialists, exacerbated by brain drain. Low pay and lack of incentives discourage veterinarians from practicing in underprivileged regions. The high cost of veterinary treatment is a challenge for livestock owners, particularly in rural locations. Additionally, underutilization and poor animal health outcomes are caused by a lack of public awareness about veterinary services in rural areas. Veterinary service delivery in Ethiopia is constrained by infrastructure gaps, workforce shortages, financial limitations, weak diagnostic capacity, poor data management, and low community awareness. Addressing these challenges requires increased investment in veterinary facilities and personnel, improved laboratory quality control and molecular diagnostic capacity, better data sharing systems, financial incentives for rural service providers, and public awareness campaigns for livestock owners.

Antimicrobial resistance (AMR) has emerged as one of the greatest threats to global health, with Africa bearing a disproportionate burden: an estimated 1.05 million deaths were associated with bacterial AMR and approximately 250,000 deaths were directly attributable to AMR in the WHO African Region in 2019 alone. This burden reflects high infectious disease prevalence, limited diagnostic capacity, weak antimicrobial stewardship, and fragmented surveillance systems. Given that resistant pathogens and resistance genes circulate across humans, animals, and the environment, effective surveillance requires a coordinated One Health approach. This narrative review synthesizes published literature (2015-2026) identified through PubMed, Scopus, Web of Science, and Google Scholar to assess the status of One Health AMR surveillance in Africa, examine progress across the human, animal, and environmental sectors, identify major implementation barriers, and propose strategic priorities for strengthening integrated surveillance systems. The evidence reviewed shows that participation in surveillance initiatives such as GLASS has expanded and laboratory capacity has improved in several countries; however, substantial gaps remain in veterinary and environmental surveillance, laboratory infrastructure, data interoperability, governance, workforce capacity, and sustainable financing. Fragmented information systems and limited cross-sectoral collaboration continue to impede timely detection of emerging resistance and evidence-informed policy action. Based on these findings, we recommend prioritizing integrated governance structures, strengthened laboratory networks, interoperable digital surveillance platforms, and sustainable domestic financing as foundational steps, with genomic technologies, wastewater surveillance, and regional collaboration serving as complementary priorities as feasibility and resources allow. Strengthening One Health surveillance will be critical for improving early detection of resistant pathogens, informing antimicrobial stewardship, supporting outbreak preparedness, and reducing the growing health and economic burden of AMR across Africa.

In October 2024, a broiler farm located south of Nouakchott, Mauritania, reported respiratory symptoms, diarrhoea, and 10% mortality within a flock of 4500 birds. Pooled organ samples (n = 6) were collected and screened by real-time RT-PCR for H5 and H9 subtype avian influenza viruses, Newcastle disease virus, infectious bronchitis virus, and infectious laryngotracheitis virus. Six samples were positive for H9. Full genome sequencing of a representative sample revealed that the viruses were H9N2 and belonged to lineage G5.5. Several molecular markers associated with adaptation to mammalian hosts were identified indicating the virus' potential to infect humans. Analysis of the eight segments showed that the virus was not a reassortant and that it was similar to H9N2 viruses identified in Senegal. This is the first report of H9N2 in Mauritania, and the data generated will be of interest to national and regional veterinary and public health authorities.

Hematopoietic stem cell transplantation (HSCT) is a therapy used to treat various malignant and non-malignant conditions and is one of the most resource-demanding medical procedures. In North Africa, the lack of cancer registries has limited insight into the regional progress of HSCT. This study provides an updated overview of the current HSCT landscape in North Africa, tracing its historical evolution and highlighting existing challenges. An electronic search was performed in scientific databases (PubMed, ResearchGate, Web of Science and Google Scholar), results of the meetings, conferences, GLOBOCAN, and other registries. Data compilation and statistical analyses concerning HSCT procedures in Morocco, Algeria, Tunisia, Libya and Egypt from 1984 to 2024 were analyzed using Microsoft Excel and IBM SPSS Statistics 25.0. During the study period, 13,129 HSCTs (6990 ASCTs, 5877 allo-HSCTs and 262 haplo-HSCTs) were performed in North Africa at 41 HSCT centers. More ASCTs (53.24%) than allo-HSCTs (44.76%) HSCTs were noted in the region. The most frequent indications were lymphomas, Multiple myeloma, leukemias, aplastic anemia, thalassemia, immune deficiency disorders, Fanconi anemia and other non-malignant disorders. Peripheral blood stem cells, bone marrow and cord blood constitute the main cell source. HSCT costs range from 11,000 to over 111,000 USD and show a moderate negative correlation with the Human Development Index (r = -0.483). Despite the efforts made to develop this therapy, HSCT represents only a minority of the therapies used in hematology in North Africa. The cost of sophisticated molecular techniques and newer drugs are sometimes limited factors in the region.

Yellow fever is a vector-borne disease with high epidemic potential. Although currently concentrated in Africa and Latin America, both climate change and human behaviour are likely to affect its future spread and epidemic risk. However, how these factors might interact to alter yellow fever distribution remains unclear. This scoping review aimed to map the available literature at the intersection of these topics and compile the trends that may influence the future spread of yellow fever. Studies were included if they reported original data on future trends in yellow fever epidemiology or vector evolution in the context of climate change, climate variability and human behaviour. Review articles, reports without original data, reports not addressing future trends in yellow fever epidemiology or vector evolution in the context of climatic factors or human behaviour were excluded. Systematic searches of PubMed, Embase and Cochrane CENTRAL were conducted from database inception up to September 2024, alongside manual searches of congress abstract books conducted in September 2024. The project followed Joanna Briggs Institute methodology for scoping reviews, using Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews guidelines. Searches focused on publications containing data relating to predicting, modelling or forecasting trends over time in yellow fever disease, virus and vector dynamics in relation to climatic factors and/or human behaviour. Search results underwent two-step screening against inclusion and exclusion criteria. Data were manually extracted using a bespoke Excel form, with results classified according to expert opinion. Trends in the dataset were identified using generative artificial intelligence as a drafting aid and all final categorisation and interpretation was determined through expert manual review. In all, 1243 studies were screened and 42 met inclusion criteria. The oldest study was published in 2009, and 67% were published between 2019 and 2024. Most (81%) were modelling studies. Most included studies projected a climate-driven expansion in the range and abundance of major yellow fever vectors, particularly The available literature suggests that changing climatic conditions and human activities such as urbanisation and land use will likely contribute to future increases in yellow fever vector abundance and geographical range. While most relevant analyses suggest that increases in human exposure and transmission risk are likely to follow, evidence related to these factors was more limited.

The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is a highly destructive pest native to the Americas that was first detected in Africa in 2016. Nearly a decade later, it continues to pose a significant threat to maize production, a staple crop for millions across the continent. The pest rapidly spread, colonizing most maize-growing regions within 2yr and causing estimated annual yield losses of up to 20 million metric tons, adversely affecting food security, rural livelihoods, and economies. Farmers who rely heavily on pesticides risk the emergence of resistance to synthetic chemicals, escalating treatment costs, and significant health and environmental hazards, emphasizing the unsustainability of this approach as a primary strategy. Over the past decade, research and development programs have broadened the range of management options available, including host plant resistance, biological control, cultural practices, and agroecological innovations such as push-pull systems. This review consolidates a decade of insights into the spread of FAW in Africa, examining its impacts and the adoption of various management practices. It highlights critical challenges such as climate variability that exacerbate impact of the pest and the limited uptake of technology, while also showcasing innovative solutions like genomics, RNA interference, predictive modeling, and cross-border collaborations that are paving the way for sustainable control of the pest. By integrating biological, socio-economic, and policy perspectives, our review offers a comprehensive overview and outlines future directions for sustainable, farmer-centered integrated pest management.

DNA library construction methods can affect the recovery of ancient DNA, thus influencing downstream analyses. While single-stranded library preparation (ssLib) has been shown to outperform double-stranded (dsLib) for highly degraded vertebrate host DNA, especially for samples older than 40,000 years, few studies have examined how library protocols shape ancient microbial community reconstruction. Here, we compare the sequencing output of paired ssLib and dsLib dental calculus libraries generated from 12 Neanderthals and two Chalcolithic humans, prepared using implementations of the Gansauge et al. and Meyer and Kircher protocols, respectively, and sequenced with identical Illumina chemistry. We compared read length and GC%, read duplication and taxonomic profiles across normalization strategies to assess protocol-specific biases. Double-stranded libraries retained a significantly higher proportion of sequenced reads throughout data processing (dsLib 72.1%, ssLib 37.9%), a higher proportion of oral reads (dsLib 9.78%, ssLib 6.75%), significantly longer median oral DNA read lengths (dsLib 57.5 bp, ssLib 50.5 bp) and more GC-rich fragments (dsLib 60.5% GC, ssLib 52.5% GC). In contrast, ssLibs exhibited slightly higher Shannon diversity and a greater proportion of unique reads. Despite these differences, species richness and overall community composition was not significantly different between protocols, with individual and preservation status explaining the most variance. Stratifying reads by length (< 50 bp vs. ≥ 50 bp) resulted in different classification rates but only had minor effects on diversity estimates. Together, these results demonstrate that dsLib and ssLib protocols impose distinct trade-offs and library choice should be guided by study-specific goals.

Several direct-to-consumer genetic tests claim to predict susceptibility to anterior cruciate ligament (ACL) rupture. Although not independently replicated, polymorphisms identified in a genome-wide association study-rs144051132 (T > A), rs186727643 (C > T), and/or rs188099931 (A > G)-have been incorporated into commercial tests to estimate cruciate ligament injury risk. This study aimed to evaluate whether these polymorphisms are associated with ACL rupture across multiple populations. We genotyped 906 clinically diagnosed ACL rupture cases, including 498 non-contact mechanism of injury ruptures (ACL-NC), and 679 controls (CON) from four European ancestry cohorts and a South African mixed-ancestry cohort. No significant differences were observed in genotype distributions between cases and controls in either the European cohorts (rs144051132 CON: 99.3% TT, 0.7% TA; ACL: 99.0% TT, 1.0% TA; rs186727643 CON: 100.0% CC; ACL: 99.9% CC, 0.1% CT or rs188099931 CON: 99.8% AA, 0.2% AG; ACL: 99.4% AA, 0.6% AG) or the mixed-ancestry cohort (rs144051132 CON: 99.0% TT, 1.0% TA; ACL: 97.9% TT, 2.1% TA; rs186727643 CON: 97.1% CC, 2.9% CT; ACL: 94.8% CC, 5.2% CT or rs188099931 CON: 99.0% AA, 1.0% AG; ACL: 100.0% AA). These polymorphisms were not associated with ACL rupture in the studied populations. The study was adequately powered to detect the larger effects previously reported but underpowered to detect the smaller effect reported for rs188099931. These results, as well as the rarity of the minor alleles, do not support the clinical validity of these polymorphisms as markers of ACL rupture risk.