Baobab Index

The narrow genetic base of cultivated wheat (

The Asian longhorned tick (

Tritrichomonas foetus is a protozoan parasite of global importance that causes significant reproductive disease in cattle and chronic diarrhea in cats, while commonly existing as a commensal in pigs. Emerging evidence of genetic diversity, transmission, and drug resistance necessitates a comprehensive understanding of its global prevalence. Here, we outline the protocol for a systematic review and meta-analysis to estimate the global prevalence of T. foetus in cattle, cats, and pigs. A comprehensive search of electronic databases, including PubMed, Scopus, Web of Science, CAB abstracts, and Embase, using a predefined search strategy, will be conducted to capture relevant studies. Observational studies reporting the prevalence or incidence of T. foetus infection in cattle, cats, or pigs will be included in the meta-analysis. There will be no language or geographic restrictions. Study selection, data extraction, and risk of bias assessment will be performed independently by at least two reviewers. The random-effects meta-analyses will be conducted to pool prevalence estimates, stratified by animal species and geographical regions. Subgroup analysis based on diagnostic methods and other animal- and management-related covariates will be conducted. Heterogeneity will be explored through subgroup analyses. Sensitivity analysis will be conducted using the leave-one-out technique. We describe a protocol for a global prevalence meta-analysis of T. foetus, providing crucial insights into its epidemiology across different host species and regions. The findings are essential to inform the status of surveillance efforts and highlight knowledge gaps, necessary for developing effective control strategies and guiding future research across the vulnerable domestic animal species. International Prospective Register of Systematic Reviews (PROSPERO) registration number CRD420261303496.

Respiratory viral infections in early childhood are major drivers of acute morbidity and long-term airway disease, yet how distinct viruses remodel the pediatric nasal mucosa at cellular resolution remains unresolved. Here, we generated a single-cell RNA sequencing atlas of 335,174 nasal epithelial and immune cells from 132 children under five years of age with SARS-CoV-2, rhinovirus, or respiratory syncytial virus (RSV) infection, alongside uninfected controls. Mapping viral transcripts to individual cells revealed virus-specific infected epithelial states: an NF-kB-responsive ciliated subset in SARS-CoV-2 and a previously undescribed

BACKGROUNDMalaria caused by Plasmodium malariae is geographically widespread and sometimes associated with prolonged infection, yet little is known about its genomic epidemiology.METHODSWe performed hybrid capture and whole-genome sequencing of 77 isolates collected from Cameroon (n = 7), the Democratic Republic of the Congo (n = 16), Nigeria (n = 4), and Tanzania (n = 50) between 2015 and 2021, analyzing parasite genetic population structure and demography.RESULTSThere is no evidence of geographic population structure. Nucleotide diversity was significantly lower than in colocalized P. falciparum isolates, while linkage disequilibrium was significantly higher. Genome-wide selection scans identified no erythrocyte invasion ligands or antimalarial resistance orthologs as top hits; however, targeted analyses of these loci revealed evidence of selective sweeps around 4 erythrocyte invasion ligands and 6 antimalarial resistance orthologs. Demographic inference modeling suggests that African P. malariae is recovering from a bottleneck.CONCLUSIONP. malariae is genomically atypical among human Plasmodium spp. and lacks strong population structure in Africa. The low diversity has potential impacts on understanding persistent versus new infection through genomic epidemiology.FUNDINGBill & Melinda Gates Foundation (grant 002202), USAID/PMI through Jhpiego and CDC, NIH (T32AI007151, T32AI070114, R01AI107949, R01AI129812, R21 AI148579, R01AI137395, R21AI152260, R01AI132547, and K24AI134990), and the DELTAS Africa initiative (DELGEME grant 107740/Z/15/Z).

Streptomyces species are prolific producers of secondary metabolites with significant pharmaceutical potential, particularly in tropical agricultural ecosystems. This study characterised rhizosphere-associated Streptomyces species from agricultural soils around Prince Abubakar Audu University, Anyigba, Nigeria, and evaluated their antimicrobial secondary metabolite production capacity through combined genomic mining and bioactivity screening. Soil samples from maize and soybean rhizospheres across five sites were analysed using 16S rRNA gene sequencing, multilocus sequence typing, and whole-genome sequencing. Biosynthetic gene clusters (BGCs) were identified using antiSMASH and PRISM, and crude extracts were evaluated for antimicrobial activity against multidrug-resistant clinical isolates via LC-MS/MS analysis. Twenty-three Streptomyces isolates representing eight species were recovered. Genomic mining revealed 187 putative BGCs, including polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and hybrid PKS-NRPS clusters. Streptomyces sp. PAU-7 and Streptomyces griseoflavus PAU-15 demonstrated significant activity against methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacteriaceae (CRE). LC-MS/MS analysis identified twelve putatively novel secondary metabolites including three polyketide derivatives and four peptide-based compounds. Nigerian agricultural soils harbour diverse Streptomyces populations with substantial biosynthetic potential for putatively novel antimicrobial compounds.

Most tuberculosis (TB) cases in The Gambia are notified in the Greater Banjul Area (GBA). We conducted an Enhanced-Case-Finding (ECF) intervention in the GBA and determined its effect on TB case notifications and ongoing TB transmission. This was a cluster randomized trial in which randomly assigned intervention areas of grouped settlements received three rounds of an ECF strategy consisting of sensitization followed by auramine microscopy, whereas people with TB in control areas continued to be identified through passive case finding. People with TB were recruited at the TB diagnostic and treatment centers serving both the intervention- and control areas. The primary outcome was TB case notification rate. To exclude that an increase in notified cases, followed by a decrease in notified cases, would hide the future impact of the intervention, we tested for changes in transmission dynamics using both genetic clustering and phylodynamic methods. 3,047 people living with TB were recruited in the study, evenly split between intervention and control regions. No significant difference in TB case notification rates, transmission clustering or effective reproductive number was detected between intervention and control areas using either a case notification rate or phylodynamic approach. Although we did not find evidence for decreased TB case notification nor TB transmission through the ECF strategy used, this approach is an examplar of how both classical epidemiology and genomic phylodynamics approaches can be integrated to better assess public health intervention outcomes.

Type 2 diabetes is rising globally, with sub-Saharan Africa facing the steepest projected increase. In low-resource settings, limited screening contributes to high rates of undiagnosed disease, delaying intervention. Traditional risk models often rely on single-factor thresholds or population averages, which can miss combinations of demographic, anthropometric, and lifestyle factors relevant in African contexts. However, emerging evidence suggests that interactions between multiple risk factors provide more accurate, region-specific characterizations of risk. We applied a multidimensional subgroup discovery algorithm to cross-sectional data from three African populations and identified combinations of risk factor cutoffs that define high-risk subgroups. The most consistent profile, such as waist-to-hip ratio greater than 0.9, physical activity less than or equal to 2448 metabolic equivalent-minutes per week, and family history, shows elevated risk across regions and outperforms guideline-based definitions. Here we show that core anthropometric and familial factors are stable across populations, while others are region-specific, improving predictive performance for screening.

Differences in body composition during childhood can influence long-term health, with notable links to cardiometabolic disorders in later life. While genetic associations with body composition traits are well-studied, less is known about the role of epigenetic mechanisms, particularly in low- and middle-income countries where the burden of cardiometabolic disease is high. We investigated links between DNA methylation and three compartments of body composition: fat mass, lean mass, and bone measures using data from children enrolled in the Epigenetic Mechanisms linking Pre-conceptional nutrition and Health Assessed in India and Sub-Saharan Africa (EMPHASIS) study. We conducted an epigenome-wide association study of 11 body composition traits assessed through dual-energy X-ray absorptiometry in children from India (mean [range] age = 5.8 [5-7] years; n = 686) and The Gambia (age = 9.0 [7-9] years; n = 284), with blood DNA methylation measured at ~ 800,000 CpGs sites on the Illumina EPIC array. Cohort-specific analysis identified 8 unique differentially methylated CpGs associated with traits across all three body composition compartments (p < 3.6 × 10 We report novel DNA methylation signatures associated with body composition traits in children from two low- and middle-income countries. Identified loci map to genes linked to inflammatory signalling, energy metabolism and cellular stress response pathways, highlighting a potential role for epigenetic mechanisms in shaping early-life body composition.