Baobab Index

Cockroaches are known reservoirs for diverse bacterial microbiomes. However, comprehensive analyses of the eukaryotic communities within cockroaches remain limited. In this study, we selected three long-term laboratory-reared cockroach species (Blattella germanica, Periplaneta fuliginosa, and Periplaneta japonica) and performed metabarcoding of the 18S rRNA V9 region using the iSeq 100 platform. The nematode Blatticola blattae was identified in B. germanica, and Leidynema appendiculata was found in both P. fuliginosa and P. japonica. The amplicon sequence variant (ASV) of Nyctotherus (Ciliophora) was detected in all three species of cockroach, while Entamoeba sp. was detected in P. fuliginosa and P. japonica. Compared with the other two species, B. germanica exhibited a higher prevalence of the fungus Nephridiophaga. Our findings showed that laboratory-reared cockroaches belonging to different species harbored distinct commensal and parasitic eukaryotic taxa. While most ASVs were of reduced clinical concern for humans as opposed to studies using wild-caught specimens, the detection of commensals, arthropod parasites and potential human pathogens illustrates the complexity of the cockroach-associated eukaryome and the influence of host identity. Our study emphasizes the importance of host-specificity in the eukaryotic community of laboratory-reared cockroach models.

Understanding the genome-wide diversity of jute mallow (Corchorus olitorius L.) is crucial for unlocking the potential of global genebank collections, enabling the discovery and use of traits that support climate resilience, improve nutrition, and increase productivity. Using 23,471 high-quality diversity array technology sequencing single-nucleotide polymorphisms (SNPs), this study assessed the genetic diversity, population structure, and linkage disequilibrium (LD) of 607 accessions. Moderate genetic diversity was detected with a total gene diversity of 0.28, an expected heterozygosity of 0.26, and a Shannon index of 0.42. Four distinct genetic clusters were identified, reflecting geographic patterns, where Cluster 1 (n = 62) and Cluster 4 (n = 354) were predominantly composed of West African accessions. An analysis of molecular variance revealed significant genetic structuring (p < 0.001), with most genetic variation occurring within countries (45.2%), followed by within individuals (32.5%), while differentiation among clusters accounted for 18.2% and variation among regions was minimal (2.9%). LD revealed low genome-wide r Jute mallow is a significant leafy vegetable and fiber crop across Africa and Asia, yet its improvement has been hindered by limited knowledge of the species’ genetic diversity. Developing resilient and high‐yielding varieties depends on understanding this diversity and how it is distributed across regions. We analyzed 607 jute mallow accessions using 23,471 genome‐wide DNA markers. Four major genetic groups were identified through ancestry analysis. Molecular variance analysis showed that most genetic variation occurs within countries rather than between regions. Rapid decay of linkage disequilibrium was observed, indicating high recombination, and hence, higher marker density is required for genome‐wide association studies. These findings help genebanks identify unique accessions, reduce redundancy, and emphasize conserving within‐country diversity, while enabling breeders to cross divergent groups to broaden the breeding base and enhance adaptation.

We present whole-genome sequence data for the

Malaria transmission in southwestern Uganda is low, but persists despite control efforts. Identifying whether infections are locally sustained or imported by travelers is critical for guiding interventions. We integrated epidemiologic surveillance with parasite genomics to characterize imported malaria episodes at three health facilities in southwestern Uganda. Between January 2023 and June 2024, we enrolled microscopy-confirmed malaria cases at three health facilities, Maziba and Muko (very low transmission) and Kamwezi (low-to-moderate transmission), administered travel history questionnaires, and collected dried blood spots for genotyping. 348 Plasmodium falciparum infections were genotyped using MAD4HatTeR, a multiplex amplicon sequencing panel targeting 165 diversity markers and 38 drug resistance loci. Complexity of infection and pairwise relatedness were estimated using MOIRE and Dcifer, respectively. Plasmotrack, a transmission network framework, was used to infer transmission networks and importation rates. Amongst malaria cases, travel was common in Maziba (87%) and Muko (96%) but infrequent in Kamwezi (12%). Most travel in Maziba and Muko was from high-transmission regions in northern and eastern Uganda. Parasites in Maziba and Muko exhibited higher within-host diversity and lower within-site relatedness compared to those in Kamwezi, with the proportion of significant related infection pairs substantially lower in Maziba (0.59%) and Muko (0.17%) than in Kamwezi (6.36%). Transmission network inference identified most infections in Maziba and Muko as imported, with the majority of inferred secondary transmission linked to recent travelers. In contrast, Kamwezi showed multiple highly related clusters, indicating sustained local transmission. Validated markers of artemisinin resistance (K13 P441L and R561H) were more prevalent in Kamwezi. Malaria in Maziba and Muko was driven largely by importation from other parts of Uganda, while local transmission predominated in Kamwezi. Tailored interventions addressing travel-associated risks and local transmission, supported by travel histories and genetic data will be valuable to advance malaria elimination in this region.

The rapid global emergence of multidrug-resistant (MDR) bacterial pathogens has significantly reduced the effectiveness of conventional antibiotics, creating an urgent need for alternative antimicrobial strategies. Among emerging precision therapeutics bacteriophage therapy and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas systems have shown to have strong potential through highly specific bacterial targeting mechanisms. Bacteriophages have the ability to replicate themselves and penetrate biofilms, and the ability of CRISPR-Cas systems to edit the genes responsible for antimicrobial resistance, virulence factors, and the mobile genetic elements that underlie bacterial resistance. The recent advancement enabled the integration of these technologies through CRISPR-armed bacteriophages, which utilize bacteriophages as delivery mechanisms for CRISPR and address the large populations of MDR bacteria. Compared to administering CRISPR and bacteriophage independently, the current data suggest that the use of these two methods synergistically will lead to greater efficacy of delivery, specific targeting of resistance determinants, decreased risk of resistance development, and minimal impact on the body's beneficial microorganisms. While the potential combination of these approaches holds great promise to help combat the issue of MDR bacteria, there are still numerous barriers to overcome in order to implement these methods which include narrow phage host range, bacterial escape mechanisms, off-target CRISPR activity, anti-CRISPR proteins, host immune responses, and unresolved manufacturing and regulatory limitations. This review critically examines bacteriophage-based antimicrobials, CRISPR-Cas therapeutic systems, and their emerging integration as CRISPR-armed phages, highlighting their comparative advantages, current limitations, and future potential as promising targeted antimicrobial approach platforms requiring further clinical validation.

Artemisinin-based combination therapies are the cornerstone of malaria treatment and control. In Africa, artemether-lumefantrine is the most widely used first-line artemisinin-based combination therapy, but its efficacy in Uganda is increasingly threatened by the emergence of artemisinin partial resistance and reduced lumefantrine susceptibility. To identify loci contributing to this decreased susceptibility, here we assessed signatures of selection in 157 whole-genome sequences of Plasmodium falciparum from Uganda. Although extended haplotypes were observed around Kelch13 C469Y and A675V mutations, the strongest signal of recent selection was centered on a segment of chr. 7 encoding the phosphoinositide-binding protein (PX1, PF3D7_0720700). A haplotype, represented by three PX1 mutations (L1222P, M1701I and D1705N) and two deletions (designated PIN), was first seen in 2008 and rapidly increased, reaching a prevalence >50% in northern Uganda by 2016 and eastern Uganda by 2023. PIN-carrying parasites showed significantly decreased ex vivo susceptibilities to lumefantrine, mefloquine and dihydroartemisinin, an active metabolite of artemether. A parasite strain in which px1 was disrupted in vitro showed increased susceptibility to the three drugs. Thus, PX1 polymorphisms appear to impact on the susceptibilities of African malaria parasites to key drugs.

Biologically defined sepsis subtypes have been identified in low- and middle-income countries (LMICs), but limited access to molecular diagnostics constrains broader evaluation and implementation in resource-limited settings. To determine whether bedside-accessible variables could approximate molecular sepsis subtype assignments among Ugandan adults with sepsis. Secondary analysis of two prospective observational sepsis cohorts conducted at Tororo General Hospital (Research in the Epidemiology of Severe and Emerging Infections in Uganda-2-Tororo [RESERVE-U-2-TOR]) and Entebbe Regional Referral Hospital (Research in the Epidemiology of Severe and Emerging Infections in Uganda-1-Entebbe [RESERVE-U-1-EBB]), Uganda. Participants were adults 18 years old or older hospitalized with sepsis who underwent transcriptomic (n = 355) and/or proteomic (n = 495) profiling. Prespecified clinical and clinico-microbiologic models were evaluated for discrimination and calibration against Uganda-derived transcriptomic and proteomic sepsis subtypes and, secondarily, high-income country (HIC)-derived sepsis subtypes and immune dysregulation frameworks. In RESERVE-U-2-TOR, clinical models incorporating demographic and physiologic variables showed moderate discrimination for transcriptomic and proteomic subtypes (area under the receiver operating characteristic curve [AUROC], 0.75 [95% CI, 0.69-0.81] and 0.73 [95% CI, 0.66-0.80], respectively), with generally acceptable calibration. Adding rapid HIV, malaria, and tuberculosis test results did not meaningfully improve performance. In RESERVE-U-1-EBB, discrimination was more variable (AUROC range, 0.63-0.75), with generally acceptable calibration. Performance was similarly modest for HIC-derived sepsis subtypes and immune dysregulation axes. Bedside-accessible clinical variables, with or without rapid microbiologic testing, only partially approximated molecular sepsis frameworks in Uganda. Scalable molecular biomarker platforms are needed to advance precision medicine for sepsis in LMICs.

Prostate cancer disproportionately affects Sub-Saharan African men, who often present with aggressive, late-stage disease. This systematic review synthesizes contemporary evidence on the immunophenotyping and molecular patterns of prostate cancer in East Africa to inform regional screening and precision oncology strategies. Following PRISMA 2020 guidelines, a systematic search was conducted across PubMed, Scopus, and Web of Science for studies published between January 1, 2011 and December 31, 2025. The review protocol was preregistered in Open Science Framework (OSF Registration ID: https://doi.org/10.17605/OSF.IO/RJZFT). Eligible studies were original research articles involving histologically confirmed prostate cancer in East African countries as classified by the United Nations Geoscheme for Africa (Eastern Africa subregion), reporting on immunohistochemical markers or genomic alterations. Preclinical studies, in vitro/in silico studies, case reports, editorials, and meeting abstracts were excluded. Quality was appraised using Joanna Briggs Institute Critical Appraisal Tools. Seven original studies involving participants from Uganda, Sudan, Kenya, and Rwanda were included. Study designs comprised 5 analytical cross-sectional studies and 2 case-control studies. Patient ages ranged from 45 to 107 years (mean ∼70-74 years across cohorts). Dominant histopathological subtype was high-grade acinar prostatic adenocarcinoma. Findings reveal mean prostate-specific antigen levels reaching 434.06 ng/mL and high-grade malignancies (Gleason Score ≥ 8) in up to 82.4% of cases. Key biomarkers identified include Cyclin D1 expression (98.3%), ERG positivity (75.4%), and pathogenic variants at the 8q24 locus (rs72725854). Loss of BRCA1/2 was noted in high-grade tumors. All included studies demonstrated a low risk of bias, though confounding management remains a recurring methodological weakness. East African prostate cancer is defined by an aggressive molecular profile and systemic diagnostic delays. The identification of population-specific genetic drivers necessitates a shift from Western-derived risk models toward decolonized precision oncology and decentralized diagnostic infrastructure to improve early detection and patient outcomes.

Comparing the genetic diversity and population structure of parasites and their hosts can improve understanding of their respective methods of dispersal, demographic histories, and factors driving genetic differentiation. In parasite taxa such as trematodes which have both intermediate and final hosts, comparative population-level analyses may also inform how each host influences gene flow among parasite populations. Here we aimed to assess how intermediate and final hosts influence trematode dispersal by examining the population genetic structure of the aquatic snail Bulinus tropicus and three trematodes that use it as intermediate host. We used high-throughput amplicon sequencing to simultaneously genotype populations of B. tropicus in two clusters of crater lakes in western Uganda (823 snails, 15 lakes) and three infecting trematode taxa (Petasiger sp., Echinoparyphium sp. and Plagiorchioidea sp.). For each taxon, we quantified genetic diversity in three mitochondrial markers and used analyses of molecular variance to test whether populations were genetically differentiated. Populations of B. tropicus were strongly genetically differentiated among individual crater lakes and lake clusters (Φ Contrasting patterns of genetic diversity and population structure among three parasitic trematodes and their common intermediate snail host illustrate how multi-host life cycles mediate dispersal dynamics and generate distinct evolutionary outcomes in hydrographically fragmented aquatic habitats. These findings demonstrate how multi-host life cycles shape parasite connectivity and evolution, and show that comparative population genetics can provide valuable insights into the dispersal ecology of understudied parasite species.