Baobab Index

BACKGROUND: Leishmaniasis is a vector-borne parasitic disease caused by Leishmania protozoa. The disease manifests in several clinical presentations including cutaneous, mucocutaneous, and visceral leishmaniasis. The diagnosis of leishmaniasis is complex and often requires a combination of clinical assessment, microscopy, serological tests, and molecular techniques especially in immunocompromised cases. However, traditional diagnostic methods have limitations in terms of accuracy, sensitivity, and the expertise required, leading to an urgent need for advanced, automated diagnostic tools. The aim of this research is to develop a deep learning-based decision-support system for the microscopic examination of tissue samples to support non-experts with the live diagnosis of the disease. METHODS: Tissue samples from lesions were collected from patients diagnosed with cutaneous leishmaniasis in Libya and Palestine for the purpose of preparing microscopic slides. The samples were then visualized using a high-performance laboratory microscope and a mobile, low-cost device. The captured images were subsequently used to train the object detection framework YOLOv8 with the aim of identifying Leishmania parasites. A graphical user interface was developed for the application of the deep learning model, which enables real-time detection of the parasites using a microscope camera, as well as recognition from previously generated images and videos. RESULTS: The deep learning YOLOv8 framework was successfully trained using data generated by the advanced microscope and employed for the detection of Leishmania parasites. Subsequent finetuning with a combined set containing the aforementioned data and microscopic images generated with the low-cost device resulted in a considerable improvement in accuracy. The efficacy of the model was demonstrated through its successful operation on previously unseen data. Object detection yielded a mean average precision of 0.78 for the combined datasets. The evaluation process for determining the presence of parasites in an image resulted in 91% accuracy, 91% sensitivity, 90% specificity and 94% precision on the test data. CONCLUSIONS: Deep learning-based YOLOv8 achieved accurate Leishmania detection in tissue samples, enhancing decision-support for non-experts via real-time graphical user interface support. This innovation can simplify diagnostics by addressing traditional method limitations, enabling early, accessible leishmaniasis detection in resource-limited settings, and potentially inspiring similar applications in other parasitic diseases. CLINICAL TRIAL NUMBER: Not applicable.

The differentiation of HL-60 cells into neutrophil-like cells is widely used to study neutrophil functions, yet no comprehensive proteomic analysis has been conducted on dimethylformamide (DMF)-induced differentiation. This study provides the first detailed proteomic characterization of DMF-differentiated (df)-HL-60 cells, demonstrating its distinct molecular and functional profiles compared to the well-established dimethyl sulfoxide (DMSO)-df-HL-60 cell model. HL-60 cells were differentiated using 1.25% DMSO or 70 mM DMF for five days. Cell proliferation, granulocytic differentiation (CD11b expression), superoxide anion production, myeloperoxidase (MPO) protein expression and enzymatic activity, and neutrophil extracellular trap (NET) formation were evaluated. Proteomic profiling was performed using LC-MS/MS, followed by gene ontology and pathway enrichment analysis to identify key molecular changes associated with differentiation. DMF-df-HL-60 cells maintained higher proliferation rates than DMSO-df-HL-60 cells. Both agents successfully induced granulocytic differentiation, with DMSO producing greater CD11b expression. Functionally, both differentiation methods enhanced superoxide anion production, but DMF-df-HL-60 cells generated distinct superoxide radical spectra when evaluated with EPR spectroscopy. MPO protein expression and activity were significantly reduced in both differentiation models, indicating a transition to a mature neutrophil-like phenotype. Proteomic analysis revealed that neutrophil degranulation was the most significantly enriched pathway in DMF-df-HL-60 cells, alongside pathways involved in oxidant production and receptor tyrosine kinase signaling. Furthermore, S100 calcium-binding protein A9 (S100A9) abundance was significantly higher in DMF-df-HL-60 cells, suggesting a novel role of DMF in modulating neutrophil differentiation. DMF-df-HL-60 cells also showed activation of MAPK, Ras, and Rap1 signaling pathways, similar to the DMSO-df-HL-60 cell model, which is crucial for differentiation and immune responses. DMF-df-HL-60 cells generated more NETs than the DMSO-df-HL-60 cell model with phorbol myristate acetate. This study emphasizes the importance of selecting the appropriate differentiation model to accurately mimic neutrophil biology and highlights DMF's unique role in neutrophil differentiation, providing novel insights into differentiation-induced functional adaptations.

Influenza sentinel surveillance in Libya was formally established in 2022 by the Libyan National Center for Disease Control (NCDC). Between 2022 and 2024, a total of 1864 nasopharyngeal specimens were collected from patients presenting with influenza-like illness and tested using the GeneXpert for influenza A virus, influenza B virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and respiratory syncytial virus (RSV). Influenza A virus was detected in 21.1% (393/1864) of samples and influenza B virus was detected in 5.4% of samples (100/1864). SARS-CoV-2 and RSV were identified in 11.6% (216/1864) and 4.1% (77/1864) of specimens, respectively. A subset of 22 influenza A-positive samples was selected based on sample availability and sufficient remaining volume after the initial test for confirmatory testing and further molecular characterization. Real-time RT-PCR subtyping identified 11 A(H1N1)pdm09 and four A(H3N2) viruses. Whole-genome sequencing was successfully performed for 11 isolates, followed by phylogenetic analysis. Genetic characterization revealed that all A(H1N1)pdm09 viruses belonged to clade 6B.1A.5a.2a (5a.2a), while A(H3N2) viruses clustered within clade 3C.2a1b.2a.2a.3a.1 (2a.3a.1) were based on hemagglutinin gene mutations. No neuraminidase mutations associated with antiviral resistance were detected. This study represents the first molecular and phylogenetic characterization of circulating human influenza viruses in Libya, with sequence data submitted to the Global Initiative on Sharing All Influenza Data (GISAID) to establish baseline genetic data for influenza viruses in Libya.

This study provides the first shotgun metagenomic characterization of infected diabetic foot ulcers (DFUs) from North Africa. We analyzed two independent datasets with distinct roles: 25 non-infected US DFUs (PRJNA506988) served as an ecological reference cohort to characterize depth-stratified microbial community patterns and pre-infection ARG ecology; 15 infected Libyan DFUs constituted the primary characterization cohort. Metagenomic sequencing, taxonomic classification, resistome and virulome profiling, and metagenome-assembled genome (MAG) reconstruction were performed. In the US reference cohort, depth-dependent community shifts were documented: Fusobacteriota predominated in deeper ulcers, while Staphylococcaceae and Pseudomonadaceae were enriched in superficial wounds. Eighty ARGs were detected across depth groups, including

Rickettsial pathogens are strictly dependent on the cellular biology of their hosts for survival and replication. Predominantly transmitted by blood-feeding arthropods, these vector-borne pathogens are forced to adapt between the disparate environments of their mammalian host and arthropod vector. To achieve this, the Rickettsial bacteria

Inbreeding depression poses a significant threat to fitness in many taxonomic groups. Studies have suggested that females may mate with multiple males to reduce inbreeding through post-copulatory discrimination against closely related males. Stored product pests are a group where inbreeding risk may arise frequently as small numbers colonies patchily distributed resources. We examined potential pre- and post-copulatory inbreeding avoidance in the red flour beetle Tribolium castaneous using direct observation of breeding behaviour and subsequent scoring of offspring parentage using phenotypical markers. Contrary to expectations, males courted and mated with related females slightly more frequently than with unrelated females. Offspring of unrelated parents were more likely to survive to adulthood, meaning that males unrelated to their mate had a higher number of adult offspring when competing for fertilisations with a male who was a full sibling to the female. When the lower survival of inbred offspring was accounted for, there was no difference in the estimated fertilisation success of males in relation to whether or not they were related to their mate. The second male to mate initially gained the majority of fertilisations, but this declined so that by week five, first and second males had similar fertilisation success. This suggests that sperm precedence in this species includes some effects of both sperm displacement and stratification of sperm within the spermatheca. We discuss our observation of a preference for mating with siblings combined with evidence for inbreeding depression in the context of potential inclusive fitness benefits of kin mating.

Two flocks of sheep suffered abortion, with the aborted fetuses varying in age from early to late term. Vaginal swabs were collected, and DNA was extracted. DNA samples were analyzed using real-time PCR coupled with high-resolution melting (HRM) analysis, and the results showed infection with the zoonotic Q fever caused by This study is the first documented evidence of Q fever in sheep in Libya and highlights the need for increased surveillance, further molecular and genomic studies, and the application of One Health approaches. The fact that the bacteria can persist in the environment and potentially cause zoonosis means that, despite being few in number, finding infected flocks could pose significant public health issues.

Despite intensive vaccination efforts, Chicken Infectious Anemia Virus (CIAV) remains a formidable threat to the Egyptian poultry industry, primarily through the emergence of vaccine-escape variants. While most studies have focused on Northern Egypt, there is a critical knowledge gap regarding the viral landscape in the Southern provinces. This study provides the most extensive surveillance to date, spanning 10 diverse Egyptian governorates with a strategic focus on Upper Egypt (2024-2025). Out of 400 collected samples, TaqMan-based qPCR revealed a high prevalence of 30% (120/400). Five representative isolates were selected for whole-genome sequencing and molecular characterization. The isolates were classified as Genotype II by phylogenetic analysis, showing a notable genetic divergence (85-87% amino acid similarity) from traditional Genotype I vaccine strains. Notably, comprehensive recombination analysis identified isolate PX96998 as a mosaic variant, with breakpoints indicating intra-genotypic recombination between closely related genotype II lineages, highlighting complex evolutionary dynamics in the field. Furthermore, 3D homology modeling of the VP1 protein identified critical structural alterations in functional loop regions, potentially hindering the binding affinity of neutralizing antibodies and facilitating immune evasion. In an experimental setting, the genotype II isolate demonstrated hypervirulence in SPF chickens, causing severe development retardation and extensive atrophy of lymphoid organs (p < 0.0001). Pathognomonic pale, fatty bone marrow with a sharp drop in PCV% to 18 ± 0.58% indicated severe aplastic anemia. By the fifth week after infection, there was a complete humoral collapse with undetectable ELISA titers due to the huge systemic replication revealed by viral load measurement, which peaked in the thymus (9.50 ± 0.25 log₁₀) and bone marrow (9.00 ± 0.22 log₁₀). These results were supported by histopathology, which revealed intranuclear inclusion bodies and systemic lymphocyte depletion. These findings support the highly pathogenic genotype II CIAV's dominance and aggressive evolution in Egypt. The emergence of recombinant variants with altered structural epitopes underscores the urgent need to replace outdated vaccination plans with genotype-matched immunogens in order to lessen the severe consequences on Egypt's poultry industry.

Acinetobacter baumannii is an opportunistic pathogen infecting immunocompromised patients, including the pediatric population. Treatment options for severe infections are challenged by the dissemination of carbapenem-resistant A. baumannii (CRAB) mostly belonging to eleven international clones (IC1-11). Unlike neighboring countries, characterization of CRAB from Libya is rare. In this study, 38 CRAB isolates collected during 2020-2021 from patients treated in the Tripoli University Hospital (TUH) were characterized by whole-genome sequencing for their antibiotic resistance genes content, their genetic elements, and phylogenetic relationship to international isolates. The 38 isolates belonged to IC1, IC2, IC6, IC7 and IC11, this latter being the most frequently identified. All isolates harbored a bla At the TUH, improvement of hygiene measures are needed to lower the burden of CRAB. At the international level, surveillance of this pathogen remains crucial to prevent its further spread from endemic regions or from conflict zones where injuries are more frequent and hygiene conditions are more precarious.