Baobab Index

Omicron sublineages have dominated global SARS-CoV-2 circulation since late 2021, but there aren't enough multi-year datasets that detail lineage dynamics and genomic surveillance performance in North Africa. The National Influenza and Other Respiratory Viruses Laboratory in Tunisia has been conducting integrated SARS-CoV-2 genomic surveillance for four years. Between 1 November 2021 and 30 September 2025, 8,635 nasopharyngeal swabs (NPS) received through the national sentinel network were tested for SARS-CoV-2 by real-time RT-PCR, of which 1,020 (11.8%) were positive. A total of 669 (65.6%) positive samples were successfully sequenced using Illumina RNA Prep with Enrichment and a respiratory virus panel. Pango lineages and GISAID clades were assigned with standard tools, and sequencing coverage, geographic representativeness, turnaround times, temporal trends, lineage diversity, mutational profiles, and phylogenetic placement were summarized descriptively. The overall SARS-CoV-2 positivity rate was 11.8%. Median governorate-level sequencing coverage among RT-PCR-positive samples was 60.0% (IQR 28.6-88.9), and the share of sequences closely matched the share of positives (r = 0.992), indicating near-proportional sampling.While SARS-CoV-2-positive NPS displayed several waves, including substantial peaks in mid-2022 and mid-2023 and subsequent winter peaks, each linked to the establishment or replacement of dominant Omicron lineages, testing volumes indicated recurrent winter rises. Among the 669 sequenced SARS-CoV-2-positive samples, 92 (13.8%) showed co-detection with at least one other respiratory virus, including 16 (2.4%) involving influenza viruses.XBB* lineages accounted for 25.0% of genomes, followed by BA.4/BA.5* (22.1%), JN.1* and descendants (13.6%), BA.2* (12.6%), and BA.1* (9.0%), while Delta represented 8.7% of genomes; the remaining 9.1% belonged to other lineages, including pre-Omicron variants and non-XBB recombinants. Almost all genomes belonged to Omicron-associated GISAID clades GK and GRA. Overall, sequencing quality was high (mapped reads typically ≥0.9), while Tunisian SARS-CoV-2 genomes showed a progressive increase in amino acid changes-from ~30-50 substitutions in early Delta/BA.1/BA.2 to >70-80 in later XBB and JN.1* sublineages, with some recombinants approaching 100 substitutions. Phylogenetic analyses showed that Tunisian genomes clustered within globally circulating Delta and Omicron clades. Rapid Omicron sublineage turnover and co-detections with other respiratory viruses, including influenza, were captured by genomic monitoring integrated into Tunisia's influenza-based sentinel network, which achieved broad sequencing coverage and overall near-proportional sampling despite subnational heterogeneity.This integrated, multi-pathogen approach provides a scalable model for sustained genomic surveillance and future respiratory pandemic preparedness in the region.

Human herpesvirus-6 (HHV-6) is involved in immune modulation and contributes to cancer development through interactions with host genetic factors. Hepcidin (

Triple-negative breast cancer is an aggressive and heterogeneous breast cancer subtype with few effective targeted therapies and frequent resistance to chemotherapy. Here, we integrate transcriptional regulatory network inference with chromatin accessibility across a large-scale multi-system collection of primary tumors, patient-derived xenografts and model cell lines to quantify transcription factor activity and identify regulators that underpin triple-negative breast cancer identity. This approach prioritizes 94 high-confidence triple-negative breast cancer transcription factors whose activity capture inter-tumor heterogeneity and independently stratify patient outcome across clinical endpoints. Linking transcription factor activity to pharmacogenomic drug sensitivity profiles identifies reproducible drug-transcription factor associations across independent datasets, including NFE2L3 and CBFB activity as predictors of sensitivity to mTOR inhibition, which we validate in everolimus-treated triple-negative breast cancer patient-derived xenograft models. Collectively, we provide a transcriptional and chromatin-informed framework to capture triple-negative breast cancer regulatory state and expand transcription factor guided precision medicine to this breast cancer subtype.

The specific pathophysiological drivers and host-pathogen-environment factors that dictate the pathogenicity of Candidatus Mycoplasma haemominutum (CMhm) remain poorly defined, hindering accurate clinical interpretation and effective disease control. This study provides detailed mechanistic insights into CMhm-associated anaemia in naturally infected cats by integrating analyses of concurrent diseases and comprehensive clinicopathological panels, alongside molecular characterisation in an under-represented region. Two groups of CMhm-infected cats (anaemic, n = 13; non-anaemic, n = 25) were systematically screened for 14 concurrent infectious, metabolic, or endocrine conditions, alongside extensive haematological, biochemical, and iron profile assessments. Multivariable logistic regression identified independent risk factors, while CMhm molecular diversity was assessed using 16S rRNA gene sequencing. Multivariable analysis identified flea infestation as the sole significant driver of anaemia (OR 7.77; P = 0.04), underscoring a key vector-trigger role and contributing evidence to the ongoing debate on CMhm's flea-borne transmission. Although specific conditions such as feline immunodeficiency virus, feline leukaemia virus, Mycoplasma haemofelis, Candidatus Mycoplasma turicensis, and hyperglycaemia were not statistically significant, they may still be biologically relevant. Notably, most cats in the non-anaemic group also had comorbidities, suggesting that disease stage or severity may be more critical than mere presence. Supporting this, the anaemic group showed significantly lower lymphocyte counts and a downward trend in other leucocytes. Anaemia appeared deceptively normocytic-normochromic and non-regenerative despite ongoing CMhm-induced haemolysis, indicating additional counteracting mechanisms. Detailed clinicopathological and concurrent disease investigations pointed to true iron deficiency (flea-related) and functional iron deficiency (inflammatory comorbidities) as contributors. The coexistence of these three opposing pathophysiological processes shaped the paradoxical haematological and iron profile. Molecular analysis identified three CMhm nucleotide sequence types (nSTs) new to the region. The results of this study suggest that CMhm-associated anaemia is likely a secondary condition, in which environmental triggers and host immune status shape disease manifestation. This study elucidates the complex pathophysiological mechanisms underlying anaemia, providing insights to enhance clinical diagnosis and inform control strategies.

This study aims to evaluate the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for species identification of human Capnocytophaga and to confirm results by whole-genome sequencing. Six reference strains, representing human Capnocytophaga species and one taxon, and a total of 126 clinical strains, selected based on their biochemical profiles from a large collection of preliminarily identified Capnocytophaga isolates, were analyzed. Of those, 125 strains (94%) were identified at least at the genus level (log score variation of 1.7-1.999), while 52 strains (39%) were identified at the species level with a cut-off score of ≥2.0. Eight strains (6%) remained unidentified with a log score of <1.69. C. leadbetteri and Capnocytophaga genospecies AHN8471 strains were accurately identified at the genus level. Minor identification errors were observed in three cases: C. leadbetteri (n=1), C. ochracea (n=2), and Capnocytophaga genospecies AHN8471 (n=38). MALDI-TOF MS was unable to distinguish between C. sputigena and Capnocytophaga genospecies AHN8471 at the species level but clustered them together in the Main Spectra Profile (MSP) dendrogram. MALDI-TOF MS shows promise as a diagnostic tool for identifying human Capnocytophaga species when correct taxonomy and sufficient reference strains are available in the database. Based on the close phenotypic, ribosomal, and genotypic structures, we propose to establish the term "C. sputigena group" encompassing C. sputigena, Capnocytophaga genospecies AHN8471, and other related Capnocytophaga variants. Nevertheless, updating and expanding the MALDI-TOF MS reference database is essential to improve identification accuracy.

Mercury (Hg) contamination and accumulation in agricultural soil represent a major hazardous environmental concern, posing serious threats to living organisms, including plants. Silicon (Si) has been widely recognized to mitigate heavy metal (loid) toxicity; however, the underlying mechanism of Si-mediated mitigation of Hg-stress in mung bean remains unclear. In this study, we addressed this research gap by thoroughly examining the potential effects of Si supplementation on Hg-stressed mung bean plants, with particular emphasis on investigating the possible effects of Si on plant biomass, nodulation traits, antioxidant defense, and expression of metal-transporter and detoxification genes. Our findings demonstrated that Hg stress significantly impaired plant growth by inducing oxidative stress and reducing biological nitrogen fixation efficiency whereas Si application significantly alleviated the Hg-induced toxicity. Specifically, Si increased shoot dry biomass by +113% (2.13-fold), root dry biomass by +60% (1.60-fold), nodule number by +152% (2.52-fold), and nodule dry weight by +273% (3.73-fold) under Hg stress compared to Hg treated plants only. Furthermore, Si enhanced antioxidant defense system, restricted the uptake and accumulation of Hg in different plant tissues, and regulated the expression of genes related to metal transport and detoxification, contributing to improved nodulation and nitrogen fixation under Hg stress. Overall, our findings demonstrate that Si application mitigates the Hg-induced toxicity in mung bean plants by enhancing antioxidant defense, improving nitrogen fixation, regulation of genes involved in metal transport and detoxification, and limiting Hg accumulation.

African rice (Oryza glaberrima) was independently domesticated in West Africa around 3000 years ago, and has long been intertwined in the history of the region. Asian rice (Oryza sativa), which was introduced in Africa when European settlers arrived, gradually replaced African rice and has since dominated rice cultivation in the continent. Domesticated rice species are affected by bacterial leaf blight (BLB), which is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Here we show that the bacterial leaf blight pathogen in Africa (AfXoo) belongs to a distinct phylogroup from the one circulating in Asia (AsXoo), and has a different evolutionary history. Analysis of 87 AfXoo genomes identified five main populations, including highly clonal ones, and a more diverse and recombinant population. Tip-dating analysis revealed that the AfXoo population went through a period of expansion, then decline and more recent recovery. We hypothesize this followed the rise and fall of African rice, and that the introduction of O. sativa served as a bottleneck leading to the emergence of current AfXoo populations. We show that AfXoo has a highly conserved repertoire of type III effectors (T3E), but that nonetheless there is variation especially between populations. In the case of transcription activator-like effectors (TALEs), variation can arise quickly through rearrangements, and we hypothesize that the TALE repertoire of AfXoo has been selected to allow the bacteria to colonize both species of cultivated rice found in the continent. Our research provides an attempt to decipher the genetic history of bacterial blight in West Africa, and its past and present impact on rice cultivation in the region.

Tuberculosis remains a major public health threat globally, with drug-resistant strains undermining treatment efficacy. We analyzed 126 Mycobacterium tuberculosis (M. tuberculosis) isolates with diverse drug resistance spectra and selected 35 for whole genome sequencing (WGS) using Illumina NextSeq, SMRT PacBio Onso and SMRT PacBio Revio sequencing platforms. The study aimed to characterize drug resistance profiles, compare short- and long-read sequencing performance, identify lineages among South African isolates, detect known drug resistance mutations and their lineage-specific patterns, and utilize long-read SMRT platforms for epigenetic profiling. Multiple drug resistance mutations were identified, some lineage-specific, and notably, East-African-Indian (EAI) Lineage 1 isolates often considered less pathogenic, showed significant potential for multidrug-resistance development, including higher fluoroquinolone resistance as compared to other lineages. Three DNA motifs with methylated adenines, namely CACGCaG, CtCCaG and GaTNNNNRtAC, were detected, with methylation patterns varying by lineage and strain due to mutations in the corresponding methyltransferases (MTases). A particularly notable finding was the stable maintenance of a genetic heterogeneity in the mamB MTase, performing methylation at CACGCaG motifs. These results highlight the combined role of genetic and epigenetic variation in M. tuberculosis adaptive evolution and underscore the value of integrating long-read sequencing into TB surveillance and research.

Escherichia coli (E. coli) F17 is one of the leading bacterial causes of diarrhea in farm livestock, which cause huge economic losses and could also pose potential risks to public health. Generally, the monitoring the E. coli F17 is based on the polymerase chain reaction (PCR) and bacteria plate counting method, which were largely limited by the time-consuming nature and susceptibility to detection errors. Hence, there is an urgent need to develop a rapid and quantitative detection method for E. coli F17. In the present study, an E. coli F17 challenge experiment in ovine intestinal epithelial cells (IECs) was employed as an in vitro model. At different post-challenge time points (1 h, 2 h, and 3 h), two conventional methods (bacteria plate counting and microplate method) were conducted as benchmarks to estimate the number of E. coli F17 adhering to the IECs. Additionally, total genomic DNA was extracted and quantitative Real-time PCR (qPCR) was performed to detect the relative abundance of E. coli F17 fimbrial pilin (F17-A) and adhesion (F17-G) genes. Subsequently, statistical analyses, including Pearson's correlation coefficient (PCC) method and linear curve-fitting, were performed to evaluate the correlation between the abundance of F17-A/G genes and the results of the benchmark methods. The results showed that the relative abundances of both genes were highly correlated with the number of E. coli F17 that adhered to the IECs, among them, the F17-A gene showed a stronger correlation with the bacterial counts, exhibiting a correlation coefficient > 0.85. Furthermore, standard curves analyses further confirmed the out-performed quantitative performance of F17-A gene and a significantly stronger correlation with bacterial counts which exhibited an outstanding linear correlation (r = -0.9534, R