Baobab Index

Middle East respiratory syndrome coronavirus (MERS-CoV) remains a low-incidence but high-consequence zoonotic coronavirus threat. Since its identification in Saudi Arabia in 2012, more than 2600 laboratory-confirmed cases have been reported from 27 countries, most from the Arabian Peninsula; the reported case fatality ratio is high but probably overestimates infection fatality because mild and asymptomatic infections are under-detected. Dromedary camels across the Middle East, North Africa, East Africa, the Horn of Africa, and parts of the Sahel show extensive evidence of MERS-CoV infection or exposure, yet PCR-confirmed human disease has rarely been reported from Africa. This "Africa paradox" is one of the most important unresolved issues in MERS-CoV epidemiology. We propose a dromedary camel-centred One Health framework for the connected Middle East-Africa dromedary belt. The framework is organised around two linked barriers: an upstream barrier that detects and reduces zoonotic spillover at the camel-human interface, and a downstream healthcare barrier that prevents amplification after human infection occurs. Preparedness should include sentinel surveillance for severe acute respiratory infection and atypical pneumonia in camel-exposed populations, linked animal-human genomic surveillance, culturally respectful and occupationally practical risk reduction, rapid diagnostic pathways, healthcare infection prevention and control, mass-gathering and travel preparedness, and pre-approved research platforms. A Middle East-Africa preparedness compact aligned with the International Health Regulations, One Health governance, and equitable pathogen access and benefit sharing could transform fragmented surveillance into a standing transregional system for early detection, prevention, and research-ready response.

Dioscorea alata L., the most widely cultivated yam species, exhibits dioecy (XY system) and a strong male-biased sex ratio. These two major constraints limit parental combinations and hinder breeding progress. To get insight into the sex chromosome structure and evolution in D. alata, we present a haplotype-resolved, near-complete genome assembly of the male cultivar "Kabusa," spanning 958 Mb across 40 chromosomes. DalaChr6A is identified as the Y chromosome which exhibits early signs of heteromorphism, including a slight reduction in size (∼400 Kb difference) and a potential centromere shift relative to the X chromosome. Our findings also reveal a sex chromosome turnover between D. alata and D. rotundata. The sex chromosomes of D. alata are evolutionarily young (approximately 4.32 million years ago) and emerged after the divergence from the D. rotundata lineage. The sex-determining region (SDR) is refined to approximately 7.6 Mb, representing approximately 44% of the Y chromosome. It contains several inversions and a divergence gradient was observed across these inversions. INV4 identified as the oldest pericentric inversion likely marks the early step in D. alata SDR evolution. Despite structural divergence, both X and Y chromosomes remain transcriptionally active. Among the 231 genes annotated in the SDR, 97 are sex-biased and enriched in functions associated with floral organ formation and hormonal signaling pathways. This study enhances our understanding of sex chromosome evolution and sex determination in dioecious plants. It provides a gold-standard reference genome for the Dioscorea genus and lays the foundation for accelerated breeding and genetic improvement in yam.

Large international gatherings such as the Grand Magal of Touba in Senegal may favor influenza A/B virus (IABV) transmission. We analyzed IABV genomes from human samples collected during the event in 2018-2024. Next-generation sequencing was performed for 190 qPCR-positive nasopharyngeal samples. Bioinformatic analyzes were performed using MAFFT v7.505, IQ-TREE v2.2.0, iTOL, Nextclade, and PREDAV-FluA. 106 (55.8%) complete genomes were obtained, including 99 type A and 7 type B. IAV genomes were classified as A/H3N2 (N = 48) and A/H1N1 (N = 43), based on hemagglutinin/neuraminidase-encoding segments. A/H3N2 was not detected in 2021 and 2023; A/H1N1 was only detected in 2018, 2021 and 2023. Phylogenies classified A/H3N2 and A/H1N1 into distinct clades varying from 1 year to the next. A single A/H1N1 sequences was predicted to be antigenic divergence from the vaccine strain concomitantly used. All IBV genomes (clades V1A.3a or V1A.3a.2) were from 2020. Some IABV genomes from the GMT were clustered together while the most similar genomes from databases were from Senegal, Subsaharan Africa or other countries. Present data describes the circulation of IABV during the GMT over time in the population studied here shedding light on the viral dynamics in such setting of mass gathering.

Listeria monocytogenes (L. monocytogenes) is a significant foodborne pathogen, posing a threat to public health. This study investigated the prevalence and genomic diversity of L. monocytogenes in 466 wild animals sampled across Central and Southern Italy (2017-2023), including species such as wild boar, red fox, and wolf, to assess their role as reservoirs and potential links to the food chain. Overall, 22.5% of the animals tested positive, and 118 L. monocytogenes strains were isolated, predominantly from wild boar (n=46), red fox (n=20), and Italian wolf (n=15). Whole Genome Sequencing (WGS) analysis revealed high genomic diversity, classifying the strains into 27 Clonal Complexes (CCs) and 31 Sequence Types (STs). Both hypervirulent clones (e.g., CC1, CC6, CC207) and hypovirulent clones (e.g., CC9, CC19), known for their persistence, were identified, with wild boars harboring a majority of the hypervirulent isolates. All strains carried key virulence genes, and accessory virulence factors, particularly LIPI-3, were detected in hypervirulent strains. Persistence factors, such as the Stress Survival Islet 1 (SSI-1) and genes for metal/disinfectant resistance (cadA, qacA), were also detected, particularly in wild boar isolates. Crucially, core-genome MLST (cgMLST) analysis demonstrated direct genomic links between the wildlife isolates and the Italian National Reference Laboratory database. Multiple clusters were identified, connecting strains from wild animals (wild boars, foxes, wolves) with those from meat products, fresh salads, and food processing environments. A persistent CC9 cluster, circulating in the meat chain for seven years, was strongly correlated with wild boar isolates, underscoring the role of wildlife as a reservoir that continuously introduces both high-virulence and highly persistent strains into the food production system. These findings emphasize the necessity of integrating wildlife surveillance into public health strategies to mitigate the risk of zoonotic transmission, particularly through game meat consumption and handling.

This study assessed Escherichia coli as an indicator of antimicrobial resistance (AMR) in retail seafood, integrating microbiological and genomic analyses within a One Health perspective. Overall, E. coli was cultured from 55 (13%) of 422 raw samples from seven seafood categories commonly consumed in Italy. E. coli was detected across multiple seafood types, but particularly in bivalves (23%) and crustaceans (20%). Because these species can accumulate or acquire faecal contaminants from the aquatic environment or along the post-harvest chain, they represent relevant matrices for AMR monitoring. In parallel, we investigated the presence of Extended-β-Lactamase ESBL-, AmpC- and carbapenemase-producing Enterobacteriaceae. Cefotaxime-resistant E. coli isolates were identified at low but relevant frequencies, especially in bivalves, and were characterised phenotypically and by whole-genome sequencing. Most isolates carried clinically important ESBL or AmpC genes, more frequently bla

BACKGROUND: The mitigation of antimicrobial resistance (AMR) has become a priority in every part of the world. Understanding AMR dynamics in Senegal is crucial for updating empirical antimicrobial treatments, adapting public health policies, and guiding future research. Therefore, this study conducted a systematic review and meta-analysis of clinical Enterobacterales resistance to 15 antimicrobials, determine AMR trends, and report the genetic determinants of AMR reported in Enterobacterales strains isolated from humans in Senegal over the past four decades. METHODS: The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PRISMA 2020) were used and the protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) database with registration number (CRD420251007413). Data analyses were conducted using Stata software, version 17.0, and consisted of a random-effects model analysis to estimate pooled AMR rates, publication bias assessments, and meta-regression analysis. RESULTS: Thirty-nine research articles met the inclusion criteria and were selected for this study. A total of 7911 Enterobacterales strains were studied. These strains were isolated between 1987 and 2022, mainly from urine [23 studies; 61% (95% CI: 45, 74)], blood [15 studies; 39% (95% CI: 26, 55)], and stool [15 studies; 39% (95% CI: 26, 55)]. The overall pooled AMR rates ranged from 3% (95% CI: 1, 5) for carbapenems to 66% (95% CI: 53, 77) for trimethoprim-sulfamethoxazole (SXT). Drastic upward trends were reported for all 15 antimicrobials tested, except for amikacin, chloramphenicol, and tetracycline, for which stable AMR trends were observed. The Klebsiella isolates presented the highest AMR rates, followed by E. coli, Shigella, and Salmonella isolates. Genetic determinants of resistance to beta-lactams, fluoroquinolones, aminoglycosides, trimethoprim, macrolides, nucleoside antibiotics, and tetracycline were reported in Senegal. In addition, class 1 and 2 integrons were reported and carried mostly aadA1, aadA2, dfrA7, dfrA1, and sat as cassettes. CONCLUSIONS: Carbapenems, amikacin, fosfomycin, and chloramphenicol could be considered good for the treatment of severe infections. In addition, there is a need to adjust empirical antimicrobial treatment guidelines in Senegal and implement whole-genome sequencing-based surveillance methods. Recommendations should include the implementation of prevention and infection control policies and the exploration of alternative therapies. CLINICAL TRIAL: Not applicable.

Genomics have become crucial in addressing the public health challenges posed by antimicrobial resistance (AMR). In this study, we performed the first whole-genome sequencing (WGS) and genomic analyses of clinical Acinetobacter baumannii (A. baumannii) strains isolated at the Sylvanus Olympio University Teaching Hospital in Lomé, Togo. This prospective study, conducted from April 19 to September 02, 2019. Susceptibility profiles were obtained using the Kirby-Bauer disc diffusion method, and the nine studied carbapenem-resistant A. baumannii strains were subjected to next generation sequencing (NGS) using an Illumina platform. All isolates exhibited resistance to imipenem, ticarcillin, clavulanic acid, cefotaxime, and ciprofloxacin, but remained susceptible to colistin, tigecycline, and rifampicin. The study identified five A. baumannii ST1 strains, two ST103 strains, one ST52 strain, and one ST1153 strain. The number of AMR genes per strain ranged from six to 24, whereas the number of virulence genes per strain varied from 32 to 67. Each isolate contained at least one plasmid, with the number of plasmids per isolate ranging from one to four per isolate. The carbapenemase-producing genes bla

Diabetic encephalopathy is a chronic neurodegenerative complication of diabetes mellitus characterized by cognitive decline, neuroinflammation, oxidative stress, and impaired insulin signaling. Semaglutide, a glucagon-like peptide-1 receptor agonist, has demonstrated neuroprotective potential; however, whether dietary antioxidant supplementation can provide additional neurobiological benefit remains unclear. This study investigated the neuroprotective effects of semaglutide alone and in combination with papaya fruit pulp in a streptozotocin-induced rat model of diabetic encephalopathy, with emphasis on oxidative stress, insulin signaling, neuroinflammation, amyloidogenesis, and neuronal integrity. Forty male rats were allocated into four groups: control, diabetic (STZ), diabetic treated with semaglutide (0.9 mg/kg), and diabetic treated with semaglutide (0.3 mg/kg) combined with 10% papaya juice for eight weeks. Notably, butyrylcholinesterase activity was normalized only in the semaglutide-papaya group, indicating a distinct cholinergic regulatory effect. Histological examination of the hippocampus and cerebral cortex confirmed superior preservation of neuronal architecture in the combination-treated animals. These findings indicate that while semaglutide mediates the primary metabolic, insulin-sensitizing, and anti-inflammatory effects, papaya provides a complementary neuroprotective contribution through selective reinforcement of antioxidant and cholinergic pathways. Rather than demonstrating global statistical synergy, the semaglutide-papaya combination exhibits pathway-specific enhancement, supporting a biologically meaningful combinatorial strategy for mitigating diabetic encephalopathy.

The reliability of the invA gene, a gold-standard target for PCR-based diagnosis of Salmonella, has been questioned due to false-negative results reported by some authors. Thus, evaluation of the inclusivity features of invA and ttrC-based real-time PCR assays and comparison of the specificity performance of both targets for the genus-specific molecular identification of Salmonella enterica has been carried out on a wide strain panel. Genus-specific identification using two real-time PCR-based assays targeting invA and ttrC gene fragments was performed on Salmonella strains (n = 421) of 50 different serovars isolated in Central Italy between 2002 and 2023 from: food and veterinary samples during poultry chain surveillance, human clinical samples, and surface water samples collected from rivers. A 99% inclusivity was recorded for both the ttrC-based and the invA-based real-time PCR assays, with perfect agreement (Cohen's Kappa = 0.991) with the ISO/TR 6579-3:2014 and with each other. Our findings suggest that both the ttrC-based and invA-based PCR assays are equally reliable for the genus-specific identification of a wide Salmonella enterica strain panel of epidemiological relevance and are in complete agreement. However, considering the genomic variability in some Salmonella serovars, a dual-target PCR approach is recommended to potentially improve diagnostic accuracy.

Early and efficient management of bloodstream infections (BSIs) reduces the risk of complications and death. Therefore, it is crucial to identify antimicrobials with good activity against bacteria isolated from BSIs. This study aimed to determine the bacterial pathogens involved in BSIs, pooled antimicrobial resistance (AMR) rate, AMR phenotype rates, and the evolution of AMR over the years in West Africa. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PRISMA 2020) were used, and the protocol for this review was registered in the International Prospective Register of Systematic Reviews (PROSPERO) database with the registration identification number (CRD420251064773). Keywords were used to conduct a systematic literature review of electronic databases such as Google Scholar, African Journals Online, PubMed, ResearchGate, Embase, and Scopus. Data analyses were conducted using Stata/MP 17.0, and a random-effects model was used to estimate pooled estimates. Twenty-three research articles, including samples collected between 2003 and 2022, were selected for this study. The prevalence of BSIs was 13.1% (95% CI: 12.8-13.3) (6,864 blood culture-positive out of the 52,566 patients screened for BSIs). A total of 4,992 bacteria were isolated, including 3,219 Gram-negative bacteria (GNB) and 1,773 Gram-positive bacteria (GPB). The pooled AMR rates of 20 antimicrobials were obtained, and the highest were for ampicillin [73% (95% CI: 66, 80)] and trimethoprim-sulfamethoxazole [72% (95% CI: 63, 80)]. The lowest pooled AMR rates were observed for the carbapenems [10% (95% CI: 1, 25)] and clindamycin [15% (95% CI: 6, 27)]. GNB were more resistant to ampicillin (P = 0.003) and amoxicillin-clavulanate (P = 0.002) than GPB, and the pooled prevalence of multidrug-resistant bacteria (MDR) was 53% (95% CI: 30, 75). There were significant upward trends for ciprofloxacin (P = 0.007), carbapenems (P = 0.010), ofloxacin (P = 0.013), and third-generation cephalosporins (3GCs) (P = 0.032) when comparing the pooled AMR rates of 2004-2013 to those of 2014-2022. Carbapenems and clindamycin showed relatively low resistance rates, but high study heterogeneity and limited data warrant caution in their empiric use. Overall, the findings highlight the need to prioritize local antibiograms and strengthen antimicrobial stewardship to address rising AMR in West Africa. Not applicable.