Baobab Index

Despite strong leprosy control measures, including effective treatment, leprosy persists in the Comoros. As of May, 2022, no resistance to anti-leprosy drugs had been reported, but there are no nationally representative data. Post-exposure prophylaxis (PEP) with rifampicin is offered to contacts of patients with leprosy. We aimed to conduct a countrywide drug resistance survey and investigate whether PEP led to the emergence of drug resistance in patients with leprosy. In this observational, deep-sequencing analysis we assessed Mycobacterium leprae genomes from skin biopsies of patients in Anjouan and Mohéli, Comoros, collected as part of the ComLep (NCT03526718) and PEOPLE (NCT03662022) studies. Skin biopsies that had sufficient M leprae DNA (>2000 bacilli in 2 μl of DNA extract) were assessed for the presence of seven drug resistance-associated genes (ie, rpoB, ctpC, ctpI, folP1, gyrA, gyrB, and nth) using Deeplex Myc-Lep (targeted next generation deep sequencing), with a limit of detection of 10% for minority M leprae bacterial populations bearing a polymorphism in these genes. All newly registered patients with leprosy for whom written informed consent was obtained were eligible for inclusion in the survey. Patients younger than 2 years or with a single lesion on the face did not have biopsies taken. The primary outcome of our study was the proportion of patients with leprosy (ie, new cases, patients with relapses or reinfections, patients who received single (double) dose rifampicin-PEP, or patients who lived in villages where PEP was distributed) who were infected with M leprae with a drug-resistant mutation for rifampicin, fluoroquinolone, or dapsone in the Comoros. Between July 1, 2017, and Dec 31, 2020, 1199 patients with leprosy were identified on the basis of clinical criteria, of whom 1030 provided a skin biopsy. Of these 1030 patients, 755 (73·3%) tested positive for the M leprae-specific repetitive element-quantitative PCR (qPCR) assay. Of these 755 patients, 260 (34·4%) were eligible to be analysed using Deeplex Myc-Lep. 251 (96·5%) were newly diagnosed with leprosy, whereas nine (3·4%) patients had previously received multidrug therapy. 45 (17·3%) patients resided in villages where PEP had been administered in 2015 or 2019, two (4·4%) of whom received PEP. All seven drug resistance-associated targets were successfully sequenced in 216 samples, 39 samples had incomplete results, and five had no results. No mutations were detected in any of the seven drug resistance-related genes for any patient with successfully sequenced results. This drug resistance survey provides evidence to show that M leprae is fully susceptible to rifampicin, fluoroquinolones, and dapsone in the Comoros. Our results also show, for the first time, the applicability of targeted sequencing directly on skin biopsies from patients with either paucibacillary or multibacillary leprosy. These data suggest that PEP had not selected rifampicin-resistant strains, although further support for this finding should be confirmed with a larger sample size. Effect:Hope, The Mission To End Leprosy, the Fonds Wetenschappelijk Onderzoek, the EU.

The Adapting Agriculture to Climate Change Project set out to improve the diversity, quantity, and accessibility of germplasm collections of crop wild relatives (CWR). Between 2013 and 2018, partners in 25 countries, heirs to the globetrotting legacy of Nikolai Vavilov, undertook seed collecting expeditions targeting CWR of 28 crops of global significance for agriculture. Here, we describe the implementation of the 25 national collecting programs and present the key results. A total of 4587 unique seed samples from at least 355 CWR taxa were collected, conserved ex situ, safety duplicated in national and international genebanks, and made available through the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture (Plant Treaty). Collections of CWR were made for all 28 targeted crops. Potato and eggplant were the most collected genepools, although the greatest number of primary genepool collections were made for rice. Overall, alfalfa, Bambara groundnut, grass pea and wheat were the genepools for which targets were best achieved. Several of the newly collected samples have already been used in pre-breeding programs to adapt crops to future challenges.

An increasing number of invasive fruit fly pests are colonizing new grounds. With this study, we aimed to uncover the invasion pathways of the oriental fruit fly,

Plants in general and mangroves in particular can harbor hyper-diverse microorganisms in their different compartments including the phyllosphere area. This study used the leaves of three mangrove species; black mangrove (Avicenia germinans), red mangrove (Rhizophora mangle) and mangrove apple (Sonneratia alba) in order to evaluate the phyllosphere epiphytic bacterial community on their leaves surface and assess the ability of some epiphytic bacteria to tolerate and survive under pyrene stress. Through the 16S rRNA genes sequencing, 380203, 405203 and 344863 OTUs were identified respectively in the leaves of mangroves apple, black and red mangroves. The identified OTUs was positively correlated with leaves-wax (p < 0.05, r

Expansion of antimicrobial resistance monitoring and epidemiological surveillance are key components of the WHO strategy towards zero leprosy. The inability to grow Mycobacterium leprae in vitro precludes routine phenotypic drug susceptibility testing, and only limited molecular tests are available. We evaluated a culture-free targeted deep sequencing assay, for mycobacterial identification, genotyping based on 18 canonical SNPs and 11 core variable-number tandem-repeat (VNTR) markers, and detection of rifampicin, dapsone and fluoroquinolone resistance-associated mutations in rpoB/ctpC/ctpI, folP1, gyrA/gyrB, respectively, and hypermutation-associated mutations in nth. The limit of detection (LOD) was determined using DNA of M. leprae reference strains and from 246 skin biopsies and 74 slit skin smears of leprosy patients, with genome copies quantified by RLEP qPCR. Sequencing results were evaluated versus whole genome sequencing (WGS) data of 14 strains, and versus VNTR-fragment length analysis (FLA) results of 89 clinical specimens. The LOD for sequencing success ranged between 80 and 3000 genome copies, depending on the sample type. The LOD for minority variants was 10%. All SNPs detected in targets by WGS were identified except in a clinical sample where WGS revealed two dapsone resistance-conferring mutations instead of one by Deeplex Myc-Lep, due to partial duplication of the sulfamide-binding domain in folP1. SNPs detected uniquely by Deeplex Myc-Lep were missed by WGS due to insufficient coverage. Concordance with VNTR-FLA results was 99.4% (926/932 alleles). Deeplex Myc-Lep may help improve the diagnosis and surveillance of leprosy. Gene domain duplication is an original putative drug resistance-related genetic adaptation in M. leprae. EDCTP2 programme supported by the European Union (grant number RIA2017NIM-1847 -PEOPLE). EDCTP, R2Stop: Effect:Hope, The Mission To End Leprosy, the Flemish Fonds Wetenschappelijk Onderzoek.

The mosquito Anopheles gambiae s.s. is a primary malaria vector throughout sub-Saharan Africa including the islands of the Comoros archipelago (Anjouan, Grande Comore, Mayotte and Mohéli). These islands are located at the northern end of the Mozambique Channel in eastern Africa. Previous studies have shown a relatively high degree of genetic isolation between the Comoros islands and mainland populations of A. gambiae, but the origin of the island populations remains unclear. Here, we analyzed phylogenetic relationships among island and mainland populations using complete mitochondrial genome sequences of individual A. gambiae specimens. This work augments earlier studies based on analysis of the nuclear genome. We investigated the source population of A. gambiae for each island, estimated the number of introductions, when they occurred and explored evidence for contemporary gene flow between island and mainland populations. These studies are relevant to understanding historical patterns in the dispersal of this important malaria vector and provide information critical to assessing their potential for the exploration of genetic-based vector control methods to eliminate this disease. Phylogenetic analysis and haplotype networks were constructed from mitogenome sequences of 258 A. gambiae from the four islands. In addition, 112 individuals from seven countries across sub-Saharan Africa and Madagascar were included to identify potential source populations. Our results suggest that introduction events of A. gambiae into the Comoros archipelago were rare and recent events and support earlier claims that gene flow between the mainland and these islands is limited. This study is concordant with earlier work suggesting the suitability of these oceanic islands as appropriate sites for conducting field trial releases of genetically engineered mosquitoes (GEMs).

FTIR-ATR spectroscopy and chemometric techniques were employed to examine the phenotypic diversity of fig seeds. The investigation was performed in detail. The research analyzed twenty-two fig genotypes to assess their nutritional properties, genetic relationships, and potential applications. The results demonstrate substantial nutritional benefits related to fig seeds, which could serve as genetic resources for selection programs for extracting vegetable oil and functional ingredients. Additionally, a detailed lipodomic profile analysis led to the categorization of the genotypes into four unique clusters. The study uncovered new insights regarding the nutritional composition of the samples, while also highlighting significant similarities and differences. The findings showcased the phenotypic diversity within the studied fig germplasm, which is likely attributed to underlying genetic factors. These accessions offer a valuable gene pool for future breeding programs and diverse applications involving fig seeds. This work contributes to the selection of potential genotypes for scientific and industrial purposes. Furthermore, the application of FTIR and chemometrics revealed a noteworthy diversity of patterns, emphasizing the previously underestimated significance of this aspect in evaluating the chemodiversity of the species.

The maize streak virus belongs in the genus Mastrevirus, in the family Geminiviridae. The A-strain of the virus (MSV-A) is recognised as the principal causative agent of the most severe manifestation of maize streak disease (MSD). This disease continues to be a persistent limitation on maize output across sub-Saharan Africa and the nearby Indian Ocean islands. Irrespective of the causes behind the spread of MSV-A, we can determine the paths and speeds with which MSV-A spreads by analysing MSV genome sequence data along with information on when and where samples were taken. This information is valuable for identifying the geographical origins of viral strains that cause sporadic MSD epidemics in specific places and the geographical regions where viruses remain in reservoirs and contribute to prolonged epidemics during outbreaks. Our aim is to utilise these analyses to estimate the timing and origin of the MSV-A that arrived on the island of Madagascar in the Indian Ocean. Specifically, we employ model-based phylogeographic analyses on 524 complete MSV-A genome sequences, which consist of 56 newly obtained genomes from infected maize plants collected in Madagascar. These studies allow us to reconstruct the most likely paths of MSV-A to Madagascar. We found strong evidence for the existence of at least four separate movements of MSV-A variants from East and southern Africa to Madagascar. These movements took place between roughly 1979 (with a 95% highest probability density interval [HPD] ranging from 1976 to 1982) and 2003 (with a 95% HPD ranging from 2002 to 2003). While we inferred that MSV-A variants are spreading at an average rate of 38.9 km/year (with a 95% highest posterior density interval of 34.0-44.4) across their geographical range. Since their arrival in Madagascar, MSV-A variants have been migrating at an average rate of 47.6 km/year (with a 95% highest posterior density interval of 36.05-61.70). Human influences are likely significant contributors to both sporadic long-range movements of MSV-A between mainland Africa and Madagascar, as well as shorter to medium range movements within the island.

In mangrove ecosystems, research on bacterial abundance in the rhizosphere and the non-rhizosphere soils remains limited. Moreover, the variation in bacterial taxonomy during the acclimation of sediment samples subjected to high-molecular-weight (HMW) organic pollutant stress remains poorly understood. This study was conducted in both rhizosphere and non-rhizosphere soils at depths ranging from 0 to 20 cm in the coastal mangrove of Yunxiao to evaluate the diversity and abundance of the bacterial community and to characterize the profile of its variation arising during acclimation under pyrene stress. Rhizosphere sediments were defined as those directly adhering to the roots of mangrove plants, while non-rhizospheres were those collected 3 m away from the roots. Each sample was divided into two groups: the first group was stored at 4 °C for the determination of the physicochemical characteristics of the sediments, and the second group, used for DNA analysis, was stored at -20 °C. A DNA isolation kit was used to extract total genomic DNA from the samples before and after acclimation. Polymerase Chain Reaction (PCR) amplification of the 16S rRNA genes targeting the V3-V4 region was performed. The results of this study showed that although the physicochemical properties of both rhizosphere and the non-rhizosphere sediments were unevenly distributed, no significant difference in bacterial abundance between the two zones was observed. Moreover, the abundance at 0-10 cm depth was significantly higher in both rhizosphere and non-rhizosphere sediments. The acclimation process revealed that pyrene significantly impacted bacterial community composition and abundance. In total, 23 genera were identified in the first transfer (G1), dominated by