Incidence and impact on clinical outcome of infections with piperacillin/tazobactam resistant Escherichia coli in ICU: A retrospective study

Escherichia coli infections are frequent in ICU patients. The increased resistance to fluoroquinolones and amoxicillin/clavulanate of this pathogen mandates the prescription of broad-spectrum antibiotics such as piperacillin/tazobactam (PIP-TAZ) or third generation cephalosporins (3GC)

Diversité agro-morphologique des accessions de fonio [Digitaria exilis (Kippist.) Stapf.] au Niger

La variablité morphologique de 67 accessions de fonio [Digitaria exilis (Kippist.) Stapf.] collectées au Niger a été évaluée au cours de deux  années (2011 et 2012). Seize (16) caractères agro morphologiques (dont 14 caractères quantitatifs et 2 caractères qualitatifs) ont été évalués en station dans deux zones agroécologiques différentes (Tarna en zone sahélo-saharienne et Tara en zone soudanienne). La classification  acsendante hierarchique (CAH) et l’analyse factorielle discriminante (AFD) ont mis en évidence quatre groupes (GI, GII, GIII et GIV). Les accessions du groupe GIV ont en moyenne un cycle de maturité compris entre 85 et 90 jours tandis que les autres groupes présentent un cycle de maturité superieur à 90 jours dans nos conditions expérimentales. Les résultats montrent que les variables les plus discriminantes qui permettent de  décrire la variabilité entre les groupes identifiés sont la biomasse sèche (tige et feuille) par hectare, la longueur des entrenoeuds, le rendement en graine par hectare et dans une certaine mesure le cycle de la plante. L’observation des caractères qualitatifs a montré que cinq accessions (représentant 7% du total) ont des graines non decortiquées de couleur rouge et quatre accessions (6% du total), une tige de couleur rouge. Les caractères analysés peuvent ainsi constituer des critères de base pour différencier les accessions des autres régions de l’Afrique de l’Ouest et servir pour une étude de variabilité entre les restes des accessions de fonio collectées au Niger. Des possiblités d’amélioration peuvent  également être envisagées une fois que le regime de réproduction de l’espèce est bien identifié.Mots clés: Digitaria exilis, variabilité morphologique, accessions, diversité, fonio, Niger

Analyse multiéchelle de la diversité génétique des sorghos : compréhension des processus évolutifs pour la conservation in situ

Using microsatellite genetic markers, we analyzed 1,518 sorghum samples collected at different spatial scales in Burkina Faso, Mali, Niger, and in the village of Wanté, from the landrace to the country scale. Genetic diversity and differentiation parameters were estimated to assess the effects of the main evolutionary processes on sorghum genetic diversity. The genetic variability found within a variety is mainly the result of the sorghum reproduction biology and the genetic drift process caused by the limited number of reproductive individuals at the time of variety introduction into a household or each year when farmers select their seeds. At the village scale, a low correlation is observed between the diversity of vernacular names and the genetic diversity assessed by microsatellites. No spatial genetic structuration is observed among villages more than 30 kilometers apart. This point highlights that traditional seed systems operate at a very local scale. In Mali, a similar proportion of allelic richness is observed along a longitudinal transect and a latitudinal gradient that crosses a larger range of agroclimatic conditions. At the country scale, sorghum exhibits more genetic diversity in Niger than in Mali despite a lower agroclimatic range in Niger. These results demonstrate that the diversity of human groups acts together with the agro-ecological factors to shape the structure of sorghum genetic diversity. An important proportion of the overall genetic diversity present in the Cirad (Centre de coopération internationale en recherche agronomique pour le développement) "core collection" is found in Mali and Niger. The tremendous diversity cultivated by farmers in traditional agroecosystems of Western Africa supports the relevance of in situ approaches for sorghum conservation programs in this region. Both conservation and crop improvement requirements can be achieved through a better use of local germplasm in decentralized breeding programs. (Summary in English)

New Disturbing Trend in Antimicrobial Resistance of Gram-Negative Pathogens

ope

New Genetic Insights into Pearl Millet Diversity As Revealed by Characterization of Early- and Late-Flowering Landraces from Senegal

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food and a drought-tolerant cereal well adapted to Sub-Saharan Africa agro-ecosystems. An important diversity of pearl millet landraces has been widely conserved by farmers and therefore could help copping with climate changes and contribute to future food security. Hence, characterizing its genetic diversity and population structure can contribute to better assist breeding programs for a sustainable agricultural productivity enhancement. Toward this goal, a comprehensive panel of 404 accessions were used that correspond to 12 improved varieties, 306 early flowering and 86 late-flowering cultivated landraces from Senegal. Twelve highly polymorphic SSR markers were used to study diversity and population structure. Two genes, PgMADS11 and PgPHYC, were genotyped to assess their association to flowering phenotypic difference in landraces. Results indicate a large diversity and untapped potential of Senegalese pearl millet germplasm as well as a genetic differentiation between early- and late-flowering landraces. Further, a fine-scale genetic difference of PgPHYC and PgMADS11 (SNP and indel, respectively) and co-variation of their alleles with flowering time were found among landraces. These findings highlight new genetic insights of pearl millet useful to define heterotic populations for breeding, genomic association panel, or crosses for trait-specific mapping

Species Discrimination, Population Structure and Linkage Disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis Using SSR Markers

Eucalyptus camaldulensis and E. tereticornis are closely related species commonly cultivated for pulp wood in many tropical countries including India. Understanding the genetic structure and linkage disequilibrium (LD) existing in these species is essential for the improvement of industrially important traits. Our goal was to evaluate the use of simple sequence repeat (SSR) loci for species discrimination, population structure and LD analysis in these species. Investigations were carried out with the most common alleles in 93 accessions belonging to these two species using 62 SSR markers through cross amplification. The polymorphic information content (PIC) ranged from 0.44 to 0.93 and 0.36 to 0.93 in E. camaldulensis and E. tereticornis respectively. A clear delineation between the two species was evident based on the analysis of population structure and species-specific alleles. Significant genotypic LD was found in E. camaldulensis, wherein out of 135 significant pairs, 17 pairs showed r2≥0.1. Similarly, in E. tereticornis, out of 136 significant pairs, 18 pairs showed r2≥0.1. The extent of LD decayed rapidly showing the significance of association analyses in eucalypts with higher resolution markers. The availability of whole genome sequence for E. grandis and the synteny and co-linearity in the genome of eucalypts, will allow genome-wide genotyping using microsatellites or single nucleotide polymorphims

Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

UMR-AGAP Equipe DAVV (Diversité, adaptation et amélioration de la vigne) ; équipe ID (Intégration de Données)International audienceAbstractBackgroundAs for many crops, new high-quality grapevine varieties requiring less pesticide and adapted to climate change are needed. In perennial species, breeding is a long process which can be speeded up by gaining knowledge about quantitative trait loci linked to agronomic traits variation. However, due to the long juvenile period of these species, establishing numerous highly recombinant populations for high resolution mapping is both costly and time-consuming. Genome wide association studies in germplasm panels is an alternative method of choice, since it allows identifying the main quantitative trait loci with high resolution by exploiting past recombination events between cultivars. Such studies require adequate panel design to represent most of the available genetic and phenotypic diversity. Assessing linkage disequilibrium extent and panel power is also needed to determine the marker density required for association studies.ResultsStarting from the largest grapevine collection worldwide maintained in Vassal (France), we designed a diversity panel of 279 cultivars with limited relatedness, reflecting the low structuration in three genetic pools resulting from different uses (table vs wine) and geographical origin (East vs West), and including the major founders of modern cultivars. With 20 simple sequence repeat markers and five quantitative traits, we showed that our panel adequately captured most of the genetic and phenotypic diversity existing within the entire Vassal collection. To assess linkage disequilibrium extent and panel power, we genotyped single nucleotide polymorphisms: 372 over four genomic regions and 129 distributed over the whole genome. Linkage disequilibrium, measured by correlation corrected for kinship, reached 0.2 for a physical distance between 9 and 458 Kb depending on genetic pool and genomic region, with varying size of linkage disequilibrium blocks. This panel achieved reasonable power to detect associations between traits with high broad-sense heritability (> 0.7) and causal loci with intermediate allelic frequency and strong effect (explaining > 10 % of total variance).ConclusionsOur association panel constitutes a new, highly valuable resource for genetic association studies in grapevine, and deserves dissemination to diverse field and greenhouse trials to gain more insight into the genetic control of many agronomic traits and their interaction with the environment

A western Sahara centre of domestication inferred from pearl millet genomes

There have been intense debates over the geographic origin of African crops and agriculture. Here, we used whole-genome sequencing data to infer the domestication origin of pearl millet (Cenchrus americanus). Our results supported an origin in western Sahara, and we dated the onset of cultivated pearl millet expansion in Africa to 4,900 years ago. We provided evidence that wild-to-crop gene flow increased cultivated genetic diversity leading to diversity hotspots in western and eastern Sahel and adaptive introgression of 15 genomic regions. Our study reconciled genetic and archaeological data for one of the oldest African crops