Caractérisation phénotypique et génétique du riz africain (Oryza glaberrima Steud) phenotypic and genetic characterization of african rice (oryza glaberrima steud)

The agronomic interest of African rice and the morphological similarities with other species, arouse the necessity to characterize African rice for recovery and conservation. The present study aims primarily to characterize phenotypically and genetically African rice for better exploitation in aid of rice producers and consumers. Indeed, the phenotypic characteristics of the rice accessions examined have been determined in two agronomics systems (upland and irrigated) carried out about 235 accessions of African rice; and afterwards, genetic characterization using a specific marker has been carried. At the end of the analyzes, with regard to the phenotypic characters, 22 O.sativa or interspecific accessions differing morphologically on several descriptors were identified. Genetically, out of 19 profiles revealed on a 935-bp band, 14 confirmed the phenotypic results. This study shows that 221 out of 235 accessions are O. glaberrima rice. These results show that the accessions of different species analyzed were confused during the collection. They also seems to validate the possibility of hybridization between the two rice species in peasant environment. The accessions characterized strengthen the conservation effort of African rice. This collection can be used for future studies, particularly with perspective to selection and running African rice with the possibility to establish a genetic model to facilitate the transfer of useful genes from O.glaberrima to O.sativa, while controlling the reproductive barrier. Thus, it will be easy to better exploit the genetic diversity of the African species of cultivated rice

Invasive atypical non-typhoidal Salmonella serovars in The Gambia.

Invasive non-typhoidal Salmonella (iNTS) disease continues to be a significant public health problem in sub-Saharan Africa. Common clinical misdiagnosis, antimicrobial resistance, high case fatality and lack of a vaccine make iNTS a priority for global health research. Using whole genome sequence analysis of 164 invasive Salmonella isolates obtained through population-based surveillance between 2008 and 2016, we conducted genomic analysis of the serovars causing invasive Salmonella diseases in rural Gambia. The incidence of iNTS varied over time. The proportion of atypical serovars causing disease increased over time from 40 to 65 % compared to the typical serovars Enteritidis and Typhimurium that decreased from 30 to 12 %. Overall iNTS case fatality was 10%, but case fatality associated with atypical iNTS alone was 10 %. Genetic virulence factors were identified in 14/70 (20 %) typical serovars and 45/68 (66 %) of the atypical serovars and were associated with: invasion, proliferation and/or translocation (Clade A); and host colonization and immune modulation (Clade G). Among Enteritidis isolates, 33/40 were resistant to four or more of the antimicrobials tested, except ciprofloxacin, to which all isolates were susceptible. Resistance was low in Typhimurium isolates, but all 16 isolates were resistant to gentamicin. The increase in incidence and proportion of iNTS disease caused by atypical serovars is concerning. The increased proportion of atypical serovars and the high associated case fatality may be related to acquisition of specific genetic virulence factors. These factors may provide a selective advantage to the atypical serovars. Investigations should be conducted elsewhere in Africa to identify potential changes in the distribution of iNTS serovars and the extent of these virulence elements

An invisible workforce: the neglected role of cleaners in patient safety on maternity units.

Hospital cleaning has been shown to impact on rates of healthcare-associated infections (HCAIs) and good environmental hygiene is critical to quality care, yet those tasked with the role of ensuring a safe and clean environment often go unrecognised as members of the healthcare workforce. Sepsis is a leading cause of maternal and newborn death, a significant proportion of these cases are estimated to be due to HCAIs. Deliveries in health institutions have now reached 75% globally, and in low and middle income countries the corresponding increased pressure on facilities  has impacted both quality of care provided and quality of the birth environment in terms of infection prevention and control (IPC) and HCAIs. The paper discusses the neglected role of health facility cleaners, providing evidence from the literature and from needs assessments conducted by The Soapbox Collaborative and partners in Bangladesh, India, The Gambia and Zanzibar. While not the primary focus of the assessments, common themes emerged consistently pointing to institutional neglect of cleaning and cleaners. The paper argues that low status within facilities, wider societal marginalisation, lack of training, and poor pay and working conditions contribute to the lack of prioritisation placed on health facility environmental hygiene. With increased international attention focused towards health facility water, sanitation and hygiene and a growing focus on IPC, now is the time to address the neglect of this frontline healthcare workforce. We propose that provision of and improved training can enable the recognition of the valuable role cleaning staff play, as well as equipping these staff with the tools required to perform their job to the highest standard. In addition to training, wider systems changes are necessary to establish improvements in environmental hygiene and the role of cleaning staff, including addressing resource availability, supportive supervision, and an increased emphasis on preventative healthcare

Refurbishment of public housing villas in the United Arab Emirates (UAE): energy and economic impact

© 2016, Springer Science+Business Media Dordrecht. This study aims at assessing the technical and economic benefits of refurbishing existing public housing villas in the UAE. Four representative federal public housing villas built between 1980s and 2010s were modeled and analyzed. The Integrated Environmental Solutions-Virtual Environment (IES-VE) energy modeling software was used to estimate the energy consumption and savings due to different refurbishment configurations applied to the villas. The refurbishment technical configurations were based on the UAE’s Estidama green buildings sustainability assessment system. The refurbishment configurations include upgrading three elements: the wall and roof insulation as well as replacing the glazing. The annual electricity savings results indicated that the most cost-efficient refurbishment strategy is upgrading of wall insulation (savings up to 20.8 %) followed by upgrading the roof’s insulation (savings up to 11.6 %) and lastly replacing the glazing (savings up to 3.2 %). When all three elements were refurbished simultaneously, savings up to 36.7 % were achieved (villa model 670). The savings translated to CO2 emission reduction of 22.6 t/year. The simple and discounted payback periods for the different configurations tested ranged between 8 and 28 and 10 and 50 years, respectively

cAMP Receptor Protein Controls Vibrio cholerae Gene Expression in Response to Host Colonization

The bacterium Vibrio cholerae is native to aquatic environments and can switch lifestyles to cause disease in humans. Lifestyle switching requires modulation of genetic systems for quorum sensing, intestinal colonization, and toxin production. Much of this regulation occurs at the level of gene expression and is controlled by transcription factors. In this work, we have mapped the binding of cAMP receptor protein (CRP) and RNA polymerase across the V. cholerae genome. We show that CRP is an integral component of the regulatory network that controls lifestyle switching. Focusing on a locus necessary for toxin transport, we demonstrate CRP-dependent regulation of gene expression in response to host colonization. Examination of further CRP-targeted genes reveals that this behavior is commonplace. Hence, CRP is a key regulator of many V. cholerae genes in response to lifestyle changes.Cholera is an infectious disease that is caused by the bacterium Vibrio cholerae. Best known for causing disease in humans, the bacterium is most commonly found in aquatic ecosystems. Hence, humans acquire cholera following ingestion of food or water contaminated with V. cholerae. Transition between an aquatic environment and a human host triggers a lifestyle switch that involves reprogramming of V. cholerae gene expression patterns. This process is controlled by a network of transcription factors. In this paper, we show that the cAMP receptor protein (CRP) is a key regulator of V. cholerae gene expression in response to lifestyle changes

The roots of future rice harvests

The authors thank the Global Rice Science Partnership and Agropolis Fondation (Special grant n° 1400–009 and Rhizopolis grant n° 1001–005) benefiting from a national ANR Investissement d’Avenir” grant ANR-10-LABX-001-01) for supporting the workshop. They acknowledge the assistance of Nathalie Pivot, Cirad and Véronique Rafin, INRA in workshop organization. The root research at Cirad and University of Aberdeen is supported by the European Grant (FP7/2007-2013) under grant agreement n° 289300.27 EURoot “Enhancing resource Uptake from ROOTs under stress in cereal crops”. Research at IRRI is supported by the Generation Challenge Program and the Bill and Melinda Gates Foundation. J.X. is supported by the AcRF Tier 2 grant (MOE2009-T2-1-060) from the Ministry of Education of Singapore and National Research Foundation Singapore under its Competitive Research Programme (CRP Award No. NRF2010 NRF-CRP002-018). Doan Trung Luu is supported by the EU Marie Curie International Outgoing Fellowship 'ORYZAQUA – Cell Biology of Rice Aquaporins' (PIOF-GA-2011-300150). AP acknowledges the Generation Challenge Programme funded project “Targeting drought avoidance root traits to enhance rice productivity under water limited environments”. Financial support for A.G. Diedhiou was provided by the Université Cheikh Anta Diop (UCAD, VE12/13, CpVIII-Ar4 ) and GRISP. *This paper is dedicated to the late memory of Pr Ping Wu who passed away in a tragic car accident on June 12th, 2014.Peer reviewedPublisher PD

Health-seeking behaviour and beliefs around sore throat in The Gambia: A qualitative study.

Group A Streptococcus (Strep A) bacteria causes a broad spectrum of diseases. The most common manifestations of Strep A infection are sore throat and pus-producing skin infections such as impetigo. Complications of Strep A infection can lead to inflammation in the bones, muscles, joints, and internal organs causing acute rheumatic fever and rheumatic heart disease (RHD). In The Gambia, the RHD burden is thought to be very high. However, epidemiological data is minimal, and Strep A control programmes do not exist. This study aimed to explore common beliefs and practices related to sore throats among primary caregivers of children, and healthcare providers in a community with a high Strep A disease burden. Four informal conversations with providers and fifteen semi-structured interviews with caregivers were conducted in the peri-urban area of Sukuta, The Gambia. Sampling was purposive and gradual, beginning from households identified to have recently experienced sore throat through a parallel cohort study. Themes explored in qualitative analysis included: sore throat causal attributions and diagnoses, care practises, health-seeking behaviour, and perceived barriers to using the biomedical sector. We found that sore throats were typically perceived to affect one child in a family, disproportionately or exclusively. Sore throats were rarely perceived as life-threatening, and awareness of links between sore throat and ARF or RHD was not reported among caregivers or providers in this study population. Most cases of sore throat were initially managed at home using traditional medicine which delayed resort to antibiotics, though in two instances of severe pain with the presence of exudate, fear that the child's life was at risk prompted care-seeking through the formal health system. Our findings can inform the development of tailored strategies to increase community knowledge of the potential long-term consequences of sore throats and appropriate care-seeking, alongside improvements in the health system, to prevent Strep A sequelae effectively

Genomic Characterization of Skin and Soft Tissue Streptococcus pyogenes Isolates from a Low-Income and a High-Income Setting.

Streptococcus pyogenes is a leading cause of human morbidity and mortality, especially in resource-limited settings. The development of a vaccine against S. pyogenes is a global health priority to reduce the burden of postinfection rheumatic heart disease. To support this, molecular characterization of circulating S. pyogenes isolates is needed. We performed whole-genome analyses of S. pyogenes isolates from skin and soft tissue infections in Sukuta, The Gambia, a low-income country (LIC) in West Africa where there is a high burden of such infections. To act as a comparator to these LIC isolates, skin infection isolates from Sheffield, United Kingdom (a high-income country [HIC]), were also sequenced. The LIC isolates from The Gambia were genetically more diverse (46 emm types in 107 isolates) than the HIC isolates from Sheffield (23 emm types in 142 isolates), with only 7 overlapping emm types. Other molecular markers were shared, including a high prevalence of the skin infection-associated emm pattern D and the variable fibronectin-collagen-T antigen (FCT) types FCT-3 and FCT-4. Fewer of the Gambian LIC isolates carried prophage-associated superantigens (64%) and DNases (26%) than did the Sheffield HIC isolates (99% and 95%, respectively). We also identified streptococcin genes unique to 36% of the Gambian LIC isolates and a higher prevalence (48%) of glucuronic acid utilization pathway genes in the Gambian LIC isolates than in the Sheffield HIC isolates (26%). Comparison to a wider collection of HIC and LIC isolate genomes supported our findings of differing emm diversity and prevalence of bacterial factors. Our study provides insight into the genetics of LIC isolates and how they compare to HIC isolates. IMPORTANCE The global burden of rheumatic heart disease (RHD) has triggered a World Health Organization response to drive forward development of a vaccine against the causative human pathogen Streptococcus pyogenes. This burden stems primarily from low- and middle-income settings where there are high levels of S. pyogenes skin and soft tissue infections, which can lead to RHD. Our study provides much needed whole-genome-based molecular characterization of isolates causing skin infections in Sukuta, The Gambia, a low-income country (LIC) in West Africa where infection and RHD rates are high. Although we identified a greater level of diversity in these LIC isolates than in isolates from Sheffield, United Kingdom (a high-income country), there were some shared features. There were also some features that differed by geographical region, warranting further investigation into their contribution to infection. Our study has also contributed data essential for the development of a vaccine that would target geographically relevant strains

Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing.

UNLABELLED: Staphylococcus aureus is an important pathogen of humans and animals. We genome sequenced 90 S. aureus isolates from The Gambia: 46 isolates from invasive disease in humans, 13 human carriage isolates, and 31 monkey carriage isolates. We inferred multiple anthroponotic transmissions of S. aureus from humans to green monkeys (Chlorocebus sabaeus) in The Gambia over different time scales. We report a novel monkey-associated clade of S. aureus that emerged from a human-to-monkey switch estimated to have occurred 2,700 years ago. Adaptation of this lineage to the monkey host is accompanied by the loss of phage-carrying genes that are known to play an important role in human colonization. We also report recent anthroponotic transmission of the well-characterized human lineages sequence type 6 (ST6) and ST15 to monkeys, probably because of steadily increasing encroachment of humans into the monkeys' habitat. Although we have found no evidence of transmission of S. aureus from monkeys to humans, as the two species come into ever-closer contact, there might be an increased risk of additional interspecies exchanges of potential pathogens. IMPORTANCE: The population structures of Staphylococcus aureus in humans and monkeys in sub-Saharan Africa have been previously described using multilocus sequence typing (MLST). However, these data lack the power to accurately infer details regarding the origin and maintenance of new adaptive lineages. Here, we describe the use of whole-genome sequencing to detect transmission of S. aureus between humans and nonhuman primates and to document the genetic changes accompanying host adaptation. We note that human-to-monkey switches tend to be more common than the reverse and that a novel monkey-associated clade is likely to have emerged from such a switch approximately 2,700 years ago. Moreover, analysis of the accessory genome provides important clues as to the genetic changes underpinning host adaptation and, in particular, shows that human-to-monkey switches tend to be associated with the loss of genes known to confer adaptation to the human host