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Aims: The main limitation of the production of potatoes (Solanum tuberosum L.) in Niger is the external dependence on the supply of quality seeds. In the context of a national potato seed system, one of the critical phases is the rapid in vitro multiplication of virus-free good quality potato plantlets. Fifteen hormonal combinations were formulated and tested to determine a suitable hormonal combination and optimum concentrations for the in vitro production of a high number of plantlets for four farmer-preferred varieties in Niger (ATLAS, PAMELA, STEMSTER and YONA). Study Design: A completely randomized design (CRD) was employed to reveal the performance of four potato varieties, as affected by fourteen combinations of NAA and BAP with four replications. Results of the study were subjected to the analysis of variance, and significant differences among treatments were determined using GENSTAT12.01. Segregation between means was made according to the Student Newman-Keuls test, at 5% threshold. Place and Duration of Study: The experiment was carried out at the laboratory of Biotechnology and plant improvement of the institute of radio-isotopes in the University Abdou Moumouni of Niamey, in Niger (latitude 13°29' North and longitude 2°10' Est), for 28 days. Methodology: Uninodal stem explants of in vitro plantlets were cultured on full-strength Murashige and Skoog media (MS) supplemented with fourteen different combinations of α-Naphthalene Acetic Acid NAA (0; 0.25; 0.50; 1.0; 2.0 mg/l) and Benzyl Amino Purine BAP (0; 0.25; 0.50 mg/l), for 28 days. Results: Statistical analysis of the results showed that the variety and hormonal significantly influenced the height of the plant, the number of leaves and number of roots. Treatments with NAA alone without BAP stimulated rhizogenesis. From a NAA concentration of 0.25 to 0.5 mg/l there is a proliferation of the roots and from 1 mg/l there is an increase in roots length. PAMELA and ATLAS cultivars showed better root production.

We sequenced 46 Vibrio cholerae isolates from Cameroon, Niger, and Nigeria, 37 of which were from 2018–2019. These sequences belong to the T12 lineage observed in the region since 2009, suggesting continuous transmission. Data were generated during a workshop in Nigeria, providing a model for future regionally coordinated surveillance efforts.

International audience; Respiratory infections remain an important cause of morbidity and mortality in children worldwide. Children aged 1 to 59 months suspect of respiratory infections were enrolled with a view to determine the etiologies of infection and improving care. In total, 767 children were enrolled. The mean age and sex ratio male/female were respectively 13.25 months and 1.3. Children aged ≤12 months and those >12 months were respectively 136/767 (17.7%) and 631/767 (82.3%). The mean hospitalization time was 6.1 days (mini=0, max=20). Of the 767 children, 714 (93.1%) had at least one sign of severe infection detected with 325/714 (42.5%) having a body temperature ≥ 38°C associated. Procalcitonin level was significant in 173/633 children (27.3%) while Binax rapid test was positive in 176/642 (27.4%). The two tests agreed in 54/159children (34.0%). Blood culture was requested for 55/767 (7.2%) children and only 11 were positive with Staphylococcus aureus being the major etiology (63%) isolated. Etiologies detected by PCR from nasopharynx were Streptococcus pneumoniae (39.3%) and respiratory syncytial virus (23.6%) with 86 children co-infected by both pathogens. Other etiologies detected were Staphylococcus aureus (17.9%), Rhinovirus (10.1%), Adenovirus (9.4%), and Parainfluenza virus (7.3%). Sixty percent of children were fully vaccinated with pentavalent vaccine but only 10% received their second dose of PCV13 vaccine. Multiple home visits for post hospitalization health monitoring did not offer better prevention of morbidity and mortality compared to a single visit (P >0.05). A rate of 42.5% severe respiratory infections was detected with Streptococcus pneumoneae and Respiratory Syncytial Virus encountered the most.

Background Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. Methods We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes. Results Population structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat pC194), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1’s rarity in carriage and consequently its lower recombination rates. Conclusions The high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversification and adaptation in different geographical regions. Such geographic adaptation reflects local variations in selection pressures in different locales. Further studies will be required to fully understand the biological mechanisms which makes the ST217 clone highly invasive but unable to successfully colonise the human nasopharynx for long durations which results in lower recombination rates. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1987-z) contains supplementary material, which is available to authorized users.

Funder: Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation), Hyper-virulent Streptococcus pneumoniae serotype 1 strains are endemic in Sub-Saharan Africa and frequently cause lethal meningitis outbreaks. It remains unknown whether genetic variation in serotype 1 strains modulates tropism into cerebrospinal fluid to cause central nervous system (CNS) infections, particularly meningitis. Here, we address this question through a large-scale linear mixed model genome-wide association study of 909 African pneumococcal serotype 1 isolates collected from CNS and non-CNS human samples. By controlling for host age, geography, and strain population structure, we identify genome-wide statistically significant genotype-phenotype associations in surface-exposed choline-binding (P = 5.00 × 10-08) and helicase proteins (P = 1.32 × 10-06) important for invasion, immune evasion and pneumococcal tropism to CNS. The small effect sizes and negligible heritability indicated that causation of CNS infection requires multiple genetic and other factors reflecting a complex and polygenic aetiology. Our findings suggest that certain pathogen genetic variation modulate pneumococcal survival and tropism to CNS tissue, and therefore, virulence for meningitis.

BACKGROUND: Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. METHODS: We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes. RESULTS: Population structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat pC194), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1's rarity in carriage and consequently its lower recombination rates. CONCLUSIONS: The high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversification and adaptation in different geographical regions. Such geographic adaptation reflects local variations in selection pressures in different locales. Further studies will be required to fully understand the biological mechanisms which makes the ST217 clone highly invasive but unable to successfully colonise the human nasopharynx for long durations which results in lower recombination rates.