scholarly journals The effect of recombination on the evolution of a population of Neisseria meningitidis

2020 ◽  
Author(s):  
Neil MacAlasdair ◽  
Maiju Pesonen ◽  
Ola Brynildsrud ◽  
Vegard Eldholm ◽  
Paul A. Kristiansen ◽  
...  
Keyword(s):  
Population Structure ◽  
Burkina Faso ◽  
Neisseria Meningitidis ◽  
Large Scale ◽  
Invasive Disease ◽  
Pathogen Transmission ◽  
Sub Saharan Africa ◽  
Health Concern ◽  
Recombination Hotspots ◽  
Sub Saharan

Neisseria meningitidis (the meningococcus) is a major human pathogen with a history of high invasive disease burden, particularly in sub-Saharan Africa. Our current understanding of the evolution of meningococcal genomes is limited by the rarity of large-scale genomic population studies and lack of in-depth investigation of the genomic events associated with routine pathogen transmission. Here we fill this knowledge gap by a detailed analysis of 2,839 meningococcal genomes obtained through a carriage study of over 50,000 samples collected systematically in Burkina Faso, West Africa, before, during, and after the serogroup A vaccine rollout, 2009-2012. Our findings indicate that the meningococcal genome is highly dynamic, with recombination hotspots and frequent gene sharing across deeply separated lineages in a structured population. Furthermore, our findings illustrate the profound effect of population structure on genome flexibility, with some lineages in Burkina Faso being orders of magnitude more recombinant than others. We also examine the effect of selection on the population, in particular how it is correlated with recombination. We find that recombination principally acts to prevent the accumulation of deleterious mutations, although we do also find an example of recombination acting to speed the adaptation of a gene. In general, we show the importance of recombination in the evolution of a geographically expansive population with deep population structure in a short timescale. This has important consequences for our ability to both foresee the outcomes of vaccination programmes and, using surveillance data, predict when lineages of the meningococcus are likely to become a public health concern.

scholarly journals The seasonality of cholera in sub-Saharan Africa

2021 ◽  
Author(s):  
Javier Perez-Saez ◽  
Justin Lessler ◽  
Elizabeth C. Lee ◽  
Francisco J. Luquero ◽  
Espoir B. Malembaka ◽  
...  
Keyword(s):  
Large Scale ◽  
Task Force ◽  
Case Fatality ◽  
Sub Saharan Africa ◽  
Health Concern ◽  
National Differences ◽  
Sub Saharan ◽  
Eastern And Southern Africa ◽  
Positive Correlations ◽  
Gates Foundation

Background Cholera remains a major threat in Sub-Saharan Africa (SSA) where some of the highest case fatality risks are reported. Knowing in what months and where cholera tends to occur across the continent can aid in improving efforts to eliminate cholera as a public health concern; though largely due to lack of unified large-scale datasets, no continent-wide estimates exist. In this study we aim to estimate cholera seasonality across SSA. Methods We leverage the Global Task Force on Cholera Control (GTFCC) global cholera database with statistical models to synthesize data across spatial and temporal scale in order to infer the seasonality of excess suspected cholera occurrence in SSA. We developed a Bayesian statistical model to infer the monthly risk of excess cholera at the first and/or second administrative levels. Seasonality patterns were then grouped into spatial clusters. Finally, we studied the association between seasonality estimates and hydro-climatic variables. Findings The majority of studied countries (24/34) have seasonal patterns in excess cholera, corresponding to approximately 85% of the SSA population. Most countries (19/24) also had sub-national differences in seasonality patterns, with strong differences in seasonality strength between regions. Seasonality patterns clustered into two macro-regions (West Africa and the Sahel vs. Eastern and Southern Africa), which were composed of sub-regional clusters with varying degrees of seasonality. Exploratory association analysis found most consistent and positive correlations between cholera seasonality and precipitation, and to a lesser extent with temperature and flooding. Interpretation Widespread cholera seasonality in SSA offers opportunities for intervention planning. Further studies are needed to study the association between cholera and climate. Funding The NASA Applied Sciences Program and the Bill and Melinda Gates Foundation.

scholarly journals Evidence supporting deployment of next generation insecticide treated nets in Burkina Faso: bioassays with either chlorfenapyr or piperonyl butoxide increase mortality of pyrethroid-resistant Anopheles gambiae s.l.

2021 ◽  
Author(s):  
Sawdetuo Aristide HIEN ◽  
Dieudonné D. Soma ◽  
Dramane Coulibaly ◽  
Abdoulaye Diabaté ◽  
Allison Belemvire ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Anopheles Gambiae ◽  
High Intensity ◽  
Large Scale ◽  
Pyrethroid Resistance ◽  
Piperonyl Butoxide ◽  
Sub Saharan Africa ◽  
Insecticide Treated Nets ◽  
Bobo Dioulasso ◽  
Sub Saharan

Abstract Background Pyrethroid resistance poses a major threat to the efficacy of insecticide treated nets (ITNs) in Burkina Faso and throughout sub-Saharan Africa, particularly when resistance is present at high intensity. For such areas there are alternative ITNs available, including the synergist piperonyl butoxide (PBO)-based ITNs and dual active ingredient ITNs such as Interceptor G2 (treated with chlorfenapyr and alpha-cypermethrin). Before deploying alternative ITNs on a large scale it is crucial to characterize the resistance profiles of primary malaria vector species for evidence-based decision making Methods Larvae from the predominant vector, Anopheles gambiae s.l., were collected from 15 sites located throughout Burkina Faso and reared to adults for bioassays to assess insecticide resistance status. Resistance intensity assays were conducted using WHO tube tests to determine the level of resistance to pyrethroids commonly used on ITNs at 1x, 5x and 10x times the diagnostic dose. WHO tube tests were also used for PBO synergist bioassays with deltamethrin and permethrin. Bottle bioassays were conducted to determine susceptibility to chlorfenapyr at a dose of 100µg/bottle. Results WHO tube tests revealed high intensity resistance in An. gambiae s.l. to deltamethrin and alpha-cypermethrin in all sites tested. Resistance intensity to permethrin was either moderate or high in 13 sites. PBO pre-exposure followed by deltamethrin restored full susceptibility in 1 site but partially restored susceptibility in all but one of the remaining sites (often reaching mortality greater than 80%). PBO pre-exposure followed by permethrin partially restored susceptibility in 12 sites. There was no significant increase in permethrin mortality after PBO pre-exposure in Kampti, Karangasso-Vigué or Mangodara; while in Seguenega, Orodara and Bobo-Dioulasso there was a significant increase in mortality, but rates remained below 50%. Susceptibility to chlorfenapyr was confirmed in 14 sites. Conclusion High pyrethroid resistance intensity in An. gambiae s.l. is widespread across Burkina Faso and may be a predictor of reduced pyrethroid ITN effectiveness. PBO + deltamethrin ITNs would likely provide greater control than pyrethroid nets. However, since susceptibility in bioassays was not restored in most sites following pre-exposure to PBO, Interceptor G2 may be a better long-term solution as susceptibility was recorded to chlorfenapyr in nearly all sites. This study provides evidence supporting the introduction of both Interceptor G2 nets and PBO nets, which were distributed in Burkina Faso in 2019 as part of a mass campaign.

scholarly journals Evidence supporting deployment of next generation insecticide treated nets in Burkina Faso: bioassays with either chlorfenapyr or piperonyl butoxide increase mortality of pyrethroid-resistant Anopheles gambiae

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Aristide S. Hien ◽  
Dieudonné D. Soma ◽  
Samina Maiga ◽  
Dramane Coulibaly ◽  
Abdoulaye Diabaté ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Anopheles Gambiae ◽  
High Intensity ◽  
Large Scale ◽  
Pyrethroid Resistance ◽  
Piperonyl Butoxide ◽  
Sub Saharan Africa ◽  
Insecticide Treated Nets ◽  
Bobo Dioulasso ◽  
Sub Saharan

Abstract Background Pyrethroid resistance poses a major threat to the efficacy of insecticide-treated nets (ITNs) in Burkina Faso and throughout sub-Saharan Africa, particularly where resistance is present at high intensity. For such areas, there are alternative ITNs available, including the synergist piperonyl butoxide (PBO)-based ITNs and dual active ingredient ITNs such as Interceptor G2 (treated with chlorfenapyr and alpha-cypermethrin). Before deploying alternative ITNs on a large scale it is crucial to characterize the resistance profiles of primary malaria vector species for evidence-based decision making. Methods Larvae from the predominant vector, Anopheles gambiae sensu lato (s.l.) were collected from 15 sites located throughout Burkina Faso and reared to adults for bioassays to assess insecticide resistance status. Resistance intensity assays were conducted using WHO tube tests to determine the level of resistance to pyrethroids commonly used on ITNs at 1×, 5 × and 10 × times the diagnostic dose. WHO tube tests were also used for PBO synergist bioassays with deltamethrin and permethrin. Bottle bioassays were conducted to determine susceptibility to chlorfenapyr at a dose of 100 µg/bottle. Results WHO tube tests revealed high intensity resistance in An. gambiae s.l. to deltamethrin and alpha-cypermethrin in all sites tested. Resistance intensity to permethrin was either moderate or high in 13 sites. PBO pre-exposure followed by deltamethrin restored full susceptibility in one site and partially restored susceptibility in all but one of the remaining sites (often reaching mortality greater than 80%). PBO pre-exposure followed by permethrin partially restored susceptibility in 12 sites. There was no significant increase in permethrin mortality after PBO pre-exposure in Kampti, Karangasso-Vigué or Mangodara; while in Seguenega, Orodara and Bobo-Dioulasso there was a significant increase in mortality, but rates remained below 50%. Susceptibility to chlorfenapyr was confirmed in 14 sites. Conclusion High pyrethroid resistance intensity in An. gambiae s.l. is widespread across Burkina Faso and may be a predictor of reduced pyrethroid ITN effectiveness. PBO + deltamethrin ITNs would likely provide greater control than pyrethroid nets. However, since susceptibility in bioassays was not restored in most sites following pre-exposure to PBO, Interceptor G2 may be a better long-term solution as susceptibility was recorded to chlorfenapyr in nearly all sites. This study provides evidence supporting the introduction of both Interceptor G2 nets and PBO nets, which were distributed in Burkina Faso in 2019 as part of a mass campaign.

scholarly journals The seasonality of cholera in sub-Saharan Africa

2021 ◽  
Author(s):  
Francisco Javier Perez-Saez ◽  
Justin Lessler ◽  
Elizabeth C. Lee ◽  
Francisco J. Luquero ◽  
Espoir B. Malembaka ◽  
...  
Keyword(s):  
Large Scale ◽  
Task Force ◽  
Case Fatality ◽  
Sub Saharan Africa ◽  
Health Concern ◽  
National Differences ◽  
Administrative Unit ◽  
Sub Saharan ◽  
Eastern And Southern Africa ◽  
Gates Foundation

BackgroundCholera remains a major threat in Sub-Saharan Africa (SSA) where some of the highest case fatality risks are reported. Knowing in what months and where cholera tends to occur across the continent can aid in improving efforts to eliminate cholera as a public health concern; though largely due to lack of unified large-scale datasets, no continent-wide estimates exist. In this study we aim to estimate cholera seasonality across SSA. MethodsWe leverage the Global Task Force on Cholera Control (GTFCC) global cholera database with statistical models to synthesize data across spatial and temporal scale in order to infer the seasonality of excess suspected cholera occurrence in SSA. Cholera excess occurrence was defined based on exceeding previously published estimates of mean monthly cholera incidence estimates in a given administrative unit. We developed a Bayesian statistical model to infer the monthly risk of excess cholera at the first and/or second administrative levels. Seasonality patterns were then grouped into spatial clusters. Finally, we studied the association between seasonality estimates and hydro-climatic variables.FindingsWe find that the majority of studied countries (26/38) have seasonal excess cholera patterns, corresponding to ~85% of the SSA population. Most countries (20/38) also had sub-national differences in seasonality patterns, with strong differences in seasonality strength between regions. Seasonality patterns clustered into two macro-regions (West Africa and the Sahel vs. Eastern and Southern Africa), which were composed of sub-regional clusters with varying degrees of seasonality. Exploratory association analysis found most consistent and positive correlations between cholera seasonality and precipitation, and to a lesser extent with temperature and flooding.InterpretationWidespread cholera seasonality in SSA offers opportunities for intervention planning. Further studies are needed to study the association between cholera and climate. FundingThe NASA Applied Sciences Program and the Bill and Melinda Gates Foundation.

scholarly journals Epidemic cerebrospinal meningitis in children at Federal Medical Centre, Gusau, Zamfara state, Nigeria

2013 ◽  
Vol 40 (2) ◽  
pp. 169-171
Author(s):  
SM Mado ◽  
U Abubakar ◽  
SO Onazi ◽  
GO Adeoye
Keyword(s):  
Neisseria Meningitidis ◽  
Large Scale ◽  
Medical Centre ◽  
Sub Saharan Africa ◽  
Treatment Modalities ◽  
Major Public Health Problem ◽  
Tropical Countries ◽  
Young Infants ◽  
Meningitis Belt ◽  
Sub Saharan

Epidemic meningococcal meningitis is a major public health problem still affecting tropical countries, particularly in Sub-Saharan Africa, which lieswithin African meningitis belt. Repeated large scale epidemics of CSM have been reported in northern Nigeria for the past four decades. It is one of the important causes of morbidity and mortality in these regions. Mortality from the CSM remains high despite advances in treatment modalities. Neisseria meningitidis serogroup A have been the major cause of large scale epidemics in tropical countries, while serogroups B, C, Y and W-135 are responsible for most of invasive disease in America and other developed countries.Objective: To determine the pattern of epidemic CSM in children atFederal Medical Centre, Gusau.Method: The study was a retrospective one carried out in children agedsix months to 12 years admitted into Emergency Paediatrics Unit (EPU) with a diagnosis of CSM within the period January to May, 2009.Results: Seventy- seven children with epidemic CSM were admittedand managed in EPU from January-May 2009.Conclusion: Neisseria meningitidis serogroup A CSM is becoming thedisease of young infants, and stresses the need for inclusion ofCSM vaccine in early infancy in routine immunization policy, in areas within the meningitis belt in Sub-Saharan Africa.

Adolescent Suicidality as Seen in Rural Northeastern Uganda

Crisis ◽  
2011 ◽  
Vol 32 (1) ◽  
pp. 43-51 ◽  
Author(s):  
Eugene Kinyanda ◽  
Ruth Kizza ◽  
Jonathan Levin ◽  
Sheila Ndyanabangi ◽  
Catherine Abbo
Keyword(s):  
Low Socioeconomic Status ◽  
Sub Saharan Africa ◽  
Psychosocial Risk ◽  
Psychiatric Nurses ◽  
Health Concern ◽  
Cross Sectional ◽  
Childhood Experiences ◽  
Low Socioeconomic ◽  
Dsm Iv ◽  
Sub Saharan

Background: Suicidal behavior in adolescence is a public health concern and has serious consequences for adolescents and their families. There is, however, a paucity of data on this subject from sub-Saharan Africa, hence the need for this study. Aims: A cross-sectional multistage survey to investigate adolescent suicidality among other things was undertaken in rural northeastern Uganda. Methods: A structured protocol administered by trained psychiatric nurses collected information on sociodemographics, mental disorders (DSM-IV criteria), and psychological and psychosocial risk factors for children aged 3–19 years (N = 1492). For the purposes of this paper, an analysis of a subsample of adolescents (aged 10–19 years; n = 897) was undertaken. Results: Lifetime suicidality in this study was 6.1% (95% CI, 4.6%–7.9%). Conclusions: Factors significantly associated with suicidality included mental disorder, the ecological factor district of residence, factors suggestive of low socioeconomic status, and disadvantaged childhood experiences.

scholarly journals Precision Agriculture for Resource Use Efficiency in Smallholder Farming Systems in Sub-Saharan Africa: A Systematic Review

2021 ◽  
Vol 13 (3) ◽  
pp. 1158
Author(s):  
Cecilia M. Onyango ◽  
Justine M. Nyaga ◽  
Johanna Wetterlind ◽  
Mats Söderström ◽  
Kristin Piikki
Keyword(s):  
Resource Use ◽  
Precision Agriculture ◽  
Large Scale ◽  
English Language ◽  
Management Practices ◽  
Smallholder Farmers ◽  
Management Strategies ◽  
Sub Saharan Africa ◽  
Smallholder Farming ◽  
Sub Saharan

Opportunities exist for adoption of precision agriculture technologies in all parts of the world. The form of precision agriculture may vary from region to region depending on technologies available, knowledge levels and mindsets. The current review examined research articles in the English language on precision agriculture practices for increased productivity among smallholder farmers in Sub-Saharan Africa. A total of 7715 articles were retrieved and after screening 128 were reviewed. The results indicate that a number of precision agriculture technologies have been tested under SSA conditions and show promising results. The most promising precision agriculture technologies identified were the use of soil and plant sensors for nutrient and water management, as well as use of satellite imagery, GIS and crop-soil simulation models for site-specific management. These technologies have been shown to be crucial in attainment of appropriate management strategies in terms of efficiency and effectiveness of resource use in SSA. These technologies are important in supporting sustainable agricultural development. Most of these technologies are, however, at the experimental stage, with only South Africa having applied them mainly in large-scale commercial farms. It is concluded that increased precision in input and management practices among SSA smallholder farmers can significantly improve productivity even without extra use of inputs.

scholarly journals Contraceptive dynamics during COVID-19 in sub-Saharan Africa: longitudinal evidence from Burkina Faso and Kenya

2021 ◽  
pp. bmjsrh-2020-200944
Author(s):  
Celia Karp ◽  
Shannon N Wood ◽  
Georges Guiella ◽  
Peter Gichangi ◽  
Suzanne O Bell ◽  
...  
Keyword(s):  
At Risk ◽  
Burkina Faso ◽  
Unintended Pregnancy ◽  
Sexual And Reproductive Health ◽  
Universal Access ◽  
Sociodemographic Factors ◽  
Sub Saharan Africa ◽  
Contraceptive Services ◽  
Logistic Regressions ◽  
Sub Saharan

IntroductionEvidence from health emergencies suggests COVID-19 will disrupt women’s sexual and reproductive health (SRH). In sub-Saharan Africa, which experiences the highest rates of unintended pregnancy and unsafe abortion globally, COVID-19 is projected to slow recent progress toward universal access to contraceptive services.MethodsWe used longitudinal data collected from women at risk of unintended pregnancy in Burkina Faso (n=1186) and Kenya (n=2784) before (November 2019–February 2020) and during (May–July 2020) COVID-19 to quantify contraceptive dynamics during COVID-19; examine sociodemographic factors and COVID-19 experiences related to contraceptive dynamics; and assess COVID-19-related reasons for contraceptive non-use. Bivariate and multivariate logistic regressions were used to examine correlates of contraceptive dynamics amid COVID-19.ResultsMost women did not change their contraceptive status during COVID-19 (68.6% in Burkina Faso and 81.6% in Kenya) and those who did were more likely to adopt a method (25.4% and 13.1%, respectively) than to discontinue (6.0% and 5.3%, respectively). Most women who switched contraceptives were using methods as or more effective than their pre-pandemic contraception. Economic instability related to COVID-19 was associated with increased contraceptive protection in Burkina Faso but not in Kenya. Altogether, 14.4% of non-contraceptive users in Kenya and 3.8% in Burkina Faso identified COVID-19-related reasons for non-use.ConclusionsThe vast majority of women at risk of unintended pregnancy did not change their contraceptive status during COVID-19, and more women adopted than discontinued methods. A minority of women reported COVID-19-related reasons for non-use, underscoring the importance of expanding safe modes of service delivery during health crises.

Intraclass Correlation Coefficients for Designing Cluster-Randomized Trials in Sub-Saharan Africa Education

2016 ◽  
Vol 40 (6) ◽  
pp. 500-525 ◽  
Author(s):  
Ben Kelcey ◽  
Zuchao Shen ◽  
Jessaca Spybrook
Keyword(s):  
Large Scale ◽  
Randomized Trials ◽  
Intraclass Correlation ◽  
Educational Interventions ◽  
Sub Saharan Africa ◽  
Design Stage ◽  
Education Outcomes ◽  
Randomized Studies ◽  
Sub Saharan ◽  
Variance Explained

Objective: Over the past two decades, the lack of reliable empirical evidence concerning the effectiveness of educational interventions has motivated a new wave of research in education in sub-Saharan Africa (and across most of the world) that focuses on impact evaluation through rigorous research designs such as experiments. Often these experiments draw on the random assignment of entire clusters, such as schools, to accommodate the multilevel structure of schooling and the theory of action underlying many school-based interventions. Planning effective and efficient school randomized studies, however, requires plausible values of the intraclass correlation coefficient (ICC) and the variance explained by covariates during the design stage. The purpose of this study was to improve the planning of two-level school-randomized studies in sub-Saharan Africa by providing empirical estimates of the ICC and the variance explained by covariates for education outcomes in 15 countries. Method: Our investigation drew on large-scale representative samples of sixth-grade students in 15 countries in sub-Saharan Africa and includes over 60,000 students across 2,500 schools. We examined two core education outcomes: standardized achievement in reading and mathematics. We estimated a series of two-level hierarchical linear models with students nested within schools to inform the design of two-level school-randomized trials. Results: The analyses suggested that outcomes were substantially clustered within schools but that the magnitude of the clustering varied considerably across countries. Similarly, the results indicated that covariance adjustment generally reduced clustering but that the prognostic value of such adjustment varied across countries.

Land conflicts and social differentiation in eastern Uganda

2017 ◽  
Vol 55 (3) ◽  
pp. 395-422 ◽  
Author(s):  
Matt Kandel
Keyword(s):  
Large Scale ◽  
Local Level ◽  
Sub Saharan Africa ◽  
Social Differentiation ◽  
Land Conflicts ◽  
Current Period ◽  
Post Conflict ◽  
Sub Saharan ◽  
Historical Developments ◽  
Eastern Uganda

ABSTRACTRising competition and conflict over land in rural sub-Saharan Africa continues to attract the attention of researchers. Recent work has especially focused on land governance, post-conflict restructuring of tenure relations, and large-scale land acquisitions. A less researched topic as of late, though one deserving of greater consideration, pertains to how social differentiation on the local-level shapes relations to land, and how these processes are rooted in specific historical developments. Drawing on fieldwork conducted in Teso sub-region of eastern Uganda, this paper analyses three specific land conflicts and situates them within a broad historical trajectory. I show how each dispute illuminates changes in class relations in Teso since the early 1990s. I argue that this current period of socioeconomic transformation, which includes the formation of a more clearly defined sub-regional middle class and elite, constitutes the most prominent period of social differentiation in Teso since the early 20th century.

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