African Water Laws: Plural Legislative Frameworks For Rural Water Management in Africa: an international workshop, Johannesburg, South Africa, 26-28 January 2005

Water law / Water management / Water policy / Poverty / River basins / Irrigation systems / Institutions / Wetlands

Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are diverse immune systems found in many prokaryotic genomes that target invading foreign DNA such as bacteriophages and plasmids. There are multiple types of CRISPR with arguably the most enigmatic being Type IV. During an investigation of CRISPR carriage in clinical, multi-drug resistant, Klebsiella pneumoniae, a Type IV-A3 CRISPR-Cas system was detected on plasmids from two K. pneumoniae isolates from Egypt (isolated in 2002-2003) and a single K. pneumoniae isolate from the UK (isolated in 2017). Sequence analysis of all other genomes available in GenBank revealed that this CRISPR-Cas system was present on 28 other plasmids from various Enterobacteriaceae hosts and was never found on a bacterial chromosome. This system is exclusively located on IncHI1B/ IncFIB plasmids and is associated with multiple putative transposable elements. Expression of the cas loci was confirmed in the available clinical isolates by RT-PCR. In all cases, the CRISPR-Cas system has a single CRISPR array (CRISPR1) upstream of the cas loci which has several, conserved, spacers which, amongst things, match regions within conjugal transfer genes of IncFIIK/ IncFIB(K) plasmids. Our results reveal a Type IV-A3 CRISPR-Cas system exclusively located on IncHI1B/ IncFIB plasmids in Enterobacteriaceae that is likely to be able to target IncFIIK/ IncFIB(K) plasmids presumably facilitating intracellular, inter-plasmid competition

Differences In \u3ci\u3eUrochloa\u3c/i\u3e Hybrids and Cultivars Biomass Production in Several Sites in Western Kenya

Forage production is at the core of improved livestock productivity, especially in sub Saharan Africa. The genetic potential of existing animals remains underutilized due to limited forage quality and quantity. Albeit wide range of forage germplasm that exists, little data is available for identifying suitable genotypes, matched to specific environments and production systems. Due to the spatial and temporal diverse environments in which livestock production happens, multi-locational screening of forage production and characterizing genotype by environment interaction is key. We selected seven Urochloa (Syn. Brachiaria) genotypes comprising three hybrids and four cultivars and established them in on-farm trials in western Kenya for dry matter evaluation and nutritional quality. We selected eight sites covering four administrative counties (Siaya, Kakamega, Busia, Bungoma), and each county hosting two replicated trials, with each trial replicated 3 times. We observed dry matter yield differences across the counties in the order Bungoma \u3e Busia \u3e Kakamega \u3e Siaya. Similarly, the genotypes returned varied performance across the sites. Hybrids did well in one of the county, a mix of hybrids and cultivars in two counties and cultivars in the last county. Amongst sites, variation was least in Busia, and more pronounced in Bungoma. Continued assessments in subsequent cuts are underway. These will feed into context-specific recommendations about suitable forages for sustainable intensification in the face of global warming

Decline in the prevalence HIV among pregnant women attending antenatal clinics in Tanzania, 2001-2011

Background: The Tanzania National AIDS Control Programme has established HIV sentinel surveillance among antenatal clinic (ANC) attendees as one of the methods for collecting data on HIV prevalence. This article provides trends on HIV prevalence for 92 sentinel sites that have constantly been part of the surveillance system since 2001 and have participated in at least three consecutive rounds.Method: The surveillance population included all pregnant women aged 15–49 years who were attending a selected sentinel ANC site for the first time for any pregnancy between 2001 and 2011. Serial testing for HIV infection was done anonymously by detecting for the presence of IgG antibodies to HIV on dried blood spot (DBS) specimens. HIV trends were calculated taking into account random effects from sites on the following variables:  region, sites and socio-demographic characteristics defined as age, marital status, parity, education level and duration of stay at present residence.Results: Overall, there was a significant decline in HIV prevalence from 9.6% in 2001 to 5.6% in 2011 (p<0.01). Specifically, the HIV prevalence among 15-24 years’ pregnant women significantly declined from 7.8% in 2001/2002 to 4% in 2011 (p<0.01). The decline in HIV prevalence occurred irrespective of residence, marital status, education level or previous pregnancies.Conclusion: There has been a significant decline in HIV infections among young pregnant women attending ANC clinics in Tanzania since 2001. This study also indicates that ANC surveillance among pregnant women over time can provide useful estimates of HIV situation between the population surveys

The risks of malariainfection in Kenya in 2009

BACKGROUND: To design an effective strategy for the control of malaria requires a map of infection and disease risks to select appropriate suites of interventions. Advances in model based geo-statistics and malaria parasite prevalence data assemblies provide unique opportunities to redefine national Plasmodium falciparum risk distributions. Here we present a new map of malaria risk for Kenya in 2009. METHODS: Plasmodium falciparum parasite rate data were assembled from cross-sectional community based surveys undertaken from 1975 to 2009. Details recorded for each survey included the month and year of the survey, sample size, positivity and the age ranges of sampled population. Data were corrected to a standard age-range of two to less than 10 years (PfPR2-10) and each survey location was geo-positioned using national and on-line digital settlement maps. Ecological and climate covariates were matched to each PfPR2-10 survey location and examined separately and in combination for relationships to PfPR2-10. Significant covariates were then included in a Bayesian geostatistical spatial-temporal framework to predict continuous and categorical maps of mean PfPR2-10 at a 1 x 1 km resolution across Kenya for the year 2009. Model hold-out data were used to test the predictive accuracy of the mapped surfaces and distributions of the posterior uncertainty were mapped. RESULTS: A total of 2,682 estimates of PfPR2-10 from surveys undertaken at 2,095 sites between 1975 and 2009 were selected for inclusion in the geo-statistical modeling. The covariates selected for prediction were urbanization; maximum temperature; precipitation; enhanced vegetation index; and distance to main water bodies. The final Bayesian geo-statistical model had a high predictive accuracy with mean error of -0.15% PfPR2-10; mean absolute error of 0.38% PfPR2-10; and linear correlation between observed and predicted PfPR2-10 of 0.81. The majority of Kenya's 2009 population (35.2 million, 86.3%) reside in areas where predicted PfPR2-10 is less than 5%; conversely in 2009 only 4.3 million people (10.6%) lived in areas where PfPR2-10 was predicted to be > or =40% and were largely located around the shores of Lake Victoria. CONCLUSION: Model based geo-statistical methods can be used to interpolate malaria risks in Kenya with precision and our model shows that the majority of Kenyans live in areas of very low P. falciparum risk. As malaria interventions go to scale effectively tracking epidemiological changes of risk demands a rigorous effort to document infection prevalence in time and space to remodel risks and redefine intervention priorities over the next 10-15 years

Monitoring prevention or emergence of HIV drug resistance: results of a population-based foundational survey of early warning indicators in mainland Tanzania

BACKGROUND: In Tanzania, routine individual-level testing for HIV drug resistance (HIVDR) using laboratory genotyping and phenotyping is not feasible due to resource constraints. To monitor the prevention or emergence of HIVDR at a population level, WHO developed generic strategies to be adapted by countries, which include a set of early warning indicators (EWIs). METHODS: To establish a baseline of EWIs, we conducted a retrospective longitudinal survey of 35 purposively sampled care and treatment clinics in 17 regions of mainland Tanzania. We extracted data relevant for four EWIs (ART prescribing practices, patients lost to follow-up 12 months after ART initiation, retention on first-line ART at 12 months, and ART clinic appointment keeping in the first 12 months) from the patient monitoring system on patients who initiated ART at each respective facility in 2010. We uploaded patient information into WHO HIVResNet excel-based tool to compute national and facility averages of the EWIs and tested for associations between various programmatic factors and EWI performance using Fisher’s Exact Test. RESULTS: All sampled facilities met the WHO EWI target (100%) for ART prescribing practices. However, the national averages for patients lost to follow-up 12 months after ART initiation, retention on first-line ART at 12 months, and ART clinic appointment keeping in the first 12 months fell short, at 26%, 54% and 38%, respectively, compared to the WHO targets ≤ 20%, ≥ 70%, and ≥ 80%. Clinics with fewer patients lost to follow-up 12 months after ART initiation and more patients retained on first-line-ART at 12 months were more likely to have their patients spend the longest time in the facility (including wait-time and time with providers), (p = 0.011 and 0.007, respectively). CONCLUSION: Tanzania performed very well in EWI 1a, ART prescribing practices. However, its performance in other three EWIs was far below the WHO targets. This study provides a baseline for future monitoring of EWIs in Tanzania and highlights areas for improvement in the management of ART patients in order not only to prevent emergence of HIVDR due to programmatic factors, but also to improve the quality of life for ART patients

Patient adherence to prescribed artemisinin-based combination therapy in Garissa County, Kenya, after three years of health care in a conflict setting.

BACKGROUND: Current day malaria cases and deaths are indicative of a lack of access to both methods of prevention, diagnosis, and treatment; an important determinant of treatment efficacy is adherence. This study is a follow up to the baseline study of adherence to artemether-lumefantrine (AL) carried out in Garissa District in 2010. The study presented evaluates any changes in adherence levels which may have occurred in the area during this period and after nearly three years of sustained use of ACT across the public health sector. METHODS: The study was carried out in Garissa County in the North Eastern Province of Kenya and included patients fitting the suspected malaria case definition and having been prescribed AL, regardless of confirmatory diagnosis. A questionnaire assessed the intake of AL via both self-reporting by the participant and observation of blister packs by the interviewer. On separate occasions exit interviews with patients and observations of prescribers were also carried out. RESULTS: Of the 218 participants enrolled, 195 were successfully followed up. 60% of participants were found to be adherent to the three-day AL regimen, this is 4.7% lower than the proportion of participants adherent in 2010; the result of a two-sided z-test was not significant (p = 0.23). The odds of the patient being adherent to AL increased by 65% with each additional correct statement regarding how to take AL that a patient could recall (between zero and four statements), this was the only variable significantly associated with patient adherence (p = 0.01). CONCLUSION: Sustaining the ACT adherence rates at the 2010 levels, through 2.5 years of insecurity in the study area is an achievement and suggests that if security can be improved barriers to improving health service quality and patient adherence to AL would be removed. This study, by looking specifically at anti-malarial adherence over a prolonged period and in a setting of severe conflict, provides a valuable and rare insight in to the challenges and barriers to ACT adherence in such settings

Plasmodium falciparum malaria parasite var gene expression is modified by host antibodies: longitudinal evidence from controlled infections of Kenyan adults with varying natural exposure.

BACKGROUND: The PfEMP1 family of Plasmodium falciparum antigens play a key role in pathogenesis of severe malaria through their insertion into the surface of parasite infected erythrocytes, and adhesion to host cells. Previous studies have suggested that parasites expressing PfEMP1 subclasses group A and DC8, associated with severe malaria, may have a growth advantage in immunologically naïve individuals. However, this idea has not been tested in longitudinal studies. METHODS: Here we assessed expression of the var genes encoding PfEMP1, in parasites sampled from volunteers with varying prior exposure to malaria, following experimental infection by sporozoites (PfSPZ). Using qPCR, we tested for associations between the expression of various var subgroups in surviving parasite populations from each volunteer and 1) the levels of participants' antibodies to infected erythrocytes before challenge infection and 2) the apparent in vivo parasite multiplication rate. RESULTS: We show that 1) expression of var genes encoding for group A and DC8-like PfEMP1 were associated with low levels of antibodies to infected erythrocytes (αIE) before challenge, and 2) expression of a DC8-like CIDRα1.1 domain was associated with higher apparent parasite multiplication rate in a manner that was independent of levels of prior antibodies to infected erythrocytes. CONCLUSIONS: This study provides insight into the role of antibodies to infected erythrocytes surface antigens in the development of naturally acquired immunity and may help explain why specific PfEMP1 variants may be associated with severe malaria. TRIAL REGISTRATION: Pan African Clinical Trial Registry: PACTR201211000433272 . Date of registration: 10th October 2012