Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya.

Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.

Seroprevalence of foot-and-mouth disease virus in cattle herds raised in Maasai Mara ecosystem in Kenya.

A cross-sectional study was carried out to determine foot-and-mouth disease (FMD) seroprevalence and identify risk factors of exposure among cattle herds raised in three zones with different types of land use and progressively distant from the Maasai Mara National Reserve (MMNR) boundary. We selected five villages purposively; two in zone 1 (area < 20 km from the MMNR), another two in zone 2 (area between 20-40 km away from the MMNR) and one in zone 3 (area >40 km away from the MMNR). A total of 1170 cattle sera were collected from 390 herds in all the zones and tested for antibodies against the non-structural proteins (NSPs) of FMD virus (FMDV) using two 3ABC-based Enzyme-Linked Immunosorbent Assay ELISA kits. All sera samples were also screened for serotype-specific antibodies using Solid Phase Competitive ELISA (SPCE) kits (IZSLER, Italy). We targeted FMDV serotypes A, O, South African Territory [SAT] 1 and SAT 2, known to be endemic in East Africa including Kenya. Data on putative risk factors for FMD seropositivity in cattle were collected using a questionnaire. The overall apparent animal-level FMD seroprevalence based on the parallel comparison of the two anti-NSPs ELISA kits was 83.8 % (95 % CI; 81.8-85.9), and differed significantly across zones. Zone 1 had a higher seroprevalence than zones 2 and 3 (χ2 = 116.1, df = 2, p < 0.001). In decreasing order, the overall seroprevalences of FMDV serotypes A, SAT 2, O and SAT 1 were 26.3 % (95 % CI; 23.5-29.2), 21.4 % (95 % CI; 18.8-24.0), 21.2 % (95 % CI; 18.7-23.9) and 13.1 % (95 % CI; 11.1-15.3), respectively. The distribution of these serotypes differed significantly between zones (p < 0.05) except for SAT 2 serotype (χ2 = 0.90, df = 2, p = 0.639). Both serotypes A and O were more prevalent in zones 1 and 2 than zone 3 while serotype SAT 1, was higher in zone 3 compared to other zones. The results of multivariable analyses identified animal sex (i.e., female), raising of cattle in zones 1 and 2 (areas < 40 km away from the MMNR); mixing of cattle from multiple herds at watering points, and pastoral husbandry practices, as significant predictors of animal-level FMD seropositivity. This study established that FMD seroprevalence declined with distance from the MMNR.

Zoonotic Pathogen Seroprevalence in Cattle in a Wildlife-Livestock Interface, Kenya.

A cross-sectional study was conducted to determine the seroprevalence of Brucella spp. and Leptospira spp. and risk factors of exposure in cattle in three zones with varying land use types and wildlife-livestock interactions. Five villages were selected purposively; two in areas with intensive livestock-wildlife interactions (zone 1), another two in areas with moderate livestock-wildlife interactions (zone 2) and one in areas where wildlife-livestock interactions are rarer (zone 3). Sera samples were collected from 1170 cattle belonging to 390 herds in all the zones and tested for antibodies against Brucella abortus and Leptospira interrogans serovar hardjo using ELISA kits. Data on putative risk factors for seropositivity of these pathogens in cattle were collected using a questionnaire. The overall apparent animal-level seroprevalence of brucellosis and leptospirosis was, respectively, 36.9% (95% CI 34.1-39.8) and 23.5% (95% CI 21.1-26.0). Brucella spp. seroprevalence was higher in zone 1 than in zones 2 and 3 (χ2 = 25.1, df = 2, P < 0.001). Zones 1 and 2 had significantly higher Leptospira spp. seroprevalence than zone 3 (χ2 = 7.0, df = 2, P = 0.029). Results of multivariable analyses identified animal sex (female) and zones (high interface area) as significant predictors (P < 0.05) of animal-level seropositivity of Brucella spp. For Leptospira spp., important predictors of animal-level seropositivity were animal sex (female), zones (moderate interface area) and herds utilizing a communal grazing reserve. The seroprevalences of Brucella spp. and Leptospira spp. in cattle were higher in areas with moderate to high wildlife-livestock interactions than those with rare interactions.

A participatory epidemiological study of major cattle diseases amongst Maasai pastoralists living in wildlife-livestock interfaces in Maasai Mara, Kenya.

Livestock-wildlife interactions promote the transmission of a wide range of infectious diseases that constraint livestock production. We used a participatory appraisal approach to find out and rank infectious diseases of concern to pastoralists in a zone of intense wildlife-livestock interaction and another zone with limited interactions. Four villages were selected purposively in areas with intensive cattle-wildlife interactions (zone 1), and another two in areas with low to moderate cattle-wildlife interactions (zone 2). Data were collected in focus group discussions (FGDs) using participatory epidemiological methods (PE); each group had 8-13 participants. Results of impact matrix scoring from all sites indicated that malignant catarrhal fever (MCF), anthrax, foot and mouth disease (FMD), contagious bovine pleuropneumonia (CBPP), east coast fever (ECF) and African animal trypanosomiasis (ATT), in decreasing order, had the highest impact on livestock production. A Kruskal-Wallis test revealed a significant difference in FMD annual prevalence between cattle age groups (p < 0.001) and was the highest in animals > 4 years (median score of 32.5, range, 10-50). FMD had the highest impact on milk production, but based on veterinary costs (treatment costs), it was ranked second to CBPP. The study provides information on disease priorities that occur in the target zones in Mara ecosystem and which the local pastoralists must consider when accessing key ecosystem services such as water and pasture.

Streptococcus pneumoniae Serotype Epidemiology among PCV-10 Vaccinated and Unvaccinated Children at Gertrude's Children's Hospital, Nairobi County: A Cross-Sectional Study.

Background: Serotype replacement and emergence of multidrug resistant S. pneumoniae has exacerbated the need for continuous regional serotype surveillance especially in the developing world. We investigated S. pneumoniae serotypes circulating among vaccinated and unvaccinated children ≤5 years in Nairobi County post PCV10 era. Methods: A total of 206 vaccinated and unvaccinated children attending Gertrude's Children's Hospital (GCH) were recruited for this study. Nasopharyngeal swabs collected using Copan Flocked Swabs were the main study specimen. Culturing and isolation of S. pneumoniae was done on BA with gentamicin and BA plates respectively at the GCH main laboratory. Serotyping was done using the Quellung reaction at the KEMRI-Wellcome Trust, Kilifi.  Results: Out of the 206 subjects sampled, 20.39% (42) were found to be carriers of S. pneumoniae. About 52% (n=22) of the S. pneumoniae carriers had received the recommended dose of PCV-10, while 48% (n=20) of the carriers had not. Almost all (n=41; 19.90% of subjects) isolates contained non-vaccine type S. pneumoniae serotypes, while n=1 of the serotypes (in 0.49% of subjects) were untypeable. Serotypes 28F, 6A, 11A, 3 and 7C were prevalent in both vaccinated and unvaccinated children, whereas serotypes 23A, 17F, 35F, 48, 13 and 35B, and 23B, 20, 19B, 21, untypeable, 15B and 39 were found among unvaccinated and vaccinated groups, respectively. Conclusions: All S. pneumoniae serotypes isolated from the subjects sampled were non PCV-10 vaccine type. These results therefore highlight the importance of monitoring and evaluation to provide epidemiological information to determine the effectiveness of PCV10 in Kenya's Public health services.

Dual African origins of global Aedes aegypti s.l. populations revealed by mitochondrial DNA.

BACKGROUND: Aedes aegypti is the primary global vector to humans of yellow fever and dengue flaviviruses. Over the past 50 years, many population genetic studies have documented large genetic differences among global populations of this species. These studies initially used morphological polymorphisms, followed later by allozymes, and most recently various molecular genetic markers including microsatellites and mitochondrial markers. In particular, since 2000, fourteen publications and four unpublished datasets have used sequence data from the NADH dehydrogenase subunit 4 mitochondrial gene to compare Ae. aegypti collections and collectively 95 unique mtDNA haplotypes have been found. Phylogenetic analyses in these many studies consistently resolved two clades but no comprehensive study of mtDNA haplotypes have been made in Africa, the continent in which the species originated. METHODS AND FINDINGS: ND4 haplotypes were sequenced in 426 Ae. aegypti s.l. from Senegal, West Africa and Kenya, East Africa. In Senegal 15 and in Kenya 7 new haplotypes were discovered. When added to the 95 published haplotypes and including 6 African Aedes species as outgroups, phylogenetic analyses showed that all but one Senegal haplotype occurred in a basal clade while most East African haplotypes occurred in a second clade arising from the basal clade. Globally distributed haplotypes occurred in both clades demonstrating that populations outside Africa consist of mixtures of mosquitoes from both clades. CONCLUSIONS: Populations of Ae. aegypti outside Africa consist of mosquitoes arising from one of two ancestral clades. One clade is basal and primarily associated with West Africa while the second arises from the first and contains primarily mosquitoes from East Africa.

Prevalence of metabolic syndrome among an urban population in Kenya.

OBJECTIVE: Developing countries are undergoing an epidemiologic transition accompanied by increasing burden of cardiovascular disease (CVD) linked to urbanization and lifestyle modifications. Metabolic syndrome is a cluster of CVD risk factors whose extent in Kenya remains unknown. The aim of this study was to determine the prevalence of metabolic syndrome and factors associated with its occurrence among an urban population in Kenya. RESEARCH DESIGN AND METHODS: This was a household cross-sectional survey comprising 539 adults (aged ≥18 years) living in Nairobi, drawn from 30 clusters across five socioeconomic classes. Measurements included waist circumference, HDL cholesterol, triacylglycerides (TAGs), fasting glucose, and blood pressure. RESULTS: The prevalence of metabolic syndrome was 34.6% and was higher in women than in men (40.2 vs. 29%; P < 0.001). The most frequently observed features were raised blood pressure, a higher waist circumference, and low HDL cholesterol (men: 96.2, 80.8, and 80%; women: 89.8, 97.2, and 96.3%, respectively), whereas raised fasting glucose and TAGs were observed less frequently (men: 26.9 and 63.3%; women: 26.9 and 30.6%, respectively). The main factors associated with the presence of metabolic syndrome were increasing age, socioeconomic status, and education. CONCLUSIONS: Metabolic syndrome is prevalent in this urban population, especially among women, but the incidence of individual factors suggests that poor glycemic control is not the major contributor. Longitudinal studies are required to establish true causes of metabolic syndrome in Kenya. The Kenyan government needs to create awareness, develop prevention strategies, and strengthen the health care system to accommodate screening and management of CVDs.

Expression of metallothionein and alpha-tubulin in heavy metal-tolerant Anopheles gambiae sensu stricto (Diptera: Culicidae).

Anopheles mosquitoes have been shown to adapt to heavy metals in their natural habitats. In this study we explored the possibility of using Anopheles gambiae sensu stricto as bio-reporters for environmental heavy metal pollution through expressions of their metal-responsive metallothionein and alpha-tubulin genes. The study was undertaken with third instar larvae after selection by cadmium, copper, or lead at LC(30) through five successive generations. Expression levels were determined in the 5th generation by semi-quantitative RT-PCR on the experimental and control populations. The data were analyzed using one-way ANOVA. The highest metallothionein (F(3,11)=4.574, P=0.038) and alpha-tubulin (F(3,11)=12.961, P=0.002) responses were observed in cadmium-tolerant treatments. There was significantly higher expression of metallothionein in cadmium or copper treatments relative to the control (P=0.012), and in cadmium than in lead treatments (P=0.044). Expressions of alpha-tubulin were significantly higher in cadmium than in control treatments (P=0.008). These results demonstrate the capacity of An. gambiae s.s. to develop tolerance to increased levels of heavy metal challenge. The results also confirm the potential of heavy metal-responsive genes in mosquitoes as possible bio-indicators of heavy metal environmental pollution. How the tolerance and expressions relate to An. gambiae s.s. fitness and vectorial capacity in the environment remains to be elucidated.

Pathogenic Escherichia coli and food handlers in luxury hotels in Nairobi, Kenya.

BACKGROUND: The epidemiology and virulence properties of pathogenic Escherichia coli among food handlers in tourist destination hotels in Kenya are largely uncharacterized. METHOD: This cross-sectional study among consenting 885 food handlers working in nine luxurious tourist hotels in Nairobi, Kenya determined the epidemiology, virulence properties, antibiotics susceptibility profiles and conjugation abilities of pathogenic Escherichia coli. RESULT: Pathogenic Escherichia coli was detected among 39 (4.4%) subjects, including 1.8% enteroaggregative Escherichia coli (EAEC) harboring aggR genes, 1.2% enterotoxigenic Escherichia coli (ETEC) expressing both LT and STp toxins, 1.1% enteropathogenic Escherichia coli (EPEC) and 0.2% Shiga-like Escherichia coli (EHEC) both harboring eaeA and stx2 genes respectively. All the pathotypes had increased surface hydrophobicity. Using multivariate analyses, food handlers with loose stools were more likely to be infected with pathogenic Escherichia coli. Majority 53.8% of the pathotypes were resistant to tetracycline with 40.2% being multi-drug resistant. About 85.7% pathotypes trans-conjugated with Escherichia coli K12 F(-) NA(r) LA. CONCLUSION: The carriage of multi-drug resistant, toxin expressing pathogenic Escherichia coli by this population is of public health concern because exposure to low doses can result in infection. Screening food handlers and implementing public awareness programs is recommended as an intervention to control transmission of enteric pathogens.

Urinary soluble egg antigen levels in Schistosoma haematobium infection in relation to sex and age of Kenyan schoolchildren following praziquantel treatment.

Schistosoma haematobium soluble egg antigen (SEA) secreted in urine can be assayed to determine egg tissue load and hence morbidity in infected individuals. A cohort of 158 infected children aged 4-18 years was followed-up for 33 days pre and post treatment with a single dose of praziquantel. There was a significant difference in the prevalence of S. haematobium between males and females (P < 0.05). There were also significant differences in egg counts between age group < or = 5 years compared with 6-8 years, 9-11 years and 12-14 years, and age group > or = 15 years compared with 6-8 years, 9-11 years and 12-14 years (P < 0.05). Comparison of SEA among age groups indicated a significant difference between age group < or = 5 years compared with 9-11 years, 12-14 years and > or = 15 years, and age group > or = 15 years compared with 9-11 years and 12-14 years (P < 0.05). There was a statistically significant correlation between levels of SEA and egg output (r2=0.961, P=0.010). These results are useful in the development of a SEA-based dipstick assay for field diagnosis of urinary schistosomiasis.

Biosafety education relevant to genetically engineered crops for academic and non-academic stakeholders in East Africa

Development and deployment of genetically engineered crops requires effective environmental and food safety assessment capacity. In-country expertise is needed to make locally appropriate decisions. In April 2007, biosafety and biotechnology scientists, regulators, educators, and communicators from Kenya, Tanzania, and Uganda, met to examine the status and needs of biosafety training and educational programs in East Africa. Workshop participants emphasized the importance of developing biosafety capacity within their countries and regionally. Key recommendations included identification of key biosafety curricular components for university students; collaboration among institutions and countries; development of informational materials for non-academic stakeholders and media; and organization of study tours for decision makers. It was emphasized that biosafety knowledge is important for all aspects of environmental health, food safety, and human and animal hygiene. Thus, development of biosafety expertise, policies and procedures can be a stepping stone to facilitate improved biosafety for all aspects of society and the environment.

Differential Induction of Proteins in Anopheles gambiae sensu stricto (Diptera: Cullicidae) Larvae in Response to Heavy Metal Selection.

Investigations were conducted to establish the magnitude and pattern of differential expression of proteins due to generational selection of third instar An. gambiae s.s. larvae by cadmium, copper and lead heavy metals, three possible common urban pollutants.A susceptible strain of An. gambiae s.s. third instar larvae was separately placed under selection pressure with cadmium, copper and lead at LC(30) and controls through five generations. First, third and fifth generation selection survivors were screened for differentially expressed proteins relative to non-exposed control by two-dimensional gel electrophoresis. Distribution patterns of the spots were analysed by Chi Square or Fishers exact test and variations in expressions between and within generation by ANOVA. Most differentially expressed spots were acidic and of low molecular weight among all metals and generations. Type of heavy metals and generation were main indicators of variations in differential expressions. Variation between generations was most significant among cadmium-selected populations of which most number of spots were induced in the fifth generation. Most spots were induced in the copper-selected population in the third generation. The induced protein spots may be products from respective genes that respond to heavy metals and counter their toxicity, thus building An. gambiae s.s. tolerance to these pollutants. The differential pattern and magnitude of expressed spots has potential application as molecular markers for assessment of anopheline adaptation status to heavy metals, and provide insight into the extent of environmental pollution.

Detection of trypanosomes in small ruminants and pigs in western Kenya: important reservoirs in the epidemiology of sleeping sickness?

BACKGROUND: Trypanosomosis is a major impediment to livestock farming in sub-Saharan Africa and limits the full potential of agricultural development in the 36 countries where it is endemic. In man, sleeping sickness is fatal if untreated and causes severe morbidity. This study was undertaken in western Kenya, an area that is endemic for both human and livestock trypanosomosis. While trypanosomosis in livestock is present at high levels of endemicity, sleeping sickness occurs at low levels over long periods, interspersed with epidemics, underscoring the complexity of the disease epidemiology. In this study, we sought to investigate the prevalence of trypanosomes in small ruminants and pigs, and the potential of these livestock as reservoirs of potentially human-infective trypanosomes. The study was undertaken in 5 villages, to address two key questions: i) are small ruminants and pigs important in the transmission dynamics of trypanosomosis? and ii), do they harbour potentially human infective trypanosomes? Answers to these questions are important in developing strategies for the control of both livestock and human trypanosomosis. RESULTS: Eighty-six animals, representing 21.3% of the 402 sampled in the 5 villages, were detected as positive by PCR using a panel of primers that identify trypanosomes to the level of the species and sub-species. These were categorised as 23 (5.7%) infections of T. vivax, 22 (5.5%) of T. simiae, 21 (5.2%) of the T. congolense clade and 20 (5.0%) of T. brucei ssp. The sheep was more susceptible to trypanosome infection as compared to goats and pigs. The 20 T. brucei positive samples were evaluated by PCR for the presence of the Serum Resistance Associated (SRA) gene, which has been linked to human infectivity in T. b. rhodesiense. Three samples (one pig, one sheep and one goat) were found to have the SRA gene. These results suggest that sheep, goats and pigs, which are kept alongside cattle, may harbour human-infective trypanosomes. CONCLUSION: We conclude that all livestock kept in this T. b. rhodesiense endemic area acquire natural infections of trypanosomes, and are therefore important in the transmission cycle. Sheep, goats and pigs harbour trypanosomes that are potentially infective to man. Hence, the control of trypanosomosis in these livestock is essential to the success of any strategy to control the disease in man and livestock.