Risk factors for diarrheagenic Escherichia coli infection in children aged 6-24 months in peri-urban community, Nairobi, Kenya.

Escherichia coli commonly inhabits the gut of humans and animals as part of their microbiota. Though mostly innocuous, some strains have virulence markers that make them pathogenic. This paper presents results of a cross-sectional epidemiological study examining prevalence of diarrheagenic E. coli (DEC) pathotypes in stool samples of asymptomatic healthy children (n = 540) in Dagoretti South subcounty, Nairobi, Kenya. E. coli was cultured and pathotyped using PCR to target specific virulence markers associated with Shiga-toxin, enteropathogenic, enterotoxigenic, enteroaggregative, entero-invasive and diffusely adherent E. coli. Overall prevalence of DEC pathotypes was 20.9% (113/540) with enteropathogenic E. coli being the most prevalent (34.1%), followed by enteroaggregative E. coli (23.5%) and Shiga-toxin producing E. coli (22.0%) among positive samples. We found evidence of co-infection with multiple pathotypes in 15% of the positive samples. Our models indicated that at the household level, carriage of DEC pathotypes in children was associated with age group [12-18 months] (OR 1.78; 95%CI 1.03-3.07; p = 0.04), eating matoke (mashed bananas) (OR 2.32; 95%CI 1.44-3.73; p = 0.001) and pulses/legumes (OR 1.74; 95%CI 1.01-2.99; p = 0.046) while livestock ownership or contact showed no significant association with DEC carriage (p>0.05). Our findings revealed significant prevalence of pathogenic DEC circulating among presumptive healthy children in the community. Since there has been no previous evidence of an association between any food type and DEC carriage, unhygienic handling, and preparation of matoke and pulses/legumes could be the reason for significant association with DEC carriage. Children 12-18 months old are more prone to DEC infections due to exploration and hand-to-mouth behavior. A detailed understanding is required on what proportion of positive cases developed severe symptomatology as well as fatal outcomes. The co-infection of pathotypes in the rapidly urbanizing environment needs to be investigated for hybrid or hetero-pathotype circulation that have been implicated in previous infection outbreaks.

Spatial-temporal distribution and sequence diversity of group a human respiratory syncytial viruses in Kenya preceding the emergence of ON1 genotype.

BACKGROUND: Human respiratory syncytial virus (HRSV) is a major cause of severe viral acute respiratory illness and contributes significantly to severe pneumonia cases in Africa. Little is known about its spatial-temporal distribution as defined by its genetic diversity. METHODS: A retrospective study conducted utilizing archived nasopharyngeal specimens from patients attending outpatient clinics in hospitals located in five demographically and climatically distinct regions of Kenya; Coast, Western, Highlands, Eastern and Nairobi. The viral total RNA was extracted and tested using multiplex real time RT-PCR (reverse transcriptase polymerase chain reaction). A segment of the G-gene was amplified using one-step RT-PCR and sequenced by Sanger di-deoxy method. Bayesian analysis of phylogeny was utilized and subsequently median joining methods for haplotype network reconstruction. RESULTS: Three genotypes of HRSVA were detected; GA5 (14.0%), GA2 (33.1%), and NA1 (52.9%). HRSVA prevalence varied by location from 33% to 13.2% in the Highlands and the Eastern regions respectively. The mean nucleotide diversity (Pi[π]) varied by genotype: highest of 0.018 for GA5 and lowest of 0.005 for NA1. A total of 58 haplotypes were identified (GA5 10; GA2 20; NA1 28). These haplotypes were introduced into the population locally by single haplotypes and additional subsidiary seeds amongst the GA2 and the NA1 haplotypes. CONCLUSIONS: HRSVA was found across all the regions throughout the study period and comprised three genotypes; GA5, GA2, and NA1 genotypes. The genotypes were disproportionately distributed across the regions with GA5 gradually increasing toward the Western zones and decreasing toward the Eastern zones of the country.

Anti-inflammatory potential of dichloromethane leaf extracts of Eucalyptus globulus (Labill) and Senna didymobotrya (Fresenius) in mice.

BACKGROUND: Inflammation is an immune response characterized by swelling, redness, pain and heat. Inflammation is mainly managed using conventional medicines that are associated with many side effects. Plant-based remedies are considerably better alternative therapies for they have fewer side effects. OBJECTIVE: This study aimed at determining the anti-inflammatory potential of dichloromethane (DCM) leaf extracts of Eucalyptus globulus and Senna didymobotrya in mice. METHODS: Fresh leaves of these plants were harvested from Embu County, Kenya. Quantitative phytochemical analysis was done using Gas Chromatography-Mass Spectrometry (GC-MS). Anti-inflammatory test comprised nine groups of five animals each: normal, negative, positive controls and 6 experimental groups. Inflammation was induced with Carrageenan. One hour post-treatment, the different groups were intraperitoneally administered with the reference drug, diclofenac, 3% DMSO and six DCM leaf extracts at doses of 25, 50, 100, 150, 200 and 250mg/kgbw. RESULTS: GC-MS results revealed α-phellandrene, camphene, terpinolene, and limonene among others. Anti-inflammatory effects showed that extract doses of 100,150,200 and 250mg/kg bw significantly reduced the inflamed paw. Doses of 200 and 250mg/kgbw in both plants were more potent and compared with diclofenac. E. globulus extract dose of 250mg kg bw reduced inflamed paw in the 1st, 2nd, 3rd and 4th hours, by 2.27,6.52,9.09 and 10.90% respectively while S.didymobotrya at similar dose ranges, inflamed paw reduced by 2.41, 5.43, 8.31 and 9.05% respectively. CONCLUSION: E. globulus and S. didymobotrya have potent anti-inflammatory activities, attributed to their constituent phytochemicals. This study confirms the traditional use of these plants in treating inflammation.

Antipyretic potential of dichloromethane leaf extract of Eucalyptus globulus (Labill) and Senna didymobotrya (Fresenius) in rats models.

INTRODUCTION: Fever is managed using synthetic drugs such as aspirin, paracetamol among others. Synthetic drugs are associated with many side effects. Herbal medicines form alternative therapy since they possess fewer side effects and are readily available. This study aimed to determine antipyretic potential of DCM extracts of E. globulus and S. didymobotrya in Swiss albino rats. MATERIALS AND METHODS: The plant leaves samples were obtained from Embu County, Kenya. Dichloromethane solvent was used to extract bioactive constituents from the plant samples. Three grams of DCM leaf extracts of Eucalyptus globulus (Labill) and Senna didymobotrya (Fresenius) samples were obtained and analyzed to determine quantitative phytochemical composition at ICIPE laboratory using GC-MS. Albino rats were used in the antipyretic activity study. Nine groups of five experimental animals were used in each test: Positive control, normal control, negative control and experimental (25, 50, 100, 150, 200 and 250 mg/kg body weight extracts) groups. Pyrexia was induced by injection of turpentine in albino rats intraperitoneally. One hour later, the pyretic animals received the leaf extracts at various dose levels, reference drug (aspirin100 mg/kg body) or the vehicle (DMSO). RESULTS: Results of antipyretic in vivo bioscreening revealed that E. globulus and S. didymobotrya possess potent antipyretic activity which was comparable to that of the reference drug aspirin. Both extracts exhibited highest antipyretic activity at a dose of 250 mg/kg bw. Results of the GC-MS revealed that these plants possess bio-compounds such as Terpinolene, Alpha-pinene, Borneol, Globulol and Terpineols that are associated with antipyretic activity. CONCLUSIONS: In conclusion, this study revealed that these plants are endowed with bioactive compounds such as terpenoids, and flavonoids that possess antipyretic activity in rats.

Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities.

Fermentation of Theobroma cacao L. beans is the most critical stage in the production of cocoa products such as chocolates and its derivatives. There is a limited understanding of the complex response of microbial diversity during cocoa bean fermentation. The aim of the present study was to investigate microbial communities in the cocoa bean fermentation heap using a culture-independent approach to elucidate microbial diversity, structure, functional annotation and mapping unto metabolic pathways. Genomic DNA was extracted and purified from a sample of cocoa beans fermentation heap and was followed by library preparations. Sequence data was generated on Illumina Hiseq 2000 paired-end technology (Macrogen Inc). Taxonomic analysis based on genes predicted from the metagenome identified a high percentage of Bacteria (90.0%), Yeast (9%), and bacteriophages (1%) from the cocoa microbiome. Lactobacillus (20%), Gluconacetobacter (9%), Acetobacter (7%) and Gluconobacter (6%) dominated this study. The mean species diversity, measured by Shannon alpha-diversity index, was estimated at 142.81. Assignment of metagenomic sequences to SEED database categories at 97% sequence similarity identified a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates and aromatic amino acids. Metabolism of aromatic compounds, amino acids and their derivatives and carbohydrates occupied 0.6%, 8% and 13% respectively. Overall, these results provide insights into the cocoa microbiome, identifying fermentation processes carried out broadly by complex microbial communities and metabolic pathways encoding aromatic compounds such as phenylacetaldehyde, butanediol, acetoin, and theobromine that are required for flavour and aroma production. The results obtained will help develop targeted inoculations to produce desired chocolate flavour or targeted metabolic pathways for the selection of microbes for good aroma and flavour compounds formation.

In Vivo Hypoglycemic Effect of Kigelia africana (Lam): Studies With Alloxan-Induced Diabetic Mice.

The claims by the traditional herbal medicine practitioners that Kigelia africana has bioactivity against several diseases, including diabetes mellitus, were investigated in this study. Type I diabetes mellitus was induced in mice by intraperitoneal administration of alloxan monohydrate followed by treatment with the therapeutic doses of the aqueous and ethyl acetate leaf extract of K africana to the experimentally diabetic mice. The treatment effects were compared with the normal control, diabetic control, and diabetic control rats treated with a standard antidiabetic drugs (insulin administered intraperitoneally at 1 IU/kg body weight in 0.1 mL physiological saline or glibenclamide administered orally at 3 mg/kg body weight in 0.1 mL physiological saline). Phytochemical composition of the leaf extract was assessed using standard procedures and mineral elements assessed using atomic absorption spectrophotometry and total reflection X-ray fluorescence system. Oral and intraperitoneal administration of the aqueous and ethyl acetate leaf extract caused a statistically significant dose-independent reduction in plasma glucose level in alloxan-induced diabetic mice. The observed hypoglycemic activity of this plant extract could be attributed to the observed phytochemicals and trace elements, which have been associated with exhibiting antidiabetic properties. Therefore, the data appear to support the hypoglycemic effects of K africana validating its folkloric usage.

Molecular characterization of group A rotaviruses in Mukuru slums Kenya: detection of novel strains circulating in children below 5 years of age.

BACKGROUND: Gastroenteritis is a public health concern due to high morbidity and mortality among children. Rotaviruses are the leading etiological agents of severe gastroenteritis in children and accounts for more than half a million deaths per year in Africa. The study aimed at investigating the rotavirus genotypes that were circulating in children aged 5 years and below in and around Mukuru slums in Nairobi County Kenya. METHODS: A purposive cross sectional sampling method was applied where 166 samples were collected from children below 5 years of age and taken to Kenya Medical Research Institute virology laboratory. Presence of rotaviruses was determined using reverse transcription polymerase chain reaction, while extraction was done using ZR Soil/Fecal RNA MicroPrep™ extraction kit. This was followed by reverse transcription and genotyping using various group A rotavirus primers. RESULTS: The G type was successfully determined in 37 (92.5%), while the P type was successfully determined in 35 (87.5%) of the 40 (24%) page positive samples. Type G1 was the most predominant of the G types (40.5%), and the incidences of G3 and G9 were 21.6 and 32.4% respectively. Mixed types G3/G9 were detected at 5.4%. Three P types existed in Mukuru slums, P[8] (60%), P[6] (22.9%), P[4] (11.4) and their relative incidence varied over the 15 months of this study. CONCLUSIONS: The G types and P types detected in this study are important causes of acute gastroenteritis in Mukuru slums Nairobi Kenya. An indication that the prevalence of certain genotypes may change over a rotavirus season is significant and mirrors observations from studies in other tropical climates. Thus monitoring of the genotypic changes among circulating viruses should be encouraged over the coming years.

How well do malaria tests correlate with disease severity? Comparison of parasite density in children with mild and severe malaria.

Background: Accurate diagnosis of malaria is key to proper management and control and an ideal diagnostic parameter that correlates to disease outcome is required. The former would be helpful in correctly identifying patients that need hospitalisation versus those that can be managed at home. This study determined how well the density estimates by microscopy, qPCR and PfHRP-2 correlate to malaria severity. Materials and Methods: Patients aged ≤ 5 yrs with severe (n = 60, Hb ≤ 6 g/dl) and mild (n = 60, Hb > 6 g/dl) malaria were enrolled to take part in a case control study at Kisumu District Hospital, Western Kenya. Parasite load was determined by microscopy, qPCR targeting the 18s rRNA gene and PfHRP-2 antigen ELISA. Results: The median parasite load and the 25th and the 75th percentile by microscopy in children with severe malaria (SM) was 49,958 parasites/µl (12,013-128,695) compared to 24,233 (6,122-103,886) in the group with mild malaria (MM), P = 0.10. By qPCR, the translated median parasite density was 31,550 parasites/µl (4,106-196,640) in the SM group compared to 24,365 parasites/µl (5,512-93,401) in the MM group (P = 0.73). According to PfHRP-2, the translated median parasite load in children with SM was 628,775 parasites/µl (332,222-1.165x106) compared to 150,453 (94,292-399,100) in children with MM (P < 0.0001). Conclusions: Unlike microscopy and qPCR, the parasite load detected by PfHRP-2 correlates with disease severity. Because of its unique attributes, PfHRP-2 is able to account for trophozoites and schizonts that are sequestered away from peripheral circulation. Because it persists in circulation, it also serves as an indicator of the magnitude of current and recent infections.

Isolation and biological characterization of non-B HIV type 1 from Kenya.

The isolation and characterization of primary strains of human immunodeficiency virus (HIV) is a vital tool for assessing properties of viruses replicating in HIV-infected subjects. HIV-1 isolation was carried out from 30 HIV-1-infected patients from a Comprehensive Care Clinic (CCC) after informed consent. Virus was successfully isolated from 9 out of the 30 samples investigated. Seven of the isolates were from drug-naive patients while two were from patients on antiretroviral drugs. The isolates were biologically phenotyped through measurement of the syncytium-inducing capacity in MT2 cells. Six of the isolates exhibited syncytia induction (SI) associated with CXCR4 coreceptor usage while three of the isolates were non-syncytia-inducing (NSI) isolates associated with CCR5 coreceptor usage. In addition, the replication capacity of the isolates was further determined in established cell line CD4(+) C8166. Indirect immunofluorescence assay was used to check the antigen expression on the cells as a supplementary test. HIV-1 isolation success was 70% (7/10) and 20% (2/20) in naive and drug-experienced patients, respectively. The majority of the viral isolates obtained (6/9) were of the SI phenotype, though SI virus strains are rare among non-B subtypes. A significant correlation between virus isolation success and viral load was established. Coreceptor use data for heavily treatment-experienced patients with limited treatment options are scanty and this is the group with perhaps the most urgent need of novel antiretroviral agents.

Reference values for some renal function parameters for adult population in north-rift valley, kenya.

A population based, cross-sectional study was carried out at Moi Teaching and Referral Hospital in collaboration with the Regional Blood Transfusion Center, North Rift. 367 participants (211 males and 156 females) were involved in the renal function reference range establishment. Reference ranges were constructed using non-parametric methods to estimate 2.5 and 97.5 percentiles of distribution as lower and upper reference limits, respectively. Results showed significant sex and age specific reference values in some of the established renal function parameters. North Rift Kenyan population clinical chemistry reference ranges differ from the American values commonly used in Kenyan Hospitals. The renal function reference values established in this study some of which are sex and age specific can be adopted for the North Rift Kenyan population.

Comparison of short-term and long-term protocols for stabilization and preservation of RNA and DNA of Leishmania, Trypanosoma, and Plasmodium.

Molecular tools continue to be important in the prevention and control of parasitic diseases. However, using these techniques directly in the field remains a major challenge. Therefore, the preservation of clinical samples collected from endemic field areas for later analysis remains an important preanalytical process. This study aimed at identifying a suitable protocol for stabilization and preservation of RNA and DNA in bioclinical specimens for Trypanosoma, Leishmania, and Plasmodium research. Both spiked and unspiked blood samples were preserved in 7 protocols (different media; storage temperatures). Samples were evaluated for possible degradation of DNA and RNA along the storage duration up to the 10th week. Nucleic acid targets were assessed as follows: (i) Trypanosoma and Plasmodium RNA analysis was done using real-time nucleic acid sequence-based amplification (RT-NASBA) for 18S rRNA and for stage-specific Pfs25 mRNA, respectively; (ii) Trypanosoma DNA assessment analysis was conducted by using a conventional PCR for 18S rDNA; (iii) Leishmania RNA analysis was performed with a quantitative NASBA for 18S rRNA and Leishmania DNA assessment with an RT-PCR for 18S rDNA. Findings suggested that a newly developed L3™ buffer proved to be reliable and suitable for both short- and long-term preservation of parasite nucleic acid material. This buffer is envisaged to be suitable for utilization in field situations where resources are limited.

Mouse cytokine profile skewed towards Th2 in pregnancy during infection with Brucella abortus S19 strain.

The two classes of cytokines Th1 and Th2 determine the type of immune response elicited. The Th2 immune response is associated with successful pregnancy. Brucellosis is an intracellular bacterium that elicits the Th1 response and is known to cause spontaneous abortion in mammalian species. This study sought to determine if Brucella infection causes spontaneous abortion by causing the circulating cytokine profile be Th1 dominant during pregnancy. Forty-eight Swiss white mice were used in this murine model and the S19 strain of Brucella abortus was used in as the infective agent. Pregnant mice in the test group were injected intraperitoneally with 10(5-8) CFU of Brucella and cytokine profile evaluated over the three trimesters of pregnancy. Pregnant mice in the control group were left to go through normal pregnancy and their cytokine profile evaluated over the three trimesters of pregnancy. Cytokines in serum samples were analyzed by Cytometric Bead Array. The data was analyzed using the Paired T- test and p < 0.05 was considered significant. IFN-γ and TNF-α represented the Th1 cytokines while IL-4 and IL-5 represented the Th2 cytokines. None of the mice in the test group had spontaneous abortion. IFN-γ and TNF-α had no significant differences between cytokine levels for infected and uninfected groups in all 3 trimesters of pregnancy. IL-4 levels had significant differences in all three trimesters of pregnancy (t = 13, P = 0.036, 0.0071 and 0.0277). IL-5 levels had significant differences second trimester (t = 14, P = 0.0075). The cytokine profile was robustly Th2. In conclusion, Brucella abortus cannot cause spontaneous abortion by altering the mouse cytokine profile towards Th1 in pregnancy. Elevated IL-4 levels with corresponding suppression of IFN-γ can be used as a marker for successful pregnancy in Brucellosis.