MST-Department of Microbiology

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Performance of Polymerase Chain Reaction, Kato-Katz, and Circulating Cathodic Antigen Techniques in Determining Schistosoma Mansoni Prevalence in Mwea, Kenya
(Kenyatta University, 2023-11) Chieng, Benard; David Mburu; Sammy Njenga
Schistosoma species are the causative agents of schistosomiasis. In the Mwea irrigation scheme, the known species is Schistosoma mansoni, which causes intestinal schistosomiasis. Kato-Katz is the primary technique employed to detect intestinal schistosomiasis, but it has weaknesses of minimal sensitivity, and it is tedious. An alteative approach is the point-of-care circulating cathodic antigen (POC-CCA) method. However, it is characterized by minimal sensitivity and high cross-reactivity. Contrarily, a polymerase chain reaction has excellent precision and sensitivity. The study aimed to evaluate the prevalence of S. mansoni in the Mwea West irrigation scheme and the efficacy of Kato-Katz, POC-CCA, and quantitative PCR methods in parasite screening. A cross-sectional analysis was adopted involving 357 individuals residing in the scheme. The three tests were employed to screen for S. mansoni in stool and urine samples. Data analysis was undertaken using STATA version 15.1. S mansoni prevalence was carried out at a confidence level of 95% McNemar's chi-square test was performed to describe data on specificity and sensitivity. As determined by the KK technique, the total prevalence rate of S. mansoni in Mwea West was 32.8%. The positivity rate was highest in individuals above 14 years (75%) and males (56%). Using the mean of the three tests as the reference, the sensitivity for KK, POC-CCA, and qPCR was 41.6%, 79.4%, and 92.5%, respectively. This study shows that S. mansoni infection remains prevalent among residents of the Mwea West irrigation scheme, posing severe public health challenges. This necessitates the implementation of enhanced measures for disease control in the region. From the study, qPCR revealed the highest sensitivity, whereas KK had the lowest sensitivity. As a result, the QPCR method can be used as a confirmatory test in research settings, whereas POC-CCA can be used in epidemiological surveillance instead of Kato-Katz.
Antimicrobial Activities and Bioassay Guided Identification and Bioactive Constituents of Selected Kenyan Medical Plants
(Kenyatta University, 2022-01) Wanjiku, Kagika W; Sumesh Chander Chhabra
Magnitude and Geographical Distribution of Nontuberculous Mycobacteria Species among Presumptive Pulmonary Tuberculosis Patients in Selected Sites in Kenya
(Kenyatta University, 2023) Aberi, Ruth Moraa; Anthony Kebira; Willie Githui
Globally, awareness of nontuberculous mycobacteria (NTM) as an agent causing pulmonary diseases is currently on the rise. Similarity in clinical manifestation with pulmonary tuberculosis (PTB) caused by Mycobacterium tuberculosis complex (MTBc) and lack of routine surveillance have led to limited information on the burden of NTM especially in sub-Saharan Africa. These challenges have led to pulmonary infections due to NTM being misdiagnosed and hence poor patient management. In Kenya, like most sub-Saharan African countries, there is scarce information on the burden of NTM due to limited laboratory diagnosis of tuberculosis (TB) using non-distinguishing sputum smear microscopy. Inorder to significantly add value on currently scarce information on the burden of pulmonary infections caused by NTM in Kenya, this study sort to determine the magnitude, drug susceptibility patterns and geographical distribution of NTM isolated from presumptive PTB patients in selected sites in Kenya. This study was part of a main East Africa Public Health Laboratory Networking (EAPHLN) study where a stratified sampling approach was used to collect sputum specimens from consenting participants. The participants were presumptive PTB patients who presented themselves at different government health facilities in Kenya. These included Wajir, Machakos, Kitale, Busia, Malindi, Lamu, Narok, Kisii and Nyahururu. In the main study, a total of 3,782 sputum specimens were collected and triple packed before shipping to Kenya Medical Research Institute TB laboratory for analysis. The sputum specimens were analyzed using GeneXpert MTB/Rif, direct sputum smear for Ziehl-Neelsen (ZN) and fluorescent microscopy. Culture was done on solid Lowenstein-Jensen and liquid Mycobacteria Growth Indicator Tube (MGIT) media. All ZN positive isolates were appropriately archived regardless of culture media used. For this study, random sampling was used to select 124 isolates that were MGIT-ZN positive but negative by TBcID-Capillia assay (Becton Dickinson, Sparks, USA). The isolates were subcultured in MGIT media (MGITTM; BD Sparks, USA) to ascertain viability after which GenoType Mycobacterium assays (HAIN Lifescience, Nehren, Germany) were used to identify NTM to species level. Drug susceptibility to the first line anti-tuberculous drugs (rifampicin, ethambutol and isoniazid) was determined using resistance ratio method. Geographical distribution of NTM was determined by correlating identified NTM with information from the facility where the specimens were collected from. Out of 124 isolates analyzed, 24 (19.3%) were identified as NTM, 20 (16.1%) as MTBc, 56 (45.2%) as other bacteria with high guanine and cytosine content, 21 (16.9%) were negative for mycobacteria while 3 (2.4%) mycobacteria could not be identified to species level. Of the 24 NTM, 15 were isolated from males and 9 from females. Out of the 24 NTM, Mycobacterium intracellulare 10/24 (41.7%) and Mycobacterium fortuitum 4/24 (16.7%) were predominant. Mycobacterium mucogenicum and Mycobacterium gordonae were the least identified at 2/24 (8.3%), each. All 24 characterized NTM were resistant to the first line anti-TB drugs. The 24 NTM were identified in 5 of the 8 facilities, with Wajir having the highest (CI95% 2046-54.27, p=0.002) compared to other facilities. The magnitude of NTM isolated from people presumed to have PTB was high in this study. There are also high levels of resistance of NTM to routinely prescribed first line anti-TB drugs. Therefore, there is need to identify mycobacteria to species level for appropriate patient management.
Determination of Bacterial Composition, Heavy Metal Pollution and Physicochemical Parameters of Fish Pond Water in Abothuguchi Central, Meru County, Kenya
(2018-11) LAIBU, PETER KABIRO; MAINGI, JOHN; KEBIRA, ANTHONY
Laibu PK, Maingi J, Kebira A. 2018. Determination of bacterial composition, heavy metal contamination and physicochemical parameters of fish pond water in Abothuguchi Central, Meru County, Kenya. Bioteknologi 15: 66-79. Humans have consumed fish as a supplementary source of proteins and as a source of income. Because fish performs all their body functions in water, the quality of water is essential to their livelihood. Fish farmers have encountered losses due to the death and stunted growth of fish due to bacterial infections and diseases among other causes. Bacteria found in fish pond water and their pathogenic effects differ with the quality of the pond water along with the variation in the frequency with which water is changed in the ponds. Physico-chemical parameters of pond water and heavy metals influence the growth and productivity of fish. This study aimed at determining the contamination levels of both fecal and pathogenic bacteria namely Salmonella spp., fecal Streptococcus, fecal coliforms Pseudomonas spp., Vibrio cholerae and E. coli in fish ponds water, the concentration of heavy metal contamination and variability of physicochemical parameters and their effects on fish. Isolation of fecal indicators and pathogens was carried out using standard laboratory methods. Some physicochemical parameters were measured in situ using a portable Universal multiline P4 WTW meter while others were analyzed in the laboratory. The determination of the heavy metal presence and concentration in the water samples was carried out by employing of Flame Atomic Absorption Spectrometer. The results indicated that the pond water was heavily contaminated with fecal streptococci and fecal coliforms and they varied significantly in the sites. Pearson correlation analysis showed a positive correlation between the prevalence of fecal streptococci and fecal coliforms. Potential pathogens such as Vibrio spp., Salmonella spp., P. aeruginosa, and E.coli were taken from the water samples with high population. Physico-chemical parameters namely pH and dissolved oxygen deviated from the permissible limits according to international standard. The study has shown that the fish ponds water was highly contaminated with both fecal and pathogenic bacteria with physicochemical parameters varying significantly. Heavy metals except for iron were within the recommended limits hence no significant contamination of the fish pond water. The study suggests the use of treated tap water, routine monitoring of fish pond water and sensitization of farmers on bacterial contamination of pond water. More studies with the aid of molecular techniques should be employed to characterize the bacteria. The finding of this study can, thereby, serve as an impetus to improve fish farming in Meru County, as a way of meeting the growing nutritional demands in the country.
Genetic Diversity and Antibiotic Resistance of Escherichia Coli Isolated from Human, Cattle, and Buffalo in the Maasai Mara Ecosystem, Kenya
(Kenyatta University, 2022) Onyari, Winfridah Bwari; Ezekiel Mugendi Njeru
Antibiotic resistance is an emerging health crisis globally with a significant impact on human and animal populations. The emergence and spread of antibiotic resistance are attributed to the wrong use of antibiotic products in human and animal health care. This is further amplified and complicated in the human-livestock-wildlife interfaces where there is selective pressure and close interaction. This interface and its impact on antibiotic resistance dynamics are inadequately evaluated in Kenya. The study aimed to establish the genetic diversity and prevalence of antibiotic resistance of Escherichia coli isolates from human, cattle, and buffalo populations in the Maasai Mara Ecosystem located in Kenya. E. coli was isolated by phenotypic and biochemical methods from stool samples of humans and fresh dung samples of cattle and buffalo collected from the Maasai Mara Ecosystem. Molecular techniques were used to characterize E. coli isolates. E. coli isolates were tested against tetracycline, gentamicin, ciprofloxacin, ceftriaxone, and amoxicillin-clavulanic acid using the Kirby-Bauer disk diffusion method and then assigned to phylogenetic groups according to chuA, yjaA, and TspE4.C2 genetic markers. E. coli isolates exhibiting resistant strains were genetically characterized based on their 16S rRNA gene region of the gDNA. Phylogenetic analysis established that all the four phylogroups (A, B1, B2, and D) were present in the E. coli isolates from the sympatric hosts except phylogroup B2 which was absent in buffalo population. E. coli isolates from the sympatric hosts were predominant in phylogroup A and B1. Buffalo was predominated by isolates of E. coli in phylogroup B1 and D. Further, the genetic sequence of resistant E. coli isolates recorded 14 unique haplotypes, with haplotype 4 and haplotype 7 being present in all the three sympatric hosts. Humans recorded the highest resistance to the tested antibiotics at 94% followed by buffalo at 50% and cattle at 45%. Humans, cattle, and buffalo recorded the highest antibiotic resistance to tetracycline at 83%, 45%, and 33%, and lowest antibiotic resistance to amoxicillin-clavulanic acid at 46%, 94%, and 100% respectively. Further, antibiotic resistance was prevalent in isolates of E. coli from buffalo with interactions and the resistant pattern exhibited those of humans and cattle against tetracycline 27%, gentamicin 23%, and ciprofloxacin 14% as compared to E. coli isolate from isolated buffalo which only recorded resistance to tetracycline antibiotic at 5%. It was concluded that isolates of E. coli from humans, cattle, and buffalo were genetically diverse. E. coli isolates from the sympatric hosts were resistant to frequently used antibiotics in human medicine and veterinary practices and finally, antibiotic-resistant in buffalo correspond to those antibiotics used in humans and food-producing animals. It was recommended that additional studies using a One-Health approach, are needed to identify the main reservoir of antibiotic resistant strains and to determine the transmission pathway in the multi-host system.
Relationship Between Microbial and Physico-Chemical Pollutants and Reistance of Water-Borne Diarrhoea-Related Bacteria Against Antibiotics in Thiba River Basin, Kenya
(Kenyatta University, 2022) Njagi, Muturi Stephen; John Maingi
Bacteria-related water-borne diarrhoea is amongst major cause of illness and death to children under five years in developing countries. Reports by health workers in Thiba river basin indicate that this diarrhoea and levels of resistance of the bacteria causing it against the commonly used antibiotics to treat it are on increase. This study was to isolate and identify the bacteria responsible for water-borne diarrhoea in Thiba river basin and to determine the levels of their resistance against commonly used antibiotics. Also the levels of microbial and physico-chemical pollutants of Thiba river basin water and rain water; and their relationship with the antimicrobial resistance of the bacteria causing water-borne diarrhoea against the commonly used antibiotics in this region were to be determined. A total of 168 water samples were obtained, distributed uniformly in upper, middle and lower zones within Thiba river basin in September 2016 during dry season and in October 2016 during wet season. Rain water samples were also taken as control. Entero-pathogenic bacteria causing water-borne diarrhoea were isolated by use of Membrane Filter Technique (MFT) and selective media. Vitek 2 System: 07.01 test and other biochemical tests were used to identify the species, which were enumerated using the most probable number (MPN). Kirby-Bauer Disc Technique was used to determine antimicrobial susceptibility. The mean levels of physico-chemical pollutants were measured using different methods. Total suspended solids were measured using glass-fibre filters; total nitrogen and total phosphorus using persulfate in acid and heavy metal ions (Cd2+, Cu2+, Zn2+ and Cr3+) using flame atomic absorption spectrometry. Microbial contaminants’ levels were estimated using the most probable number (MPN) of coliforms and pathogenic E. coli bacteria. Of the total 168 samples analysed, 143 samples were detected with at least pathogenic bacteria. Those identified were Salmonella paratyphi, Pseudomonas aeruginosa, Salmonella enteritidis, Shigella flexineri, Klebsiella pneumonia, Enterobacter liquefaciens, Proteus mirabilis and Escherichia coli. Salmonella spp., Pseudomonas aeruginosa, Shigella flexineri and E. coli were resistant to erythromycin, with Salmonella showing the highest resistance; while Klebsiella pneumoniae and Shigella flexineri were resistant to methicillin. Of the bacteria tested, 75 % showed moderate sensitivity to minocycline, cotrimoxazole, chloramphenicol, ampicillin, ciprofloxacin, metronidazole and lincomycin antibiotics, with highest sensitivity during dry season. Student’s T-test and Single-factor ANOVA statistical tests showed no significance difference on mean values of levels of these microbial and physico-chemical pollutants in the Thiba river basin water across the sampled zones and within the two seasons at p=0.05. However, the mean values of these pollutants were found to be significant as they were higher than those admissible by World Health Organisation, except for Cu2+. Positive correlation was established between the increased levels of physico-chemical pollutants and increased resistance of the pathogenic bacteria causing water-borne diarrhoea against commonly used antibiotics in Thiba river basin using Pearson’s Correlation Coefficient and Bivalent Regression (R2=0.58) tests. Therefore, the study showed that the Thiba river basin river water had significant levels of water-borne bacteria pathogens, with 53 % of them showing some resistance against commonly used antibiotics for treatment of the diarrhoea they cause to the basin residents living there. It also found some modulating effect of the Thiba river water contaminants on bacteria antimicrobial resistance, as increase in pollutants increased bacteria resistance against the antibiotics. The national government and county governments of Embu and Kirinyaga should have constant surveillance of microbial resistance of bacteria causing water-borne diarrhoea for prompt treatment. In addition, there should be improvement of sanitation of Thiba river basin water and beyond.
Genetic Diversity and Antibiotic Resistance of Escherichia Coli Isolated from Human, Cattle, and Buffalo in the Maasai Mara Ecosystem, Kenya
(Kenyatta University, 2022) Onyari, Winfridah Bwari; Ezekiel Mugendi Njiru; Vincent Obanda
Antibiotic resistance is an emerging health crisis globally with a significant impact on human and animal populations. The emergence and spread of antibiotic resistance are attributed to the wrong use of antibiotic products in human and animal health care. This is further amplified and complicated in the human-livestock-wildlife interfaces where there is selective pressure and close interaction. This interface and its impact on antibiotic resistance dynamics are inadequately evaluated in Kenya. The study aimed to establish the genetic diversity and prevalence of antibiotic resistance of Escherichia coli isolates from human, cattle, and buffalo populations in the Maasai Mara Ecosystem located in Kenya. E. coli was isolated by phenotypic and biochemical methods from stool samples of humans and fresh dung samples of cattle and buffalo collected from the Maasai Mara Ecosystem. Molecular techniques were used to characterize E. coli isolates. E. coli isolates were tested against tetracycline, gentamicin, ciprofloxacin, ceftriaxone, and amoxicillin-clavulanic acid using the Kirby-Bauer disk diffusion method and then assigned to phylogenetic groups according to chuA, yjaA, and TspE4.C2 genetic markers. E. coli isolates exhibiting resistant strains were genetically characterized based on their 16S rRNA gene region of the gDNA. Phylogenetic analysis established that all the four phylogroups (A, B1, B2, and D) were present in the E. coli isolates from the sympatric hosts except phylogroup B2 which was absent in buffalo population. E. coli isolates from the sympatric hosts were predominant in phylogroup A and B1. Buffalo was predominated by isolates of E. coli in phylogroup B1 and D. Further, the genetic sequence of resistant E. coli isolates recorded 14 unique haplotypes, with haplotype 4 and haplotype 7 being present in all the three sympatric hosts. Humans recorded the highest resistance to the tested antibiotics at 94% followed by buffalo at 50% and cattle at 45%. Humans, cattle, and buffalo recorded the highest antibiotic resistance to tetracycline at 83%, 45%, and 33%, and lowest antibiotic resistance to amoxicillin-clavulanic acid at 46%, 94%, and 100% respectively. Further, antibiotic resistance was prevalent in isolates of E. coli from buffalo with interactions and the resistant pattern exhibited those of humans and cattle against tetracycline 27%, gentamicin 23%, and ciprofloxacin 14% as compared to E. coli isolate from isolated buffalo which only recorded resistance to tetracycline antibiotic at 5%. It was concluded that isolates of E. coli from humans, cattle, and buffalo were genetically diverse. E. coli isolates from the sympatric hosts were resistant to frequently used antibiotics in human medicine and veterinary practices and finally, antibiotic-resistant in buffalo correspond to those antibiotics used in humans and food-producing animals. It was recommended that additional studies using a One-Health approach, are needed to identify the main reservoir of antibiotic resistant strains and to determine the transmission pathway in the multi-host system.
Prevalence and Genetic Diversity of Hepatitis B and C Viruses among Human Immunodeficiency Virus Infected Individuals in Siaya County, Kenya
(Kenyatta University, 2020-09) Onyango, Omondi Kevin
Viral hepatitis B and C co-infections among Human immunodeficiency virus infected patients is significantly becoming a worrying public health problem worldwide. The three infectious viruses’ shares common routes of transmission including, blood transfusion, sexual intercourse, and injecting drug users among others, which could be the reason for the co-infections observed in the previous studies in sub-Sahara Africa. In Kenya, the documented data from the studies conducted indicate that Nyanza recorded the highest HIV prevalence at 15.1% with Siaya County at 17.8% of the total national population. The invention of Highly Active Antiretroviral Therapy was thought to reduce morbidity and mortality rate of HIV patients, however, HIV patients continue to suffer from liver related illness due to the co-infections with hepatitis B and C viruses, in addition to the emergence of drug resistant strains. Despite this there is scarcity of information on hepatitis B and C co-infections, circulating virus genotypes and drug resistant strains in Kenya. This study evaluated the co-infections of viral hepatitis B/C and genetic diversity and drug resistance of HBV among HIV infected individuals in Siaya County. Approval to conduct this study was sought from Kenyatta University Research and Ethical Review Committee and SCRH Institutional review Committee. This was a hospital based cross-sectional study in which a total of 225 blood samples were aseptically collected from consenting participants. The blood samples were separated and plasma used for serological assays. Serological detection of HBsAg and anti-HCV IgM was performed using On Site Rapid Test Kits as prescribed by the manufacture (CTK Biotech, Inc, San Diego, USA).Viral DNA was extracted from positive HBsAg plasma samples using QiampTMDNA Mini kit as per the manufactures’ instructions. HBV-pol gene was amplified by nested PCR using specific primers and the amplicons directly sequenced by automated ABI 377 DNA sequencer (Applied Biosystem, Foster City, USA) using BigDye Terminator Kit (Applied Biosystem®). Generated sequences were phylogenetically analyzed together with references sequences using Molecular Evolutionary Genetics Analysis (MEGA X version 10.0.4) software. Of (225) individuals who participated in this study, 157(69.8%) were female and 68(30.2%) were males. Their ages were ranged between 3 and 76 years with mean of 38.26 years. Majority of the participants were married (146/225) with most of them having secondary education level (116/225). Gender, age and level of education were not significantly associated with HBV infection. However, place of residence was associated with HBV infection. In addition, only gender and marital status were significantly associated with HCV infections. Overall prevalence for HBV/HIV was 6.2% (14/225); HCV/HIV was 4.0% (9/225) while that of HIV mono-infection was 89.8% (202/225). Nevertheless, none of the study participants was infected with all the three viruses. HBV drug resistance mutation rt169F was detected in one participant. However, the rest of the 10 Individuals were infected with HBV drug susceptible strains. Of the 11 samples that were successfully sequenced, the phylogenetic analysis revealed the sequences belonged to HBV genotype A1. The study findings reveal that the levels of HBV/HIV and HIV/HCV co-infections could be higher than reported here with circulating strains remaining susceptible to treatment. There is therefore a need for continuous surveillance of HBV, HCV infections and monitoring circulating trends of these viral genotypes and drug resistance in this region in order to guide vaccine design and optimize treatment.
Analysis of Microbial Load And Diversity in Crickets (Gryllus Bimaculatus and Scapsipedus Marginatus) Used as A Source of Protein for Food
(Kenyatta University, 2019-04) Jedida Wanjiru, Gatheru
Crickets are drawing interest as sustainable source of protein for food and feed worldwide. However, there is little information on microbial quality of edible crickets thus the need for a profound insight into their safety. The objective of the study was to determine the microbial load of two edible cricket species Scapsipedus marginatus and Gryllus bimaculatus and to evaluate the efficiency of different processing methods (boiling, sun-drying, freeze-drying, snap freezing and deep frying) in reducing microbial counts. The wild-caught crickets were obtained from Nguruman (Kajiado County) and Mbita (Homa Bay County) while the farmed crickets were reared at Animal Rearing and Containment Unit at the International Centre of Insect Physiology and Ecology (icipe). The cricket samples were screened for microbiota using culture-dependent method. Fifteen adult crickets were pooled together and homogenized in Phosphate-buffered Saline (PBS). The solution was used for mycological and bacterial isolation and analysis. Bacterial microbiota was isolated using Nutrient agar (NA) and MacConkey agar (MCA). Fungal microbiota was isolated using Sabouraud Dextrose Agar (SDA) and Potato Dextrose Agar (PDA). The isolates were characterized morphologically and through sequencing of bacterial 16S SSU rRNA genes and fungal internal transcribed spacer (ITS) rRNA gene. Most of the bacterial isolates (70 %) on NA had characteristics typical of members of Bacillus spp. while on MCA, most bacteria (90 %) had characteristics suggestive of members of E. coli. Majority (80 %) of the fungal isolates on PDA had characteristics similar to those of Aspergillus spp. while most isolates (80 %) on SDA were members of Trichoderma spp. Microbial counts of fresh cricket samples were generally high, with bacterial population ranging from 2.5 × 104 - 3.8 x 104 CFU /g fresh weight. The fungal populations ranged from 2.0 × 104 – 3.0 × 104 CFU /g fresh weight. Upon processing the microbial counts reduced considerably with bacterial counts ranging from 0.1 x 102 – 0.8 x 102 CFU /g dry weight (boiled) and 0.7 x 103 – 2.2 x 103 CFU /g dry weight (sun dried). The fungal counts ranged from 0.7 x 102 - 0.9 x 102 CFU /g dry weight (boiled) and 0.9 x 103- 1.7 x103 CFU /g dry weight (sun-dried). Freeze-dried and deep fried samples had no microbial counts. The diversity of bacteria and fungi species in wild-caught crickets was considerably high compared to the lab-reared crickets with most isolates belonging to species pathogenic to humans. Phylogenetic analysis revealed that most bacterial isolates from the wild-caught crickets related to members of Bacillus spp. (57 %), Staphylococcus spp. (43 %) and E. coli (14 %). Fungal isolates related to Aspergillus spp. (57 %) and Penicillium roseopurpureum (29 %). From the farmed crickets, most of the bacterial isolates related to E. coli (60 %), Enterobacter (40 %) and Lactococcus garvieae (20 %). The fungal isolates related to Trichoderma asperellum (75 %), Aspergillus spp. (25 %) and Tetrapisispora fleetii (12.5 %). From the cricket samples processed by boiling and sun drying, the microbial diversity was very low with only two bacterial isolates related to Rickettsiella grylli (42 %) and Wolbachia spp. (29 %), while the two fungal isolates related to members of Aspergillus spp. (67 %) and Trichoderma asperellum (33 %). Thirteen potentially novel bacterial and fungal isolates from wild and reared crickets had no close matches from gene bank and need further investigation. This study shows that crickets harbor diverse microbial communities some of which are potentially pathogenic. Deep-frying, freeze drying and snap freezing completely eliminated bacterial and fungal contaminants thus minimizing microbial risks in crickets meant for food.
Determination of Biodiversity and Symbiotic Efficiency of Native Rhizobia Isolated from Different Regions in Kenya
(Kenyatta University, 2020-10) Jalloh, Abdul A.
Crop production has continued to decline in sub-Saharan Africa due to soil infertility and increased cost of farm inputs. To enhance food security, farmers have adopted the use of both inorganic and organic fertilizers on their farms. The production and use of inorganic chemical fertilizers are not only expensive for family farming systems but also contribute significantly to environmental pollution. Biological nitrogen fixation using rhizobia has proven to be a cost-effective and environmentally friendly alternative to inorganic nitrogen fertilizers. Rhizobia interact with legumes symbiotically, improving soil fertility and legume plants productivity. The present study aimed at determining the morphological and genetic diversity, cross-inoculation ability, and symbiotic efficiency of native rhizobia isolates in sterile and non-sterile soils. Greenhouse experiments were set to trap rhizobia from soil from smallholder farms from Kitui, Embu, and Tharaka Nithi Counties using cowpea as the trap host. The cowpea crops were harvested after one month, and a total of 311 nodule isolates were purified from the crop nodules. Based on morphological characteristics, the nodule isolates were clustered into 42 different groups. The effect of the soil on cowpeas nodulation was determined using redundancy analysis where soil characteristics including P, Zn, Mn, and total organic carbon correlated positively with cowpea nodulation and nodule dry weight. Soil pH and Ca correlated negatively with nodule number and weight. In addition, 53 glycerol stocks nodule isolates (archived samples) from previous studies were revived. Revived cultures were clustered based on morphological characteristics into 11 different groups. The isolates were tested for symbiotic efficiency using common bean, cowpea, green gram and soyabean seeds planted in sterile and non-sterile soils in the greenhouse. Un-inoculated plants were used as controls, while the treatments included the revived native isolates and commercial rhizobia inocula. The experiments were laid out in a completely randomized design. Plants grown in both sterilized and non-sterilized soils and inoculated with the different isolates varied significantly (p<0.05) in the shoot, root, and nodule dry weights. Some of the isolates, including; IsAS14, IsAS11, IsAS10, IsAMR6, IsAMR22, IsAMR23, IsAMR27, and IsAGR5 significantly (P<0.05) outperformed commercial isolates in influencing the plants growth parameters. Forty-six revived nodule isolates had the ability to infect, induce nodule formation and influence the growth of the non-original host. The best performing native rhizobia isolate IsAS14, IsAMR3, IsAMR27, IsAMR18 and IsAMR22 outperformed the commercial inocula in terms of symbiotic efficiency of 104.97 %, 136.86 %, 136.99 %, 138.88 % and 155.05 %. DNA from representative isolates was extracted using ZYMO research DNATM extraction Kit. The 16S rRNA region was then amplified using universal primers and sequenced using the same primers. Based on the sequencing of 16S rDNA of representative revived nodule isolates, most of the isolates were rhizobia but clustered with different species with the most dominant cluster being isolates related to Rhizobium leguminosarum and Rhizobium etli. Nodule number and nodule dry weight were dependent on soil physico-chemical characteristics. Rhizobia isolates also had the ability to form symbiotic interaction with non-original host legume crops. These rhizobia isolates can be used as bio-inoculants to improve the production of the different legumes, and to enhance food security.
Microbial Contamination of Nile Tilapia (Oreochromis Niloticus) and African Catfish (Clarias Gariepinus) Fingerlings Reared in Hatchery Tanks at Sagana, Jambo, and Mwea Fish Farms
(Kenyatta University, 2019-03) Njagi, Isaac G
In Kenya, aquaculture continues to expand as a source of food production and livelihood in all the counties. Mortality of Nile Tilapia and African Catfish fingerlings constitute the biggest loss in extensive and intensive fish farms. The main objective of this stud y was to determine contamination by bacteria and fungi in Nile Tilapia and African Catfish fingerlings . The study was carried out from March 2014 to July 2014 in fish farms with different water sources, hatchery systems and feed sources. These were; Jambo fish farm in Kiambu County which utilizes borehole water and has a recirculation aquaculture system also known as (RAS).Sagana and Mwea fish farms in Kirinyaga County. Four weeks old and weighing 5 7 g, Nile Tilapia ( Oleochromis niloticus ) and African Catf ish ( Clarias gariepinus ) 60 each in number were stocked as follows; in every hatchery tank 10 fingerlings of each species regardless of sex. Data obtained from samples was analyzed using descriptive statistics . Fish fingerlings samples and fish feeds were collected from three fish farms and taken to the Laboratory. The bacterial load of the samples was determined using the pour plate method. Identification and characterization of various isolates were based on gram staining technique, biochemical tests and subculture on selective media . Fungi were isolated on SDA agar, Macroscopy of hyphae and mycelium, microscopic identification of subcultured fungal isolates using LCBS stain and Mycology charts . The mean of bacteria isolated in the two fish species from th ree farms per cfu/mL was as follows: African Catfish had 9.00 ±3.85a, 27.752.85a and 21.67±4.82a for the Bacillus spp, Escherichia spp and Salmonella spp, respectivelly while Nile Tilapia had 8.58±3.68a, 25.25±3.54a and 22.83±4.95a, for the Bacillus spp, Es cherichia spp and Salmonella spp, respectivelly. Penicillium spp 33.1±2.5 cfu/g and Rhizopus spp 27.6±2.8 cfu/g occurred less frequently. There was a significant variation (p = 0.015) in the means of bacteria contaminants isolated in Sagana fish farm from N ile Tilapia and African Catfish species. Escherichia spp in the skin did not vary significantly (P= 0.0684) between the fish species, however African catfish skin had the highest 27.7± 2.8 Escherichia spp contamination. There was also significant (p< 0.0001) variation in Bacillus spp contamination in fingerlings skins from different farms. The occurrence of Klebsiella species 22.0±4.7 cfu/ml , Salmonella species 22 80±4.9 cfu/ml , Streptococcus spp 25.0±5 .4 cfu/ml while Vibrio spp had a mean of 2 0.0±3.6 cfu/m l There was no significant (P= 0.4857) interaction between fish species and farm in determining the Klebsiella spp in fish skin. Formulated feeds were more contaminated (25.58) than commercial feeds (1.15) (Table 4.6). Formulated feeds had higher contamin ations attributable to high moi sture, poor storage facilities, h andling and preparation methods For physiochemical parameters Salinity varied from 155.47±6.49 to 94.70 ±0.33 mg/L in Sagana and Mwea respectively with Mwea recording the least levels of salini ty . Water temperature in the morning ranged from 20.55±0.49 °C to 25.30±0.26 °C. I n the evening time, there was also a significant variation in the levels of temperature with Sagana recording the highest at 27.10±0.63, followed by Jambo 25.00±0.41 and Mwea h ad the lowest temperature of 20.15±0.43 Variations of salinity, temperature oxygen levels are among the parameters which determine the contamination for the two fish species among the three farms. It i s recommended that all farms supplying fingerlings appl y frequent assessment of water parameters, fish feeds and water analysis F ish farmers should be educated on best practices in aquaculture in order to prevent bacterial and fungal contamination.
Detection of Pathogenic Human Adenoviruses and Enteroviruses in Water Samples Collected from Lake Victoria along Homa Bay Town, Homa Bay County, Kenya
(Kenyatta University, 2019-07) Wasonga, Michael Opere
Lake Victoria is the main source of water in Homa Bay town as well as the surrounding community. Increase in population in the resent past has led to intensified human activities with a possible compromise on the sanitation standards around the town consequently resulting into increased fecal load to the lake through fecal pollution. Increased fecal contamination of the lake has consequently led to an increase in pathogenic microorganisms including waterborne enteric viruses. These viruses can affect both human and animals health by causing diseases such as gastrointestinal infections. Research on viral water quality in Lake Victoria is limited. The objectives of this study were to determine the occurrence of these pathogenic enteric viruses with respect to human adenoviruses and enteroviruses in Lake Victoria Waters. Factors that may have influenced the levels of contamination of the lake water by the viruses such as physical water parameters, seasonal variations, proximity to sewage effluent and pit latrines were assessed. Water samples were collected from six sites commonly used for domestic and commercial purposes spanning approximately 3 km along the shoreline for analysis for the presence or absence of the two groups of enteric viruses over a seven month period. A total of 216 water samples were analysed for possible contamination with the viruses using nested PCR method. Paired t test, ANOVA, Odds Ratios, Correlation and Regression analysis (STATA ver.13.0) were performed to determine factors associated with the virus contamination of the waters. P-values<0.05 were considered significant at 95 % confidence interval. Analysis showed that the lake is contaminated with adenoviruses and enteroviruses which were discovered in 11(5.09 %) and 7(3.24 %) of the samples, respectively. The presence of the enteric viruses was strongly associated with the distance from possible sources of contamination (odds ratio 20.28 and 4.86, confidence interval 2.42, and 0.95) for pit latrines and the sewage treatment plant respectively. Neither wet season nor dry season was associated with the prevalence of the viruses. Of the 72 samples collected from the sites (L5 and L6) closer to the sewage effluent points 13(18 %) tested positive for the two types of viruses. This research clearly signifies that waste water discharge and wastewater-impacted surface waters along the shores of Lake Victoria contain some enteric viruses. This contamination may be due to the fact that the enteric viruses can highly persist in the environmental waters due to their ability to be resistant to environmental conditions. This viral analysis will provide the much needed information in controlling the source of pollution of the lake, such as untreated sewage effluents. It will be useful in ascertaining health risks from the analysis of viral exposure. Further research and analysis is recommended to ascertain the true position concerning the public heath implication and whether the contamination may be as a result of ineffective waste water treatment.
Antimicrobial Susceptibility Profile of Neisseria Gonorrhoeae Isolated from Urethral Discharges and Men Who Have Sex with Men in Nairobi
(Kenyatta University, 2018-12) Lewa, Pole Said
Neisseria gonorrhoea has progressively developed resistance to previously used drugs and recently to fluoroquinolones. Currently, there have been reports of emergency of N. gonorrhoea strains with reduced susceptibility and some exhibiting extensive multidrug resistant to the cephalosporin class of antibiotics that remains to be the remaining option for management of gonorrhoea. In Kenya, published reports regarding the drug susceptibility of N. gonorrhoea is scanty because of lack of surveillance programs and reliance of syndromic management established 20 years ago. Currently, management of gonococcal infections still utilizes a fluoroquinolone in combination with a macrolide; a treatment option that was revised more than three years ago. This study was undertaken in order to determine the antimicrobial susceptibility profile of Neisseria gonorrhoea cultured from symptomatic men and asymptomatic men who have sex with men (MSM) attending Casino Special Treatment Centre (STC) clinic in Nairobi. A total of 264 participants were consecutively sampled of which 73 were symptomatic men patients that presented with urethral discharges and 191 were asymptomatic MSM during the period between September 2015 and August 2016. Swabs were directly inoculated on modified thayer martin agar plates and transported to the University of Nairobi department of medical microbiology laboratory in candle jars for analysis. Colonies that were suggestive of gonococci were identified and N. gonorrhoeae was confirmed using standard procedures. The Minimum Inhibitory Concentrations (MIC) using Etest for penicillin, tetracycline, ciprofloxacin, spectinomycin, erythromycin, azithromycin, gentamicin, cefixime and ceftriaxone were determined and WHO reference strains used as controls. Data analysis was done using SPSS and descriptive statistics used to analyse both demographic and risk sexual behaviour of MSM. The Chi-square test was used to determine level of significance age category and risk sexual behaviour. There was a significant association between age category and the variables of number of partners and insertive anal sex one MSM was engaged for the last 3 months. The overall isolation rate was 23.8% (63/264) where 20.1% (53/264) were recovered from symptomatic men and 3.7% (10/264) from symptomatic MSM. All N. gonorrhoea strains recovered urethral discharges were highly susceptible to cefixime, ceftriaxone and spectinomycin; gentamicin demonstrated moderate susceptibility (94.3%) levels. High resistance levels were observed in penicillin (49.1%), tetracycline (96.2%), ciprofloxacin (49.1%) and azithromycin 16.9%). Of the total 3.7% N. gonorrhoea strains isolates from asymptomatic MSM, 4/9 (1.5%) were recovered from the pharynx, 5/9 (1.9%) urethral and 0/9 from the rectal. All the gonococci isolated from the pharynx were highly susceptible to cefixime, ceftriaxone, spectinomycin and gentamicin (100%). Urethral strains were highly sensitive (100%) to spectinomycin and gentamicin only. Susceptibility to both cefixime and ceftriaxone was at 80% and 60% respectively. One strain showed high level MIC to both ceftriazone and cefixme; while one showed cefixime MIC increased level (≥2.0μg/ml) and (≥0.160μg/ml) respectively both recovered from the urethra. Cefixime and ceftriaxone currently used in the management of gonorrhoea are still effective in our local gonorrhoea conditions. The traditional antibiotics previously used to manage gonorrhoea are not effective and there is an emerging resistance of N. gonorrhoea strains towards azithromycin. There is therefore a need to conduct continuous surveillance of gonococcal strains and screen high risk group as they harbour gonococcal strains that are resistant to antibiotics. The study recommends molecular characterization of these two gonococcal strains isolated from the urethra of MSM to further understand if they are the same strains previously associated with extensive multidrug resistance in other parts of the world.
Prevalence and detection of drug resistant mutations in mycobacterium tuberculosis among patients visiting selected health centres in Nairobi, Kenya
(Kenyatta University, 2018) Ogari, Collins Otieno
Tuberculosis (TB), an ancient scourge of humanity known for several thousands of years, is still a main public health challenge in many countries today even though some progress has been made recently in curbing the disease. Deferred diagnosis, poor treatment regimens and fatality qualify drug-resistant and multi-drug resistant tuberculosis (MDR TB). Unlike other bacterial pathogens, Mycobacterium tuberculosis lacks plasmid mediated mechanisms of resistance. Drug resistance in M. tuberculosis is entirely due to chromosomal changes that occur within the genes, for instance deletions or mutations. These chromosomal modifications influence the drug target or bacterial enzymes that are responsible for activating or customizing the drug. Inadequate or incomplete chemotherapy also enables M. tuberculosis to become drug resistant due to mutants that exist by nature in the mycobacterial community. Since the frequency of mutations vary geographically and limited data is available on the patterns of gene mutation in Kenya, insight of the rates of geographic specific mutations can enable the evolution of internal, PCR-based techniques for targeting mutations relevant in a specific setting. In addition to crafting new molecular biology-based techniques for the examination of MDR tuberculosis and advancement of new drugs, heightened rates of MDR and extremely-drug resistant tuberculosis (XDR TB) worldwide need to be controlled and profiled. Therefore, the main objective of this study was to evaluate the prevalence and detection of drug resistant mutations in Mycobacterium tuberculosis among patients visiting selected health centers in Nairobi, Kenya. The current study employed a cross-sectional study design which involved collecting sputum samples from 132 patients visiting Mbagathi district hospital and Chandaria community hospital. Of the 132 patients, male subjects were seventy-two (54%), while women were 60 (46%), all averaging 35 years and having a range of 18 to 60 years. Overall, 132 sputum samples were collected from patients who were all smear-positive for pulmonary TB and included for processing. Sample processing involved decontamination of collected sputum samples with NALC/NaOH/sodium citrate, thereafter, direct sputum smear microscopy using Ziehl-Neelsen stain for Acid Fast Bacteria (AFB). DNA was then extracted from the positive samples and analyzed by means of Genotype MTBDRplus (Rapid test for rifampicin and/or isoniazid resistance) and Genotype MTBDRsl (Rapid test for fluoroquinolones, aminoglycosides, and low-level kanamycin resistance in addition to confirmation of M. tuberculosis). Data analysis was carried out using chi-square test to analyze the difference in mutations detected. In total, the prevalence for the resistance to first and second-line TB drugs was 1.5% (2/132). Rifampicin resistant strain had the rpoB mutation S531L; isoniazid resistant strains had the mutations katG S315T; AG/CP resistant strains had the rrs mutation G1484T. The molecular analysis indicates confirmation of the transmission of resistant strain. The data suggested that there is homogeneity when it comes to the type of drug resistance and mutation that occurs in the region. This calls for intensified drug resistance surveillance and drug adherence among patients infected with TB. In addition, there is an urgent need for randomized controlled trials to discover the most effective treatment regimen for managing INH resistant TB.
Nodulation and Nitrogen Fixation Potential of Sesbania Spp. Rhizobia on Sesbania Sesban (L.) Merr. and Rose Coco (Phaseolus Vulgaris L.)
(Kenyatta University, 2018-03) Makatiani, Emmanuel Tendwa
Global crop and energy production are fast dwindling inversely to population growth. Common bean (Phaseolus vulgaris L.) yield has reduced worldwide due to soil infertility which can be reversed through application of chemical fertilizers. The chemical fertilizers used to ameliorate nitrogen, phoshorus and potassium are expensive and cause both deleterious physico‒chemical modification of soil and water mass eutrophication. The common bean has ability to fix atmospheric nitrogen symbiotically with rhizobia but only a few effective strains have been recovered from African soils, most of them ineffective under field conditions. Prospecting from local pool of strains trapped by wild native species like sesbania can increase the number of elite inoculant production strains for both species in agroforestry systems practiced under diverse soil and eco-climatic conditions. The specific objectives of this study were: to assess the phenotypic and genotypic characteristics of rhizobia from root nodules of East Africa and Namibia Sesbania spp. (here after referred to as sesbania) using morpho-cultural characteristics and PCR‒RFLP methods; to assess the nitrogen fixation potential of sesbania isolates on S. sesban using growth parameters; and to determine the infectiveness and symbiotic effectiveness of sesbania rhizobia on common beans. Experiments were carried out at the Kenya Forestry Research Institute, Muguga‒Nairobi, Kenya. Morpho-cultural techniques were used to characterize and cluster 128 presumptive sesbania rhizobia collected from Kenya, Uganda, Tanzania and Namibia. The diverse growth characteristics of rhizobia on YEMA media, intrinsic antibiotic resistance and salt tolerance were used to select for 79 sesbania isolates that were later subjected to fingerprinting assays using PCR‒RFLP of the 16S rDNA in comparison with 17 reference strains. The presumptive sesbania rhizobial isolates were used to inoculate S. sesban and common bean under glasshouse controlled conditions to test for their infectiveness and symbiotic effectiveness. Reference inoculants strains KFR647 and BA37 for S. sesban and bean respectively, were included in the test. Uninoculated positive control (70 ppm N as KNO3) and a negative control (0 ppm N) were included for strain effectiveness comparison and to check for contamination. The sesbania rhizobia were grouped into nine morphotypes and various ribotypes per site. The rhizobia varied in their infectiveness and symbiotic effectiveness on S. sesban and the common bean resulting in three categories viz: (1) highly effective (2) effective and (3) ineffective. The mean shoot dry weight, nodule number and nodule dry weight were all significantly different (p < 0.001). The shoot N content range was 0.16‒5.66 mg plant-1 and 0.34‒3.08 mg plant-1 for S. sesban and common beans at 8 and 4 weeks of growth respectively. Based on shoot dry weight due to inoculation, rhizobial isolate KFR402 was preferred as a common inoculant production strain for both common beans and S. sesban. However, data in the present study shows that the highest shoot dry weight was obtained with strain MASS133 (S. sesban) inoculated on Rose coco bean variety (0.87 g plant-1) and MASS172 (S. sesban) on S. sesban (1.06 g plant-1). Rhizobia recovered from sesbania grown in East Africa and Namibia are phenotypically and genetically diverse. The isolates exhibit great variations in effectiveness and nitrogen fixation efficiency on S. sesban and common beans (variety: Rose coco). Prospecting for elite rhizobia inoculant strains should be prioritized and tested for effectiveness on both S. sesban and common bean grown in diverse edaphic and agro-ecological conditions under agroforestry systems.
Antibiotic Susceptibility Pattern of Bacterial Uropathogens Isolated From Patients in Nakuru Level 5 Hospital, Kenya
(Kenyatta University, 2017) Gachuhi, George Tibi
Urinary tract infections (UTI) are bacterial infections encountered in the hospital and community and is preventable. It is among bacterial infection encountered with increasing antibiotic resistance to uropathogens, although there is availability of antibiotics. Despite the wide spread of antibiotics, it remains the common bacterial infections. Antibiotic susceptibility testing therefore provides information that allows clinicians to select the most appropriate antimicrobial drugs. Over the years, the UTIs antimicrobial resistance patterns have been changing. The study was carried out to establish the prevalence of bacterial isolates and their drug susceptibility patterns among the study population. A descriptive cross-sectional study was conducted in outpatients and inpatients presenting with symptoms of UTI. Purposeful sampling was used to obtain 385 respondents. Mid-stream urine sample were obtained from respondents using sterile bottles and bacterial isolates identification was done using biochemical tests. Culture and sensitivity pattern of uropathogens were determined using disc diffusion method. A questionnaire was administered to consenting respondents and data associated with risk factors was collected and analyzed at ɑ=0.05. Out of 385 urine samples 112 (29 %) patients were confirmed positive for UTI. The prevalence of UTI was higher among females (62.1 %) compared to males (37.9 %). Escherichia coli 66 (55 %) was the most predominant followed by Klebsiella pneumoniae 12 (10 %), coagulase negative staphylococci 25 (20.9 %), Staphylococcus aureus 11 (9.2 %) and Proteus mirabilis 6 (5 %). Antimicrobial profiles of E. coli strains showed the following susceptibility pattern to nitrofuratoin (100 %), cefotaxime (86.3 %), ciprofloxacin (83.3 %), gentamicin (81.7 %), ampicillin (45.3 %) nalidixic acid (48.5 %) and cotrimoxazole (44.1 %). Further 85% of the isolates were observed to be multidrug resistant, limiting treatment of UTIs with routinely used antibiotics. Hence, there is need for constant monitoring of antibiotic resistance for better management of patients on antibiotic treatment. In addition, the collected data could be use in determination of trends in antimicrobial susceptibility patterns and therefore assisting in policy formulation on the currently used antibiotics for management of UTIs.
Prevalence of plasmodium species infection among primary school children and performance of malaria rapid diagnostic test kits in Baringo county, Kenya.
(2017-09) Omondi, Collince Jared
Malaria causes the greatest public health burden in sub-Saharan Africa where high mortality mainly occurs in children under five years of age and pregnant women. Majority of Kenyan population are at risk of malaria infection. Traditionally, malaria has been studied mainly in Western and Coastal Kenya while the rift valley especially Baringo County few malaria studies have been conducted indicating seasonal transmission. This has resulted in scanty information on actual malaria prevalence and transmission patterns which may hinder setting up of proper control strategies. Moreover, primary school children seem to be endangered due to minimal protection by insecticide treated nets. The purpose of this study was to determine the prevalence of Plasmodium species infection among primary school children and to evaluate the performance of malaria rapid diagnostic test kits in diagnosis of malaria in Baringo County, Kenya. One thousand six hundred and sixty eight (1668) children from fifteen primary schools located in 4 ecological zones (lowlands, midlands, highlands and riverine) of three sub-Counties of Baringo County were recruited into the study. Finger prick blood sampling was done every four months (during the dry season in January/ February, during the long rains in June/July, short rains in November 2015 and during dry season in January/ February 2016). Plasmodium species infection was tested using three rapid diagnostic test kits (CareStart Pf, SD Bioline Ag Pf and SD Bioline Ag P.f/ Pan). Microscopic examination was done on all RDT positive and 10% of negative cases. A total of 268 (16.1%), out of 1668 pupils tested positive for P. falciparum by RDT; 78% had a single episode of infection, 16.8% had 2 episodes, 4.9% had 3 episodes and 0.4% had 4 episodes of infections. Plasmodium species infection varied within local ecological zones. For instance, the riverine zone had the highest cases of Plasmodium species infection compared to lowland, highland and midland (Fisher’s exact test = 0.005). More cases of Plasmodium species infection (10.7 and 6.2%) were reported in dry season compared to 2.6% in the long rains (Fisher’s exact test= 1.000) and 5.7% in short rains (Fisher’s exact test= 0.197). Risk of Plasmodium species infection was significantly higher in riverine zone compared to midland, lowland and highland (IRR= 40.24165 (95% CI: 7-1623). Infection rate for males and females was similar (IRR = 1.02 (95% CI: 0.55-1.88). The study also established that children aged between 10 – 15 years were at higher risk of Plasmodium species infection than those aged between 5- 9 (IRR 1.6 (95% CI: 0.9- 3.1). The kits performed relatively well in the diagnosis of malaria using microscopy as reference. SD Bioline Ag-Pf/ Pan RDT kit had a higher sensitivity (90%) compared to that of CareStart Pf (70%) (McNemar's χ² = 0.5, df = 1, p-value = 0.4795). Similarly, the sensitivity of SD Bioline Pf was the same as that of CareStart Pf (82.4%). The kits can therefore be used to guide treatment of febrile illness within Baringo County. In addition, present study findings, indicate that Plasmodium species infection was relatively low within Baringo County compared to endemic regions of Kenya; however, there is a need for continued monitoring of transmission dynamics under changing climatic conditions as well as establishing expanded malaria control strategies especially within the riverine zone.
Prevalence of plasmodium infection and anaemiain primary school children following universal distribution of insecticide treated bed nets inkasipul, Homa-Bay county, Kenya
(2017-10) Robert, Omondi
Malaria is devastating diseases afflicting humans, in Kenya; the disease is endemic in areas around Lake Victoria and along the southern coast. Untreated malaria in school children, result in anaemia, reduced ability to concentrate and learn in school and if fallen sick may lead to school absenteeism. Insecticide treated nets (ITN) have been shown to provide significant protection against Plasmodium infection. Available data show that the overall prevalence of Plasmodium and anaemia among primary school aged children in Kasipul is 25.8 % and 14.1%, respectively. However, there is limited information on the Plasmodium and anaemia prevalence in Kasipul following mass distribution of ITN in 2014. The objective of this study was to assess the prevalence of Plasmodium and anaemia among school children living in Kasipul and their reported use of insecticide treated bed nets, one year after mass distribution of ITN in Kasipul, Homa-Bay County. A descriptive cross-sectional study of 398 primary school pupils was conducted in Kasipul. Pupil’s fingers were pierced using a lancet to obtain blood sample for malaria parasite detection and haemoglobin level determination. Data on insecticide net use was collected using self-administered questionnaire. The overall prevalence of Plasmodium among children was 10.05% and anaemia was 2.3%. The association between net ownership and Plasmodium prevalence among pupils was significant (2= 14.46, df =1, p = 0.000). The difference in malaria prevalence in terms of sex was not statistically significant (2= 0.814, df= 1, p = 0.367). However, anaemia was slightly more prevalent in girls (3.6%) than boys (1.0%) were. Although the difference was not statistically significant (2= 3.217, df= 1, p = 0.073). The study established that only 51.0 % of the study population owned ITN, which is below the 80% target set by the government. A negative correlation of -0.3874 existed between the use of ITN and malaria prevalence. The study observed a significant decline in Plasmodium prevalence from 25.8% in 2011 to 10.05% in 2016, which is evidence that ITN, which was the major control strategy implemented in Kasipul reduced Plasmodium infection in the study population. Decline in Plasmodium infection could also have reduced the prevalence of anaemia in the study area from 14 % in 2010 to 2.3% in 2016. In conclusion, this inquiry revealed that the prevalence of Plasmodium and anaemia has significantly reduced following distribution of free ITN in Kasipul. Plasmodium prevalence was lower in schools, which recorded a large number of pupils using ITN. Prevalence of Plasmodium in Kasipul is still high compared to the national average of 5%; this study recommends that other control measures apart from insecticidal nets should also be introduced in Kasipul, by the Kenya government to eliminate Plasmodium. Ministry of health and other stakeholders should ensure that hang-up’ campaigns to sensitize residence on the relationship between ITN and Plasmodium prevalence, forms an integral part of future treated nets distributions. Further studies using households as sampling units need to be conducted in Kasipul, since this study did not include pupils absent from school on the sampling days.
Symbiotic efficiency and diversity of native rhizobia isolated from climbing beans (phaseolus vulgaris l.) in Embu and Tharaka Nithi Counties, Kenya
(2016-11) Koskey, Gilbert
Kenya is the eighth highest producer of common beans (Phaseolus vulgaris L.) worldwide with a production of 529,265 tons annually. Climbing beans are highly productive, and can produce yields 2 to 3 times higher than bush beans and is therefore a promising option to increase bean yields in Kenya. However, climbing bean production is greatly affected by the decline in soil fertility, particularly low nitrogen levels in the soil. Replenishment of soil nitrogen using effective rhizobia inoculants presents a sustainable solution to climbing bean production. The objectives of this study were to assess climbing bean varieties grown by smallholder farmers in Eastern Kenya, to determine the genetic diversity of native rhizobia strains that nodulate climbing beans and to determine nodulation and symbiotic nitrogen fixation efficiencies of native rhizobia strains isolated from climbing beans grown in Eastern Kenya. Questionnaires were used to obtain information on climbing bean varieties grown in Eastern Kenya. The experiments involved laboratory analysis, greenhouse and on farm activities. A complete randomized design and a randomized complete block design were used in the greenhouse and field experiments respectively. Five climbing bean varieties were identified in Embu and Tharaka Nithi Counties of Eastern Kenya; Gatune, Raila, Mama safi, Kithiga and Muviki, of which Gatune was the most preferred variety. In regards to bean diversity, Embu Lower Midland zone had the highest Shannon-Wiener diversity index (H’) of 2.01, while Embu Upper Midland zones had the lowest diversity index (H’) of 1.83. From the laboratory analysis, 41 native rhizobia isolates were isolated from the root nodules of mid-altitude climbing beans (MAC 13 and MAC 64) and placed into 9 groups based on their morphological characteristics. Rhizobia diversity was determined based on restriction digestion of PCR amplified 16S rRNA genes using Msp I, EcoR I and Hae III enzymes. Analysis of molecular variance based on restriction digestion of 16S rRNA genes showed that there was a 100 % genetic variation within population and no variation (0 %) among the four rhizobia populations and across the two regions (0 %). Nine representative native rhizobia isolates were tested in the greenhouse for their symbiotic nitrogen fixation efficiency on MAC 13 and MAC 64 climbing bean varieties. Four native isolates ELM3, ELM5, ELM8 and ELM4 with symbiotic efficiency (SE) of 123.72%, 99.21%, 98.24% and 96.75%, respectively, compared favorably with the commercial rhizobia inoculant (Biofix-CIAT 899) (SE of 95.21%). The best native rhizobia isolate (ELM3) was evaluated in the field experiment using MAC 13 and MAC 64 climbing beans. The mean nodule number of climbing beans differed significantly (p < 0.0001) among the test isolates. Climbing beans inoculated with test isolate ELM3 recorded a higher mean nodule number (85.58 plant-1) compared to the Biofix-CIAT 899 (76.13 plant-1) and non-inoculated control plants (52.08 plant-1). There was a significant effect of rhizobia isolates on shoot dry weight (p < 0.0001) and total bean seed yield (p < 0.0001). Climbing beans inoculated with native isolate ELM3 produced the highest mean seed yield of 4,397.75 kg/ha, indicating 89 % increase over non-inoculated control which yielded 2,334.81 kg/ha. This study demonstrated the presence of diverse native rhizobia isolates that are potentially superior over the commercial inoculant (Biofix-CIAT 899) bean inoculants. However, these isolates need to be identified and tested further in different geographical locations to determine their efficiency and stability on bean production.
Nitrogen fixing potential of indigenous bradyrhizobia nodulating soybean varieties grown in Embu and Thara Kanithi Counties in Eastern Kenya
(Kenyatta University, 2016-11) Wambui, Simon Mburu
Nitrogen deficiency in most African soils is the main factor limiting crop productivity. Grain legumes such as soybean (Glycine max (L.) Merril) can form a symbiotic association with soil root nodule bacteria (rhizobia) and the process can provide sufficient nitrogen for crop production. Continuous cultivation without nutrient replenishment, leaching and poor soil fertility are the major limitations for soybean production by smallholder farmers in Embu and Tharaka-Nithi Counties. The objectives of this study were to assess the soybean varieties grown by smallholder farmers from Embu and Tharaka-Nithi Counties, to determine the diversity of indigenous bradyrhizobia nodulating soybean varieties and to determine symbiotic effectiveness of bradyrhizobia isolates on biological nitrogen fixation. DNA fingerprinting was carried out using 16S rRNA gene for polymerase chain reaction (PCR) products based on restriction digest using HaeIII, Msp 1 and Eco RI enzymes. The symbiotic effectiveness of isolates was carried out both in greenhouse and field conditions. A split plot arrangement in a randomized complete block design (RCBD) replicated three times was used. During the study, four soybean varieties namely Gazelle, Nyala, Namsoy, and Mausoy were recorded where Gazelle was most abundant with 85 % of smallholder farmers surveyed. Thirty-nine (39) isolates were obtained from trapping experiments and placed into nine groups based on their morphological characteristics. Analysis of molecular variance (AMOYA) on genetic data based on restriction digest revealed significant (p < 0.015) variation within populations and not among the zones or populations. Based on principal coordinate analysis (PCA), there was sympatric speciation of indigenous rhizobia isolates. EUMZ rhizobia isolates had the highest genetic diversity estimates (H = 0.419) compared to other agroecological zones according to Shannon's Information Index I (H). Authentication experiment showed that most of the isolates were bradyrhizobia due to their ability to infect soybeans. The test isolates had varied ability to infect and fix nitrogen. The best performing indigenous isolates (R19 ad R14) in greenhouse outperformed commercial bradyrhizobia (Bio-fix) in terms of symbiotic effectiveness with 119.17 %,142.35 %, and 101.01 %, respectively, when compared to nitrogen controls. Results from the field experiment indicated that indigenous isolates were competitive where they improved significantly soybean shoot biomass (p < 0.001). Different zones were found to have a significant influence on yield after use of inoculants (p = 0.00 I). The indigenous isolate RI9 scored highest grain yield of 823 kg ha' when compared to other treatments. The effective indigenous bradyrhizobia therefore showed the potential of being sources of inocula for soybean smallholder farmers.

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