MST-Department of Microbiology

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Browsing MST-Department of Microbiology by Subject "Genetic Diversity"

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    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.
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    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.
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    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.