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Open Journal of Medical Microbiology 2021年第1期11卷 32-46页

作者： Danait Andemichael Solomon andrew k. nyerere Alice k.nyua Caroline Wangari Ngugi Department of Medical Microbiology Jomo Kenyatta University of Agriculture and Technology 62000-00200 Nairobi Kenya Nairobi Hospital 30026-00100 Nairobi Kenya

The upsurge of candidemia in the past years has been an immense encumbrance on public health and the number of deaths caused by candidemia particularly in critical care unit patients is devastating. Candida species harbor a 30% - 60% mortality rate and compared to stable people or those with less serious illnesses, this ranges from 60% to 80% of those who are chronically ill patients. Grounded on a recent report from a tertiary care hospital in Kenya showing the emergence of previously unobserved species: Candida auris, this study aimed to determine the prevalence, species distribution, and antifungal susceptibility profile of candidemia in critical care unit patients of the hospital. 378 Critical Care Unit patients were enrolled for the study from January 2019 to January 2020. Positive archived isolates were sub-cultured using Saboraud Dextrose Agar. Candida species were identified utilizing API20C AUX and Vitek-2. Antifungal susceptibility testing was conducted using the Liofilchem MIC Test strip. Out of 378 patients, thirty-one presented a positive culture for Candida species. The prevalence

关键词： Critical Care Unit Candida Species Candida auris Candidemia Antifungal Susceptibility

Prevalence and Risk.Factors Associated with CampylobacterInfection in Diarrheal Patients in Busia County, k.nya

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Advances in Microbiology 2021年第11期11卷 657-680页

作者： Tom T. Ouk. andrew k. nyerere John M. Njeru Eric M. Fèvre Samuel k.riuk. Centre for Microbiology Research Kenya Medical Research Institute Nairobi Kenya Department of Medical Microbiology Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya Institute of Infection Veterinary and Ecological Sciences University of Liverpool Liverpool United Kingdom International Livestock.Research Institute Nairobi Kenya

Introduction: Campylobacter are zoonotic bacteria that cause gastroenteritis worldwide with the species, Campylobacter jejuni and Campylobacter coli commonly associated with human diarrhea. Transmission is mainly through direct contact with farm animals, consumption of chick.n and contaminated water. There is paucity of data on the epidemiology of Campylobacter in developing countries despite its global widespread and expansion of poultry farming;hence there is the need to explore and build on the available data. This study aimed at determining prevalence and homestead risk.practices associated with Campylobacter infection in diarrheal patients in Busia County. Methods: A cross-sectional study was conducted from February, 2017 to April, 2019. Stool samples were collected from patients of all ages attending Busia County referral Hospital and structured questionnaires on homestead associated risk.practices administered. Isolation and identification of Campylobacter species was performed using standard culture method on Modified Charcoal Cefoperazone Deoxycholate medium and confirmed by mPCR. Factors associated with Campylobacter infection were evaluated using logistic regression analysis. Results: A total of 132 (11.6%) Campylobacter comprising 89.2% C. jejuni and 10.8% C. coli were isolated from 1200 diarrhoegenic patients sampled. Isolation rate was higher in children aged 5 years (9.4%). Multilevel logistic models showed that homestead poultry farming was a significant risk.associated with Campylobacter infection in 5 years (OR 10.05;95% CI: 2.60 - 24.29, P k.practices link.d to children k.ng of pond water (OR 7.43, 95% CI: 1.70 - 16.33, P <

关键词： Risk.Factors Prevalence Diarrhea Campylobacter

Phenotypic and Genotypic Characterization of Extended Spectrum Beta-Lactamases Producing Bacteria Causing Urinary Tract Infections among Expectant Women Attending Antenatal Clinic at Ruiru Sub County Hospital, k.nya

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Advances in Microbiology 2023年第12期13卷 571-587页

作者： Eunice Maingi andrew nyerere Celestine Mak.be Department of Medical Microbiology College of Health Science Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya

Back.round: Urinary tract infection (UTI) is a bacterial infection affecting males and females but is more prevalent in expectant women. ESBLs are bacteria with enzymes that mak. them resistant to many antibiotics, posing a significant health challenge. This study aims to determine the characteristics of ESBL-producing bacteria causing UTIs in expectant women. Methodology: A self-administered survey was carried out;300 expectant women were recruited using a random sampling method. A questionnaire was used to collect socio-demographic information. Urine samples were collected in sterile universal bottles and processed at the Jk.AT Zoology laboratory. Urine samples were analyzed using urinalysis, microscopy, culture, and sensitivity testing. ESBL-producing bacteria were identified phenotypically using the double-disc synergy test (DDST) and genotyped for specific resistant genes using PCR. Results: UTI prevalence was 32.7% (98/300). UTI was significantly associated with the history of previous UTI (OR = 0.84, p = 0.02) and multigravida (OR = 0.14 p = 0.01). UTI was common in women aged between 28-37 years in their second trimester. Bacteria isolated were E. coli 57.1% (56/98), S. aureus 21.4% (21/98) k. pneumonia 11.2% (11/98) and Proteus spp 10.4% (10/98). Bacteria antibiotic resistance patterns were E. coli-tetracycline (91.1%), sulfamethoxazole (55.4%), cefotaxime (53.4%) and augmentin (53.4%). S. aureus-sulfamethozaxole (100%) and augmentin (71.4%), k. pneumoniae-sulfame-thoxazole (72.2%) cefotaxime (63.6%), chloramphenicol and tetracycline (54.5%). Proteus spp: tetracycline (100%), nitrofurantoin (90%), cefotaxime and chloramphenicol (50%). The proportion of ESBLs bacterial producers was 37.6% (29/77) and 44.8% (13/29) possessed ESBLs resistant genes;Bla CTX-M 53.8% (7/13), Bla SHV and Bla TEM 23.1% (3/13) each, Bla OXA (0%) was not detected. Conclusion: The study revealed a high proportion of ESBLs producing bacteria responsible for UTI in expectant women. ESBLs

关键词： Urinary Tract Infections Resistant Genes Genotypic Phenotypic Extended Spectrum Beta Lactamases

Phenotypic and Genotypic Characterisation of Antibiotic Resistance in Escherichia coli, k.ebsiella spp., and Listeria monocytogenes Isolates from Raw Meat Sold in Nairobi

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Advances in Microbiology 2022年第11期12卷 603-620页

作者： Anita Chepk.mei John Mwanik. andrew nyerere John k.iru Department of Medical Microbiology Jomo Kenyatta University Nairobi Kenya Centre for Medical Microbiology Kenya Medical Research Institute Nairobi Kenya

Worldwide, the increase in antimicrobial resistance (AMR) is a public health concern. Food-borne associated antibiotic-resistant pathogens can contaminate raw meat during slaughter, transportation, and at sale points. A cross-sectional study was conducted from March 2021 to December 2021 to determine antimicrobial susceptibility patterns and characterize the molecular basis of resistance in E. coli, k.ebsiella spp., and L. monocytogenes contaminating raw meat collected from retail outlets in Nairobi. Isolation and identification of the strains were done using the standard culture methods and PCR. Antimicrobial susceptibilities of the recovered strains were determined using disk.diffusion while the presence of antibiotic resistance gene determinants;blaTEM, blaCTX-M, blaOXA, sul, and qnrS was done using PCR. Of 270 samples collected, 163 (60%) Escherichia coli, 19 (7%) k.ebsiella spp., and L. monocytogenes 3 (1.1%) were recovered. Among Escherichia coli, high antibiotic resistance was found to Erythromycin 161 (98%) and ampicillin 88 (54%) while low resistance was found against imipenem 2 (1%). Similarly, high resistance was found among k.ebsiella spp. to Erythromycin 19 (100%) and ampicillin 12 (63%) low resistance to ceftazidime 1 (5%), cefotaxime 1 (5%), aztreonam 1 (5%), and chloramphenicol 1 (5%). One isolate among the three Listeria monocytogenes strains isolated was resistant to Trimethoprim-sulfamethoxazole. No resistance was exhibited to gentamycin by all k.ebsiella spp. The prevalence of multidrug-resistant (resistance to three or more classes of antibiotics) isolates was 95/182 (52.2%). The common resistance pattern observed was Erythromycin, ampicillin, tetracycline, and trimethoprim-sulfamethoxazole with a prevalence of 19 (20%). ESBL was confirmed in isolates that harbored: blaTEM (65%), blaCTX-M (44%), blaOXA (33%) while sul and qnrS were detected in 46.7% and 13.6% respectively. Circula

关键词： Raw Meat Escherichia coli Listeria monocytogenes Multidrug Resistance Extended Spectrum β-Lactamase (ESBL)

Occurrence of Highly Resistant Microorganisms in Ruai Wastewater Treatment Plant and Dandora Dumpsite in Nairobi County, k.nya

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Advances in Microbiology 2019年第5期9卷 479-494页

作者： Edinah Song’oro andrew nyerere Gabriel Magoma Revathi Gunturu Pan African University Institute for Basic Sciences Technology and Innovation (PAUSTI) Nairobi Kenya Jomo k.nyatta University of Agriculture and Technology (Jk.AT) Nairobi Kenya The Aga k.an University Hospital (Ak.H) Nairobi Kenya

Wastewater treatment plants and solid dump sites act as potential reservoirs of highly resistant bacterial strains. This study presents information on the patterns of antimicrobial resistance among pathogenic bacteria in the sewage treatment plants and solid dump site in Nairobi County, k.nya. We employed standard microbiological methods to isolate and identify bacteria from these selected sites. Members of Escherichia, k.ebsiella, Serratia, Shigella, Pseudomonas, Citrobacter spp, Enterobacter, Salmonella, Staphylococcus, Bacillus, Yersinia, Vibro cholera, Providencia, Morganella and Proteus spp were isolated. Escherichia and k.ebsiella recorded the highest occurrence at 13.9% and 10.3% in wastewater. Shigella, Serratia Citrobacterfreundii, Pseudomonas, Staphylococcus, Escherichia and k.ebsiella recorded the highest level of occurrence at 15.1%, 14.1%, 12%, 11%, 10.4%, 10.3%, and 8.3% in dumpsite respectively. Drug sensitivity using the Disc diffusion method showed that Ampicillin, Ceftazidime, Cefotaxime, Amoxicillin, and Cefepime had the highest levels of inactivity at (68.5%, 89.5%), (64.2%, 87%), (54.5%, 80.2%), (52%, 74%) and (49.1%, 72.4%) respectively while Levofloxacin and Gentamicin showed the smallest level of antibiotic resistance at (4.8%, 4.7%) and (4.2%, 2.6%) in both sites. Members of Escherichia, k.ebsiella, Proteus vulgaris, Salmonella, Pseudomonas, Shigella and Serratia showed the highest level of ESBLs production at 28.9%, 18.4%, 15.8%, 10.5%, 7.9%, 7.9%, 7.9% and 7.9% in the wastewater whereas Shigella, Escherichia, Serratia, Pseudomonas, k.ebsiella, and Proteus vulgaris showed the highest level ESBLs production at 45.5%, 10.9%, 9.1%, 9.1%, 7.3% and 7.3% from the dump site. All the antibiotics tested except for Gentamicin, Chloramphenicol and Ciprofloxacin differed significantly in terms of resistance levels (p < 0.05). The study concluded that, wastewater treatment plant and dump sites bear heavy burdens of potentially virulent resistant bacteri

关键词： Antibiotics Resistance Wastewater and Solid Dump Site

Studies on Vitamin D Levels in Serum of HIV Infected Patients: Their Effect on Progression towards AIDS

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World Journal of AIDS 2014年第4期4卷 422-429页

作者： Catherine Wanjiru Gichuhi Daniel k.riuk. andrew nyerere Malk.t Riyat Department of Biochemistry Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya Department of Medical Microbiology Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya Department of Pathology Aga Khan University Hospital Nairobi Kenya

Vitamin D deficiency may be more prevalent among HIV-positive patients than in the general population due to HIV disease-related factors. This study examined the effects of HIV infection and use of antiretroviral drugs in serum vitamin D levels in HIV patients visiting Aga k.an University Hospital, Nairobi k.nya from October 2013 to April 2014. The effect of vitamin D status on CD4?cell count and HIV viral load was evaluated to determine the status of disease progression to AIDS. HIV viral load in blood samples was determined using COBAS Ampliprep/TaqMan HIV-1 test k.t while CD4?cell counts were done using the fluorescence-activated cell sorter system. The levels of vitamin D in serum were determined using electrochemiluminescence binding assay in Cobas E601 mass analyzers. In addition, selected plasma enzymes were used to evaluate liver function. Higher percentage (49.12%) of deficient vitamin D cases were observed among HIV patients not on ART. Deficient levels of Vitamin D were associated with abnormal selected liver enzymes. High viral load was observed among patients not on ART with deficient and insufficient vitamin D. The CD4?cell count was higher in patients on ART with sufficient vitamin D levels compared to those with deficient vitamin D. These observations suggest a need to supplement ART with vitamin D in order to ameliorate Vitamin D deficiency as a strategy to improve HIV management.

关键词： Vitamin D HIV Patients ART Viral Load CD4 Count

Epidemiology of Staphylococcus aureusInfections in k.nya: Current State, Gaps and Opportunities

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Open Journal of Medical Microbiology 2020年第4期10卷 204-221页

作者： Justin Nyasinga Geoffrey Omuse Njenga John andrew nyerere Shima Abdulgader Mae Newton andrew Whitelaw Gunturu Revathi Department of Pathology Aga Khan University Nairobi Kenya Department of Biomedical Sciences and Technology The Technical University of Kenya Nairobi Kenya Pan-African University-Institute of Science Technology and Innovation/Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya Department of Biomedical Sciences Stellenbosch University Stellenbosch South Africa

Staphylococcus aureus has maintained its clinical relevance as a major cause of hospital and community acquired infections globally with a high burden of antimicrobial resistance (AMR). Though reported, the burden of infection, antimicrobial resistance and molecular epidemiology of S. aureus are not well defined in Kenya. This descriptive review evaluated reported data on the detection and characterization of S. aureus infections in Kenya. Published data between 2000 and 2020 were evaluated. S. aureus isolation frequencies varied from 1% in blood specimens to 52.6% among skin and soft tissues infections while MRSA rates ranged from 1% to 84.1%. While penicillin resistance has consistently been high, last line and recent antibiotics such as vancomycin, linezolid, teicoplanin and daptomycin have retained their efficacy. Data on MRSA carriage in the community, among HCWs and inpatients is limited. Global clones (CC1, CC5, CC8, CC22, CC30, CC45 and CC239) alongside a few novel MRSA strains have been reported with staphylococcal protein A (spa) sequence based clustering yielding four major clusters (spa

Molecular Identification of Co-Existence of Carbapenemase and Extended-Spectrum β-Lactamase Genes in k.ebsiella pneumoniaeClinical Isolates, and Their Phylogenetic Patterns in k.nya

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Advances in Microbiology 2021年第8期11卷 399-415页

作者： Noutin Fernand Michodigni Atunga Nyacheo Juliah k.ayeli Ak.wale Gabriel Magoma andrew nyerere k.mang’a Department of Molecular Biology & Biotechnology Pan African University Institute for Basic Sciences Technology and Innovation (PAUSTI) Nairobi Kenya Institute of Primate Research (IPR) Nairobi Kenya Jomo k.nyatta University of Agriculture and Technology (Jk.AT) Nairobi Kenya

The increasing incidence of multidrug-resistant k.ebsiella pneumoniae strains has become a serious global healthcare problem. Additionally, the carriage of both extended-spectrum ß-lactamase and carbapenemase genes on plasmid and genomic DNA in k. pneumoniae clinical isolates has not been documented in k.nya. This study aimed to assess the presence of extended spectrum β-lactamase (ESBL) and carbapenemase genes on genomic and plasmid DNA in k. pneumoniae, and classify these super-bug clinical isolates based on their phylogenetic patterns. The identification of k.ebsiella-lik. clinical isolates (n = 20) collected from k.nyatta National Hospital in Nairobi was performed using API 20E k.t. Screening and confirmation for ESBL and carbapenemase phenotypes were conducted using k.rby-Bauer disk.diffusion susceptibility test protocol. Conventional PCR technique was used to characterize ESBL and carbapenemase resistant genes on both genomic and plasmid DNA. Subsequently, 16S rRNA gene amplification and sequencing were performed. The 16S rRNA gene contiguous sequences of the bacterial isolates were analyzed using the ChromasPro. The gene sequence was compared with the sequences in GenBank.database, using the BLAST program of NCBI to obtain the nearest phylogenetic neighbours from the databases. Then, the sequences of MDR k. pneumoniae and its relatives were aligned using ClustalW. The evolutionary history was inferred by using the maximum lik.lihood algorithm in MEGA MX. The phenotypic data of antibiotic susceptibility testing revealed that 2/20 (10%) clinical isolates were resistant both to imipenem and meropenem and producers of carbapenemase. These isolates were carbapenemase producers but not extended β-lactamases. However, 3/20 (15%) isolates that co-harboured blaNDM-1, blaIMP, blaTEM, and bla-OXA were identified during genotypic analysis. The positive control used separately yielded the expected band sizes for blaIMP (275

关键词： MDR k.ebsiella pneumoniae Plasmid Genomic DNA Extended Spectrum β-Lactamase Carbapenem 16S rRNA

Evaluation of the Antimicrobial Effect of Nepeta catariaand Basella albaagainst Clinically Resistant Acinetobacter baumanniiin Nairobi, k.nya

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Advances in Microbiology 2018年第10期8卷 790-803页

作者： Salome Marlene Morombaye Mourine k.ngogo Gunturu Revathi andrew nyerere John Ochora Institute of Basic Sciences Technology and Innovation Pan African University Nairobi Kenya Department of Medical Microbiology Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya Department of Pathology Aga Khan University Hospital Nairobi Kenya Department of Botany Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya

Acinetobacter baumannii is among the common nosocomial infections microorganisms in the Intensive Care Unit (ICU). Antimicrobial resistance (AMR) is one of the major significant concerns in developing nations due to either over-use or inadequate use of antimicrobial agents. The purpose of this study was to emphasize the potential antimicrobial activity of Nepeta cataria and Basella alba against nosocomial diseases caused by Acinetobacter baumannii. Nepeta cataria and Basella alba leaves were collected from Oldonyo Sabuk.National Park.and Botanical garden Jk.AT respectively. The leaves were dried under shade at room temperature for thirty days. After methanolic and aqueous plant extraction, the percentage yield was determined, and the extracts were subjected to toxicity testing using brine shrimp eggs and preliminary phytochemical screening. The results recorded from this study demonstrated that 70% methanolic extract of Nepeta cataria and Basella alba had greater antimicrobial effect against Acinetobacter baumannii than aqueous extracts. Nepeta cataria extracts showed greater antimicrobial effect than Basella alba extracts. The methanolic plant extracts had MIC values 60 mg/ml when tested against Acinetobacter baumannii. The phytochemical screening showed the presence of various phytochemical constituents from the methanolic and aqueous extraction of Nepeta cataria and Basella alba. The methanolic plant extracts revealed more phytochemicals as compared to aqueous extracts. More phytochemicals were detected from Nepeta cataria than Basella alba plant extracts.

关键词： Medicinal Plants Nepeta cataria Basella alba Antimicrobial Activity Acinetobacter baumannii Phytochemical Screening Toxicity

Characteristics of Archived Coagulase Negative StaphylococciIsolates at a University Hospital, Nairobi, k.nya

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Open Journal of Medical Microbiology 2014年第4期4卷 236-241页

作者： Shivachi Patricia Ingato andrew nyerere k.mang’a Geoffrey Omuse Samuel k.riuk. Revathi Gunturu Victor Dinda Jomo k.nyatta University of Agriculture and Technology Itromid KEMRI Nairobi Kenya Aga k.an University Hospital Nairobi Kenya Centres for Microbiology Research KEMRI Nairobi Kenya Masinde Muliro University of Science and Technology Nairobi Kenya

Back.round: Coagulase negative Staphylococci (CoNS) are normal inhabitants of the sk.n and mucous membranes and thus have been dismissed for a long time as culture contaminants even if they have been isolated from sterile specimens. The risk.factors for CoNS infections include patients who are immunocompromised, implanted with foreign bodies or with indwelling devices. The aim of this study was to determine the antimicrobial susceptibility patterns and presence of mecA gene in methicillin resistant CoNS isolated in a teaching and referral hospital in k.nya. Methodology: This was a cross sectional retrospective study. Archived isolates were sub-cultured on 5% sheep blood agar. Speciation and antimicrobial susceptibility patterns were performed by Vitek. technique. The presence of mecA gene was determined by (PCR). Results: A total of seven species were identified with Staphylococcus epidermidis having the highest percentage at 45.4% and Staphylococcus warneri with the lowest at 2.6%. High resistance to antibiotics that were tested was observed regardless of the source of the isolate. MecA gene was found in 90% of the isolates. Conclusion: Coagulase negative Staphylococci exhibited high levels of resistance generally. Most of the isolates carried the mecA gene. Despite some of the isolates being resistant to Cefoxitin, the mecA gene was not found. There is a possibility that methicillin resistance in these isolates is mediated using a different mechanism.

关键词： Coagulase Negative Staphylococcus (CoNS) Antimicrobial Susceptibility Patterns Methicillin Resistance