Prevalence and Antibiotic Resistance Patterns of Escherichia coli among Hospitalised Patients at Thika District Hospital

Background: Emerging resistance to antimicrobial drugs increases morbidity and mortality by hampering the provision of effective chemotherapy; and makes treatment more costly. The emergence of resistance to antimicrobial agents is a global public health problem; especially in pathogens causing nosocomial infections. Objectives: To determine the carriage of E. coli from wounds and urine in catheterised inpatients at Thika District Hospital (TDH) and to determine antimicrobial resistance patterns to Beta-lactams; aminoglycosides and (fluoro) quinolones. Design: A cross-sectional study. Setting: Thika District Hospital among hospitalised patients. Subjects: A total of 450 specimens were collected and forty two (42) Escherichia coli isolated. Pus swabs were collected from wounds and urine was collected aseptically from the inpatients with catheters. Escherichia coli were identified by culture methods and biochemical tests. Antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion method and interpreted according to Clinical Laboratory Standards Institute recommendations. Results: Susceptibility results in aminoglycosides were; resistance for amikacin; gentamicin and kanamycin was 20; 39 and 51 respectively. Resistance in penicillin was ampicillin 85 and piperacillin 83 . Resistance for sulfamethoxazole was 83; tetracycline 66 ; nalidixic acid 44; nalidixic acid 44 and chloramphenicol 39and chloramphenicol 39. In amoxicillin/clavulanic acid; resistance was 68 . Cephalosporins' resistance was ceftazidime 22 ; cefotaxime 56 . Resistance for imipenem and tazobactam was 7 and 12 respectively. Conclusion: Due to observations on resistance to antimicrobial agents commonly used in Thika District Hospital; this shows that there is need to revise antimicrobial policy in this region in the treatment of E. coli infections

MOLECULAR CHARACTERISATION AND ANTIMICROBIAL RESISTANCE PATTERNS OF ESCHERICHIA COLI ISOLATES FROM GOATS SLAUGHTERED IN PARTS OF KENYA.

OBJECTIVE: To determine the antibiotic resistance patterns of pathogenic Escherichia coli on goat meat carcass at Huruma and Kiserian abattoirs in Kenya. DESIGN: Laboratory based study. SETTING: Huruma and Kiserian abattoirs in Kenya, SUBJECTS: 400 slaughtered goats inspected by veterinary health officers and approved for human consumption. METHODS: A Total of 400 slaughtered goats which were inspected by veterinary health officers and approved for human consumption were sampled from Huruma and Kiserian abattoir. Goat carcass swabs were collected by passing each swab tissue on four parts of the carcass mainly neck, right and left forelimbs, right and left hind limbs, and brisket. RESULTS: A total of 54 E. coli isolates were isolated and confirmed to be pathogenic. The percentage of isolates resistant to various microbial agents was recorded as follows: ampicillin (26 %), amoxycillin-clavulanic acid (17%), tetracycline (15%), chroramphenicol (4%), and ceftrixone (2% each). All Escherichia coli isolates were susceptible to gentamicin sulphamethaxazole-trimethomprin, kanamycin, cetriazididine (CAZ, 30pg), ciproxacin, nalidixic acid and chloramphenicol. Isolates were resistant to one or more of the antibiotics tested. Among the drugs tested, resistance was more frequently observed against ampicillin, amoxycillin-clavulanic acid, tetracycline, ceftrixone and chroramphenicol antibiotics. Among the isolates 26(48%) were positive for the stx1 gene, 19(35%) had the eae gene, 10(19%) possessed est gene,while 8(15%) harboured elt gene. Overall five isolates (10%) possessed aspu gene and two (4%) had aggR gene. No isolate possessed ipah gene. CONCLUSION: This study demonstrated that there is a significant level of antimicrobial resistance in pathogenic E. coli isolated from goat meat from Huruma and Kiserian abattoir. This indicates that goat meat from abattoirs could pose a risk of transmission of pathogenic antibiotic resistant strains to human. Poor hygienic standards and indiscriminate use of antimicrobials are the two main reasons for the presence of resistant pathogens in goat carcasses. RECOMMENDATIONS: Implemention of appropriate hygiene measures to control contamination of meat with pathogenic E. coli.

Bacterial diversity in the haloalkaline Lake Elmenteita, Kenya.

Lake Elmenteita is one of the alkaline saline lakes within the Kenyan Rift valley. The lake is situated on the floor of the Kenyan Rift Valley at 1,776 m above sea level and has no direct outlet. The microbial diversity of the lake was investigated using a culture-independent approach. Five different sampling points were selected randomly within the lake. Wet sediments and water samples were collected from each sampling point. In addition, dry mud cake was collected from three points where the lake had dried. DNA was extracted from the samples and the 16S rRNA genes amplified using universal primers for Bacteria. Thirteen clone libraries were constructed using the PCR amplified 16S rRNA genes. A total of 1,663 clones were picked. Representative clones were selected using ARDRA technique for sequencing. 655 partial and non-chimeric clone sequences indicated the presence of 37 orders in the Domain Bacteria. Cyanobacteria were the most abundant clones in terms of numbers whereas members of the phylum Firmicutes group were the second in terms of numbers but the most diverse in terms of genera represented. All clones affiliated to the class Betaproteobacteria originated from DNA obtained from the water samples. Analysis using BLAST showed that 93.1% of the sequenced clones had similarity values below 98% to both cultured and as yet uncultured bacteria, resulting in 596 phylotypes. Therefore, it can be concluded that Lake Elmenteita harbours phylogenetically diverse groups of bacteria involved in complex metabolic interactions within the Lake's ecosystem.

Reverse transcriptase inhibitors drug resistance mutations in drug-naive HIV type 1 positive Kenyans.

OBJECTIVE: To evaluate the extent of HIV-1 drug resistance among drug naive Kenyan individuals. DESIGN: Cross-sectional study. SETTING: Kenya Medical Research Institute HIV laboratory Nairobi, Kenya. SUBJECTS: A total of seventy eight HIV-1 positive drug naive subjects randomised from five Kenyan provincial hospitals between April and June 2004. RESULTS: A major non-nucleoside reverse transcriptase (NNRTI) an associated mutation was found in one patient (1.3%). NNRTI associated resistance mutations were present at amino acid codon sites G98A (2.56%); K103E (1.3%) and L100F (3.57%) prevalences. Baseline resistance may compromise the response to standard NNRTI-based first-line ART in 1.3 % of the study subjects. CONCLUSION: This indicates in general, that drug resistance among HIV-1 positive drug naive individual is at low thresholds (1.3%) but the problem could be more serious than reported here. Continuous resistance monitoring is therefore warranted to maintain individual and population-level ART effectiveness.

Isolation and characterisation of bacteria from the haloalkaline Lake Elmenteita, Kenya.

Culture-independent studies show that soda lake environments harbour diverse groups of bacteria and archaea. In this study different enrichment and isolation media were used in an attempt to isolate novel groups of bacteria from Lake Elmenteita. Different media were prepared using filter-sterilised water from the lake. The isolates recovered were purified on tryptic soy agar supplemented with 1% sodium carbonate and 4% sodium chloride. Phylogenetic analysis of 181 partial 16S rRNA gene sequences with excellent quality showed that the majority of the isolates were affiliated to the class Gammaproteobacteria and to the genus Bacillus. Isolates from the genus Halomonas and Bacillus constituted 37 and 31% of the total sequenced isolates, respectively. Other groups recovered were related to Marinospirillum, Idiomarina, Vibrio, Enterococcus, Alkalimonas, Alkalibacterium, Amphibacillus, Marinilactibacillus and the actinobacteria Nocardiopsis and Streptomyces. Fifty-one different genera were represented with 31 and 15 cultures scoring with their nearest neighbour similarities below 98 and 97%, respectively. Some novel taxa were identified which had not been isolated previously from the soda environment. The results show that the use of different media with varying compositions can help retrieve novel bacterial diversity from the soda lake environment.