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 β-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 % and 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

Phylogenetics in plant biotechnology: principles, obstacles and opportunities for the resource poor

Phylogenetic inference has become routine for most studies of genetic variation among plant taxa. However, inferring phylogenies can be confounded by both biological and computational or statisticalcomplexities, resulting in misleading evolutionary hypotheses. This is particularly critical because the “true tree” can only truly be known in exceptional circumstances. Moreover, selecting appropriatemarker(s), characters, sample sizes and the appropriate reconstruction methods offers a challenge to most evolutionary geneticists. Textbooks are generic (and sometimes outdated), and in resource poor labs, they may altogether be inaccessible. In this review, we take the worker through the low-down on reconstructing a phylogeny, review the enigmatic biological and computational problems, and examine cases where cheaper markers and extremely small sample sizes can recover a reliable phylogeny

Localizing genes using linkage disequilibrium in plants: integrating lessons from the medical genetics

Finding genes controlling quantitative traits will aid molecular breeding for crops and livestock with superior yields, growth rates, and evolutionary potential. Such genes can be located using thecandidate gene approach, genome wide scans, or by within family mapping. Linkage disequilibrium (LD) or association mapping, is a candidate gene approach that relies on detecting a statisticalassociation between the desired quantitative trait and a molecular marker allele. This approach is emerging as a leading tool for precise estimation of QTL positions, because it offers several advantages over family-based mapping: LD mapping detects associations with greater resolution, the associations detected are relevant population wide, and in plants, the use of natural populations would circumvent the need to raise large controlled crosses. However, LD approach is facing obstacles, with well over 60% of studies reporting associations in the medical genetics disapproved in subsequent tests. A large proportion of these false associations (or lack of it) result from population stratification, while the rest may be caused by other demographic and evolutionary processes that create a statistical association between a marker allele and the trait, such as bottlenecks, natural selection, hybridization and genetic drift. The problem is expected to escalate in plants, owing to the complex population structures. Regardless of the many recent methods that purport to take into account populationstratification during association tests, we discuss the reasons why in plants, a priori knowledge of population structures is essential in any robust association analysis

Comparative performance of Anigen © FMD NSP Ab ELISA (Korea), NSP Priocheck® kit, liquid phase blocking ELISA kits and virus neutralisation tests in the detection of foot and mouth disease virus antibodies in animals sera from Kilifi county, Kenya

Background: Foot and mouth disease (FMD) is a highly contagious viral infection of hoof cloven animals. Performance of serological tests used for FMD is faced with challenges like low test sensitivity, low tests agreement levels, in concise test cut-offs, cost of the tests and numerous FMD serotypes which may lead to misdiagnosis.Objective: To determine the sensitivity of assays Anigen © FMD NSP Ab ELISA –Korea, NSP Priocheck® kits with Liquid Phase Blocking Enzyme Linked Immunosorbent Assay compared with Virus neutralisation test ( the gold standard).Design: A cross-sectional study design.Setting: Kilifi County.Subjects: Four hundred and twenty one cattle.Results: The results showed that both Anigen © FMD NSP Ab ELISA (Korea), NSP Priocheck® Netherlands assays had low sensitivity but high specificity. Liquid Phase Blocking ELI SA had the highest sensitivity 100%. LPBE had a Positive Predictive Value (PPV) =100%, Anigen © FMD NSP Ab ELISA–Korea 94.44% and NSP Priocheck® Netherlands had the lowest 44.74% compared with the VNT 100%. The Cohen's kappa coefficient showed a perfect agreement level of 90%, 93%, 100 and 100% respectively.Conclusion: This study showed no significant difference in sensitivity and both structural and non-structural proteins tests should always be used concurrently

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,30ìg), 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.Key words: Escherichia. coli pathotypes, Antibiotic resistance, Goat meat, Abattoir

Chemical composition and antimicrobial activity of the essential oil of Ocimum gratissimum L. growing in Eastern Kenya

Hydro-distilled volatile oils from the leaves of Ocimum gratissimum L. (Lamiaceae) from Meru district in Eastern Kenya were analysed by gas chromatography-mass spectrometry (GC-MS) and also evaluatedfor antimicrobial activity. The oil was dominated by monoterpens which accounted for 92.48%. This monoterpene fraction was characterized by a high percentage of eugenol (68.8%). The other major monoterpenes were methyl eugenol (13.21%), cis-ocimene (7.47%), trans-ocimene (0.94%), -pinene (1.10%) and camphor (0.95%). The sesquiterpenes present in fairly good amounts were germacrene D(4.25%) and trans-caryophyllene (1.69%). The minor  sesquiterpenes were -farnesene (0.85%) and -bisabolene (0.74%). The antimicrobial activities of the essential oils were evaluated against both Gram positive (Staphylococcus aureus, Bacillus spp.) and Gram negative (Escherichia coli, Pseudomonasaeruginosae, Salmonella typhi, Klebisiella pneumoniae, Proteus mirabilis) bacteria and a pathogenic fungus Candida albicans. The oil had pronounced antibacterial and antifungal activities on all themicrobes

Characterization of Kenyan sweet potato genotypes for SPVD resistance and high dry matter content using simple sequence repeat markers

Simple sequence repeat (SSR) markers were used to characterize Kenyan sweet potato genotypes for resistance to the sweet potato virus disease (SPVD) and high dry matter content. Eighty nine (89)genotypes with a mean symptom severity score of between 1 and 1.5 were selected following graft inoculation with SPVD-infected scions and characterized using 6 SSR primers. The 6 SSR primer pairshad an average polymorphic information content (PIC) of 0.47. The average number of alleles within the 89 genotypes across the 6 loci was 13.52. Cluster analyses revealed a 50% variation among the 89genotypes. The dendrogram did not reveal any unique clustering of the genotypes according to dry matter content and reaction to SPVD. The genetic differences among the SPVD resistant genotypes andthose with high dry matter revealed by the distinct groups suggest a significant genetic variability and the presence of different sources of resistance to SPVD and high dry matter. This characterization willgive valuable information for breeders and serve as a baseline for efficient development of new cultivars resistant to SPVD and containing high dry matter

Leaf storage conditions and genomic DNA isolation efficiency in Ocimum gratissimum L. from Kenya

Storage of plant tissues for DNA is important to avoid degradation of DNA. Preliminary studies were conducted on Ocimum gratissimum L. in order to establish the storage conditions for the collected samples before DNA extraction. Secondly, the aim was to determine the best protocol for the extraction of high quality DNA, which would later be used for molecular analysis. DNA was extracted from thesamples one month after field sampling. During the DNA extraction, four protocols were used; the modified hexadecyltrimethyl ammonium bromide (CTAB) mini preparation method described by Doyleand Doyle (1990), with reductants either mercaptoethanol or dithiothreitol; the modified sodium dodecyl sulphate (SDS) mini preparation method of Edwards et al. (1991) with redundant either mercaptoethanol or dithiothreitol. The DNA was purified, treated with RNase, quantified and examined for intactness using gel electrophoresis method. Good quality and high yield DNA  could only be extracted with the buffer containing the detergent SDS and the reducing agent dithiothreiotol

Genetic diversity and population structure of the endangered Namaqua Afrikaner sheep

The Namaqua Afrikaner is an endangered sheep breed indigenous to South Africa, primarily used in smallholder farming systems. Genetic characterization is essential for the breed’s conservation and utilization. In this study, a genetic characterization was performed on 144 Namaqua Afrikaner sheep kept at the Karakul Experimental Station (KES), Carnarvon Experimental Station (CES), and a private farm Welgeluk (WGK) using 22 microsatellite markers. The mean number of alleles observed was low (3.7 for KES, 3.9 for CES, and 4.2 for WGK). Expected heterozygosity values across loci ranged between 46 % for WGK, 48 % for KES, and 55 % for CES, indicating low to moderate genetic variation. The analysis of molecular variance revealed that 89.5 % of the genetic variation was due to differences within populations. The population structure confirmed the differentiation of three clusters with high relationships between the CES and WGK populations. In the population structure comparison with Pedi and South African Mutton Merino sheep, limited hybridization between the Namaqua Afrikaner sheep and both of these breeds was observed. The results of this study will serve as a reference for genetic management and conservation of Namaqua Afrikaner sheep.Department of Agriculture, Forestry and Fisherieshttp://www.springerlink.com/content/0049-4747hb201