Abstract
Molecular epidemiology of human ecovariants of Escherichia coli from different regions of Nigeria were studied using their antibiotic susceptibility patterns, plasmid profile and DNA microarray techniques. E. coli was isolated using Eosin Methylene Blue agar (EMB) and identified by conventional microbiological technique. The isolates were tested against 14 antibiotics using the disc diffusion method. Genotyping was done using DNA microarray. Overall, 42 different antibiotics resistance clusters were observed, with each isolate showing resistance to at least four or more drugs tested. Of the 60 isolates genotyped with DNA microarray, 57 were identified as having, at least, one antimicrobial resistance gene. Among the 90 antibiotic resistance genes detected, bla-CMY-2 was the most prevalent occurring in 38 (63.3%) of the isolates. Other highly prevalent genes occurring in the human isolates, include strA 28(70%) aadE 28(70%); TEM1 11(27.5%); Sul2 14(35%); andTetA 21(52.5%). The microarray genotyping corresponded with the phenotype of the strains. Presence of drug-resistance genes/plasmids in commensal strains isolated from apparently healthy individuals is of great public health importance. Key words: DNA microarray, E. coli, Nigeria.
Highlights
The large-scale genome sequencing effort and the ability to immobilize thousands of DNA fragments on a surface, such as coated glass slide or membrane, have led to the development of DNA microarray technology (Cassone et al, 2006)
An entire microbial genome can be represented in a single array, making it feasible to perform genome-wide analysis (Ye et al, 2006) The two common applications of DNA microarray technology in molecular biology are the exploration of genome-wide transcripttional profiles and the measurement of the similarities or differences in genetic contents among different microbes (Peterson et al, 2010)
The sequence identity of each gene was compared with GenBank sequences, all the 90 genes were used to construct the DNA microarray; biotin was used as the positive control and 16s rDNA as orientation
Summary
The large-scale genome sequencing effort and the ability to immobilize thousands of DNA fragments on a surface, such as coated glass slide or membrane, have led to the development of DNA microarray technology (Cassone et al, 2006). An entire microbial genome can be represented in a single array, making it feasible to perform genome-wide analysis (Ye et al, 2006) The two common applications of DNA microarray technology in molecular biology are the exploration of genome-wide transcripttional profiles and the measurement of the similarities or differences in genetic contents among different microbes (Peterson et al, 2010). DNA microarray technology is being used to study many bacterial species ranging from standard laboratory strains and pathogens to environmental isolates (Murakami et al, 2002). DNA microarrays are basically a miniaturized form of dot blot, but in a high-throughput format. A DNA microarray experiment consists of array fabrication, probe preparation, hybridization and data analysis (Call et al, 2001). The basic array technology is the same, there are fundamental differences in its application to prokaryotes and eukaryotes
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