Abstract
PCR-based fingerprinting using random amplified polymorphic DNA (RAPD) has been used widely for genome identification. In this study, 13 Salmonella Typhi strains were isolated from typhoid patients from Aswan, Cairo, Fayoum, and Monofya Governorates of Egypt. The isolates, along with three reference strains, i.e., O901, H901, and Ty2 were subjected to whole genome typing by RAPD PCR. Three RAPD-PCR 10-mer primers generated a total of 85 RAPD bands (81 polymorphic bands), 12 distinct PCR profiles, and proved to be useful for discriminating the isolates and strains studied. Interestingly, the B1 and C1 PCR profile were found only in Cairo and Monofya, respectively; and some PCR types appeared only in certain Governorates of Egypt. By combining the profiles obtained with the primer trio used in this study, an excellent discrimination index (D) of 0.942 was reached. Pairwise comparisons of Jaccard’s similarity coefficients calculated among the 12 PCR types identified three major clusters; i.e., O901 branch and Ty2 and H901 sub-branches. Principal component analysis adequately resolved each of these three major clusters. Three principal components accounted for about 72% of the variation, with the first two components accounting for about 62% of the total variance among the genotypes studied. Biclustering improved the display of groups of RAPD amplicons (markers) that cluster similarly across the genomes and could delineate features pertaining to genome structure. In conclusion, RAPD PCR provided a fast method with high potentials in surveillance and epidemiological investigations of Salmonella Typhi infections.
Highlights
Typhoid fever is a systemic infection with the bacterium Salmonella enterica serotype Typhi
The objective of this study is to develop a simple, easy to interpret, and low cost random amplified polymorphic DNA (RAPD)-based method, for typing Salmonella Typhi isolated from Egyptian patients suffering from typhoid fever
Out of the nine primers tested, only three primers, i.e., B02, E10, and E18 were suitable for discrimination (Table 2)
Summary
Typhoid fever is a systemic infection with the bacterium Salmonella enterica serotype Typhi. This fever is an important cause of illness and death with a global occurrence of 21.6 million infections and about 200,000 deaths from typhoid fever per year (Bhutta 2006). A concerning prevalence of multidrug-resistant Salmonella Typhi (29%) was reported (Srinkantiah et al 2006). Salmonella Typhi has evolved a genetic mechanism for the expression of virulence genes located at pathogenicity islands in the bacterial genome. As revealed by sequencing and microarray analyses, the genome of Salmonella Typhi accumulated many pseudogenes (McClelland et al 2004)
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