Typing of Salmonella Typhi strains isolated from Egypt by RAPD PCR

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.

Molecular techniques for detecting and typing of bacteria, advantages and application to foodborne pathogens isolated from ducks

“…This process leads to the amplification of one or more DNA sequences and generates a set of finger printing patterns of different sizes specific to each strain (Farber 1996, Trindade et al 2003). The advantages of RAPD are that, it is relatively cheap, rapid, readily available, and easy to perform (Wassenaar and Newell 2000; Shi et al 2010; Rezk et al 2012). In RAPD, the efficiency of amplification, annealing and the length of the product varies with the primed sites, giving rise to both weak and strong amplicons which make interpretation of the results difficult (Wassenaar and Newell 2000).…”

Molecular typing of Salmonella from Sergipe, Northeastern Brazil, showing the epidemiological relationship between poultry and human infection

“…It does not require any previous knowledge of the DNA sequence of the target organisms, and results in simpler, low-cost, and rapid detection of the genetic variations present in isolated samples (Colauto et al, 2002;Ruiz et al, 2003;Santos and Bäumler, 2004). RAPD has been used as a tool to trace Salmonella epidemiologically, to distinguish Salmonella strains from different geographical origins, and for complementing serotyping and phage typing methods (Soto et al, 1999;De Cesare et al, 2001;Quintaes et al, 2002;Lim et al, 2005;Smith et al, 2011;Rezk et al, 2012).…”

Genotyping of Salmonella strains isolated from ducks, their rearing and processing environments in Penang, Malaysia, using RAPD

“…and their outbreak investigations largely depend on efficient isolation, detection and typing methods. A wide range of molecular typing methods have been used to study the genetic relatedness or diversity of bacterial pathogens and even plants (Wassenaar and Newell 2000 ; Elmeer et al 2011 ; Adzitey et al 2012c , d ; Rezk et al 2012 ; Tripathi et al 2012 ). Genotyping methods such as pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), random amplified polymorphic deoxyribonucleic acid (RAPD), enterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic palindromic (REP), are among those routinely used to type Salmonellae to study their genetic diversity or relatedness (Chansiripornachai et al 2000 ; Khoodoo et al 2002 ; Lim et al 2005 ; Albufera et al 2009 ; Smith et al 2011 ; Noble et al 2012 ).…”