Abstract
We investigated the 16S-23S rRNA intergenic spacer region (ISR)-PCR and the phylogenetic PCR analyses of 150 Escherichia coli isolates as tools to explore their diversity, according to their sampling origins, and their relative dominance in these sampling sources. These genetic markers are used to explore phylogenetic and genetic relationships of these 150 E. coli isolates recovered from different environmental sources (water, food, animal, human and vegetables). These isolates are tested for their biochemical pattern and later genotyped through the 16S-23S rRNA intergenic spacer PCR amplification and their polymorphism investigation of PCR-amplified 16S-23S rDNA ITS. The main results of the pattern band profile revealed one to four DNA fragments. Distributing 150 E. coli isolates according to their ITS and using RS-PCR, revealed four genotypes and four subtypes. The DNA fragment size ranged from 450 to 550bp. DNA band patterns analysis revealed considerable genetic diversity in interspecies. Thus, the 450 and 550bp sizes of the common bands in all E. coli isolates are highly diversified. Genotype I appeared as the most frequent with 77.3% (116 isolates), genotype II with 12% (18 isolates); genotype III with 9.7% (14 isolates), and the IV rarely occurred with 4% (2 isolates). Distributing the E. coli phylogroups showed 84 isolates (56%) of group A, 35 isolates (23.3%) of group B1, 28 isolates (18.7%) of group B2 and only three isolates (2%) of group D.
Highlights
Escherichia coli is associated with a variety of intestinal diseases in humans and animals (Fröhlicher et al, 2008; Martinez-Medina and Garcia-Gil, 2014)
This study was conducted between January and July 2012, and 150 E. coli isolates are collected from various biotopes, distributed: 22 from animal organs and meats, 21 from varied kinds of soil, 45 from different types of water, 16 from feces of varied animals, 27 from different foods, 5 from humans, and 14 from different nosocomial and abattoir environment
Distributing the phylogroups of 150 E. coli isolates showed that 84 strains belonged to group A (56%), including subgroups A1 (37, 24.7%) and A0 (47, 31.3%), and 35 strains (23.3%) belonged to the phylogroup B1 (Figure 1, Table 2)
Summary
Escherichia coli is associated with a variety of intestinal diseases in humans and animals (Fröhlicher et al, 2008; Martinez-Medina and Garcia-Gil, 2014). The recently developed DNA fingerprinting method is based on the repeated intergenic consensus sequence (ERIC) of intestinal bacteria, and has described repeated foreign palindrome (REP) and BOX elements for distinguishing bacterial strains (Xin Wang et al 2015; Tacao et al 2005). The length polymorphism in the internal transcription spacer (ITS) of 16 S-23S ribosomal DNA is a stable genetic marker for studying bacterial phylogeny. RRNA (and rRNA genes) are highly conserved, nucleotide variation between rDNA sequences is usually large enough to be used to estimate the relationship between bacterial phylogenetic profiles (Gutellet et al 1994). We used 16S-23S ITS genetic markers to study the phylogenetic relationships of some E. coli strains isolated from various environmental biomes (water, animals, humans, and vegetables). The relationship between these E. coli isolates and their system group members and their origins will be studied
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