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 550 bp. DNA band patterns analysis revealed considerable genetic diversity in interspecies. Thus, the 450 and 550 bp 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.
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Acknowledgements
The authors are grateful to the University of Tunis El Manar for providing partial financial support. This study is output Research Program Contract (2015–2018) titled 'Study of bio-filtration and UV disinfection for the simultaneous elimination of pathogenic bacteria, enteric viruses, nitrates and phosphates from wastewater', funded by the Tunisian Ministry of Higher Education and Scientific Research and Technology. Thanks to experimental CERTE and IRVT staff for their help during the experimentation.
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SB analyzed and interpreted the patient data. RWA major contributor in writing the manuscript, and was a corresponding author, MSA major contributor in E. coli strain selection, MS analyzed the strain characterization, PC, ML and BC a major contributor in molecular analysis, AH a major contributor in writing the manuscript. All authors read and approved the final manuscript.
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Badi, S., Ammeri, R.W., Abbassi, M.S. et al. Study of the diversity of 16S–23S rDNA internal transcribed spacer (ITS) typing of Escherichia coli strains isolated from various biotopes in Tunisia. Arch Microbiol 204, 32 (2022). https://doi.org/10.1007/s00203-021-02684-x
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DOI: https://doi.org/10.1007/s00203-021-02684-x