Ehsan Moglad posteradmin
A NOVEL MUTATION IN 16S RIBOSOMAL RNA GENES OF ESCHERICHIA COLI ISOLATED FROM CLINICAL SPECIMENS
Ahmed. S. Kabbashi1,2, Arwa M. Hassan1, Mohammed I. Garbi2 , Hisham N. Altayb3, Salah Eldin G Elzaki4, Ashraf Siddig Yousif 5,6 and Ehssan H. Moglad1*
1Department of Microbiology, Medicinal and Aromatic Plants and Traditional Medicine Research Institute (MAPTMRI), P.O. Box 2404, National Center for Research, Khartoum, Sudan.
2Department of Parasitology, Faculty of Medical Laboratory Sciences, International University of Africa. Khartoum, Sudan.
3Faculty of Medical Laboratory Science, Sudan University of Science and Technology, Sudan
4Department Epidemiology, Molecular Epidemiology Laboratory Biology, Tropical Medicine Research Institute, National Centre for Research, Khartoum, Sudan.
5Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge 02139 USA
6Department of Immunology and Biotechnology, Tropical Medicine Research Institute. National Centre for Research, Khartoum, Sudan
*Corresponding author: email@example.com
Background: New pathogens in clinical samples that are suspected to carry bacterial infection can be effectively characterized by sequence analysis of the rrs gene (16S rRNA).
Aim: this study aimed to characterize E. coli isolated from clinical samples (wound, urine and stool) by sequencing of the 16S rRNA E. coli strain.
Methods: Forty E. coli isolates were collected from different sites of infections (29 from urine culture, 2 from stool culture and 9 from wound infection), and identified using enrichment selective media and biochemical tests. Control strain in all procedures was E. coli (ATCC 25922). DNA was isolated from E. coli by Chelex® method and universal primers were used subsequently to amplify 16S rRNA genes through a conventional PCR technique. The amplified PCR product was sequenced by Macrogen Campany, Korea. The chromatogram sequences were visually analyzed using Finch TV program version 1.4. The similarity and identity of the nucleotide sequence from the isolated strains were compared sequences published in the NCBI database applying the local alignment search tool BLASTn. A Phylogenetic tree was generated via the Phylogeny.fr software.
Results: Sequencing revealed that isolates 76 and 77 contain a novel inserted G at position 884 (Domain II at the conservation region between the hypervariable region V and VI) of reference from France (FJ544921), China (KU156692), Portugal (JQ781608), Argentina (FJ997269), Korea (FJ4638197), China (FJ803886), USA (KF574802), Korea (FJ405334), Pakistan (KR822241) and Belgium (KJ016265).
Conclusions: This finding further supports considering and adopting 16S rRNA sequence’s analysis as a powerful method for the identification and investigation of phylogenetic relationships among bacterial isolates in particular medically important bacteria. It also raises the important issue whether conserved regions are totally conserved or not, which has implications for the use of 16S rRNA as biomarker.