Dissecting the genomics structure of proteus mirabilis strain PR03 using whole genome sequencing approach / Mohd Ikhmal Hanif Abdul Khalid

Study background: Proteus mirabilis is a common Gram-negative bacterium which causes upper urinary tract infection and re-current infection. With cutting-edge technology such as whole genome sequencing, the genome sequence could be fully explored to understand its pathogenic and virulence genes. Thi...

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Main Author:	Abdul Khalid, Mohd Ikhmal Hanif
Format:	Thesis
Language:	English
Published:	2014
Online Access:	http://ir.uitm.edu.my/id/eprint/18391/ http://ir.uitm.edu.my/id/eprint/18391/2/TM_MOHD%20IKHMAL%20HANIF%20ABDUL%20KHALID%20PH%2014_5.pdf

id	uitm-18391
recordtype	eprints
spelling	uitm-183912019-02-21T07:37:55Z http://ir.uitm.edu.my/id/eprint/18391/ Dissecting the genomics structure of proteus mirabilis strain PR03 using whole genome sequencing approach / Mohd Ikhmal Hanif Abdul Khalid Abdul Khalid, Mohd Ikhmal Hanif Study background: Proteus mirabilis is a common Gram-negative bacterium which causes upper urinary tract infection and re-current infection. With cutting-edge technology such as whole genome sequencing, the genome sequence could be fully explored to understand its pathogenic and virulence genes. This study aims to provide better understanding on its mechanisms to invade, infect, colonize host epithelial cells and evade host immune system. Method: DNA of local clinical isolate of Proteus mirabilis strain PR03 was extracted and subjected to whole genome sequencing using the Illumina second generation sequencer, Genome Analyzer II (Illumina, California, USA). The genomic data was trimmed, analyzed, assembled and annotated using bioinformatics pipeline to identify genes that contribute to the pathogenicity and virulence of the strain. The genome was compared with P. mirabilis strain HI4320 to identify genes of similarities and differences. Results: The genome size of P. mirabilis strain PR03 is 3.9 Mbp with a G+C content of 38.6%. This strain has 3 465 genes and 53 RNA. Flagella, fimbriae, capsule, cell membrane, cell wall, urease, invasion proteins and stress respond genes were identified that contribute to the pathogenic and virulence factors of this strain. Genomes comparison showed this species has 56.25% of essential genes, 39.25% of dispensable genes and 4.47% of strain specific genes. Conclusion: P. mirabilis strain PR03 was successfully sequenced, assembled and annotated. 23.39% of P. mirabilis strain PR03 total genes were identified to contribute it pathogenicity and virulence. The genome sequences were successfully deposited in NCBI genomic database. 2014 Thesis NonPeerReviewed text en http://ir.uitm.edu.my/id/eprint/18391/2/TM_MOHD%20IKHMAL%20HANIF%20ABDUL%20KHALID%20PH%2014_5.pdf Abdul Khalid, Mohd Ikhmal Hanif (2014) Dissecting the genomics structure of proteus mirabilis strain PR03 using whole genome sequencing approach / Mohd Ikhmal Hanif Abdul Khalid. Masters thesis, Universiti Teknologi MARA.
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Teknologi MARA
building	UiTM Institutional Repository
collection	Online Access
language	English
description	Study background: Proteus mirabilis is a common Gram-negative bacterium which causes upper urinary tract infection and re-current infection. With cutting-edge technology such as whole genome sequencing, the genome sequence could be fully explored to understand its pathogenic and virulence genes. This study aims to provide better understanding on its mechanisms to invade, infect, colonize host epithelial cells and evade host immune system. Method: DNA of local clinical isolate of Proteus mirabilis strain PR03 was extracted and subjected to whole genome sequencing using the Illumina second generation sequencer, Genome Analyzer II (Illumina, California, USA). The genomic data was trimmed, analyzed, assembled and annotated using bioinformatics pipeline to identify genes that contribute to the pathogenicity and virulence of the strain. The genome was compared with P. mirabilis strain HI4320 to identify genes of similarities and differences. Results: The genome size of P. mirabilis strain PR03 is 3.9 Mbp with a G+C content of 38.6%. This strain has 3 465 genes and 53 RNA. Flagella, fimbriae, capsule, cell membrane, cell wall, urease, invasion proteins and stress respond genes were identified that contribute to the pathogenic and virulence factors of this strain. Genomes comparison showed this species has 56.25% of essential genes, 39.25% of dispensable genes and 4.47% of strain specific genes. Conclusion: P. mirabilis strain PR03 was successfully sequenced, assembled and annotated. 23.39% of P. mirabilis strain PR03 total genes were identified to contribute it pathogenicity and virulence. The genome sequences were successfully deposited in NCBI genomic database.
format	Thesis
author	Abdul Khalid, Mohd Ikhmal Hanif
spellingShingle	Abdul Khalid, Mohd Ikhmal Hanif Dissecting the genomics structure of proteus mirabilis strain PR03 using whole genome sequencing approach / Mohd Ikhmal Hanif Abdul Khalid
author_facet	Abdul Khalid, Mohd Ikhmal Hanif
author_sort	Abdul Khalid, Mohd Ikhmal Hanif
title	Dissecting the genomics structure of proteus mirabilis strain PR03 using whole genome sequencing approach / Mohd Ikhmal Hanif Abdul Khalid
title_short	Dissecting the genomics structure of proteus mirabilis strain PR03 using whole genome sequencing approach / Mohd Ikhmal Hanif Abdul Khalid
title_full	Dissecting the genomics structure of proteus mirabilis strain PR03 using whole genome sequencing approach / Mohd Ikhmal Hanif Abdul Khalid
title_fullStr	Dissecting the genomics structure of proteus mirabilis strain PR03 using whole genome sequencing approach / Mohd Ikhmal Hanif Abdul Khalid
title_full_unstemmed	Dissecting the genomics structure of proteus mirabilis strain PR03 using whole genome sequencing approach / Mohd Ikhmal Hanif Abdul Khalid
title_sort	dissecting the genomics structure of proteus mirabilis strain pr03 using whole genome sequencing approach / mohd ikhmal hanif abdul khalid
publishDate	2014
url	http://ir.uitm.edu.my/id/eprint/18391/ http://ir.uitm.edu.my/id/eprint/18391/2/TM_MOHD%20IKHMAL%20HANIF%20ABDUL%20KHALID%20PH%2014_5.pdf
first_indexed	2023-09-18T23:00:25Z
last_indexed	2023-09-18T23:00:25Z
_version_	1777418135531421696

Dissecting the genomics structure of proteus mirabilis strain PR03 using whole genome sequencing approach / Mohd Ikhmal Hanif Abdul Khalid

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