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

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.

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Abstract

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.

Item Type: Thesis (Masters)
Creators:
CreatorsEmail
Abdul Khalid, Mohd Ikhmal HanifUNSPECIFIED
Divisions: Faculty of Pharmacy
Item ID: 18391
Uncontrolled Keywords: Genomics structure; Gram-negative bacterium; genome
Last Modified: 21 Feb 2019 07:37
Depositing User: Staf Pendigitalan 2
URI: http://ir.uitm.edu.my/id/eprint/18391

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