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GG3 Lab Report

This document summarizes an experiment that involved isolating and sequencing the genome of a strain of Pseudomonas aeruginosa to analyze its antibiotic resistance. DNA was extracted from the bacteria and sequenced using various computational tools. The genome was then annotated and analyzed to identify genes associated with antibiotic resistance as well as other phenotypes such as biofilm formation and fluorescent markers.

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Wulfrun Godson
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22 views

GG3 Lab Report

This document summarizes an experiment that involved isolating and sequencing the genome of a strain of Pseudomonas aeruginosa to analyze its antibiotic resistance. DNA was extracted from the bacteria and sequenced using various computational tools. The genome was then annotated and analyzed to identify genes associated with antibiotic resistance as well as other phenotypes such as biofilm formation and fluorescent markers.

Uploaded by

Wulfrun Godson
Copyright
© © All Rights Reserved
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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Genome sequencing and analysis of antibiotic resistance in a strain of Pseudomonas aeruginosa

Abstract (150)

Introduction (200)

Methods, Core Data and Species Identification (600)

Methods

This experiment involved the isolation and purificication of P. aeruginosa chromosomal DNA and
construction of a genome sequencing library in accordance with a protocol provided by the
University of Edinburgh (Guschanski, 2022). The resulting raw data was assessed for quality then the
genome was assembled, annotated and analysed using a variety of computational tools.

Pseudomonas aeruginosa cells were cultured, lysed and stored before DNA extraction. RNAs were
removed from the cell debris as if sequenced, these would only characterise the transcribed regions
of the genome and some genes would be overrepresented; removal was carried out using an RNase
treatment followed by cleaning of the DNA (Schulthaus et al., 2019). DNA was extracted from the
sample using a Qiagen DNaeasy Blood and Tissue Kit (Ayana et al., 2019); the integrity of the DNA
was then tested with gel electrophoresis and the concentration was determined using a Qubit
Fluorimiter.

- Protocol
(Guschanski, 2022)
- Qiagen DNaesy Blood and Tissue Kit
(Ayana et al., 2019)
- ZymoResearch Genomic DNA Clean & Concentrator
(Schultzhaus et al., 2019)
- NextERA XT Tagmentation Illumina sequencing library kit
(Sato et al., 2019)

Antibiotic Resistance/Sensitivity (500)

Fluorescent Markers (50)

Biofilm Formation and Regulation (350)

Summary and Conclusions (150)

Ayana, M., Cools, P., Mekonnen, Z., Biruksew, A., Dana, D., Rashwan, N., Prichard, R., Vlaminck, J.,
Verweij, J. and Levecke, B., 2019. Comparison of four DNA extraction and three preservation
protocols for the molecular detection and quantification of soil-transmitted helminths in
stool. PLOS Neglected Tropical Diseases, 13(10), p.e0007778.

Guschanski, K., 2022. Genomes and Genomics 3 Practical Manual 2022 - Wet lab protocols.

Sato, M., Ogura, Y., Nakamura, K., Nishida, R., Gotoh, Y., Hayashi, M., Hisatsune, J., Sugai, M.,
Takehiko, I. and Hayashi, T., 2019. Comparison of the sequencing bias of currently available
library preparation kits for Illumina sequencing of bacterial genomes and metagenomes. DNA
Research, 26(5), pp.391-398.
Schultzhaus, J., Taitt, C., Orihuela, B., Smerchansky, M., Schultzhaus, Z., Rittschof, D., Wahl, K. and
Spillmann, C., 2019. Comparison of seven methods for DNA extraction from prosomata of the
acorn barnacle, Amphibalanus amphitrite. Analytical Biochemistry, 586, p.113441.

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