Lanterna Rally

Author: Theodore Ngwana

Publisher: GRIN Verlag

Published: 2018-02-05

Total Pages: 29

ISBN-13: 3668630100

Scientific Essay from the year 2018 in the subject Medicine - Diagnostics, University of Salford (College of Science and Technology), course: Msc Biomedical Science, language: English, abstract: Next Generation Sequencing, one of the applications of genomics, employs bioinformatics tools and other molecular biology techniques such as the Polymerase Chain Reaction (PCR) and electrophoresis to diagnose diseases. Once sequenced, our assembled genome sequenced can be annotated to identify target genes and compared to a reference genome for similarities such as the case of BLAST, which is used to establish evolutionary relationships between species. The sequences can also be compared for variants. In this report Illumina-based next generation sequencing was used to sequence the genomes of three Staphylococcus aureus strains which are the methicillin resistant strain (MRSA), methicillin sensitive strain (MSSA) and an unknown strain of S. aureus (U). This involved an array of techniques, from the extraction of genomic DNA by way of the QIAGEN DNeasy DNA extraction kit, to quality control of our purified DNA by 1% agarose gel electrophoresis, Nanodrop and Qubit. It then moved on to preparation of DNA libraries from our genomic DNA extract, with the QIAGEN® QIAseq FX DNA Library Kit, from where the libraries went through an Illumina MiSeq sequencer. Raw sequence data was then assembled and analysed with genome annotation tools such as Atermis, Artemis Comparison Tool, WGSA and Abricate. Annotation of our S. aureus species revealed antimicrobial resistance genes. Abricate produced 10 antimicrobial genes for MRSA, 5 for MSSA and 6 for U. Meanwhile Artemis annotation gave 16 antimicrobial resistance genes for MRSA, 13 for MSSA and 14 for U. Information on antibiotic susceptibility of the three bacterial species can then be used to determine the best possible treatment for individuals with S. aureus infections, thus proving that next generation sequencing and genome annotation can serve as an alternative for routine disc antimicrobial susceptibility techniques to diagnose and treat infectious diseases.