Characterization of multi-drug resistant salmonella using long read genome sequencing
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Date
2022-01-19
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Kamuzu University of Health Sciences
Abstract
Introduction
Salmonella Typhimulium is a Gram negative bacteria of the Enterobacteriaceae family that has
been reported to cause an epidemic of invasive non-typhoidal Salmonella disease. The strain
responsible is reported to be sequence type ST313. From the data gathered ST313 encodes the
gene ctx-m-15 which is responsible for production of an extended spectrum beta lactamase
enzyme. Since the introduction of sequencing technologies the data about bacterial genomes has
been generated at a rapid pace owing to the fact that second and third generation sequencing
technologies have improved and enhanced the analysis of bacterial genome sequence data. Third
generation sequencing technologies have provided long reads which have enabled whole genome
sequencing for both prokarytotes which includes Salmonella Typhimurium and eukaryotic
genomes.
Methodology
This is a retrospective study that’s looking at one sample and sample analysis will begin with
genome assembly, then polishing and annotation of the gene of interest will be done. The data in
the form of gff files will be visualized on artemis and location of the gene will be established.
Objectives
Providing the location of the ctx-m-15 will tell us whether the production of the enzyme ESBL
has been established and stabilized within the pathogen. Research has shown this Salmonella
Typhimurium ST313 to have ctx-m-15 gene with illumna sequencing, however; the location is
not known. Therefore the aim of this study is to locate the position of the gene with regard to its
stability within the genome of the pathogen.
Specific objectives
1. To perform assembly of Salmonella Typhimurium ST313 disjointigs through De novo
genome assembly using the long reads to come up with contigs that facilitate a
complete genome from the disjointigs.Identify drug resistant genes for Salmonella Typhimurium ST313 through database
that will locate points of mutations within the long reads genome.
3. Identify the location of ctx-m-15 gene for Salmonella Typhimurium ST313 genome
through annotation of the genome by using a database that will allow the location of
the gene to be identified on the contigs of the pathogen.
Expected Outcomes
The study will help in understanding of the evolution of the strain of Salmonella Typhimurium
ST313 and be able to trace evolution of new clade of the organism since it is suggested that the
organism is going through a phase of evolutionary bottleneck. Though the results of the project
may not be conclusive, but they will provide insightful knowledge on how ST313 is evolving of
which this could be used by big projects on a larger scale.