Microbial genomics exercise
EX03: What sequence type is the genome?
In addition to species identification, sequence typing is commonly used in clinical microbiology to compare isolates and support outbreak investigations.
Multilocus Sequence Typing (MLST) assigns isolates to a sequence type (ST) based on the allelic profiles of a defined set of housekeeping genes.
The assembled genomes are available in:
/home/projects/microbial_genomics/ex02_assemblies
Run the MLST tool to determine the sequence type of each genome.
Start by inspecting the available options:
mlst.sh -h
Then run MLST on the genome assemblies:
mlst.sh /home/projects/microbial_genomics/ex02_assemblies/*.fna
Questions:
- What MLST scheme is used for each genome?
- What sequence type (ST) is assigned to each isolate?
- Are all genomes assigned to the same ST?
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EX04: Which antimicrobial resistance genes are present?
Detection of antimicrobial resistance (AMR) genes is an important part of microbial diagnostics.
The tool ABRicate can be used to screen genome assemblies against curated resistance gene databases.
Run ABRicate on the assembled genomes using a resistance gene database.
First, inspect the available options and databases:
abricate.sh -h abricate.sh --list
Then screen the genomes using the ResFinder database:
abricate.sh --db resfinder /home/projects/microbial_genomics/ex02_assemblies/*.fna
Questions:
- Which antimicrobial resistance genes are detected in each genome?
- Are the resistance profiles identical across the isolates?
- Based on the detected genes, which antibiotic classes might be ineffective?
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Whole-genome comparisons are frequently used to assess the relatedness of bacterial isolates, for example during suspected outbreaks.
The tool Parsnp performs core-genome alignment and identifies single nucleotide polymorphisms (SNPs) between closely related genomes.
Use Parsnp to compare the assembled genomes.
First, view the help information:
parsnp.sh -h
Then run Parsnp using one genome as the reference:
parsnp.sh -r /home/projects/microbial_genomics/ex02_assemblies/genome1.fna \
-d /home/projects/microbial_genomics/ex02_assemblies \
-o $HOME/parsnp_out
Parsnp produces a core-genome alignment and a phylogenetic tree.
Questions:
- How many SNPs separate the isolates?
- Do the genomes cluster closely together?
- Based on the results, do the isolates appear to be clonally related?
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Summary
In this exercise you have:
- Identified the species of bacterial genomes using GTDB-Tk
- Determined sequence types using MLST
- Screened for antimicrobial resistance genes using ABRicate
- Assessed genomic relatedness using Parsnp
Together, these analyses reflect a typical bioinformatics workflow used in microbial diagnostics and epidemiological investigations.