Question

I am interested in antibiotic resistance. How might I identify all genes that contribute to resistance to a given antibiotic in a particular isolate of bacteria all at once, using an approach that involves illumina sequencing? (note – this is not simply by genome sequence analysis – it’ll take a more complex experiment coupled to sequencing).

Answer 1

Illumina sequencing is a next generation sequencing technique that is being widely used recently to study the antibiotic resistant genes in the bacterial cells. The overview of the steps that might be used to study the antibiotic genes are:

• Growing the bacterial cell containing all the antibiotic genes in selective media
• Isolation of a colony and extraction of the DNA from the culture by WGS-AST method or any simple DNA extraction method
• The extracted DNA is used then to create a gene pool and create a library by adapter attachments
• Cluster generation and multiplication or amplification of the DNA library to study
• Then shotgun sequencing can be done with higher accuracy by using smaller fragments of the amplified DNA. A better way is using one base at a time to sequence.
• The genomes can be assembled and then imaged in order to study the specific sights and sequences of the antibiotic resistance genes found in the bacterial genome. Illuma sequencing uses basecalls or reads to study the sequenced genome.