Identify AMR genes from WGS bacterial sequence

Question

[bioinforesearchquestions]

Hi folks,

I have the WGS data from Illumina for a bacterial strain. I would like to do the following task,

• Compare the sequence of B. mayonii to other bacterial sequences that are deposited in NCBI. We are interested in knowing how the sequence of this strain compares to other Borrelia
• Determine if there are any AMR genes encoded on a plasmid.

How to accomplish both these tasks?

Any suggestions and relevant papers are welcomed.

Answer 1

[ctseto]

"Compare the sequence of B. mayonii to other bacterial sequences that are deposited in NCBI" De novo assembly (SPAdes or Megahit with appropriate read QCing), followed by similar annotation techniques as those in the B. mayonii paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5193363/pdf/pone.0168994.pdf); though in the latter case they benefit from a long read platform. Not familiar with the genome topology or the assembly graph of Borrelia, but hopefully it's straightforward.

"Determine if there are any AMR genes encoded on a plasmid."

In re AMR genes in a fasta I've been evaluating Abricate (https://github.com/tseemann/abricate ); in your case a positive control against existing Borrelia strains to see if it picks up everything you expect it to may be a useful first step.