how to determine the gene involved in antibiotic resistance?

Question

[sharmilla_487]

My project is to test the antibiotic susceptibility of abscessus strains, and then use WGS to find for the genes that cause the resistance. Here is where i got stuck as i have 0 knowledge in bioinformatics =(. I have used CARD, ARG ANNOT and Resfinder to blast my WGS. They all give me a long list of possible AR genes with various e value and bit score. How do i move from here?

I have aligned probable resistant gene (Ex: gyr A) sequences in MEGA6, to see if there are any difference between the Resistant and Susceptible strains.20 strains all together. I can't see any clear pattern between the resistant and susceptible strains by comparing their amino acid sequences. Where did i go wrong?

[GenoMax]

I can't see any clear pattern between the resistant and susceptible strains by comparing their amino acid sequences. Where did i go wrong?

What kind of pattern are you referring to? Sensitive/resistant strains not forming blocks with identical AA changes? Perhaps gyrA gene is not involved in antibiotic resistance in these strains.

Answer 1

[swbarnes2]

You will never be able to prove with electronic data alone what mutation is granting resistance. You can investigate, and see if any of the mutated genes have been shown by someone else to grant resistance. And, you can give the ranked list of mutations to the biologist, and they do wet lab work, like knocking in a mutation to a sensitive strain, to see if the mutation grants resistance.

Answer 2

[Hussain Ather]

Have you looked at this database? https://ardb.cbcb.umd.edu/documentations.shtml