Species-specific phenotype for gene

[Former user]

Thanks for the great tool.

Some genes only exhibit a phenotype in a specific species. For example, OXA-2 in Acinetobacter baumannii displays carbapenem resistance vs in E. coli does not: https://journals.asm.org/doi/10.1128/AAC.02522-13

Is it possible to do this with ResFinder? If not, would appreciate if you could add this feature...thanks!

[CGE Helpdesk]

Dear Mr./Mrs.

Thank you for your interest in ResFinder.

I believe what you are asking is possible within ResFinder. If you add the -s flag and specify the species, you will get two pheno_table outputs. The first one is the regular pheno_table.txt containing all antimicrobials while the second one, pheno_table_species_name.txt, will only contain the antimicrobials relevant for the selected species.

Best Regards

Maja, CGE Helpdesk