No Klebsiella panel found in Pointfinder db?

[Former user]

Hi there,

I have been trying to run resfinder along with the Pointfinder db option but this won't work for Klebsiella spp. Is it a matter of adding a Klebsiella panel to the phenotype_panel.txt file in the resfinder_db?

Thanks, Ann-Marie

[Edison Alain von Matt]

Dear Ann-Marie,

Thank you for your message.

We currently do not have a panel for the Klebsiella species, which is why it is not defined in the file phenotype_panels.txt.

It is still possible to run the Pointfinder service for Klebsiella species to detect chromosomal mutations predictive of drug resistance for all antimicrobial drugs. The missing panel only means we have not defined a specific selection of drugs relevant to Klebsiella.

The script should actually display a warning message if Klebsellia is specified but still terminate successfully.

Do you receive a result?

Best regards
Eddy

[Ann-Marie Keane]

Hi Eddy,

Thanks for your reply. Unfortunately it falls over when Klebsiella is specified with the following error:

Traceback (most recent call last):
File "/usr/local/lib/python3.8/dist-packages/resfinder/run_resfinder.py", line 533, in <module>
sys.exit(main())
File "/usr/local/lib/python3.8/dist-packages/resfinder/run_resfinder.py", line 469, in main
isolate = Isolate(name=conf.sample_name, species=conf.species,
File "/usr/local/lib/python3.8/dist-packages/resfinder/cge/phenotype2genotype/isolate.py", line 30, in init
self.amr_panel = Isolate.load_amr_panel(species, amr_panel_file)
File "/usr/local/lib/python3.8/dist-packages/resfinder/cge/phenotype2genotype/isolate.py", line 67, in load_amr_panel
return set(panels[species_key])
KeyError: False

It does appear to gives result files that look reasonable though, even if it then falls over.

I use the -acq -c -s and --ignore_missing_species flags.

Let me know if you need more info.

Thanks,

Ann-Marie

[Edison Alain von Matt]

Dear Ann-Marie,

I believe that is because you are using an outdated version of ResFinder - the following command should work:

pip install resfinder --upgrade

Please let me know if this resolved your issue.

Best regards

Eddy