Fluoroquinolones

[Jan M]

I ran ResFinder 4.0 on the 390 DE raw reads from the paper. For Nalidixic Acid, I find 22% concordance (expected 99.2% from the paper), with no resistance found in any sample (0/99). For Ciprofloxacin I find 38% concordance (expected 99.2%), with resistance found in under half of the samples (105/275).

For the remaining antimicrobials, I either find the same concordance (ampicillin, chloramphenicol, cefotaxime, tetracylcine) or extremely close (ceftazidime, gentamicin).

There is a ‘fluoroquinolone' row in the ResFinder output that says 'under_development’. Is this a separate entry under development or is it indicating that the fluoroquinolones, ciprofloxacin and nalidixic acid, are under development and should not be used at this time?

[RolfKaas]

Dear Jan

Thanks for reporting this issue.

I will try and see if I can recreate it, and figure out whats going on.

Best regards,

Rolf

[RolfKaas]

Dear Jan,

I just ran a few isolates from the German dataset through ResFinder 4.0 and I am not able to recreate the issue. This is the command I used to run ResFinder:

python3 run_resfinder.py -ifq data/SRR11454052_* -o SRR11454052 -s "Escherichia coli" --acquired --point

Got these results:

# Antimicrobial Class   WGS-predicted phenotype Match   Genetic background
gentamicin  aminoglycoside  No resistance   0   
ciprofloxacin   fluoroquinolone Resistant   3   gyrA (p.S83L)
azithromycin    macrolide   Resistant   3   mph(A) (mph(A)_D16251), mph(A) (mph(A)_U36578)
ceftazidime beta-lactam Resistant   3   blaCTX-M-102 (blaCTX-M-102_HQ398215), blaCTX-M-27 (blaCTX-M-27_AY156923)
ampicillin+clavulanic acid  beta-lactam No resistance   0   
tetracycline    tetracycline    Resistant   1   tet(A) (tet(A)_AF534183)
tigecycline tetracycline    No resistance   0   
ampicillin  beta-lactam Resistant   3   blaCTX-M-102 (blaCTX-M-102_HQ398215), blaCTX-M-27 (blaCTX-M-27_AY156923)
colistin    polymyxin   No resistance   0   
amikacin    aminoglycoside  No resistance   0   
fosfomycin  fosfomycin  No resistance   0   
meropenem   beta-lactam No resistance   0   
imipenem    beta-lactam No resistance   0   
cefoxitin   beta-lactam No resistance   0   
chloramphenicol phenicol    No resistance   0   
temocillin  beta-lactam No resistance   0   
tobramycin  aminoglycoside  No resistance   0   
trimethoprim    folate pathway antagonist   Resistant   3   dfrA17 (dfrA17_FJ460238)
ertapenem   beta-lactam No resistance   0   
piperacillin+tazobactam beta-lactam No resistance   0   
cefepime    beta-lactam Resistant   3   blaCTX-M-102 (blaCTX-M-102_HQ398215), blaCTX-M-27 (blaCTX-M-27_AY156923)
cefotaxime  beta-lactam Resistant   3   blaCTX-M-102 (blaCTX-M-102_HQ398215), blaCTX-M-27 (blaCTX-M-27_AY156923)
nalidixic acid  fluoroquinolone Resistant   3   gyrA (p.S83L), gyrA (p.D87N)
sulfamethoxazole    folate pathway antagonist   Resistant   3   sul1 (sul1_U12338), sul2 (sul2_AY034138)

‌

Did you remember the “--point” flag. It sounds like you are missing the point mutations.

Else try and upgrade your cgecore module by:

sudo pip3 install cgecore --upgrade

‌

If none if this works, post the exact results you got from one of the isolates along with the exact command you used.

Thanks.

Best regards,

Rolf

[Jan M]

Thank you, the issue was with --point. I had run --acquired --point, but had failed to remove the results of a previous run with only --acquired. There was an error with --point, but since the intermediate files (PointFinder_prediction.txt etc.) and final output (pheno_table files) file were present, I didn't realize the output wasn't updated, and was still from --acquired only.

With the same command, python3 run_resfinder.py -ifq data/SRR11454052_* -o SRR11454052 -s "Escherichia coli" --acquired --point and either an empty or non-empty output folder, the error is:

Traceback (most recent call last):
  File ".../resfinder/run_resfinder.py", line 521, in <module>
    "PointFinder")
  File ".../resfinder/cge/standardize_results.py", line 346, in standardize_results
    res_collection, mismatch, gene_results, ref_db_name)
  File ".../resfinder/cge/standardize_results.py", line 27, in __init__
    region_name = region_results[0]["ref_id"]
IndexError: list index out of range

If I switch from 4.0 to master, there is no error, so it appears this error has already been addressed.

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