Nucleotide variant mutations not reported by hAMRonize from AMRfinderplus

[leosanbu]

Hi,
I have run hAMRonize from AMRfinderplus and noticed that for non-coding mutations (in ribosomal rDNA or promoter regions), the hAMRonize results do not include the mutation itself. It reports the gene involved but not the mutation, i.e.

AMRfinderplus line:
HAV_067 NA NODE_62_length_5566_cov_494.005101 1802 4704 + 23S_A2062G Neisseria gonorrhoeae azithromycin resistant 23S core AMR POINT MACROLIDE AZITHROMYCIN POINTN 2903 2910 100.00 99.35 2910 NC_002946.2:1119158-1116249 23S ribosomal RNA NA NA NA

hAMRonize line:
HAV_067 23S Neisseria gonorrhoeae azithromycin resistant 23S NCBI Reference Gene Database 2024-07-22.1 NC_002946.2:1119158-1116249 amrfinderplus 3.12.8 nucleotide_variant_detected AZITHROMYCIN 100.0 MACROLIDE 2903 2910 99.35

I am using hamronize 1.1.4 on a an iOS system.

Thanks very much in advance!
Best,
Leo

[fmaguire]

Hi @leosanbu I just tested this out but wasn't able to replicate the issue, which version of amrfinderplus and which options are you using to run it? It may be specific to certain options or I may have just fixed it dealing with another issue (#89)!

I've added these files to hAMRonization/test/data/raw_outputs/amrfinderplus for testing:

amrfinder -d /home/fin/miniforge3/envs/hamronization/share/amrfinderplus/data/2024-07-22.1/ -O Neisseria_gonorrhoeae --nucleotide non_coding_contig.fasta --name "DAWXTK010000082_noncoding_test" --output afp_non_coding.tsv

Then:
hamronize amrfinderplus --input_file_name DAWXTK010000082_noncoding_test --analysis_software_version 3.12.18 --reference_database_version 2024-07-22.1 afp_non_coding.tsv > hamronized_non_coding.tsv

Produces:
hamronized_non_coding.tsv with a nucleotide_mutation field containing c.2062A>G