Is it possible to apply this method to environmental metagenomic sequencing data?

[M-o-Y-u]

Great work！
I am wondering whether it will be possible in the future to detect fungal AMR genes in environmental metagenomic sequencing data in the same way as antibiotic resistance genes, which may help to quantify the risks posed by fungal AMR.
Thank you in advance for your reply.

[nmquijada]

Hi @M-o-Y-u

Thanks a lot!
That's definitely the next step we are willing to do! ;)
There are some challenges to overcome... particularly when closely related strains (that might have a different fAMR profile) are present. In such cases, metagenomic assembly and binning would probably resolve "just" the most abundant genotype for each particular gene/protein.
If you have metagenomic contigs/bins/MAGs with a taxonomic assignation you can definitely use ChroQueTas for them (you might need to adjust the --species flag). But please note that ChroQueTas will return the fAMR profile of that particular contig/bin/MAG and it won't be a reflection of the whole community.

As I said, we are working on that so I hope I can come with better news soon!

N

[M-o-Y-u]

Thank you very much for your reply. Considering that the number of sequences from fungi in environmental metagenomic data is very limited, is metatranscriptomics a more promising technical approach for detecting AMR in fungal communities?