Antimicrobial resistance genes (ARGs) are genes that encode resistance determinants capable of conferring to the bacteria the ability to tolerate or resist some antibiotics or antimicrobials, making bacteria less susceptible to its effects. In this pipeline, ARGs have been predicted/detected with four main AMR resources:
All the predictions were passed through a user defined threshold for minimum coverage and identity:
> 90
> 90
CARD RGI have their own detection models thresholds obtained by curation. Therefore, the only result from CARD that have been filtered like that is their final tabular output (shown in this report).
The results used to create this report are under the directory called
resistance
in the output folder of the query ecoli.
No AMR gene was annotated either because Resfinder has not been executed (based on user’s input parameters) or the given alignment thresholds were too strict. If you believe that at least one gene should be present in the query genome you may try different thresholds.
The results obtained with RGI tool are summarized in the heatmap produced by the tool itself (Figure 1). Additionally, the annotation results are also shown in an interactive table displaying the tool’s complete annotation information (Table 1). They can be roughly divided into two main categories:
Obs: CARD RGI tool always tries to annotate functional AMR genes, however, depending on the assembly, a not functional gene may yet be annotated. Therefore, users are advised to double check genes annotated under Strict category.
The AMRFinderPlus annotation results are summarized below in an interactive table containing the complete annotation information (Table 2) and an image displaying the targeted drug classes (Figure 2). Whenever possible, features are linked to the NCBI database marking the closest reference sequence to each annotated gene. The results obtained with AMRFinderPlus can be roughly divided into two main categories:
ARGminer is an online resource for the inspection and curation of ARGs based on crowdsourcing as well as a platform to promote interaction and collaboration for the ARG scientific community. We put this database here in the report and annotation in order to support the initative and to help it go towards nomenclature simplification. Genes are scanned via BLASTp
since ARGminer is a protein database. This alignment is summarized in table 3.
It must be used with caution. Remember, it is a super new database thus it is rapidly changing and may yet contain errors.
Additionally, Prokka generically annotates a few proteins that are related to any type of resistance. These are showed in Table 4.
When using Prokka, one must take caution when evaluating this result because this annotation can be very generic and therefore not so meaningful. Because it only uses hmms, sometimes the annotation of genes can be based on a single detected motif thus its results must be checked whether they are correctly annotated and/or functional.