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Annotation of ARGs

WY Wei Yan
AH A. Brantley Hall
XJ Xiaofang Jiang
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We extracted the genes in the operons downstream the putative invertible promoters. We searched the protein sequences of these genes for known ARGs from the Comprehensive Antibiotic Resistance Database (CARD) (v3.0.7)62 using BLASTn (v2.10.0)41. The BLAST results were filtered using the parameters: -perc_identity 80, -evalue 1e-10, and -culling_limit 1. Resistance Gene Identifier (RGI, v5.0.0)62 was also used to predict known antibiotic-resistance elements using the following parameters: rgi main --t contig -a BLAST -n 8 -d wgs --local. ARGs located in the operon immediately downstream of the identified invertible promoters were kept for further analysis. Pairwise BLASTn searches were performed between each pair of contigs with putative IP-ARG from samples of the same individual. If multiple contigs from samples of the same individual likely originated from the same genomic region, only the longest contig was selected as a representative in further analysis.

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