Antibiotic resistance genes (ARGs) were identified using the Resistance Gene Identifier (RGI, v4.2.2) with default parameters and the CARD database (The Comprehensive Antibiotic Resistance Database, v3.0.7) [70]. DIAMOND was utilized for alignment [71]. In order to identify the species origins of drug resistance genes, the similarity of the predicted ARG segments to known species was estimated by aligning the predicted ARGs to the NCBI-NT using BLASTN (v2.7.1, default parameters except that -evalue 1e-10 outfmt 6 -word_size 16), and identified genes had an alignment coverage greater than 70%.

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