We identified the antimicrobial resistance genes present in our sequenced genomes using the EPI2ME Fastq Antimicrobial Resistance workflow (Oxford Nanopore Technologies). This workflow consists of three processes, including 1) quality control of the reads, 2) WIMP analysis (v2020.03.11) using centrifuge and NCBI RefSeq database (v88), and 3) detection of antimicrobial genes using the CARD database (v1.1.3) [53].

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