Sequencing of Erythromycin-Resistant Bacteria

Total DNA of erythromycin-resistant colonies was purified using the DNeasy Blood & Tissue Kits (Qiagen). Genomic DNA library preparation and sequencing were performed at the SeqCenter (Pittsburgh, PA) by using Illumina NextSeq 2000 and NovaSeq 6000 technology. Sample libraries were prepared using the Illumina DNA Prep kit and IDT 10 bp unique dual indices (UDI). Demultiplexing, quality control and adapter trimming were performed with BCL Convert (Version 4.1.5). To analyze genetic alterations by HGT, paired-end sequencing reads (2 × 151 bp) were assembled by SPAdes (Version 3.15.2)^{62 (link)}. The sequencing reads (2 × 151 bp) were also mapped to the plasmid bearing the thyA gene (shown in Fig. 4a) and the plasmid with transgenes (shown in Fig. 5a), using Bowtie 2 (Version 2.4.5)^{63 (link)}. Raw sequencing data and assembled genomes have been deposited at DDBJ/ENA/GenBank under the accession number: PRJNA754595.