We ran BLASTn (version 2.6.0)66 on the de novo assemblies using a query rplD sequence from FA1090 (RefSeq accession: NC_002946.2). rplD sequences were aligned using MAFFT (version 7.450)67. Binding site mutations were identified after in silico translation of nucleotide alignments in Geneious Prime (version 2019.2.1, https://www.geneious.com). Subsequent analyses identifying prevalence, geometric mean azithromycin MIC, and MIC distribution differences were conducted in Python (version 3.6.5) using the Biopython package (version 1.69)68 and R (version 3.5.1).
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