Long-Read Genome Sequencing and Plasmid Analysis for ST171 Strains

We determined plasmid replicons of all ST171 strains in this study by using PlasmidFinder version 2.0 (https://cge.cbs.dtu.dk/services/PlasmidFinder). The first blaNDM-5–harboring ST171 strain (090011) in this study and the only blaNDM-1–harboring ST171 strain (045001) were selected for whole-genome sequencing by using the long-read MinION sequencer (Nanopore, https://nanoporetech.com) to obtain complete chromosomal and plasmid sequences. De novo hybrid assembly of short Illumina reads and long MinION reads was performed by using Unicycler version 0.4.3 (15) in conservative mode for increased accuracy. Complete circular contigs were then corrected by using Pilon version 1.22 (18) with Illumina reads for several rounds until no further improvements were reported. Short reads of the remaining four blaNDM-5–harboring ST171 strains (090022, 090023, 090055, and 090059) were mapped against the blaNDM-5-carrying plasmid (designated pNDM5_090011) of strain 090011 by using BWA version 0.7.17 (H. Ling, unpub. data, https://arxiv.org/abs/1303.3997) at default settings.

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