WGS of Shigella flexneri from MSM in Southern California
The isolate (UCLA689) was sequenced on Miseq (Illumina, CA, USA) using 2X250bp protocol. Analysis was performed using CLC genomic workbench (Qiagen, CA, USA) and Geneious Prime software (Biomatters, New Zealand). AMR genes and plasmid replicons were identified using ResFinder and PlasmidFinder (https://cge.cbs.dtu.dk/services). Reference sequences used include S. flexneri type 2a ATCC strain 700930 (GenBank: AE014073), and 2 plasmids pMHMC-004 (GenBank: CP053755) and pMHMC-012 (GenBank: CP053763).