SRX5171148 SEETm_RM14512 SRP174079 PRJNA175692 Illumina MiSeq Illumina libraries were prepared for all strains using the KAPA Low-Throughput Library Preparation Kit with Standard PCR Amplification Module (Kapa Biosystems, Wilmington, MA), following manufacturer's instructions except for the following changes: 750 ng DNA was sheared at 30 psi for 40 s and size selected to 700-770 bp following Illumina protocols. Standard desalting TruSeq LT and PCR Primers were ordered from Integrated DNA Technologies (Coralville, IA) and used at 0.375 and 0.5 M final concentrations, respectively. PCR was reduced to 3-5 cycles. Libraries were quantified using the KAPA Library Quantification Kit (Kapa), except with 10 l volume and 90-s annealing/extension PCR, then pooled and normalized to 4 nM. Pooled libraries were requantified by ddPCR on a QX200 system (Bio-Rad), using the Illumina TruSeq ddPCR Library Quantification Kit and following manufacturer's protocols, except with an extended 2-min annealing/extension time. The libraries were sequenced 2 250 bp paired end v2 on a MiSeq instrument (Illumina) at 13.5 pM, following manufacturer's protocols. SRS4178771 SAMN10617425 SEETm_RM14512 WGS GENOMIC RANDOM Illumina MiSeq