Xt library kit

All cultured microbes were collected in toto from culture plates (see above) with 1ml PBS and a cell spreader (plate swipe). Bacterial cells were pelleted with centrifugation at 5,000rpm, 10min. DNA was extracted with Maxwell tissue DNA kit following the manufacturer’s instructions. DNA libraries were prepared using Nextera XT Library Kit and sequenced on Illumina MiSeq (2 × 250 bp). Raw sequence data were demultiplexed into sample-specific fastq files using bcl2fastq conversion software from Illumina. Adaptor-trimmed, high-quality reads were then used to calculate relative abundances of microbes, using MetaPhlAn2(71 (link)).

Individual isolates were picked from culture plates (see above) and streaked on a new plate, to ensure single clone. After 16 hours, a single colony from each streaked plate was picked, and DNA was extracted with Maxwell tissue DNA kit following manufacturer’s instructions. DNA libraries were prepared using Nextera XT Library Kit and sequenced on Illumina MiSeq (2 × 250 bp). Raw sequence data were demultiplexed into sample-specific fastq files using bcl2fastq conversion software from Illumina. Multilocus sequence typing (MLST) was performed using SRST2(72 (link)) with MLST database from (https://pubmlst.org/sepidermidis/, https://pubmlst.org/shominis/).
For phylogenetic analysis of S. epidermidis, reads from each isolate were mapped, and variants called using Snippy core (https://github.com/tseemann/snippy), with S. epidermidis ATCC12228 (accession no: GCA_000007645.1) as a reference. Predicted recombination was identified using Gubbins(73 (link)). Core genome SNPs, following removal of recombination, were then used to construct a phylogeny with FastTree(74 (link)). Resistance gene content in isolate sequencing data was detected by mapping to a reference database of known AMR determinants, as derived from previous reports(75 , 76 (link)), using SRST2(72 (link)).