Gaiix sequencing platform

Target gene capture was performed using SureSelect custom designs (Agilent Technologies, Inc., Santa Clara, CA) targeting 1,321 genes (Supplementary Table 2). Sequencing was performed using an Illumina GAIIx sequencing platform (Illumina, Inc., San Diego, CA) at the Beijing Genomics Institute (BGI, Shenzhen, China).
Sequences were aligned to the human genome reference hs37d5 using the Burrows-Wheeler Aligner (BWA)^{54 (link)}. The Genome Analysis ToolKit (GATK)^{55 (link)} was used for insertion/deletion realignment, quality score recalibration, and variant identification. ANNOVAR^{58 (link)} was used to annotate mutations. Matched normal samples were not available for comparison so somatic mutations were enriched via population filtering, including 1000 Genomes and 238 unmatched normal samples. Final read depth averaged ~140x across the targeted regions and a median of ~94% of bases across samples had ≥10 reads (Supplementary Figure 2).

Isolates were grown on trypticase soy agar media and DNA was prepared using DNeasy Blood & Tissue Kit as described by the manufacturer (Qiagen, Valencia, CA) with the addition of lysostaphin to the gram-positive extraction protocol from Qiagen. The DNA samples were prepared for multiplexed, paired-end sequencing with a 500 base pair insert using Library Preparation Kit with Standard PCR Library Amplification (KAPA Biosystems, Woburn, MA). A 100 bp read paired-end run was used for all twenty-four isolates on the GAIIx sequencing platform (Illumina, Inc. San Diego, CA).

Genomic DNA was extracted using the PeqGold DNA Isolation Kit (PEQLAB, Germany) according to the manufacturer’s instructions. The genome was sequenced with Illumina technology using a GAIIx sequencing platform on paired-end libraries prepared with the Nextera XT DNA Kit (Illumina, San Diego, CA). A total of 83 contigs (0.5–330 kb, average 55 kb) were assembled using SPAdes v3.0 (Bankevich et al., 2012 (link)), followed by error correction using BayesHammer (Nikolenko et al., 2013 (link)) and gene prediction using the IMG pipeline (Markowitz et al., 2012 (link)). The draft genome has been converted to EMBL format using EMBLmyGFF3 (Norling et al., 2018 (link)) and deposited at ENA under PRJEB40942. Phylogenetic analysis was carried out with 92 core genes identified using UBCG (Na et al., 2018 (link)), with Capnocytophaga ochracea DSM 7271 as outgroup. The resulting nucleotide alignment was visually confirmed for consistency and the best substitution model (GTR + G) computed using ModelTest-NG (Darriba et al., 2020 (link)). A maximum-likelihood phylogeny with 1000 bootstrap replicates was calculated using RaxML v8.2 (Stamatakis, 2014 (link)) on the CIPRES Science Gateway (Miller et al., 2010 ).