Viral.Bacteria.Genomes
DNA was extract using QIAampDNA mini Cat (Qiagen, Dusseldorf, Germany). DNA was cleaned using Ampure beads, eluted in 23 ul of elution buffer. Library preparation was performed using Nextera DNA Flex Library Prep Kit (Illumina, San Diego, CA Cat#20018704). Total DNA input was 10 ng for MWF and 100ng for lung tissue, we utilized 6 PCR cycles. Sequencing was performed on an Illumina NovaSeq with a sp300 cartridge (Illumina, San Diego, CA) and sp 2 lane flow cell. Runs were paired-ends 150 bp. We obtained 150-1600 million total reads per sample. Raw shotgun sequencing data was processed using Kraken (20). Reads from tissue samples were further aligned to metal working fluid reads annotated to Pseudomonas pseudoalcaligenes using VSEARCH (21) using usearch_global and 100% identity parameters. Only reads with complete alignment over the whole sequence were considered as exact matches. All WGS Sequences are available through the NIH SRA archive at PRJNA635410.