Dnaesy blood and tissue kit

Sequencing data of SSMs are as previously described [31 (link)]. Sequencing data from pool samples derive from pools of 30 Ae. albopictus mosquitoes each. Mosquitoes were collected on the island of La Reunion Island, France in 2017. DNA was extracted using the DNAesy Blood and Tissue Kit following manufacturer’s recommendations (Qiagen, Hilden Germany). DNA-seq library preparation and sequencing on an Illumina HiSeq4000 was performed at Biodiversa srl (Rovereto, Italy).

Genomic DNA was isolated and purified from bacterial cultures grown overnight using the Mo Bio Powersoil® DNA Isolation kit (Mo Bio, Carlsbad, CA, USA) or the DNAesy Blood and Tissue kit (Qiagen, Hilden, Germany), according to manufacturer’s instructions. Long-read sequencing was performed on the three E. coli isolates on a PacBio RSII Instrument at the Ramaciotti Centre for Genomics (UNSW, Sydney, Australia). Polishing and assembly of sequenced reads was performed at the Ramaciotti Centre using HGAP and CANU, and plasmids were closed using Circlator^{48 (link)}. Errors in PacBio assemblies were checked and curated by alignment with Illumina short reads from whole genome sequencing of the E. coli hosts. P1-like genomes were first annotated using RASTtk^{49 (link)}, then manually curated using BLAST functions^{50 (link)}, SnapGene (GSL Biotech; available at SnapGene.com) and Geneious v.9.1 (https://www.geneious.com). Plasmid virulence and resistance regions were also annotated using web-based software [Center for Genomic Epidemiology, www.genomicepidemiology.org; Galileo^TM AMR (formerly MARA), galileoamr.arcbio.com/mara/^{51 (link)}]. All allelic variants of IS26^{52 (link)} detected in pTZ20_1P are referred to as IS26 throughout. Comparisons with the reference P1 genome (P1 mod749::IS5 c1.100 mutant; GenBank NC_005486)^{19 (link)} were visualized using EasyFig.^{53 (link)}.

DNA was isolated from blood and saliva using Gentra Purgene Blood Kit (Qiagen, Germantown, MD), or from frozen lung tissue using DNeasy Blood and Tissue Kit (Qiagen). RNA from frozen lung or FFPE lung tissues was extracted using miRNeasy Mini Kit (Qiagen) or Quick-RNA FFPE Kit (Zymo Research, Irvine, CA), respectively. DNA and RNA from cultured IMR-90 cells was isolated using DNaesy Blood and Tissue Kit (Qiagen) and miRNeasy Mini Kit (Qiagen), respectively.