Nextera xt preparation kit

For sequencing, the 23 Salmonella isolates were grown overnight at 37°C in 3 mL of Luria-Bertani broth (Mast Diagnostica GmbH, Reinfeld, Germany). DNA extraction was performed using the DNeasy blood and tissue kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer's instructions for Gram-negative bacteria. DNA sequencing libraries were constructed using the Nextera XT Preparation Kit (Illumina Inc., San Diego, CA) following the manufacturer's instructions. Paired-end sequencing was performed on an Illumina MiSeq platform (Illumina Inc.) using a 300-cycle MiSeq reagent kit.
One strain (19CS0402) was additionally sequenced using the MinION platform to analyze the complete genome sequence and the plasmid structure. High-molecular-weight DNA was extracted using Genomic-tip 100/G and genomic DNA buffer kit (QIAGEN GmbH). The sequencing library was prepared using the Oxford Nanopore Technologies 1D Ligation Sequencing Kit (SQK-LSK109) with the Native Barcoding Expansion Kit (EXP-NBD104) as recommended by the manufacturer.

Filters and cells possibly detached from the filters were subjected to three successive rinsing/centrifugation steps using a phosphate buffer solution (PBS) to remove the RNAlater reagent. Total nucleic acids were extracted using the Power Water RNA isolation kit (Machery-Nagel), following manufacturer instructions, except that the DNAse treatment step was omitted (DNA and RNA were co-extracted but only the DNA fraction was further analyzed in the present study). Libraries of total genomic DNA were prepared using Nextera XT preparation kit (Illumina) following the manufacturer’s instructions, except that we increased the number of PCR amplifications to 13 cycles as indicated for low DNA input (0.1 ng/µl in our case)^{53 (link)}. Libraries were purified using AMPure XP beads (New England Biolabs) and their concentration was normalized following Illumina Nextera XT protocol. Bioanalyzer and High Sensitivity DNA Kit (Agilent) were used to check the fragment size distribution of each library. Libraries were sequenced on an Illumina Miseq sequencer based at the Environmental Microbial Genomics group in Laboratoire Ampère (Ecole Centrale de Lyon) with 2 × 250 bp chemistry (MiSeq Reagent Kit v2).

Bacterial genomic DNA was isolated using a DNeasy blood and tissue kit (Qiagen) as per manufacturer’s specifications for Gram negative bacteria. A DNA sequencing library of bacterial genomic DNA was created using an Illumina Nextera XT preparation kit adding flow cell attachment and bar code through transposon insertion. These libraries were sequenced using Illumina V2 2 × 250 bp chemistry on the Illumina MiSeq Platform.