Genomic dna buffer kit

B. anthracis strains (Data Set 2) were sequenced using Illumina MiSeq (Illumina, USA). DNA was extracted using the Genomic-tip 100/G and genomic DNA buffer kit (Qiagen, Germany) for the German strains. For the 35 strains from Italy, the DNAeasy blood and tissue kit (Qiagen, Germany) was used. Paired-end sequencing libraries were prepared using the Nextera XT DNA Library Preparation kit (Illumina, USA) with an average sequencing depth of between 40× and 104× for the strains. Genome assembly was performed for sequence data produced in this study or downloaded from the NCBI using shovill v.1.0.4 (option -trim [https://github.com/tseemann/shovill]) for paired-end Illumina data or SPAdes v.3.12.0 (-careful option) (27 (link)) for single-end Illumina data. Assembly statistics were obtained using the program Quast v.5.0.2 (28 (link)).

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.

Genomic DNA from the isolated colonies was extracted at the end of the assay using the Qiagen Genomic-tip 100/G together with the genomic DNA buffer kit (Qiagen) following the manufacturer’s protocol. The quality of the extracted DNA was assessed by electrophoresis in agarose gel, and DNA quantity was measured with a Qubit 2.0 fluorometer. WGS was performed with a MiSeq instrument (Illumina) in-house at the department of Medical Biochemistry and Microbiology. The libraries were prepared with the Nextera XT DNA library preparation kit, and the sequencing was done with a V3 600-cycle reagent cartridge. The sequencing was achieved to an average of at least 30× coverage. Data analysis was accomplished with CLC Genomics Workbench software (Qiagen), and the genetic changes were identified through the mapping of the obtained reads to the S. maltophilia D457 reference genome (GenBank accession number NC_017671.1). The given variants were then filtered against those of the D457 laboratory wild-type strain.