Sequencing and Analysis of Salmonella Genomes

Bacterial genome sequencing was performed at the DNA Sequencing Service of the University of Seville (Servicio General de Biología, CITIUS, Universidad de Sevilla, Spain). Sample preparation included gDNA isolation by phenolic extraction and ethanol precipitation. Genome sequencing employed Roche 454 FLX + technology on a GS FLX titanium system. Emulsion PCR and 454 pyrosequencing were performed and 1,031,375 reads with an average read length of 810 base pairs, totaling 1000 Mb. Whole genome sequences were analyzed using the Burrow-Wheeler Alignment tool (BWA), specifically the BWA-MEM algorithm^{29 (link),30} . As a reference, the genome sequence of the laboratory stock of S. enterica SL1344 was also analyzed. Genomes were submitted to NCBI GenBank and are available as SUB3834111 “Salmonella typhimurium isolates from Balb/c mice gall bladders (Urdaneta & Casadesus)”. PCR amplification of regions harboring mutations was performed using the primers listed in Table S1. Chromosomal DNA samples obtained by PCR were sequenced by Stab Vida (Caparica, Portugal).