Computational protocol: Draft Genome Sequences of 20 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Swine in Santa Catarina, Brazil

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Protocol publication

[…] Salmonella enterica subsp. enterica serovar Typhimurium has often been isolated from pigs, among which it generally does not cause severe diseases and can be asymptomatic (). According to the Brazilian Association of Animal Protein (ABPA), pork production in Brazil was 3.73 billion tons in 2016. Furthermore, exports to Russia, Hong Kong, China, and Singapore, among other countries, reached 733 million tons in 2016, and Santa Catarina has been the largest pork producer in recent years in Brazil (http://abpa-br.com.br/storage/files/final_abpa_relatorio_anual_2017_ingles_web.pdf). In this report, we announce 20 draft genome sequences from a collection of S. Typhimurium strains isolated from swine between 2000 and 2012 in Santa Catarina, Brazil.DNA from each strain was extracted according to the method used by Campioni and Falcão (). Libraries were prepared using 1 ng of genomic DNA with the Nextera XT DNA library preparation kit (Illumina, San Diego, CA, USA), and the genomes were sequenced using the NextSeq 500 desktop sequencer with the NextSeq 500/500 high-output version 2 kit (Illumina) for 2 × 151 cycles according to the manufacturer’s instructions. De novo assemblies were generated from all raw sequence data. The Illumina reads were assembled using CLC Genomics Workbench version 10.0.1. The contigs for each isolate (draft genomes) were annotated with NCBI’s Prokaryotic Genome Annotation Pipeline (PGAP) ().The genomes ranged from 4.6 to 5.1 Mb in size, as described for other Salmonella strains (). Sequencing generated an average G+C content of 52.03%, which is similar to that reported previously for other Salmonella isolates (). The number of contigs per assembly for each isolate ranged between 63 and 152.These data will provide support for understanding the molecular epidemiology of S. Typhimurium strains isolated from swine in Brazil. It will also provide phylogenetic insights into their evolution. More information about these genomic features will be detailed in future publications. […]

Pipeline specifications

Software tools CLC Genomics Workbench, PGAP
Application Phylogenetics
Organisms Salmonella enterica subsp. enterica serovar Typhimurium, Salmonella enterica subsp. enterica, Sus scrofa