Computational protocol: Draft Genome Sequences of Salmonella enterica Isolates Containing Incompatibility Group I1 Plasmids from Swine, Poultry, and Human Sources

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[…] Salmonella enterica is one of the top five bacterial pathogens contributing to foodborne illnesses. Salmonella is also a leading foodborne pathogen associated with hospitalizations and deaths in the United States (, ). Food products originating from diverse sources like poultry, swine, and cattle are commonly associated with disease outbreaks caused by Salmonella enterica (). Some serotypes of Salmonella, including Enteritidis, Typhimurium, and Heidelberg, are more prevalent as foodborne pathogens than other serotypes, such as Kentucky (). Isolates containing certain mobile genetic elements, such as plasmids, have been associated with clinical manifestations of Salmonella infection (). Plasmids encode genes responsible for antimicrobial resistance and virulence, which may have clinical significance associated with severe manifestations of diseases (). Incompatibility group I1 (IncI1) plasmids have been reported to carry genes related to antimicrobial resistance and virulence ().Eight strains of Salmonella enterica containing IncI1 plasmids were sequenced (). Four of these strains were isolated from swine, two from poultry-related sources, and two from human patients. Previous studies showed that SE1148 and SE146 carried IncI1 plasmids and antimicrobial resistance genes (). In addition to resistance genes, SE146 also contained an IncX4 plasmid which encodes a VirB/D4 type 4 secretion system that is likely involved in the increased virulence potential of this strain (). Strains SE142, SE143, SE144, and SE146 were found to contain one or more plasmids and were resistant to commonly used antimicrobial agents (). Overall analysis of the whole-genome sequences of these strains will improve our current understanding of the potential role of IncI1 plasmids in the pathogenicity of Salmonella enterica isolated from various foods and hosts.To conduct the sequencing, total DNA was extracted using a DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA). Nextera XT DNA sample kits (Illumina, San Diego, CA, USA) were used to construct a DNA library. Sequencing reactions were carried out at the DNA Sequencing Core at the University of Arkansas for Medical Sciences (UAMS) (Little Rock, AR, USA) and the Division of Microbiology, National Center for Toxicological Research (NCTR) (Jefferson, AR, USA) on an Illumina MiSeq instrument to generate 2 × 250 (UAMS) or 2 × 300 (NCTR) paired-end reads (). Trimming and de novo assembly of the paired-end reads was performed using CLC Genomics Workbench versions 8.5.1 and 9 (Qiagen, Germantown, MD, USA). The Rapid Annotation using Subsystem Technology (RAST) server (), the Pathosystems Resource Integration Center (PATRIC) (), and the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) () were employed to annotate the draft genomes of these strains (). The average G+C content of these strains is estimated to be 51.81%, as determined by PATRIC. lists individual G+C content (%) and numbers of contigs, coding sequences, and functional proteins for respective strains. […]

Pipeline specifications

Software tools CLC Genomics Workbench, RAST, PGAP
Databases PATRIC
Application WGS analysis
Organisms Salmonella enterica, Sus scrofa, Homo sapiens