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

The draft genome sequences of eight Salmonella enterica isolates from various sources were evaluated for the influence of incompatibility group I1 (IncI1) plasmids on virulence. Strains SE142, SE143, SE144, and SE146 originated from swine, SE36N and SE89N from poultry-related sources, and SE991 and SE1148 from human patients.

GENOME ANNOUNCEMENT

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 (1, 2). Food products originating from diverse sources like poultry, swine, and cattle are commonly associated with disease outbreaks caused by Salmonella enterica (2). Some serotypes of Salmonella, including Enteritidis, Typhimurium, and Heidelberg, are more prevalent as foodborne pathogens than other serotypes, such as Kentucky (3). Isolates containing certain mobile genetic elements, such as plasmids, have been associated with clinical manifestations of Salmonella infection (4). Plasmids encode genes responsible for antimicrobial resistance and virulence, which may have clinical significance associated with severe manifestations of diseases (5). Incompatibility group I1 (IncI1) plasmids have been reported to carry genes related to antimicrobial resistance and virulence (6).

Eight strains of Salmonella enterica containing IncI1 plasmids were sequenced (Table 1). 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 (5). 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 (7). Strains SE142, SE143, SE144, and SE146 were found to contain one or more plasmids and were resistant to commonly used antimicrobial agents (8). 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.

TABLE 1 

Summary of the genome sequence analysis of Salmonella enterica strains containing IncI1 plasmids

Strain	Serovar	Source	Location, yr of isolation	No. of contigs	Assembly size (bp)	G+C content (%)	No. of CDSa	No. of functional proteins	Accession no.
SE142	Heidelberg	Swine	Indiana, 2002	205	5,197,369	51.85	5,450	4,683	NPFC00000000
SE143	Heidelberg	Swine	Minnesota, 2002	306	5,361,922	51.69	5,718	4,779	NPEL00000000
SE144	Heidelberg	Swine	Minnesota, 2002	111	5,279,737	51.82	5,488	4,673	NPEQ00000000
SE146	Heidelberg	Swine	Minnesota, 2002	221	5,356,597	51.59	5,704	4,801	NPEM00000000
SE36N	Typhimurium	Chicken	West Virginia, 2000	158	5,160,965	51.90	5,358	4,705	NPER00000000
SE89N	Kentucky	Poultry house water	West Virginia, 2000	120	5,146,652	51.69	5,799	4,811	NPES00000000
SE991	Heidelberg	Human feces	Arkansas, 2009	98	5,053,493	51.82	5,161	4,493	NPEP00000000
SE1148	Heidelberg	Human blood	Wisconsin, 2007	166	4,867,737	52.17	4,995	4,435	NPEO00000000

CDS, coding sequences.

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 (9). 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 (10), the Pathosystems Resource Integration Center (PATRIC) (11), and the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) (12) were employed to annotate the draft genomes of these strains (Table 1). The average G+C content of these strains is estimated to be 51.81%, as determined by PATRIC. Table 1 lists individual G+C content (%) and numbers of contigs, coding sequences, and functional proteins for respective strains.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers listed in Table 1.