Genome Sequences of Salmonella enterica subsp. enterica Serovar Lubbock Strains Isolated from Liver Abscesses of Feedlot Cattle.

The genome sequencing of 13 Salmonella enterica subsp. enterica serovar Lubbock strains isolated from liver abscesses of feedlot cattle is reported here. The availability of these genomes will help to further understand the etiologic role of Salmonella strains in liver abscesses of cattle and will serve as references in microbial trace-back studies to improve food safety.

GENOME ANNOUNCEMENT

Liver abscesses occur in feedlot cattle as a consequence of feeding them a high-grain diet (1). Cattle with severely abscessed livers have lower feed intake, reduced weight gain, and a decreased gain-to-feed ratio (2). The primary causative agent of liver abscess is Fusobacterium necrophorum (3). The ruminal acidosis resulting from the highly fermentable starch contained in the grains, and subsequent rumenitis, facilitate the migration of F. necrophorum from the rumen to the liver via portal circulation (1). Recently, for the first time, we reported the occurrence, along with F. necrophorum, of a novel Salmonella serotype, designated 6,7:g,m,s:e,n,z15, now named Salmonella enterica subsp. enterica serovar Lubbock (4), in liver abscesses of cattle (5). The newly reported serotype S. Lubbock is closely related to S. enterica subsp. enterica serovar Mbandaka and has been isolated from subiliac lymph nodes of healthy cattle (4). It is not known whether S. Lubbock is a causative agent of liver abscesses or is a secondary invader, via or lymph or blood, of an abscess initiated by F. necrophorum. In a recent study, we observed that Salmonella was prevalent in 20 to 25% of the abscesses cultured, and S. Lubbock was the predominant serotype. Here, we report the availability of draft genomes of 13 S. Lubbock strains isolated from liver abscesses.

S. Lubbock strains were isolated from liver abscesses of feedlot cattle, as per a previously described protocol (5). The serotypes of the isolates were determined at the National Veterinary Service Laboratory (NVSL), Ames, Iowa. Strains were grown in brain heart infusion broth for 12 h at 37°C. DNA from each strain was isolated from 1.0-ml cultures using the E.Z.N.A. bacterial DNA kit (Omega Bio-tek, Norcross, GA). According to the manufacturer’s protocol, sequencing libraries were prepared using 1.0 ng of genomic DNA using the Nextera XT kit (Illumina, San Diego, CA). We used V2 paired-end chemistry (2 × 250 bp) to sequence the genomes on an Illumina MiSeq platform. De novo genome assembly was performed using SPAdes version 3.5.0 (6), available at http://bioinf.spbau.ru/spades. Genome annotation was performed using the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) (7).

The genome characteristics of the 13 S. Lubbock strains are summarized in Table 1. The serotypes of the 13 strains were confirmed using SeqSero (8). Genome size and G+C content were estimated for all contigs of each strain. Among the 13 strains, the median values for genome size and G+C content were 4.97 Mb and 52.1%, respectively (Table 1), and were similar to those of previously published S. enterica genomes.

TABLE 1 

Characteristics of 13 S. Lubbock strains isolated from liver abscesses of cattle

Strain name	GenBank accession no.	Genome size (bp)	G+C content (%)	Total no. of contigs
LA-10-2013	LSMA00000000	4,973,701	52.1	128
LA-1-2013	LSLN00000000	4,955,079	52.1	100
LA-2-2013	LSLO00000000	4,959,869	52.1	108
LA-3-2013	LSLP00000000	4,988,702	52.1	174
LA-4-2013	LSLQ00000000	4,964,148	52.1	112
LA-5-2013	LSLR00000000	5,174,970	52.1	479
LA-5-2014	LSLS00000000	5,032,588	52.1	267
LA-6-2013	LSLT00000000	4,983,284	52.1	184
LA-7-2013	LSLU00000000	4,992,701	52.0	175
LA-7-2014	LSLV00000000	4,979,081	52.1	142
LA-8-2013	LSLW00000000	4,979,081	52.1	142
LA-8-2014	LSLX00000000	4,961,787	52.1	106
LA-9-2014	LSLZ00000000	4,870,086	52.1	159

The availability of the genomes of 13 S. Lubbock strains is the first report of this serotype isolated from liver abscesses of cattle. The availability of these genomes will help to further understand the etiologic role of Salmonella strains in liver abscesses in cattle and will serve as references in microbial trace-back studies to improve food safety.

Nucleotide sequence accession numbers.

The sequences have been deposited as whole-genome shotgun projects at GenBank under the accession numbers listed in Table 1.