Abstract
Here, we report draft genome sequences of 26 isolates of Salmonella enterica subsp. enterica, representing eight serotypes, which were isolated from cows in a Pennsylvania dairy herd, the farm on which they were reared, and the associated off-site heifer-raising facility over an 8-year sampling period.
GENOME ANNOUNCEMENT
Salmonella enterica is a leading cause of gastroenteritis among humans worldwide, with cases estimated at 93.8 million per year and deaths from nontyphoidal S. enterica estimated at 155,000 per year (1). Salmonellosis is typically ascribed to the consumption of contaminated poultry, beef, milk, and dairy products, nonanimal products, such as produce, and occasionally, contaminated drinking water (2–4). Poultry and cattle frequently harbor these organisms, sometimes as pathogens resulting in illness or death of the animal, but sometimes as nonpathogenic commensals, thereby presenting a difficult-to-detect public health risk to humans and other animals (5). Further, those people in contact with animals known to be sources of Salmonella are at increased risk of infections by these organisms (6).
As part of a long-term longitudinal study of Salmonella prevalence in a commercial dairy herd and its associated heifer-rearing facility, samples were collected from feces, composite manure (feces, urine, bedding), trough water, feed, flies caught on the farm, bedding, bulk milk, and milk filters and fecal grab samples, composite manure samples, and water trough samples were also obtained from the farm that raises the postweaned heifers before they are brought back to the farm at which they were born (7, 8). These samples were processed for S. enterica using traditional bacteriology methods (7). We selected a subset of Salmonella strains from the fecal grab samples for whole-genome sequence analysis.
The 17 S. enterica subsp. enterica serovar Cerro and two S. enterica subsp. enterica serovar Kentucky strains were sequenced using 454 Titanium GS FLX+ pyrosequencing (Roche, Branford, CT) to obtain high-quality draft genomes (18 to 23× coverage). The genome contigs were assembled de novo with 454 Life Sciences Newbler software package version 2.6 (9). The other Salmonella isolates were sequenced using Illumina MiSeq technology (Illumina, Inc., San Diego, CA) to obtain high-quality draft genomes. Genome contigs generated from MiSeq runs were assembled de novo with the Velvet software package version 1.2.09 (10). The genome sequencing statistics for these isolates are listed in Table 1. The results describing the evolution and comparative genomics of these isolates will be reported elsewhere.
TABLE 1.
Genome statistics for the S. enterica subsp. enterica strains sequenced in this study
| Salmonella enterica subsp. enterica serovar | USDA ID | CFSAN ID | No. of contigs | Genome size (bp) | N50 contig size (bp) | Accession no. |
|---|---|---|---|---|---|---|
| Cerro | 818 | CFSAN001330 | 78 | 4,736,638 | 193,703 | AOZJ00000000 |
| Cerro | 6827 | CFSAN001587 | 71 | 4,699,129 | 219,427 | AYVG00000000 |
| Cerro | 7001 | CFSAN001588 | 81 | 4,699,438 | 145,279 | AYVF00000000 |
| Cerro | 7002 | CFSAN001589 | 65 | 4,701,086 | 174,094 | AYVE00000000 |
| Cerro | 7004 | CFSAN001590 | 74 | 4,699,430 | 184,318 | AYVD00000000 |
| Cerro | 7005 | CFSAN001669 | 97 | 4,682,990 | 189,203 | AYVC00000000 |
| Cerro | 7006 | CFSAN001670 | 75 | 4,691,976 | 218,403 | AYVB00000000 |
| Cerro | 7007 | CFSAN001671 | 76 | 4,696,980 | 195,832 | AYVA00000000 |
| Cerro | 7009 | CFSAN001673 | 79 | 4,690,427 | 141,968 | AYUZ00000000 |
| Cerro | 7010 | CFSAN001674 | 90 | 4,694,516 | 140,791 | AYUY00000000 |
| Cerro | 7020 | CFSAN001679 | 102 | 4,674,873 | 140,217 | AYUX00000000 |
| Cerro | 7021 | CFSAN001680 | 86 | 4,689,127 | 162,579 | AYUW00000000 |
| Cerro | 7022 | CFSAN001681 | 82 | 4,685,594 | 151,097 | AYUV00000000 |
| Cerro | 7032 | CFSAN001690 | 65 | 4,712,966 | 211,782 | AYUU00000000 |
| Cerro | 7033 | CFSAN001691 | 68 | 4,712,532 | 222,383 | AYUT00000000 |
| Cerro | 7034 | CFSAN001692 | 76 | 4,705,937 | 131,290 | AYUS00000000 |
| Cerro | 7036 | CFSAN001697 | 81 | 4,711,367 | 142,132 | AYUR00000000 |
| Typhimurium var. Copenhagen | 084 | CFSAN001284 | 217 | 5,103,297 | 50,576 | AYVJ00000000 |
| Typhimurium var. 5- | 6190 | CFSAN004345 | 227 | 4,732,039 | 45,480 | AYUO00000000 |
| Enteriditis | 3402 | CFSAN001333 | 191 | 4,912,750 | 52,316 | AYVI00000000 |
| Muenster | 5914 | CFSAN004344 | 271 | 4,836,971 | 35,024 | AYUP00000000 |
| Montevideo | 6180 | CFSAN004346 | 258 | 4,897,282 | 35,493 | AYUN00000000 |
| Give var. 15 | 117 | CFSAN004343 | 143 | 4,972,238 | 76,600 | AYUQ00000000 |
| Kentucky | 0253 | CFSAN001286 | 108 | 4,814,097 | 98,447 | AYDR00000000 |
| Kentucky | 5349 | CFSAN001337 | 128 | 4,811,416 | 84,872 | AOYZ00000000 |
| Oranienburg | 250 | CFSAN001285 | 138 | 4,602,146 | 81,627 | AOYM00000000 |
Nucleotide sequence accession numbers.
The sequences for the S. enterica subsp. enterica strains were deposited at NCBI under the accession no. listed in Table 1.
ACKNOWLEDGMENTS
This project was supported by internal FDA/CFSAN and USDA/ARS research funding.
The mention of a trade name, proprietary product, or specific equipment does not constitute a guarantee or warranty by the USDA and does not imply approval to the exclusion of other products that might be suitable.
Footnotes
Citation Haley BJ, Luo Y, Wang C, Pettengill J, Allard M, Brown E, Karns JS, Van Kessel JA. 2014. Genome sequences of eight Salmonella enterica subsp. enterica serovars isolated from a single dairy farm. Genome Announc. 2(2):e00082-14. doi:10.1128/genomeA.00082-14.
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