Abstract
Salmonella enterica is an important pathogen transmitted by numerous vectors. Genomic comparisons of Salmonella strains from disparate hosts have the potential to further our understanding of mechanisms underlying host specificities and virulence. Here, we present the closed genome and plasmid sequences of 10 Salmonella enterica subsp. enterica serovar Anatum isolates from bovine and human sources.
GENOME ANNOUNCEMENT
Infections by Salmonella enterica (nontyphoidal) are one of the most common causes of foodborne illnesses, with over a million estimated cases in the United States and an economic impact of $3.66 billion in 2013 (1). The far-reaching impact of this pathogen can be attributed to the many niches and vectors it is able to occupy. Yet in spite of this source diversity, the majority of fully sequenced S. enterica isolates to date are of strains isolated from humans. Expanding the genomic purview of Salmonella from human food sources will facilitate epidemiological tracking as well as comparative genomic methods of source attribution. Salmonella enterica subsp. enterica serovar Anatum is frequently found to be associated with animals in production agriculture (2, 3), including cattle, and yet is not commonly attributed to human salmonellosis (4). Additional genomic and plasmid sequence data for S. Anatum will improve phylogenetic comparisons in different niches. Here, we announce the complete closed genome and plasmid sequences of 10 S. Anatum isolates from cattle (ground beef, hide, and pre-evisceration carcasses) and human salmonellosis.
DNA was isolated from overnight cultures grown at 37°C in Trypticase soy broth (Becton, Dickinson, Franklin Lakes, NJ) and was purified using Genomic-tip 100/G columns and a DNA isolation kit, as per the included protocol (Qiagen, Valencia, CA). Sequencing libraries for single-molecule real-time sequencing (SMRT) on a PacBio RS II instrument (Pacific Biosciences, Menlo Park, CA) were prepared as per the recommendation for P4-C2/P5-C3 chemistry. SMRT produced average subreads of >7 kb and mean coverage of 157×. Complete single-contig chromosomes were assembled using the Celera assembler version 7.0 (5) and then polished by Quiver (6). Use of a self/self-dot plot of consensus sequences in Geneious 8.1.6 (Biomatters Ltd., New Zealand) (7) revealed duplicated ends that were then trimmed at the 3′ end to generate a circularized sequence. Ori-Finder (8) was used to determine the origin of replication and to reset base position 1 of the chromosome.
The average size of the S. Anatum genomes in this report was 4.77 Mb, with a range of 4.64 to 4.95 Mb (Table 1). Five plasmids associated with S. Anatum were assembled from four strains reported here and one previously reported strain, ranging in size from 9,323 bp to >160 kb (Table 1). Isoforms of plasmid pSAN1-2010K-2577 were detected, due to the presence of a shufflon (9). The sequence of the predominant isoform (103.8 kb) is reported here.
TABLE 1 .
Chromosome and plasmid sequence accession numbers and additional information for 10 Salmonella enterica subsp. enterica serovar Anatum strains
| Strain or plasmid | NCBI accession no. | Size (bp) | Coverage (×) | Antibiotic resistance phenotypea | Source of isolation |
|---|---|---|---|---|---|
| pSAN1-1735b | CP014707 | 101,118 | 273.8 | Bovine PREc | |
| USMARC-1676 | CP014620 | 4,676,958 | 125.7 | PS | Ground beef |
| USMARC-1677 | CP014663 | 4,836,394 | 113.0 | PS | Ground beef |
| USMARC-1727 | CP014621 | 4,894,060 | 125.3 | PS | Bovine PRE |
| pSAN1-1727 | CP014622 | 97,041 | 225.1 | ||
| USMARC-1728 | CP014664 | 4,783,492 | 136.2 | PS | Ground beef |
| USMARC-1736 | CP014657 | 4,704,371 | 192.4 | Am Ap F Ax C K S Su Te | Bovine hide |
| pSAN1-1736 | CP014658 | 160,227 | 225.0 | ||
| CDC 06-0532 | CP007211 | 4,667,736 | 111.5 | PS | Human stool |
| CDC 06-0624 | CP014659 | 4,946,108 | 262.0 | Te | Human stool |
| pSAN1-06-0624 | CP014660 | 9,323 | 369.7 | ||
| CDC 06-0855 | CP014665 | 4,751,034 | 134.3 | PS | Human stool |
| CDC 08-1092 | CP014666 | 4,636,307 | 184.9 | PS | Human stool |
| CDC 2010k-2577 | CP014661 | 4,700,848 | 146.3 | Su Sxt | Human stool |
| pSAN1-2010K-2577 | CP014662 | 103,851 | 288.2 |
PS, pansusceptible; Am, amoxicillin-clavulanic acid; Ap, ampicillin; F, cefoxitin; Ax, ceftriaxone; C, chloramphenicol; K, kanamycin; S, streptomycin; Su, sulfisoxazole; Sxt, sulfamethoxazole-trimethoprim; Te, tetracycline.
Host strain USMARC-1735 was previously submitted to NCBI GenBank (10).
PRE, pre-evisceration carcass.
Nucleotide sequence accession numbers.
Genome and plasmid sequence data of the 10 S. Anatum isolates were annotated using the NCBI Prokaryotic Genome Annotation Pipeline and deposited into NCBI GenBank; the accession numbers are listed in Table 1.
ACKNOWLEDGMENTS
We are grateful for the technical assistance of Kerry Brader, Renee Godtel, Bob Lee, Steve Simcox, Sandy Bradley, and Kim Kucera, USDA.
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. The United States Meat Animal Research Center is an equal opportunity employer and provider.
The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.
Funding Statement
S.V.N., D.M.H., J.L.B., T.P.L.S., C.M.K., R.W., J.M.B., and G.P.H. are funded by the Agricultural Research Service of the United States Department of Agriculture. This project was funded in part by the Beef Checkoff.
Footnotes
Citation Nguyen SV, Harhay DM, Bono JL, Smith TPL, Fields PI, Dinsmore BA, Santovenia M, Kelley CM, Wang R, Bosilevac JM, Harhay GP. 2016. Complete and closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Anatum isolates from human and bovine sources. Genome Announc 4(3):e00447-16. doi:10.1128/genomeA.00447-16
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