ABSTRACT
Salmonella enterica serovar Dublin is a strongly adapted serovar that causes enteritis and/or systemic disease in cattle and results in high rates of mortality. Here, we report the draft genome sequences of 112 S. Dublin strains isolated from humans and animals in Brazil. These draft genome sequences will help enhance our understanding of this serovar in Brazil.
GENOME ANNOUNCEMENT
Salmonellosis by nontyphoidal serovars is among the most common foodborne infections worldwide, causing around 93.8 million cases of gastroenteritis and 155,000 deaths annually (1). Salmonella enterica serovar Dublin is a strongly adapted serovar that causes enteritis and/or systemic disease in cattle and results in high rates of mortality. However, sporadically, it can be isolated from humans, usually causing serious disease, especially in patients with underlying chronic diseases (2–4).
In this report, we announce 112 draft genome sequences from a collection of S. Dublin strains isolated from humans and animals in several states of Brazil.
DNA from each strain was extracted according to Campioni and Falcão (5). Libraries were prepared using 1 ng of genomic DNA with the Nextera XT DNA library preparation kit (Illumina, San Diego, CA). The genomes were then sequenced using the Illumina NextSeq 500 desktop sequencer using the NextSeq 500/500 high-output kit version 2 (300 cycles; Illumina) at 2 × 151 cycles, according to the manufacturer’s recommendations. De novo assemblies were generated from all the Illumina sequence data using CLC Genomics Workbench version 9.5.2 (Qiagen Bioinformatics, Denmark). The contigs for each isolate (draft genomes) were annotated using NCBI’s Prokaryotic Genome Annotation Pipeline (PGAP) (6). The genomes ranged between 4.7 and 5.0 Mb in size, as described for other Salmonella genomes (4.6 Mb to almost 5.1 Mb) (7). The number of contigs per assembly for each isolate ranged from 46 to 179.
The data provided will help in the understanding of the epidemiology of Salmonella Dublin strains isolated in Brazil from different sources. It will also provide phylogenetic insights into the evolution of these strains. A more detailed report of these genomic features will be addressed in a future publication.
Accession number(s).
The draft genome sequences for these 112 S. Dublin isolates are available in GenBank and are listed in Table 1.
TABLE 1.
Metadata for the 112 Salmonella Dublin strains isolated from humans and animals in Brazil
| CFSAN no. | WGS accession no.a |
|---|---|
| CFSAN060419 | QBMT00000000 |
| CFSAN060420 | QBMU00000000 |
| CFSAN060421 | QBMV00000000 |
| CFSAN060422 | QBMW00000000 |
| CFSAN060423 | QBMX00000000 |
| CFSAN060424 | QBMY00000000 |
| CFSAN060425 | QBMZ00000000 |
| CFSAN060426 | QBNA00000000 |
| CFSAN060427 | QBNB00000000 |
| CFSAN060428 | QBNC00000000 |
| CFSAN060429 | QBND00000000 |
| CFSAN060430 | QBNE00000000 |
| CFSAN060431 | QBNF00000000 |
| CFSAN060432 | QBNG00000000 |
| CFSAN060433 | QBNH00000000 |
| CFSAN060434 | QBNI00000000 |
| CFSAN060435 | QBNJ00000000 |
| CFSAN060436 | QBNK00000000 |
| CFSAN060437 | QBNL00000000 |
| CFSAN060438 | QBNM00000000 |
| CFSAN060439 | QBNN00000000 |
| CFSAN060440 | QBNO00000000 |
| CFSAN060441 | QBNP00000000 |
| CFSAN060442 | QBNQ00000000 |
| CFSAN060443 | QBNR00000000 |
| CFSAN060444 | QBNS00000000 |
| CFSAN060445 | QBNT00000000 |
| CFSAN060446 | QBNU00000000 |
| CFSAN060447 | QBNV00000000 |
| CFSAN060449 | QBNW00000000 |
| CFSAN060450 | QBNX00000000 |
| CFSAN060451 | QBNY00000000 |
| CFSAN060452 | QBNZ00000000 |
| CFSAN060453 | QBOA00000000 |
| CFSAN060454 | QBOB00000000 |
| CFSAN060455 | QBOC00000000 |
| CFSAN060456 | QBOD00000000 |
| CFSAN060457 | QBOE00000000 |
| CFSAN060458 | QBOF00000000 |
| CFSAN060459 | QBOG00000000 |
| CFSAN060460 | QBOH00000000 |
| CFSAN060461 | QBOI00000000 |
| CFSAN060462 | QBOJ00000000 |
| CFSAN060463 | QBOK00000000 |
| CFSAN060464 | QBOL00000000 |
| CFSAN060465 | QBOM00000000 |
| CFSAN060466 | QBON00000000 |
| CFSAN060467 | QBOO00000000 |
| CFSAN060468 | QBOP00000000 |
| CFSAN060469 | QBRY00000000 |
| CFSAN060470 | QBRZ00000000 |
| CFSAN060471 | QBSA00000000 |
| CFSAN060472 | QBSB00000000 |
| CFSAN060473 | QBSC00000000 |
| CFSAN060474 | QBSD00000000 |
| CFSAN060475 | QBSE00000000 |
| CFSAN060476 | QBSF00000000 |
| CFSAN060477 | QBSG00000000 |
| CFSAN060478 | QBSH00000000 |
| CFSAN060479 | QBSI00000000 |
| CFSAN060480 | QBSJ00000000 |
| CFSAN060481 | QBSK00000000 |
| CFSAN060482 | QBSL00000000 |
| CFSAN060483 | QBSM00000000 |
| CFSAN060484 | QBSN00000000 |
| CFSAN060485 | QBSO00000000 |
| CFSAN060486 | QBSP00000000 |
| CFSAN060487 | QBSQ00000000 |
| CFSAN060488 | QBSR00000000 |
| CFSAN060489 | QBSS00000000 |
| CFSAN060491 | QBST00000000 |
| CFSAN060492 | QBSU00000000 |
| CFSAN060493 | QBSV00000000 |
| CFSAN060494 | QBSW00000000 |
| CFSAN060495 | QBSX00000000 |
| CFSAN060496 | QBSY00000000 |
| CFSAN060497 | QBSZ00000000 |
| CFSAN060498 | QBTA00000000 |
| CFSAN060499 | QBTB00000000 |
| CFSAN060500 | QBTC00000000 |
| CFSAN060501 | QBTD00000000 |
| CFSAN060502 | QBTE00000000 |
| CFSAN060503 | QBTF00000000 |
| CFSAN060504 | QBTG00000000 |
| CFSAN060505 | QBTH00000000 |
| CFSAN060506 | QBTI00000000 |
| CFSAN060507 | QBTJ00000000 |
| CFSAN060508 | QBTK00000000 |
| CFSAN060509 | QBTL00000000 |
| CFSAN060510 | QBTM00000000 |
| CFSAN060511 | QBTN00000000 |
| CFSAN060512 | QBTO00000000 |
| CFSAN060513 | QBTP00000000 |
| CFSAN060514 | QBTQ00000000 |
| CFSAN060515 | QBTR00000000 |
| CFSAN060516 | QBTS00000000 |
| CFSAN060517 | QBTT00000000 |
| CFSAN060518 | QBTU00000000 |
| CFSAN060519 | QBTV00000000 |
| CFSAN060520 | QBPE00000000 |
| CFSAN060521 | QBPD00000000 |
| CFSAN060522 | QBPC00000000 |
| CFSAN060523 | QBPB00000000 |
| CFSAN060524 | QBPA00000000 |
| CFSAN060526 | QBOZ00000000 |
| CFSAN060527 | QBOY00000000 |
| CFSAN060528 | QBOX00000000 |
| CFSAN060529 | QBOW00000000 |
| CFSAN060530 | QBOV00000000 |
| CFSAN060531 | QBOU00000000 |
| CFSAN060532 | QBOT00000000 |
| CFSAN060533 | QBOS00000000 |
WGS, whole-genome sequencing.
ACKNOWLEDGMENTS
The study was supported by FDA/CFSAN under Marc William Allard’s supervision and by the Sao Paulo Research Foundation-FAPESP (Proc. 2016/24716-3) and CNPq (473043/2013-0) under Juliana Pfrimer Falcão’s supervision. During the course of this work, Fabio Campioni was supported by a fellowship from the Sao Paulo Research Foundation-FAPESP (grants 2013/25191-3 and 2016/05817-3) and Felipe Pinheiro Vilela by a scholarship from the Sao Paulo Research Foundation-FAPESP (grants 2015/10818-6 and 2017/05756-7).
Footnotes
Citation Campioni F, Vilela FP, Cao G, Kastanis G, Miller D, Sanchez Leon M, Tiba-Casas MR, Fernandes SA, Rodrigues DDP, Costa RG, Allard MW, Falcão JP. 2018. Draft genome sequences of 112 Salmonella enterica serovar Dublin strains isolated from humans and animals in Brazil. Genome Announc 6:e00405-18. https://doi.org/10.1128/genomeA.00405-18.
REFERENCES
- 1.Majowicz SE, Musto J, Scallan E, Angulo FJ, Kirk M, O’Brien SJ, Jones TF, Fazil A, Hoekstra RM, International Collaboration on Enteric Disease ‘Burden of Illness’ Studies . 2010. The global burden of nontyphoidal Salmonella gastroenteritis. Clin Infect Dis 50:882–889. doi: 10.1086/650733. [DOI] [PubMed] [Google Scholar]
- 2.Pezoa D, Blondel CJ, Silva CA, Yang H-J, Andrews-Polymenis H, Santiviago CA, Contreras I. 2014. Only one of the two type VI secretion systems encoded in the Salmonella enterica serotype Dublin genome is involved in colonization of the avian and murine hosts. Vet Res 45:2. doi: 10.1186/1297-9716-45-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Uzzau S, Brown DJ, Wallis T, Rubino S, Leori G, Bernard S, Casadesús J, Platt DJ, Olsen JE. 2000. Host adapted serotypes of Salmonella enterica. Epidemiol Infect 125:229–255. doi: 10.1017/S0950268899004379. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Nielsen LR. 2013. Review of pathogenesis and diagnostic methods of immediate relevance for epidemiology and control of Salmonella Dublin in cattle. Vet Microbiol 162:1–9. doi: 10.1016/j.vetmic.2012.08.003. [DOI] [PubMed] [Google Scholar]
- 5.Campioni F, Falcão JP. 2014. Genotypic diversity and virulence markers of Yersinia enterocolitica biotype 1A strains isolated from clinical and non-clinical origins. APMIS 122:215–222. doi: 10.1111/apm.12126. [DOI] [PubMed] [Google Scholar]
- 6.Klimke W, Agarwala R, Badretdin A, Chetvernin S, Ciufo S, Fedorov B, Kiryutin B, O’Neill K, Resch W, Resenchuk S, Schafer S, Tolstoy I, Tatusova T. 2009. The National Center for Biotechnology Information’s Protein Clusters Database. Nucleic Acids Res 37:D216–D223. doi: 10.1093/nar/gkn734. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Cao G, Meng J, Strain E, Stones R, Pettengill J, Zhao S, McDermott P, Brown E, Allard M. 2013. Phylogenetics and differentiation of Salmonella Newport lineages by whole genome sequencing. PLoS One 8:e55687. doi: 10.1371/journal.pone.0055687. [DOI] [PMC free article] [PubMed] [Google Scholar]