ABSTRACT
Salmonella enterica serovar Typhimurium strains isolated from systemic sites outside sub-Saharan Africa have been rarely sequenced. Here, we report the draft genome sequences of S. Typhimurium sequence type 19 (ST19) (n = 9), ST1649 (n = 1), and ST313 (n = 1) strains isolated from human systemic (e.g., blood) and nonsystemic (e.g., stool and wounds) sites in Brazil.
GENOME ANNOUNCEMENT
Nontyphoidal Salmonella (NTS) is one of the major causes of diarrheal disease worldwide, with an estimated 93 million enteric infections and 155,000 deaths annually (1). However, these estimates do not include the infections caused by invasive nontyphoidal Salmonella (iNTS) enterica serovar Typhimurium sequence type 313 (ST313), which is often associated with systemic infection. S. Typhimurium ST313 strains account for >50% of the systemic infections in sub-Saharan Africa (2, 3). Two genetic lineages of S. Typhimurium ST313 have been linked with the emergence of iNTS across sub-Saharan Africa (4). In Brazil, S. Typhimurium is frequently isolated from systemic sites, such as blood and cerebrospinal fluid (CSF), from human patients (5, 6); however, the genetic underpinning of S. Typhimurium isolates recovered from systemic sites in Brazil remains unknown. We sequenced 11 S. Typhimurium strains isolated from blood (n = 4), stool (n = 4), and extraintestinal (n = 3) sites between 2010 and 2014 from different geographic regions of Brazil (Table 1).
TABLE 1 .
GenBank accession numbers of Salmonella Typhimurium strains isolated from human clinical samples in Brazil
| Strain | SRA accession no. | WGS accession no.a | No. of contigs | N50 (bp) | Length (bp) | Sourceb | Yr | State |
|---|---|---|---|---|---|---|---|---|
| PP_BR007 | SAMN05505504 | NPJP00000000 | 156 | 57,229 | 4,632,574 | Blood | 2014 | Rio de Janeiro |
| PP_BR026 | SAMN05505503 | NPJQ00000000 | 149 | 62,099 | 4,777,031 | Blood | 2012 | Rio Grande do Sul |
| PP_BR027 | SAMN05505502 | NPJR00000000 | 175 | 44,398 | 4,626,743 | WS | 2012 | Rio Grande do Sul |
| PP_BR031 | SAMN05505501 | NPJS00000000 | 190 | 46,721 | 4,594,320 | WS | 2012 | Rio Grande do Sul |
| PP_BR032 | SAMN05505500 | NPJT00000000 | 122 | 99,313 | 4,650,556 | ABS | 2012 | Rio Grande do Sul |
| PP_BR045 | SAMN05505499 | NPJU00000000 | 147 | 76,702 | 4,827,606 | RS | 2011 | Santa Catarina |
| PP_BR057 | SAMN05505498 | NRDL00000000 | 131 | 103,073 | 4,787,663 | Blood | 2011 | Amapá |
| PP_BR060 | SAMN05505496 | NPMT00000000 | 123 | 96,334 | 4,776,943 | Feces | 2011 | Minas Gerais |
| PP_BR062 | SAMN05505495 | NRDM00000000 | 118 | 142,310 | 4,958,705 | Feces | 2010 | Santa Catarina |
| PP_BR063 | SAMN05505494 | NRDN00000000 | 161 | 50,016 | 4,365,189 | Blood | 2010 | Rio Grande do Sul |
| PP_BR076 | SAMN05505493 | NSDQ00000000 | 125 | 120,490 | 5,065,902 | Feces | 2010 | Rio Grande do Sul |
WGS, whole-genome sequencing.
WS, wound secretion; ABS, abdominal abscess; RS, rectal swab.
Paired-end sequencing libraries (2 × 250 bp) were prepared using the Nextera XT kit (Illumina, San Diego, CA) following the protocol described in the DNA library reference guide (7), size selected to be in the range of 600 to 1,000 bp (average peaks, ~800 bp), and sequenced using the MiSeq Illumina version 2 kit, according to the manufacturer’s instructions. The number of paired reads per sample ranged from 941,320 to 1,389,798. The average G+C content was 52.5% (8). De novo assembly was performed using Velvet 1.2.10 set at default for all parameters (9). Contigs were organized by aligning to the genome sequence of the reference strain S. Typhimurium LT2 (accession no. NC_003197) using Mauve multiple alignments (10). Whole-genome multilocus sequence typing was performed using EnteroBase (https://enterobase.warwick.ac.uk/). A total of three sequence types, ST19 (n = 9), ST1695 (n = 1), and ST313 (n = 1), were identified. Detailed comparative genomics analysis of these strains is currently ongoing and will be published independently. These genome sequences will provide better insights into the molecular epidemiology of invasive S. Typhimurium strains in Brazil.
Accession number(s).
The draft genome sequences are available in GenBank under the accession numbers listed in Table 1.
ACKNOWLEDGMENTS
We thank Li Zhen at the Washington Department of Health (WADOH) and Mark Allard at the FDA Center for Food Safety and Applied Nutrition (CFSAN) for sequencing the strains used in this study.
This research was funded by the Safe Food Initiative and Agricultural Animal Health Program at the Washington State University, Pullman, WA. Pedro Henrique N. Panzenhagen received scholarship support by the Doctoral Sandwich Abroad Program CAPES/PDSE at the Federal University of Rio de Janeiro.
We declare no conflicts of interest.
Footnotes
Citation Panzenhagen PHN, Paul NC, Conte Junior CA, Costa RG, Rodrigues DP, Shah DH. 2018. Draft genome sequences of 11 Salmonella enterica serovar Typhimurium strains isolated from human systemic and nonsystemic sites in Brazil. Genome Announc 6:e01223-17. https://doi.org/10.1128/genomeA.01223-17.
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