Abstract
Salmonellosis is an important health problem worldwide and Salmonella enterica serovar Typhimurium is one of the most common isolated serovars. Here, we reported the draft genomes of 40 S. Typhimurium strains isolated from humans and food in Brazil. These draft genomes will improve phylogenetic analysis and will help enhance our understanding of strains of this serovar isolated in Brazil.
GENOME ANNOUNCEMENT
Salmonella enterica is recognized as one of the most common pathogen causes of foodborne disease worldwide (1). In the United States, S. enterica causes approximately 1.0 million cases in humans, resulting in nearly 20,000 hospitalizations and more than 378 deaths each year (2). Salmonella enterica subsp. enterica serovar Typhimurium is one of the most common serovars isolated worldwide, including in Brazil (3).
In this report, we announce 40 draft genome sequences from a collection of S. Typhimurium strains isolated from humans and food between 1983 and 2013 from different geographical locations in Brazil.
DNA from each strain was extracted according to published methods (4). Libraries were prepared using 1 ng of genomic DNA with the Nextera XT kit (Illumina, San Diego, CA), and the genomes were sequenced using NextSeq Illumina for 2 × 151 cycles according to the manufacturer’s instructions. De novo assemblies were generated from all raw sequence data. The Illumina reads were assembled with SPAdes (5). The contigs for each isolate (draft genomes) were annotated using NCBI’s Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (6).
The average G+C mol% of these strains was 52.05%, similar to the reported G+C content for other Salmonella strains (7). The genome length was also within the range described for Salmonella (4.6 Mb to almost 5.1 Mb) (8). The number of contigs per assembly for each isolate ranged from 47 to 286.
The data provided will help in understanding the molecular epidemiology of Salmonella Typhimurium strains isolated from humans and food in Brazil. It will also provide phylogenetic insights into their evolution. A more detailed report of these genomic features will be addressed in a future publication.
Accession number(s).
The draft genome sequences for these 40 Salmonella Typhimurium isolates are available in GenBank and are listed in Table 1.
TABLE 1 .
Metadata for Salmonella Typhimurium strains isolated from humans and food between 1983 and 2013 in Brazil
| CFSAN no.a | Isolate name | WGS accession no.b | Source | Year of isolation | State |
|---|---|---|---|---|---|
| CFSAN033848 | STm01 | LVHC00000000 | Human feces | 1983 | SP |
| CFSAN033851 | STm04 | LVGZ00000000 | Human feces | 1983 | SP |
| CFSAN033852 | STm05 | LVGY00000000 | Human feces | 1983 | SP |
| CFSAN033859 | STm12 | LUJG00000000 | Human feces | 1984 | SP |
| CFSAN033865 | STm18 | LVGN00000000 | Human feces | 1985 | SP |
| CFSAN033866 | STm19 | LVGM00000000 | Human feces | 1986 | SP |
| CFSAN033875 | STm28 | LUJE00000000 | Human feces | 1988 | SP |
| CFSAN033876 | STm29 | LVGE00000000 | Human feces | 1989 | SP |
| CFSAN033877 | STm30 | LVGD00000000 | Human feces | 1990 | SP |
| CFSAN033878 | STm31 | LUJD00000000 | Human feces | 1991 | SP |
| CFSAN033881 | STm34 | LVGA00000000 | Human feces | 1993 | SP |
| CFSAN033882 | STm35 | LVFZ00000000 | Human feces | 1995 | SP |
| CFSAN033883 | STm36 | LVFY00000000 | Cold chicken | 1995 | SP |
| CFSAN033884 | STm37 | LVFX00000000 | Raw pork sausage | 1996 | SP |
| CFSAN033885 | STm38 | LUJC00000000 | Human feces | 1997 | SP |
| CFSAN033886 | STm39 | LUJB00000000 | Human feces | 1998 | SP |
| CFSAN033887 | STm40 | LUJA00000000 | Lettuce | 1998 | SP |
| CFSAN033889 | STm42 | LUIZ00000000 | Human feces | 1999 | SP |
| CFSAN033890 | STm43 | LVFV00000000 | Human feces | 2000 | SP |
| CFSAN033891 | STm44 | LVFU00000000 | Blood | 2000 | SP |
| CFSAN033892 | STm45 | LUIY00000000 | Raw pork sausage | 2000 | SP |
| CFSAN033893 | STm46 | LVFT00000000 | Raw Tuscan sausage | 2002 | SP |
| CFSAN033894 | STm47 | LUIX00000000 | Human feces | 2003 | SP |
| CFSAN033895 | STm48 | LUIW00000000 | Brain abscess | 2005 | SP |
| CFSAN033896 | STm49 | LVFS00000000 | Human feces | 2010 | SP |
| CFSAN033898 | 12288/06 | LUIV00000000 | Swine | 2006 | SC |
| CFSAN033904 | 5937/06 | LUIQ00000000 | Cold chicken | 2006 | SC |
| CFSAN033913 | 16240/09 | LUIJ00000000 | Ready-to-eat dish | 2009 | MS |
| CFSAN033914 | 16202/09 | LUII00000000 | Industrialized product | 2009 | RS |
| CFSAN033918 | 9461/10 | LUIF00000000 | In natura meat | 2010 | SC |
| CFSAN033921 | 3057/10 | LUID00000000 | Frozen chicken carcass | 2010 | PR |
| CFSAN033922 | 6346/10 | LUIC00000000 | Chicken | 2010 | SP |
| CFSAN033923 | 5635/10 | LVFL00000000 | Unknown (food) | 2010 | RS |
| CFSAN033924 | 9109/10 | LVFK00000000 | Swine | 2010 | PR |
| CFSAN033925 | 426/10 | LUIB00000000 | Chicken | 2010 | SC |
| CFSAN033928 | 6709/11 | LVFJ00000000 | Cold chicken | 2011 | RS |
| CFSAN033929 | 948/12 | LUHY00000000 | Raw salad | 2012 | BA |
| CFSAN033930 | 1103/12 | LUHX00000000 | Swine (homemade salami) | 2012 | RS |
| CFSAN033932 | 3330/12 | LUHW00000000 | Roast beef | 2012 | SC |
| CFSAN033933 | 994/13 | LUHV00000000 | Final product sales (animal origin) | 2013 | SP |
CFSAN, Center for Food Safety and Applied Nutrition.
WGS, Whole-Genome Shotgun.
Footnotes
Citation Almeida F, Medeiros MIC, Rodrigues DP, Payne J, Timme RE, Allard MW, Falcão JP. 2016. Draft genome sequences of 40 Salmonella enterica serovar Typhimurium strains isolated from humans and food in Brazil. Genome Announc 4(5):e00892-16. doi:10.1128/genomeA.00892-16.
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