Literature DB >> 28705959

Draft Genome Sequences of 256 Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Humans, Food, Chickens, and Farm Environments in Brazil.

Fábio Campioni1, Guojie Cao2, George Kastanis2, Maria Sanchez Leon2, Alzira Maria Morato Bergamini3, Dália Dos Prazeres Rodrigues4, Marc William Allard5, Juliana Pfrimer Falcão6.   

Abstract

Salmonella enterica subsp. enterica serovar Enteritidis emerged in the late 1980s as the most isolated Salmonella serovar worldwide. Here, we report the draft genomes of 256 S Enteritidis strains isolated from humans, food, chickens, and farm environments in Brazil. These draft genomes will help enhance our understanding of this serovar in Brazil.
Copyright © 2017 Campioni et al.

Entities:  

Year:  2017        PMID： 28705959      PMCID： PMC5511898          DOI： 10.1128/genomeA.00399-17

Source DB:  PubMed          Journal:  Genome Announc


GENOME ANNOUNCEMENT

Salmonellosis caused by Salmonella enterica serovars has been a major health problem worldwide in terms of morbidity and mortality (1). S. enterica subsp. enterica serovar Enteritidis emerged in the late 1980s as one of the most isolated serovars from gastroenteritis cases linked to the consumption of raw or undercooked eggs and chickens in several countries (2, 3). In Brazil, the increase of S. Enteritidis isolation started in the late 1990s and currently remains one of the most isolated serovars in this country (4–7). Here, we announce 256 draft genome sequences from a collection of S. Enteritidis strains isolated in several states of Brazil from humans, food, chickens, and farm environments. DNA from each strain was extracted according to Campioni et al. (8). Libraries were prepared using 1 ng of genomic DNA with the Nextera XT DNA library preparation kit (Illumina, San Diego, CA, USA), and the genomes were sequenced using the NextSeq 500 desktop sequencer with the NextSeq 500/500 high-output version 2 kit (300 cycles) (Illumina, San Diego, CA, USA) 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 CLC Genomics Workbench version 9.5.2. The contigs for each isolate (draft genomes) were annotated using NCBI’s Prokaryotic Genome Annotation Pipeline (PGAP) (9). The genomes ranged between 4.6 and 4.8 Mb in size, as described for previous Salmonella isolates (4.6 Mb to almost 5.1 Mb) (10). The number of contigs per assembly for each isolate ranged from 52 to 183. The data provided will help in understanding the epidemiology of S. Enteritidis strains isolated in Brazil from different sources. 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 the 256 S. Enteritidis isolates reported here are available in GenBank under the accession numbers listed in Table 1.
TABLE 1 

Metadata for the 256 S. Enteritidis strains isolated from humans, food, chickens, and farm environments in Brazil

CFSANa no.GenBank accession no.
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CFSAN057776MZTR00000000
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CFSAN057810MZUZ00000000
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CFSAN057820MZVJ00000000
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CFSAN057842MZWC00000000
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CFSAN057845MZWF00000000
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CFSAN057850MZWK00000000
CFSAN057851MZWL00000000
CFSAN057852MZWM00000000
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CFSAN057855MZWP00000000
CFSAN057858MZWQ00000000
CFSAN057859MZWR00000000
CFSAN057860MZWS00000000
CFSAN057861MZWT00000000
CFSAN057862MZWU00000000
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CFSAN057864MZWW00000000
CFSAN057865MZWX00000000
CFSAN057866NBNA00000000
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CFSAN057868MZWZ00000000
CFSAN057869MZXA00000000
CFSAN057870MZXB00000000
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CFSAN057873MZXD00000000
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CFSAN057875MZXF00000000
CFSAN057880MZXG00000000
CFSAN057881MZXH00000000
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CFSAN057884MZXK00000000
CFSAN057885MZXL00000000
CFSAN057888MZXM00000000
CFSAN057889MZXN00000000
CFSAN057890MZXO00000000
CFSAN057891MZXP00000000

CFSAN, Center for Food Safety and Applied Nutrition (FDA).

Metadata for the 256 S. Enteritidis strains isolated from humans, food, chickens, and farm environments in Brazil CFSAN, Center for Food Safety and Applied Nutrition (FDA).
  9 in total

1.  Phage types of Salmonella enteritidis isolated from clinical and food samples, and from broiler carcasses in southern Brazil.

Authors:  Luciana Ruschel dos Santos; Vladimir Pinheiro do Nascimento; Sílvia Dias de Oliveira; Dália P Rodrigues; Eliane Moura Falavina dos Reis; Liliane Miyuki Seki; Aldemir Reginato Ribeiro; Sueli A Fernandes
Journal:  Rev Inst Med Trop Sao Paulo       Date:  2003 Jan-Feb       Impact factor: 1.846

Review 2.  Salmonella, stress responses and food safety.

Authors:  Tom Humphrey
Journal:  Nat Rev Microbiol       Date:  2004-06       Impact factor: 60.633

Review 3.  Mechanisms of egg contamination by Salmonella Enteritidis.

Authors:  Inne Gantois; Richard Ducatelle; Frank Pasmans; Freddy Haesebrouck; Richard Gast; Tom J Humphrey; Filip Van Immerseel
Journal:  FEMS Microbiol Rev       Date:  2009-01-21       Impact factor: 16.408

4.  Genotypic diversity and virulence markers of Yersinia enterocolitica biotype 1A strains isolated from clinical and non-clinical origins.

Authors:  Fábio Campioni; Juliana P Falcão
Journal:  APMIS       Date:  2013-06-14       Impact factor: 3.205

5.  The global burden of nontyphoidal Salmonella gastroenteritis.

Authors:  Shannon E Majowicz; Jennie Musto; Elaine Scallan; Frederick J Angulo; Martyn Kirk; Sarah J O'Brien; Timothy F Jones; Aamir Fazil; Robert M Hoekstra
Journal:  Clin Infect Dis       Date:  2010-03-15       Impact factor: 9.079

6.  The role of public health laboratory in the problem of salmonellosis in São Paulo, Brazil.

Authors:  A E Taunay; S A Fernandes; A T Tavechio; B C Neves; A M Dias; K Irino
Journal:  Rev Inst Med Trop Sao Paulo       Date:  1996 Mar-Apr       Impact factor: 1.846

7.  Phenotypic and molecular characterization of Salmonella Enteritidis strains isolated in São Paulo, Brazil.

Authors:  Sueli A Fernandes; Angela C R Ghilardi; Ana T Tavechio; Antonia M O Machado; Antonio C C Pignatari
Journal:  Rev Inst Med Trop Sao Paulo       Date:  2003-05-14       Impact factor: 1.846

8.  Phylogenetics and differentiation of Salmonella Newport lineages by whole genome sequencing.

Authors:  Guojie Cao; Jianghong Meng; Errol Strain; Robert Stones; James Pettengill; Shaohua Zhao; Patrick McDermott; Eric Brown; Marc Allard
Journal:  PLoS One       Date:  2013-02-11       Impact factor: 3.240

9.  The National Center for Biotechnology Information's Protein Clusters Database.

Authors:  William Klimke; Richa Agarwala; Azat Badretdin; Slava Chetvernin; Stacy Ciufo; Boris Fedorov; Boris Kiryutin; Kathleen O'Neill; Wolfgang Resch; Sergei Resenchuk; Susan Schafer; Igor Tolstoy; Tatiana Tatusova
Journal:  Nucleic Acids Res       Date:  2008-10-21       Impact factor: 16.971
  9 in total

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