Literature DB >> 29903808

Draft Genome Sequences of 112 Salmonella enterica Serovar Dublin Strains Isolated from Humans and Animals in Brazil.

Fábio Campioni1, Felipe Pinheiro Vilela2, Guojie Cao3, George Kastanis3, Daniela Miller3, Maria Sanchez Leon3, Monique Ribeiro Tiba-Casas4, Sueli Aparecida Fernandes4, Dália Dos Prazeres Rodrigues5, Renata Garcia Costa5, Marc William Allard6, Juliana Pfrimer Falcão7.   

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.

Entities:  

Year:  2018        PMID： 29903808      PMCID： PMC6003729          DOI： 10.1128/genomeA.00405-18

Source DB:  PubMed          Journal:  Genome Announc


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
CFSAN060419QBMT00000000
CFSAN060420QBMU00000000
CFSAN060421QBMV00000000
CFSAN060422QBMW00000000
CFSAN060423QBMX00000000
CFSAN060424QBMY00000000
CFSAN060425QBMZ00000000
CFSAN060426QBNA00000000
CFSAN060427QBNB00000000
CFSAN060428QBNC00000000
CFSAN060429QBND00000000
CFSAN060430QBNE00000000
CFSAN060431QBNF00000000
CFSAN060432QBNG00000000
CFSAN060433QBNH00000000
CFSAN060434QBNI00000000
CFSAN060435QBNJ00000000
CFSAN060436QBNK00000000
CFSAN060437QBNL00000000
CFSAN060438QBNM00000000
CFSAN060439QBNN00000000
CFSAN060440QBNO00000000
CFSAN060441QBNP00000000
CFSAN060442QBNQ00000000
CFSAN060443QBNR00000000
CFSAN060444QBNS00000000
CFSAN060445QBNT00000000
CFSAN060446QBNU00000000
CFSAN060447QBNV00000000
CFSAN060449QBNW00000000
CFSAN060450QBNX00000000
CFSAN060451QBNY00000000
CFSAN060452QBNZ00000000
CFSAN060453QBOA00000000
CFSAN060454QBOB00000000
CFSAN060455QBOC00000000
CFSAN060456QBOD00000000
CFSAN060457QBOE00000000
CFSAN060458QBOF00000000
CFSAN060459QBOG00000000
CFSAN060460QBOH00000000
CFSAN060461QBOI00000000
CFSAN060462QBOJ00000000
CFSAN060463QBOK00000000
CFSAN060464QBOL00000000
CFSAN060465QBOM00000000
CFSAN060466QBON00000000
CFSAN060467QBOO00000000
CFSAN060468QBOP00000000
CFSAN060469QBRY00000000
CFSAN060470QBRZ00000000
CFSAN060471QBSA00000000
CFSAN060472QBSB00000000
CFSAN060473QBSC00000000
CFSAN060474QBSD00000000
CFSAN060475QBSE00000000
CFSAN060476QBSF00000000
CFSAN060477QBSG00000000
CFSAN060478QBSH00000000
CFSAN060479QBSI00000000
CFSAN060480QBSJ00000000
CFSAN060481QBSK00000000
CFSAN060482QBSL00000000
CFSAN060483QBSM00000000
CFSAN060484QBSN00000000
CFSAN060485QBSO00000000
CFSAN060486QBSP00000000
CFSAN060487QBSQ00000000
CFSAN060488QBSR00000000
CFSAN060489QBSS00000000
CFSAN060491QBST00000000
CFSAN060492QBSU00000000
CFSAN060493QBSV00000000
CFSAN060494QBSW00000000
CFSAN060495QBSX00000000
CFSAN060496QBSY00000000
CFSAN060497QBSZ00000000
CFSAN060498QBTA00000000
CFSAN060499QBTB00000000
CFSAN060500QBTC00000000
CFSAN060501QBTD00000000
CFSAN060502QBTE00000000
CFSAN060503QBTF00000000
CFSAN060504QBTG00000000
CFSAN060505QBTH00000000
CFSAN060506QBTI00000000
CFSAN060507QBTJ00000000
CFSAN060508QBTK00000000
CFSAN060509QBTL00000000
CFSAN060510QBTM00000000
CFSAN060511QBTN00000000
CFSAN060512QBTO00000000
CFSAN060513QBTP00000000
CFSAN060514QBTQ00000000
CFSAN060515QBTR00000000
CFSAN060516QBTS00000000
CFSAN060517QBTT00000000
CFSAN060518QBTU00000000
CFSAN060519QBTV00000000
CFSAN060520QBPE00000000
CFSAN060521QBPD00000000
CFSAN060522QBPC00000000
CFSAN060523QBPB00000000
CFSAN060524QBPA00000000
CFSAN060526QBOZ00000000
CFSAN060527QBOY00000000
CFSAN060528QBOX00000000
CFSAN060529QBOW00000000
CFSAN060530QBOV00000000
CFSAN060531QBOU00000000
CFSAN060532QBOT00000000
CFSAN060533QBOS00000000

WGS, whole-genome sequencing.

Metadata for the 112 Salmonella Dublin strains isolated from humans and animals in Brazil WGS, whole-genome sequencing.
  7 in total

Review 1.  Host adapted serotypes of Salmonella enterica.

Authors:  S Uzzau; D J Brown; T Wallis; S Rubino; G Leori; S Bernard; J Casadesús; D J Platt; J E Olsen
Journal:  Epidemiol Infect       Date:  2000-10       Impact factor: 2.451

2.  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

3.  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

Review 4.  Review of pathogenesis and diagnostic methods of immediate relevance for epidemiology and control of Salmonella Dublin in cattle.

Authors:  Liza Rosenbaum Nielsen
Journal:  Vet Microbiol       Date:  2012-08-09       Impact factor: 3.293

5.  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.

Authors:  David Pezoa; Carlos J Blondel; Cecilia A Silva; Hee-Jeong Yang; Helene Andrews-Polymenis; Carlos A Santiviago; Inés Contreras
Journal:  Vet Res       Date:  2014-01-09       Impact factor: 3.683

6.  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

7.  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
  7 in total
  2 in total

1.  High similarity and high frequency of virulence genes among Salmonella Dublin strains isolated over a 33-year period in Brazil.

Authors:  Felipe Pinheiro Vilela; Dália Dos Prazeres Rodrigues; Renata Garcia Costa; Monique Ribeiro Tiba Casas; Juliana Pfrimer Falcão; Fábio Campioni
Journal:  Braz J Microbiol       Date:  2019-11-08       Impact factor: 2.476

2.  Whole genome sequencing analyses revealed that Salmonella enterica serovar Dublin strains from Brazil belonged to two predominant clades.

Authors:  Fábio Campioni; Felipe Pinheiro Vilela; Guojie Cao; George Kastanis; Dália Dos Prazeres Rodrigues; Renata Garcia Costa; Monique Ribeiro Tiba-Casas; Lanlan Yin; Marc Allard; Juliana Pfrimer Falcão
Journal:  Sci Rep       Date:  2022-06-22       Impact factor: 4.996
  2 in total

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