Complete genome sequence data of two Salmonella enterica subsp. enterica serovar Gallinarum: A 9R vaccine strain and a virulent Brazilian field strain

Salmonella Gallinarum (SG) is a host-restricted enterobacteria and the causative agent of fowl typhoid in poultry. Here, we report the complete genomes of two strains belonging to this serotype. SA68 is a field strain isolated from the livers of dead hen carcasses of a commercial layer farm presenting high mortality located in São Paulo city, Brazil, in 1990. Strain 9R corresponds to a live attenuated SG commercial vaccine. DNA was extracted from pure cultures and subjected to whole genome sequencing (WGS) using the Ion Torrent PGM System. The assemblies reached lengths of 4,657,435 (SA68) and 4,657,471 (9R) base pairs. Complete genomes were deposited in GenBank under the accession numbers CP110192 (SA68) and CP110508 (9R). Both genomes were analyzed and compared in terms of molecular typing, antibiotic resistance genes, virulence genes, Salmonella pathogenic islands (SPIs), insertion sequences and prophages. The data obtained show many similarities in the genetic content, with the exception of the SPI-12 and CS54 pathogenic islands, which are exclusive to the field strain. The information generated will help to understand the virulence differences of field and vaccinal SG strains and can be used to perform evolutionary and epidemiologic studies.


a b s t r a c t
Salmonella Gallinarum (SG) is a host-restricted enterobacteria and the causative agent of fowl typhoid in poultry. Here, we report the complete genomes of two strains belonging to this serotype. SA68 is a field strain isolated from the livers of dead hen carcasses of a commercial layer farm presenting high mortality located in São Paulo city, Brazil, in 1990. Strain 9R corresponds to a live attenuated SG commercial vaccine. DNA was extracted from pure cultures and subjected to whole genome sequencing (WGS) using the Ion Torrent PGM System. The assemblies reached lengths of 4,657,435 (SA68) and 4,657,471 (9R) base pairs. Complete genomes were Keywords: Fowl typhoid Multilocus sequence typing Serotype Pathogenicity island Virulence factor Antimicrobial Resistance gene Mobile genetic element Prophages deposited in GenBank under the accession numbers CP110192 (SA68) and CP110508 (9R). Both genomes were analyzed and compared in terms of molecular typing, antibiotic resistance genes, virulence genes, Salmonella pathogenic islands (SPIs), insertion sequences and prophages. The data obtained show many similarities in the genetic content, with the exception of the SPI-12 and CS54 pathogenic islands, which are exclusive to the field strain. The information generated will help to understand the virulence differences of field and vaccinal SG strains and can be used to perform evolutionary and epidemiologic studies. ©

Value of the Data
• The available complete genome sequencing data of field and vaccinal Salmonella Gallinarum strains provides insight into genetic differences among this avian serovar. • The data also help to understand the increased virulence of field strains carrying additional virulence factors. • The data can be used to perform comparative and evolutionary genomics for Salmonella Gallinarum and other Salmonella serovars.

Introduction
We aimed to sequence the complete genome of a field and a vaccinal strain of Salmonella enterica subsp. enterica serovar Gallinarum and compare their genomic characteristics.

Data Description
Salmonella enterica subsp. enterica serovar Gallinarum is a gram-negative Enterobacteriaceae that is flagellated and nonmotile. It is the major cause of fowl typhoid in mature birds, producing acute or chronic septicemic disease and significant economic losses in the poultry industry [1] . It is usually controlled by using live attenuated vaccines; however, it remains endemic to Asia and South America and causes outbreaks in developed countries [2] . Genetic and genomic approaches have shown differences in the virulence gene composition and the importance of horizontal gene transfer in genome evolution and host adaptation in chicken-associated serovars [3][4][5] . In this sense, the availability of SG genomes from distinct geographical and temporal locations allows for a deeper understanding of this pathogen [6 , 7] .
The complete genomic data reported here include the whole-genome sequencing, assembly, annotation and comparative genomic data of two Salmonella isolates (SA68 and 9R) corresponding to field and vaccine strains. The raw reads from both genomes were trimmed and assembled. The genome assembly results, annotation, typification and genetic features and gene content are listed in Table 1 .

Bacterial isolation, genomic DNA extraction and sequencing
Field strain SA68 originated from a liver sample and was cultured in tetrathionate for 48 hrs at 37 °C and then cultured in xylose lysine tergitol 4 (XLT4) agar for 24 h at 37 °C. Typical colonies were detected and subjected to biochemical testing using Enterokit B (Probac, SP, Brazil). Vaccinal strain SG 9R was obtained from Cevac® S. Gallinarum lyophilized live vaccine. Colonies were cultured in LB broth for 18 hrs at 37 °C for DNA extraction using the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany). Samples were submitted for whole genome sequencing. Libraries were prepared using the Ion Torrent RNA-Seq kit and sequenced on the Ion Torrent PGM.

Genome assembly, annotation, descriptive and comparative genomic analysis
The nucleic acid sequences of each sample were assembled using SeqMan NGen software (DNASTAR Lasergene, Madison, WI, USA). The S. Gallinarum 287/91 strain (GenBank Accession Number: AM933173) was used as the reference scaffold for the templated assembly. The Q-score for all sequences included in the assembly was Q > 28. The average read length was ∼140 bp. The genomes were annotated by NCBI Prokaryotic Genome Annotation Pipeline (PGAP v. 6.3) [16] .

Ethics Statements
The study was conducted according to the guidelines of the Declaration of Helsinki

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Data Availability
Salmonella enterica subsp. enterica Genome sequencing and assembly (Original data) (Bio-Project NCBI).