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Genome Announc. 2017 March; 5(10): e01585-16.
Published online 2017 March 9. doi:  10.1128/genomeA.01585-16
PMCID: PMC5347240

Draft Genome Sequences of 18 Salmonella enterica subsp. enterica Serovar Oranienburg Strains Isolated from Rivers in Northwestern Mexico


Salmonella enterica subsp. enterica serovar Oranienburg is recognized as a foodborne pathogen widely distributed in the environment. Here, we report 18 draft genomes of S. Oranienburg strains isolated from rivers in the northwestern region of Mexico.


In Mexico, the Dirección General de Epidemiología (General Directorate of Epidemiology), highlights Salmonella as one of the main etiological agents of gastroenteritis, and reports 72,000 nontyphoid salmonellosis (NTS) cases annually ( However, it should be noted that serotypes linked to these cases and the infection route were not clearly defined. Salmonella enterica subsp. enterica serovar Oranienburg is a nontyphoid serotype associated with foodborne outbreaks worldwide, including México (1). The rivers located in the northwestern region of Mexico have been recognized as a harboring source of different clones of S. Oranienburg strains and are irrigation sources of crop-exported production, exposing the potential risk of Salmonella dissemination (2). Irrigation water used in agriculture has been linked to NTS outbreaks in the United States (3). Hence, we report here the availability of draft-genome sequences of 18 S. Oranienburg strains isolated from diverse river points in northwestern Mexico.

The bacterial strains samples were prepared by a modified High Pure PCR template preparation kit (Roche, Indianapolis, IN) that carried out genomic DNA extraction. Following the manufacturer’s protocol, sequencing libraries were prepared using the Nextera XT kit (2 × 251 bp) (Illumina, San Diego, CA). Whole genomes were sequenced on an Illumina MiSeq platform (Illumina, San Diego, CA). PEAT-V1-2.1.4 (4) and Trimmomatic version 0.36 (5) were used for adapter and quality trimming, respectively. Assembling analysis was performed with the pipeline A5-miseq (6), and the Rapid Annotations using Subsystems Technology (RAST) server ( and NCBI Prokaryotic Genomes Automatic Annotation Pipeline ( were used to annotate the assembled genomes. Genome size and G+C content were estimated with all contigs of each strain. Also, the serotype was determined by SeqSero software (7).

The in silico serotyping confirmed that all of the strains belong to the S. Oranienburg (7:m,t:-) serotype, as previously reported by a conventional serological test (2). Table 1 summarizes the general characteristics of the draft-genomes of the 18 S. Oranienburg strains isolated from rivers in northwestern Mexico. Briefly, the draft genomes among the strains consist of ~4.57 to ~5.00 Mb with a median value for G+C of 52.0%, and on average a total of ~4,714 and 4,591 coding DNA sequences and proteins were identified, respectively (Table 1). At least 2.2% of proteins might be related to virulence functions, which could be used to infer phylogenetic relationships between strains. These genome sequences have been deposited in GenBank, contributing to the number of S. Oranienburg genomes and biological evolutionary knowledge. Additionally, these references can be used to contribute to epidemiological surveillance studies to control this foodborne pathogen.

Metadata for Salmonella Oranienburg strains isolated from river water in northwestern Mexico

Accession number(s).

The genome sequences of these 18 S. Oranienburg strains are part of GenBank BioProject PRJNA186035 under the accession numbers listed in Table 1.


We thank the Laboratorio Nacional para la Investigación en Inocuidad Alimentaria at the Centro de Investigación en Alimentación y Desarrollo in Mexico for sharing the strains and permitting their use in this research.

This work was supported by the Consejo Nacional de Ciencia y Tecnología in Mexico (CONACyT) grant CB-2014/235989.


Citation Casteñeda-Ruelas GM, Carreón-Gaxiola C, Castelán-Sánchez HG, Acatzi-Silva A, Romero-Martínez S, García-Molina A, Jiménez-Edeza M. 2017. Draft genome sequences of 18 Salmonella enterica subsp. enterica serovar Oranienburg strains isolated from rivers in northwestern Mexico. Genome Announc 5:e01585-16.


1. Vázquez-Garcidueñas MS, Romero-Pérez NL, Figueroa-Aguilar GA, Jaime-Sánchez JL, Vázquez-Marrufo G 2014. Investigation of a food-borne Salmonella Oranienburg outbreak in a Mexican prison. J Infect Dev Ctries 8:143–153. doi:.10.3855/jidc.3367 [PubMed] [Cross Ref]
2. Jiménez M, Martinez-Urtaza J, Rodriguez-Alvarez MX, Leon-Felix J, Chaidez C 2014. Prevalence and genetic diversity of Salmonella spp. in a river in a tropical environment in Mexico. J Water Health 12:874–884. doi:.10.2166/wh.2014.051 [PubMed] [Cross Ref]
3. Behravesh CB, Mody RK, Jungk J, Gaul L, Redd JT, Chen S, Cosgrove S, Hedican E, Sweat D, Chávez-Hauser L, Snow SL, Hanson H, Nguyen T, Sodha SV, Boore AL, Russo E, Mikoleit M, Theobald L, Gerner-Smidt P, Hoekstra RM, Angulo FJ, Swerdlow DL, Tauxe RV, Griffin PM, Williams IT 2011. 2008 Outbreak of Salmonella Saintpaul infections associated with raw produce. N Engl J Med 364:918–927. doi:.10.1056/NEJMoa1005741 [PubMed] [Cross Ref]
4. Li YL, Weng JC, Hsiao CC, Chou MT, Tseng CW, Hung JH 2015. PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm. BMC Bioinformatics 16:S2. doi:.10.1186/1471-2105-16-S1-S2 [PMC free article] [PubMed] [Cross Ref]
5. Bolger AM, Lohse M, Usadel B 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi:.10.1093/bioinformatics/btu170 [PMC free article] [PubMed] [Cross Ref]
6. Coil D, Jospin G, Darling AE 2015. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31:587–589. doi:.10.1093/bioinformatics/btu661 [PubMed] [Cross Ref]
7. Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X 2015. Salmonella serotype determination utilizing high-throughput genome sequencing data. J Clin Microbiol 53:1685–1692. doi:.10.1128/JCM.00323-15 [PMC free article] [PubMed] [Cross Ref]

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