Abstract
The draft genome of Salmonella enterica serovar Enteritidis phage type 4 (PT4) strain IOC4647/2004, isolated from a poultry farm in São Paulo state, was obtained with high-throughput Illumina sequencing platform, generating 4,173,826 paired-end reads with 251 bp. The assembly of 4,804,382 bp in 27 scaffolds shows strong similarity to other S. Enteritidis strains.
GENOME ANNOUNCEMENT
Nontyphoidal Salmonella (NTS) is one of the commonest bacterial pathogens causing gastrointestinal infection worldwide. Salmonella enterica serovar Enteritidis is the most prevalent serovar (1); it accounts for huge global disease burden and causes human gastroenteritis and bacteremia (2, 3). Since 1993, S. Enteritidis has been the main serovar underlying human infections isolated from poultry materials in Brazil. This serovar is still the cause of many losses faced by the national poultry industry (4).
Although our understanding of the host immune response to S. enterica infections has improved considerably, some important questions remain unanswered (5). Comparative analysis of different Salmonella genomes revealed that core regions resembled each other closely, and that continuous genetic re-assortment increased virulence and generated multiple-drug resistant isolates, which is of significant public health concern (6). An important feature among different S. Enteritidis isolates is the genetic similarity they share, which makes their discrimination by traditional genotyping methods difficult (7). Hence, sequencing samples from different locations worldwide is crucial to detect specific differences that might be related to factors driving the evolution of this pathogen.
Here we announce a whole-genome sequence of Brazilian S. Enteritidis phage type 4 strain IOC4746, considered a representative strain isolated in the state of São Paulo in 2004 (FIOCRUZ, unpublished data). DNA was isolated from overnight Luria-Broth culture using a DNA purification kit (Promega Corporation, Madison, WI, USA). Libraries were prepared with the Nextera mate-pair sample preparation kit and the TruSeq DNA PCR-free LT sample prep kit according to the manufacturer’s instructions (Illumina, San Diego, CA, USA). The genome was sequenced with the Illumina HiSeq2500 platform, which produced 4,173,826 paired-end reads with 251 bp. The reads were de novo assembled using SPAdes version 3.6.0 (8). Contigs larger than 1,000 bp were scaffolded using SSPACE version 2.0 (9), which gave 27 scaffolds and totaled 4,804,382 bp (largest: 1,549,687 bp; N50: 490,431 bp; mean: 177,940 bp).
The contigs were aligned with the reference S. Enteritidis strain P125109 using MAUVE (10), and an automated annotation was made with RAST (11). Two scaffolds containing 51,142 and 7,763 bp, respectively, perfectly aligned with the virulence plasmid of P125109, but it was not possible to close it. The alignment showed that this S. Enteritidis isolate presents high identity with the P125109 strain. A kmerfinder (12) confirmed this observation, and multilocus sequencing typing (13) indicated that strain IOC4746 is sequence type 11 (ST 11), the most common ST among “classic” S. Enteritidis isolates (14).
Nucleotide sequence accession numbers.
The whole-genome sequence generated in this project has been deposited at DDBJ/ENA/GenBank under the accession no. LTDW00000000. The version described in this paper is the first version, LTDW01000000.
ACKNOWLEDGMENT
We thank Cynthia Manso for English grammar review.
Funding Statement
G.P.M. was supported by a FAPESP fellowship (2012/05382-6).
Footnotes
Citation Milanez GP, Nascimento LC, Tirabassi AH, Zuanaze M, Rodrigues DP, Pereira GAG, Brocchi M. 2016. Whole-genome sequence of Salmonella enterica serovar Enteritidis phage type 4, isolated from a Brazilian poultry farm. Genome Announc 4(3):e00340-16. doi:10.1128/genomeA.00340-16.
REFERENCES
- 1.Hendriksen RS, Vieira AR, Karlsmose S, Lo Fo Wong DM, Jensen AB, Wegener HC, Aarestrup FM. 2011. Global monitoring of Salmonella serovar distribution from the World Health Organization global Foodborne Infections Network Country Databank: results of quality assured laboratories from 2001 to 2007. Foodborne Pathog Dis 8:887–900. doi: 10.1089/fpd.2010.0787. [DOI] [PubMed] [Google Scholar]
- 2.Majowicz SE, Musto J, Scallan E, Angulo FJ, Kirk M, O’Brien SJ, Jones TF, Fazil A, Hoekstra RM, International Collaboration on Enteric Disease “Burden of Illness” Studies . 2010. The global burden of nontyphoidal salmonella gastroenteritis. Clin Infect Dis 50:882–889. doi: 10.1086/650733. [DOI] [PubMed] [Google Scholar]
- 3.Feasey NA, Dougan G, Kingsley RA, Heyderman RS, Gordon MA. 2012. Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa. Lancet 379:2489–2499. doi: 10.1016/S0140-6736(11)61752-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Silva E, Duarte A. 2002. Salmonella Enteritidis em aves: retrospectiva no Brasil. Rev Bras Cienc Avic 4:85–100. doi: 10.1590/S1516-635X2002000200001. [DOI] [Google Scholar]
- 5.Mastroeni P, Grant AJ. 2011. Spread of Salmonella enterica in the body during systemic infection: unravelling host and pathogen determinants. Expert Rev Mol Med 13:e12. doi: 10.1017/S1462399411001840. [DOI] [PubMed] [Google Scholar]
- 6.Chen HM, Wang Y, Su LH, Chiu CH. 2013. Nontyphoid salmonella infection: microbiology, clinical features, and antimicrobial therapy. Pediatr Neonatol 54:147–152. doi: 10.1016/j.pedneo.2013.01.010. [DOI] [PubMed] [Google Scholar]
- 7.Betancor L, Yim L, Fookes M, Martinez A, Thomson NR, Ivens A, Peters S, Bryant C, Algorta G, Kariuki S, Schelotto F, Maskell D, Dougan G, Chabalgoity JA. 2009. Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates. BMC Microbiol 9:237. doi: 10.1186/1471-2180-9-237. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578–579. doi: 10.1093/bioinformatics/btq683. [DOI] [PubMed] [Google Scholar]
- 10.Darling AE, Mau B, Perna NT. 2010. progressiveMauve: multiple genome alignment with Gene gain, loss and rearrangement. PLoS One 5:e11147. doi: 10.1371/journal.pone.0011147. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O. 2014. Benchmarking of methods for genomic taxonomy. J Clin Microbiol 52:1529–1539. doi: 10.1128/JCM.02981-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O. 2012. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–1361. doi: 10.1128/JCM.06094-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Langridge GC, Fookes M, Connor TR, Feltwell T, Feasey N, Parsons BN, Seth-Smith HMB, Barquist L, Stedman A, Humphrey T, Wigley P, Peters SE, Maskell DJ, Corander J, Chabalgoity JA, Barrow P, Parkhill J, Dougan G, Thomson NR. 2015. Patterns of genome evolution that have accompanied host adaptation in Salmonella. Proc Natl Acad Sci USA 112:863–868. doi: 10.1073/pnas.1416707112. [DOI] [PMC free article] [PubMed] [Google Scholar]