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Phylogenetic analysis revealed that Salmonella Typhimurium ST313 isolated from humans and food in Brazil presented a high genomic similarity

  • Amanda Ap. SeribelliEmail author
  • Júlia C. Gonzales
  • Fernanda de Almeida
  • Leandro Benevides
  • Marta I. Cazentini Medeiros
  • Dália dos Prazeres Rodrigues
  • Siomar de C. Soares
  • Marc W. Allard
  • Juliana P. Falcão
Bacterial Fungal and Virus Molecular Biology - Research Paper

Abstract

Salmonella Typhimurium sequence type 313 (S. Typhimurium ST313) has caused invasive disease mainly in sub-Saharan Africa. In Brazil, ST313 strains have been recently described, and there is a lack of studies that assessed by whole genome sequencing (WGS)—the relationship of these strains. The aims of this work were to study the phylogenetic relationship of 70 S. Typhimurium genomes comparing strains of ST313 (n = 9) isolated from humans and food in Brazil among themselves, with other STs isolated in this country (n = 31) and in other parts of the globe (n = 30) by 16S rRNA sequences, the Gegenees software, whole genome multilocus sequence typing (wgMLST), and average nucleotide identity (ANI) for the genomes of ST313. Additionally, pangenome analysis was performed to verify the heterogeneity of these genomes. The phylogenetic analyses showed that the ST313 genomes were very similar among themselves. However, the ST313 genomes were usually clustered more distantly to other STs of strains isolated in Brazil and in other parts of the world. By pangenome calculation, the core genome was 2,880 CDSs and 4,171 CDSs singletons for all the 70 S. Typhimurium genomes studied. Considering the 10 ST313 genomes analyzed the core genome was 4,112 CDSs and 76 CDSs singletons. In conclusion, the ST313 genomes from Brazil showed a high similarity among them which information might eventually help in the development of vaccines and antibiotics. The pangenome analysis showed that the S. Typhimurium genomes studied presented an open pangenome, but specifically tending to become close for the ST313 strains.

Keywords

Salmonella Typhimurium ST313 Phylogeny Pangenome 

Notes

Funding information

We thank São Paulo Research Foundation (FAPESP) (Proc. 2016/24716-3) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Finance Code 001 for financial support. During this work, Seribelli, A.A. was supported by a scholarship from São Paulo Research Foundation (FAPESP) (Proc. 2017/06633-6). Falcão, J.P. received a productive fellowship from Council for Scientific and Technological Development (CNPq) grants CNPq 303475/2015-3 and CNPq 304399/2018-3.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

42770_2019_155_MOESM1_ESM.pdf (50 kb)
Supplementary Table 1 (PDF 49 kb)
42770_2019_155_MOESM2_ESM.pdf (46 kb)
Supplementary Table 2 (PDF 46 kb)
42770_2019_155_MOESM3_ESM.pdf (21 kb)
Supplementary Table 3 (PDF 20 kb)

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Copyright information

© Sociedade Brasileira de Microbiologia 2019

Authors and Affiliations

  • Amanda Ap. Seribelli
    • 1
    Email author
  • Júlia C. Gonzales
    • 1
  • Fernanda de Almeida
    • 1
  • Leandro Benevides
    • 2
  • Marta I. Cazentini Medeiros
    • 3
  • Dália dos Prazeres Rodrigues
    • 4
  • Siomar de C. Soares
    • 5
  • Marc W. Allard
    • 6
  • Juliana P. Falcão
    • 1
  1. 1.Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão PretoUniversidade de São Paulo – USPRibeirão PretoBrazil
  2. 2.National Laboratory of Scientific Computation – LNCCPetrópolisBrazil
  3. 3.Instituto Adolfo Lutz de Ribeirão Preto – IALSão PauloBrazil
  4. 4.Fundação Instituto Oswaldo Cruz – FIOCRUZRio de JaneiroBrazil
  5. 5.Universidade Federal do Triângulo Mineiro – UFTMUberabaBrazil
  6. 6.Food and Drug Administration – FDACollege ParkUSA

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