Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil

Detalhes bibliográficos
Autor(a) principal: Seribelli, Amanda Aparecida
Data de Publicação: 2021
Outros Autores: da Silva, Patrick [UNESP], Frazão, Miliane Rodrigues, Kich, Jalusa Deon, Allard, Marc W., Falcão, Juliana Pfrimer
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1016/j.meegid.2021.104977
http://hdl.handle.net/11449/229034
Resumo: Salmonella Typhimurium has been transmitted between humans and animals. Although, Brazil has been one of the largest pork meat exporters worldwide, there are few studies that characterized epidemiologically S. Typhimurium strains from swine. The aims of this work were to study the phylogenetic relationship of S. Typhimurium genomes isolated from swine in Brazil among themselves and with other genomes isolated from several sources and countries using wgMLST and cgMLST and to perform the search of Salmonella pathogenicity islands (SPIs). In addition, for S. Typhimurium strains from swine to compare the virulence and antimicrobial resistance genes by VFDB and ResFinder, genetic content by BLAST Atlas and orthologous proteins clusters by OrthoVenn. The constructed phylogenetic trees by wgMLST and cgMLST grouped the majority (92.3% and 80.7%, respectively) of the strains isolated from swine in Brazil into the same group. All the isolates contained important SPIs (SPI-1, SPI-2, SPI-3, SPI-5 and SPI-9). A total of 100 and 31 virulence and resistance genes were detected in the S. Typhimurium strains isolated from swine, respectively. The BLAST Atlas and orthologous proteins analysis found regions of phages and differences in metabolic, regulatory and cellular processes among S. Typhimurium LT2 and S. Typhimurium isolates from swine. In conclusion, molecular typing based in the wgMLST and cgMLST suggested that the S. Typhimurium isolates from swine studied were genetically related. The pathogenic potential of the strains studied was corroborated by the presence of important SPIs and virulence genes. The high number of antimicrobial resistance genes detected is worrying and reinforced their potential risk in swine in Brazil. The comparison by BLAST Atlas suggested differences in mobile genetic elements among S. Typhimurium LT2 and S. Typhimurium isolates from swine in Brazil. The orthologous proteins analysis revealed unique genes related to important cellular processes in the strains from swine.
id UNSP_11e4f035588d0c6d09c6949f4729fbba
oai_identifier_str oai:repositorio.unesp.br:11449/229034
network_acronym_str UNSP
network_name_str Repositório Institucional da UNESP
repository_id_str 2946
spelling Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in BrazilBLAST AtlasOrthologous proteinsPhylogenetic analysesSPIsVirulence and resistance genesSalmonella Typhimurium has been transmitted between humans and animals. Although, Brazil has been one of the largest pork meat exporters worldwide, there are few studies that characterized epidemiologically S. Typhimurium strains from swine. The aims of this work were to study the phylogenetic relationship of S. Typhimurium genomes isolated from swine in Brazil among themselves and with other genomes isolated from several sources and countries using wgMLST and cgMLST and to perform the search of Salmonella pathogenicity islands (SPIs). In addition, for S. Typhimurium strains from swine to compare the virulence and antimicrobial resistance genes by VFDB and ResFinder, genetic content by BLAST Atlas and orthologous proteins clusters by OrthoVenn. The constructed phylogenetic trees by wgMLST and cgMLST grouped the majority (92.3% and 80.7%, respectively) of the strains isolated from swine in Brazil into the same group. All the isolates contained important SPIs (SPI-1, SPI-2, SPI-3, SPI-5 and SPI-9). A total of 100 and 31 virulence and resistance genes were detected in the S. Typhimurium strains isolated from swine, respectively. The BLAST Atlas and orthologous proteins analysis found regions of phages and differences in metabolic, regulatory and cellular processes among S. Typhimurium LT2 and S. Typhimurium isolates from swine. In conclusion, molecular typing based in the wgMLST and cgMLST suggested that the S. Typhimurium isolates from swine studied were genetically related. The pathogenic potential of the strains studied was corroborated by the presence of important SPIs and virulence genes. The high number of antimicrobial resistance genes detected is worrying and reinforced their potential risk in swine in Brazil. The comparison by BLAST Atlas suggested differences in mobile genetic elements among S. Typhimurium LT2 and S. Typhimurium isolates from swine in Brazil. The orthologous proteins analysis revealed unique genes related to important cellular processes in the strains from swine.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São PauloFaculdade de Ciências Farmacêuticas de Araraquara UNESP – Departamento de Ciências Biológicas, Rodovia Araraquara-Jaú Km 1Empresa Brasileira de Pesquisa Agropecuária – Suínos e Aves – EMBRAPAFood and Drug Administration - FDA College ParkFaculdade de Ciências Farmacêuticas de Araraquara UNESP – Departamento de Ciências Biológicas, Rodovia Araraquara-Jaú Km 1CAPES: 001FAPESP: 2016/24716-3FAPESP: 2017/06633-6FAPESP: 2019/19338-8Universidade de São Paulo (USP)Universidade Estadual Paulista (UNESP)Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)College ParkSeribelli, Amanda Aparecidada Silva, Patrick [UNESP]Frazão, Miliane RodriguesKich, Jalusa DeonAllard, Marc W.Falcão, Juliana Pfrimer2022-04-29T08:30:03Z2022-04-29T08:30:03Z2021-09-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1016/j.meegid.2021.104977Infection, Genetics and Evolution, v. 93.1567-72571567-1348http://hdl.handle.net/11449/22903410.1016/j.meegid.2021.1049772-s2.0-85108641753Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengInfection, Genetics and Evolutioninfo:eu-repo/semantics/openAccess2024-06-24T13:06:50Zoai:repositorio.unesp.br:11449/229034Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T14:14:47.779705Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil
title Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil
spellingShingle Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil
Seribelli, Amanda Aparecida
BLAST Atlas
Orthologous proteins
Phylogenetic analyses
SPIs
Virulence and resistance genes
title_short Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil
title_full Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil
title_fullStr Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil
title_full_unstemmed Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil
title_sort Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil
author Seribelli, Amanda Aparecida
author_facet Seribelli, Amanda Aparecida
da Silva, Patrick [UNESP]
Frazão, Miliane Rodrigues
Kich, Jalusa Deon
Allard, Marc W.
Falcão, Juliana Pfrimer
author_role author
author2 da Silva, Patrick [UNESP]
Frazão, Miliane Rodrigues
Kich, Jalusa Deon
Allard, Marc W.
Falcão, Juliana Pfrimer
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade de São Paulo (USP)
Universidade Estadual Paulista (UNESP)
Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
College Park
dc.contributor.author.fl_str_mv Seribelli, Amanda Aparecida
da Silva, Patrick [UNESP]
Frazão, Miliane Rodrigues
Kich, Jalusa Deon
Allard, Marc W.
Falcão, Juliana Pfrimer
dc.subject.por.fl_str_mv BLAST Atlas
Orthologous proteins
Phylogenetic analyses
SPIs
Virulence and resistance genes
topic BLAST Atlas
Orthologous proteins
Phylogenetic analyses
SPIs
Virulence and resistance genes
description Salmonella Typhimurium has been transmitted between humans and animals. Although, Brazil has been one of the largest pork meat exporters worldwide, there are few studies that characterized epidemiologically S. Typhimurium strains from swine. The aims of this work were to study the phylogenetic relationship of S. Typhimurium genomes isolated from swine in Brazil among themselves and with other genomes isolated from several sources and countries using wgMLST and cgMLST and to perform the search of Salmonella pathogenicity islands (SPIs). In addition, for S. Typhimurium strains from swine to compare the virulence and antimicrobial resistance genes by VFDB and ResFinder, genetic content by BLAST Atlas and orthologous proteins clusters by OrthoVenn. The constructed phylogenetic trees by wgMLST and cgMLST grouped the majority (92.3% and 80.7%, respectively) of the strains isolated from swine in Brazil into the same group. All the isolates contained important SPIs (SPI-1, SPI-2, SPI-3, SPI-5 and SPI-9). A total of 100 and 31 virulence and resistance genes were detected in the S. Typhimurium strains isolated from swine, respectively. The BLAST Atlas and orthologous proteins analysis found regions of phages and differences in metabolic, regulatory and cellular processes among S. Typhimurium LT2 and S. Typhimurium isolates from swine. In conclusion, molecular typing based in the wgMLST and cgMLST suggested that the S. Typhimurium isolates from swine studied were genetically related. The pathogenic potential of the strains studied was corroborated by the presence of important SPIs and virulence genes. The high number of antimicrobial resistance genes detected is worrying and reinforced their potential risk in swine in Brazil. The comparison by BLAST Atlas suggested differences in mobile genetic elements among S. Typhimurium LT2 and S. Typhimurium isolates from swine in Brazil. The orthologous proteins analysis revealed unique genes related to important cellular processes in the strains from swine.
publishDate 2021
dc.date.none.fl_str_mv 2021-09-01
2022-04-29T08:30:03Z
2022-04-29T08:30:03Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1016/j.meegid.2021.104977
Infection, Genetics and Evolution, v. 93.
1567-7257
1567-1348
http://hdl.handle.net/11449/229034
10.1016/j.meegid.2021.104977
2-s2.0-85108641753
url http://dx.doi.org/10.1016/j.meegid.2021.104977
http://hdl.handle.net/11449/229034
identifier_str_mv Infection, Genetics and Evolution, v. 93.
1567-7257
1567-1348
10.1016/j.meegid.2021.104977
2-s2.0-85108641753
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Infection, Genetics and Evolution
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv Scopus
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv
_version_ 1808128335267495936