Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics
Autor(a) principal: | |
---|---|
Data de Publicação: | 2021 |
Outros Autores: | , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/s13099-021-00423-7 http://hdl.handle.net/11449/207667 |
Resumo: | Background: Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is an important zoonotic agent worldwide. The aim of this work was to compare genetically 117 S. Typhimurium isolated from different sources over 30 years in Brazil using different genomics strategies. Results: The majority of the 117 S. Typhimurium strains studied were grouped into a single cluster (≅ 90%) by the core genome multilocus sequence typing and (≅ 77%) by single copy marker genes. The phylogenetic analysis based on single nucleotide polymorphism (SNP) grouped most strains from humans into a single cluster (≅ 93%), while the strains isolated from food and swine were alocated into three clusters. The different orthologous protein clusters found for some S. Typhimurium isolated from humans and food are involved in metabolic and regulatory processes. For 26 isolates from swine the sequence types (ST) 19 and ST1921 were the most prevalent ones, and the ST14, ST64, ST516 and ST639 were also detected. Previous results typed the 91 S. Typhimurium isolates from humans and foods as ST19, ST313, ST1921, ST3343 and ST1649. The main prophages detected were: Gifsy-2 in 79 (67.5%) and Gifsy-1 in 63 (54%) strains. All of the S. Typhimurium isolates contained the acrA, acrB, macA, macB, mdtK, emrA, emrB, emrR and tolC efflux pump genes. Conclusions: The phylogenetic trees grouped the majority of the S. Typhimurium isolates from humans into a single cluster suggesting that there is one prevalent subtype in Brazil. Regarding strains isolated from food and swine, the SNPs’ results suggested the circulation of more than one subtype over 30 years in this country. The orthologous protein clusters analysis revealed unique genes in the strains studied mainly related to bacterial metabolism. S. Typhimurium strains from swine showed greater diversity of STs and prophages in comparison to strains isolated from humans and foods. The pathogenic potential of S. Typhimurium strains was corroborated by the presence of exclusive prophages of this serovar involved in its virulence. The high number of resistance genes related to efflux pumps is worrying and may lead to therapeutic failures when clinical treatment is needed. |
id |
UNSP_622698522c680d40b01389723e04376d |
---|---|
oai_identifier_str |
oai:repositorio.unesp.br:11449/207667 |
network_acronym_str |
UNSP |
network_name_str |
Repositório Institucional da UNESP |
repository_id_str |
2946 |
spelling |
Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomicsEfflux pumpsPhylogenetic treesProphagesProtein orthologous clustersSalmonella TyphimuriumBackground: Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is an important zoonotic agent worldwide. The aim of this work was to compare genetically 117 S. Typhimurium isolated from different sources over 30 years in Brazil using different genomics strategies. Results: The majority of the 117 S. Typhimurium strains studied were grouped into a single cluster (≅ 90%) by the core genome multilocus sequence typing and (≅ 77%) by single copy marker genes. The phylogenetic analysis based on single nucleotide polymorphism (SNP) grouped most strains from humans into a single cluster (≅ 93%), while the strains isolated from food and swine were alocated into three clusters. The different orthologous protein clusters found for some S. Typhimurium isolated from humans and food are involved in metabolic and regulatory processes. For 26 isolates from swine the sequence types (ST) 19 and ST1921 were the most prevalent ones, and the ST14, ST64, ST516 and ST639 were also detected. Previous results typed the 91 S. Typhimurium isolates from humans and foods as ST19, ST313, ST1921, ST3343 and ST1649. The main prophages detected were: Gifsy-2 in 79 (67.5%) and Gifsy-1 in 63 (54%) strains. All of the S. Typhimurium isolates contained the acrA, acrB, macA, macB, mdtK, emrA, emrB, emrR and tolC efflux pump genes. Conclusions: The phylogenetic trees grouped the majority of the S. Typhimurium isolates from humans into a single cluster suggesting that there is one prevalent subtype in Brazil. Regarding strains isolated from food and swine, the SNPs’ results suggested the circulation of more than one subtype over 30 years in this country. The orthologous protein clusters analysis revealed unique genes in the strains studied mainly related to bacterial metabolism. S. Typhimurium strains from swine showed greater diversity of STs and prophages in comparison to strains isolated from humans and foods. The pathogenic potential of S. Typhimurium strains was corroborated by the presence of exclusive prophages of this serovar involved in its virulence. The high number of resistance genes related to efflux pumps is worrying and may lead to therapeutic failures when clinical treatment is needed.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Departamento de Análises Clínicas Toxicológicas e Bromatológicas Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo - USPFaculdade de Ciências Farmacêuticas de Araraquara UNESP – Departamento de Ciências Biológicas, Rodovia Araraquara-Jaú Km 1Instituto Adolfo Lutz de Ribeirão PretoFundação Oswaldo Cruz – FIOCRUZEmpresa Brasileira de Pesquisa Agropecuária – Suínos e Aves – EMBRAPAUniversidade Federal do Triângulo Mineiro – UFTMFood and Drug Administration-FDAFaculdade de Ciências Farmacêuticas de Araraquara UNESP – Departamento de Ciências Biológicas, Rodovia Araraquara-Jaú Km 1FAPESP: 2016/24716-3FAPESP: 2017/06633-6FAPESP: 2019/19338-8CNPq: 304399/2018-3CAPES: Finance code 001Universidade de São Paulo (USP)Universidade Estadual Paulista (Unesp)Instituto Adolfo Lutz de Ribeirão PretoFundação Oswaldo Cruz – FIOCRUZEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Universidade Federal do Triângulo Mineiro – UFTMFood and Drug Administration-FDASeribelli, Amanda Ap.da Silva, Patrick [UNESP]da Cruz, Marcelo Ferreirade Almeida, FernandaFrazão, Miliane R.Medeiros, Marta I. C.Rodrigues, Dália dos P.Kich, Jalusa D.de Jesus Benevides, LeandroSoares, Siomar de C.Allard, Marc W.Falcão, Juliana Pfrimer.2021-06-25T10:59:02Z2021-06-25T10:59:02Z2021-12-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1186/s13099-021-00423-7Gut Pathogens, v. 13, n. 1, 2021.1757-4749http://hdl.handle.net/11449/20766710.1186/s13099-021-00423-72-s2.0-85104996583Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGut Pathogensinfo:eu-repo/semantics/openAccess2024-06-24T13:07:14Zoai:repositorio.unesp.br:11449/207667Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T15:41:48.924832Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics |
title |
Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics |
spellingShingle |
Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics Seribelli, Amanda Ap. Efflux pumps Phylogenetic trees Prophages Protein orthologous clusters Salmonella Typhimurium |
title_short |
Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics |
title_full |
Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics |
title_fullStr |
Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics |
title_full_unstemmed |
Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics |
title_sort |
Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics |
author |
Seribelli, Amanda Ap. |
author_facet |
Seribelli, Amanda Ap. da Silva, Patrick [UNESP] da Cruz, Marcelo Ferreira de Almeida, Fernanda Frazão, Miliane R. Medeiros, Marta I. C. Rodrigues, Dália dos P. Kich, Jalusa D. de Jesus Benevides, Leandro Soares, Siomar de C. Allard, Marc W. Falcão, Juliana Pfrimer. |
author_role |
author |
author2 |
da Silva, Patrick [UNESP] da Cruz, Marcelo Ferreira de Almeida, Fernanda Frazão, Miliane R. Medeiros, Marta I. C. Rodrigues, Dália dos P. Kich, Jalusa D. de Jesus Benevides, Leandro Soares, Siomar de C. Allard, Marc W. Falcão, Juliana Pfrimer. |
author2_role |
author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade de São Paulo (USP) Universidade Estadual Paulista (Unesp) Instituto Adolfo Lutz de Ribeirão Preto Fundação Oswaldo Cruz – FIOCRUZ Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Universidade Federal do Triângulo Mineiro – UFTM Food and Drug Administration-FDA |
dc.contributor.author.fl_str_mv |
Seribelli, Amanda Ap. da Silva, Patrick [UNESP] da Cruz, Marcelo Ferreira de Almeida, Fernanda Frazão, Miliane R. Medeiros, Marta I. C. Rodrigues, Dália dos P. Kich, Jalusa D. de Jesus Benevides, Leandro Soares, Siomar de C. Allard, Marc W. Falcão, Juliana Pfrimer. |
dc.subject.por.fl_str_mv |
Efflux pumps Phylogenetic trees Prophages Protein orthologous clusters Salmonella Typhimurium |
topic |
Efflux pumps Phylogenetic trees Prophages Protein orthologous clusters Salmonella Typhimurium |
description |
Background: Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is an important zoonotic agent worldwide. The aim of this work was to compare genetically 117 S. Typhimurium isolated from different sources over 30 years in Brazil using different genomics strategies. Results: The majority of the 117 S. Typhimurium strains studied were grouped into a single cluster (≅ 90%) by the core genome multilocus sequence typing and (≅ 77%) by single copy marker genes. The phylogenetic analysis based on single nucleotide polymorphism (SNP) grouped most strains from humans into a single cluster (≅ 93%), while the strains isolated from food and swine were alocated into three clusters. The different orthologous protein clusters found for some S. Typhimurium isolated from humans and food are involved in metabolic and regulatory processes. For 26 isolates from swine the sequence types (ST) 19 and ST1921 were the most prevalent ones, and the ST14, ST64, ST516 and ST639 were also detected. Previous results typed the 91 S. Typhimurium isolates from humans and foods as ST19, ST313, ST1921, ST3343 and ST1649. The main prophages detected were: Gifsy-2 in 79 (67.5%) and Gifsy-1 in 63 (54%) strains. All of the S. Typhimurium isolates contained the acrA, acrB, macA, macB, mdtK, emrA, emrB, emrR and tolC efflux pump genes. Conclusions: The phylogenetic trees grouped the majority of the S. Typhimurium isolates from humans into a single cluster suggesting that there is one prevalent subtype in Brazil. Regarding strains isolated from food and swine, the SNPs’ results suggested the circulation of more than one subtype over 30 years in this country. The orthologous protein clusters analysis revealed unique genes in the strains studied mainly related to bacterial metabolism. S. Typhimurium strains from swine showed greater diversity of STs and prophages in comparison to strains isolated from humans and foods. The pathogenic potential of S. Typhimurium strains was corroborated by the presence of exclusive prophages of this serovar involved in its virulence. The high number of resistance genes related to efflux pumps is worrying and may lead to therapeutic failures when clinical treatment is needed. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-06-25T10:59:02Z 2021-06-25T10:59:02Z 2021-12-01 |
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/10.1186/s13099-021-00423-7 Gut Pathogens, v. 13, n. 1, 2021. 1757-4749 http://hdl.handle.net/11449/207667 10.1186/s13099-021-00423-7 2-s2.0-85104996583 |
url |
http://dx.doi.org/10.1186/s13099-021-00423-7 http://hdl.handle.net/11449/207667 |
identifier_str_mv |
Gut Pathogens, v. 13, n. 1, 2021. 1757-4749 10.1186/s13099-021-00423-7 2-s2.0-85104996583 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Gut Pathogens |
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_ |
1808128552150761472 |