Analyses of the genomes, transcriptomes and phenotypic characterization of Salmonella Typhimurium strains isolated from humans, food and swine in Brazil

Detalhes bibliográficos
Autor(a) principal: Seribelli, Amanda Aparecida
Data de Publicação: 2021
Tipo de documento: Tese
Idioma: eng
Título da fonte: Biblioteca Digital de Teses e Dissertações da USP
Texto Completo: https://www.teses.usp.br/teses/disponiveis/60/60141/tde-29092021-052421/
Resumo: Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) has been an important cause of gastroenteritis in various countries worldwide. In addition, S. Typhimurium sequence type (ST) 313 has been emerging as a cause of invasive disease mainly in sub-Saharan Africa and its presence was recently described in Brazil. However, in Brazil there are few studies that have elucidated possible differences in the genotypic diversity, gene expression and virulence of S. Typhimurium strains isolated from different sources and belonging to important STs. In the present thesis, six important questions were addressed: (1) What is the diversity of single nucleotide polymorphism (SNP) and resistance genes among S. Typhimurium strains isolated from humans and food? (2) Are genetically distinct the S. Typhimurium ST313 strains isolated from humans and food among each other and in comparison to other STs? (3) How do S. Typhimurium strains isolated from humans and food behave in phenotypic tests related to virulence? (4) What is the genetic diversity of S. Typhimurium strains isolated from swine? (5) What are the genomic differences of S. Typhimurium strains isolated from humans, food and swine? (6) How do the S. Typhimurium ST313 strain behave in a classic animal model and what are their differences in gene expression in comparison to ST19 strains? Phylogenetic results placed the S. Typhimurium strains into two major clades suggesting the existence of a prevalent subtype, likely more adapted, among strains isolated from humans, with some diversity in subtypes in isolates from food. The variety and prevalence of resistant genes found in these Salmonella Typhimurium strains reinforced their potential hazard for humans under treatment and the risk of its presence in foods in Brazil. 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 closed for the ST313 strains. The ability of the studied S. Typhimurium to invade Caco-2 epithelial cells was strain dependent and was not related to the source or the year of isolation. However, S. Typhimurium strains isolated from humans showed greater survival rates in U937 human macrophages and presented higher proportion of isolates with a virulent related profile in G. mellonella larvae in comparison to strains isolated from food suggesting that this difference may be related to the higher frequency of human isolates which contained plasmidial genes, such as spvABCDR operon, pefABCD operon, rck and mig-5. The cgMLST and BLAST Atlas were more efficient at discriminating the swine isolates studied in comparison to wgMLST. The pathogenic potential of the swine strains studied was corroborated by the presence of important Salmonella pathogenicity islands (SPIs) related to the pathogenesis of S. Typhimurium. Phylogenetic analyses grouped the majority of the S. Typhimurium strains of diverse origins into a single cluster suggesting that there was one prevalent subtype that has successful contaminated human, food and animal sources for 30 years in Brazil. The orthologous protein clusters analysis revealed unique genes in the S. Typhimurium studied mainly related to bacterial metabolism and that may be important in their pathogenicity. S. Typhimurium isolates from swine showed greater diversity of STs and prophages in comparison to S. Typhimurium 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 treatment is needed. S. Typhimurium STm30 (ST313) isolated from human feces in Brazil demonstrated greater expression of genes related to pathogenesis at 37°C, besides better colonization and invasion in the murine colon due to higher levels of expression of virulence genes and pro-inflammatory cytokines were also more expressed in this organ, suggesting greater tissue damage in comparison to S. Typhimurium SL1344 (ST19) and S. Typhimurium STm11 (ST19) isolated from human feces in Brazil. Finally, the results obtained contributed for a better characterization of the virulence and genotypic diversity of this important enteropathogen worldwide.
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spelling Analyses of the genomes, transcriptomes and phenotypic characterization of Salmonella Typhimurium strains isolated from humans, food and swine in BrazilAnálises dos genomas, transcriptomas e caracterização fenotípica de linhagens de Salmonella Typhimurium isoladas de humanos, alimentos e suínos no BrasilPhenotypic tests related to virulenceSalmonella TyphimuriumSalmonella TyphimuriumSequenciamento do genoma completoTestes fenotípicos relacionados à virulênciaTranscriptomaTranscriptomeWhole genome sequencingSalmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) has been an important cause of gastroenteritis in various countries worldwide. In addition, S. Typhimurium sequence type (ST) 313 has been emerging as a cause of invasive disease mainly in sub-Saharan Africa and its presence was recently described in Brazil. However, in Brazil there are few studies that have elucidated possible differences in the genotypic diversity, gene expression and virulence of S. Typhimurium strains isolated from different sources and belonging to important STs. In the present thesis, six important questions were addressed: (1) What is the diversity of single nucleotide polymorphism (SNP) and resistance genes among S. Typhimurium strains isolated from humans and food? (2) Are genetically distinct the S. Typhimurium ST313 strains isolated from humans and food among each other and in comparison to other STs? (3) How do S. Typhimurium strains isolated from humans and food behave in phenotypic tests related to virulence? (4) What is the genetic diversity of S. Typhimurium strains isolated from swine? (5) What are the genomic differences of S. Typhimurium strains isolated from humans, food and swine? (6) How do the S. Typhimurium ST313 strain behave in a classic animal model and what are their differences in gene expression in comparison to ST19 strains? Phylogenetic results placed the S. Typhimurium strains into two major clades suggesting the existence of a prevalent subtype, likely more adapted, among strains isolated from humans, with some diversity in subtypes in isolates from food. The variety and prevalence of resistant genes found in these Salmonella Typhimurium strains reinforced their potential hazard for humans under treatment and the risk of its presence in foods in Brazil. 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 closed for the ST313 strains. The ability of the studied S. Typhimurium to invade Caco-2 epithelial cells was strain dependent and was not related to the source or the year of isolation. However, S. Typhimurium strains isolated from humans showed greater survival rates in U937 human macrophages and presented higher proportion of isolates with a virulent related profile in G. mellonella larvae in comparison to strains isolated from food suggesting that this difference may be related to the higher frequency of human isolates which contained plasmidial genes, such as spvABCDR operon, pefABCD operon, rck and mig-5. The cgMLST and BLAST Atlas were more efficient at discriminating the swine isolates studied in comparison to wgMLST. The pathogenic potential of the swine strains studied was corroborated by the presence of important Salmonella pathogenicity islands (SPIs) related to the pathogenesis of S. Typhimurium. Phylogenetic analyses grouped the majority of the S. Typhimurium strains of diverse origins into a single cluster suggesting that there was one prevalent subtype that has successful contaminated human, food and animal sources for 30 years in Brazil. The orthologous protein clusters analysis revealed unique genes in the S. Typhimurium studied mainly related to bacterial metabolism and that may be important in their pathogenicity. S. Typhimurium isolates from swine showed greater diversity of STs and prophages in comparison to S. Typhimurium 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 treatment is needed. S. Typhimurium STm30 (ST313) isolated from human feces in Brazil demonstrated greater expression of genes related to pathogenesis at 37°C, besides better colonization and invasion in the murine colon due to higher levels of expression of virulence genes and pro-inflammatory cytokines were also more expressed in this organ, suggesting greater tissue damage in comparison to S. Typhimurium SL1344 (ST19) and S. Typhimurium STm11 (ST19) isolated from human feces in Brazil. Finally, the results obtained contributed for a better characterization of the virulence and genotypic diversity of this important enteropathogen worldwide.Salmonella enterica subsp. enterica sorovariedade Typhimurium (S. Typhimurium) é uma das principais causas de gastroenterite em vários países ao redor do mundo. Ademais, S. Typhimurium sequence type (ST) 313 é emergente e tem causado doença invasiva principalmente na África Subsaariana e sua presença foi recentemente descrita no Brasil. Entretanto, no país há poucos estudos que elucidaram possíveis diferenças na diversidade genotípica, expressão gênica e virulência de linhagens de S. Typhimurium isoladas de diferentes fontes e pertencentes a importantes STs. Na presente tese, seis importantes questões foram abordadas: (1) Qual é a diversidade de single nucleotide polymorphism (SNP) e de genes de resistência entre linhagens de S. Typhimurium isoladas de humanos e alimentos? (2) As linhagens de S. Typhimurium ST313 isoladas de humanos e alimentos são geneticamente distintas entre si e em comparação a outros STs? (3) Como linhagens de S. Typhimurium isoladas de humanos e alimentos se comportam diante de testes fenotípicos relacionados à virulência? (4) Qual é a diversidade genética de linhagens de S. Typhimurium isoladas de suínos? (5) Quais são as diferenças genômicas das linhagens de S. Typhimurium isoladas de humanos, alimentos e suínos? (6) Como a linhagem de S. Typhimurium ST313 se comporta em um modelo animal clássico e quais são as suas diferenças de expressão gênica em comparação a linhagens do ST19? Foi evidenciado que o resultado filogenético baseado em SNP agrupou as linhagens de S. Typhimurium em dois grandes grupos, sugerindo a existência de um subtipo prevalente, provavelmente mais adaptado para as linhagens isoladas de humanos e com alguma diversidade de subtipos para as linhagens de alimentos. A variedade e prevalência de genes de resistência encontrados nessas linhagens de S. Typhimurium reforçaram o potencial perigo destas para humanos sob tratamento e o risco da sua presença em alimentos no Brasil. Os genomas de linhagens de S. Typhimurium ST313 do Brasil mostraram grande semelhança entre si, cujas informações podem eventualmente ajudar no desenvolvimento de vacinas e antimicrobianos. A análise do pangenoma mostrou que os genomas de S. Typhimurium estudados apresentavam um pangenoma aberto, mas especificamente tendendo a se tornar fechado para as linhagens de S. Typhimurium ST313. A capacidade das S. Typhimurium estudadas invadirem as células epiteliais Caco-2 foi variável e não está relacionada com a fonte ou o ano de isolamento. Contudo, linhagens de S. Typhimurium isoladas de humanos mostraram maiores taxas de sobrevivência em macrófagos humanos U937 e apresentaram maior proporção de isolados com perfil virulento em larvas de G. mellonella quando comparadas com as linhagens isoladas de alimentos, sugerindo que essa diferença pode estar relacionada à maior frequência de isolados humanos que continham genes plasmidiais, tais como operon spvABCDR, operon pefABCD, rck e mig-5. O cgMLST e BLAST Atlas foram mais eficientes na discriminação das linhagens isoladas de suínos estudadas em comparação com o wgMLST. O potencial patogênico dessas linhagens de suínos foi corroborado pela presença de importantes Salmonella pathogenicity islands (SPIs) relacionadas à patogênese de S. Typhimurium. As análises filogenéticas agruparam a maioria dos isolados de S. Typhimurium de origens diversas em um único grupo, sugerindo a presença de um subtipo prevalente que contaminou com sucesso fontes humanas, alimentares e animais há 30 anos no Brasil. A análise de agrupamentos de proteínas ortólogas revelou genes únicos nas linhagens de S. Typhimurium estudadas, principalmente relacionados ao metabolismo bacteriano e que podem ser importantes em sua patogenicidade. Isolados de S. Typhimurium de suínos apresentaram maior diversidade de STs e profagos em comparação com as linhagens de S. Typhimurium isoladas de humanos e alimentos. O potencial patogênico das linhagens de S. Typhimurium foi corroborado pela presença de profagos exclusivos dessa sorovariedade envolvidos em sua virulência. O elevado número de genes de resistência relacionados às bombas de efluxo é preocupante e pode levar a falhas terapêuticas quando houver necessidade de tratamento. S. Typhimurium STm30 (ST313) isolada de fezes de humano no Brasil demonstrou maior expressão de genes relacionados à patogênese a 37°C, além de melhor colonização e invasão no cólon murino, devido aos maiores níveis de expressão de genes de virulência e as citocinas pró-inflamatórias também foram mais expressas nesse órgão, sugerindo maior dano tecidual em comparação com as linhagens de S. Typhimurium SL1344 (ST19) e S. Typhimurium STm11 (ST19) isoladas de fezes humanas no Brasil. Finalmente, os resultados obtidos contribuíram para uma melhor caracterização da virulência e da diversidade genotípica desse importante enteropatógeno mundial.Biblioteca Digitais de Teses e Dissertações da USPFalcão, Juliana PfrimerSeribelli, Amanda Aparecida2021-04-05info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesisapplication/pdfhttps://www.teses.usp.br/teses/disponiveis/60/60141/tde-29092021-052421/reponame:Biblioteca Digital de Teses e Dissertações da USPinstname:Universidade de São Paulo (USP)instacron:USPLiberar o conteúdo para acesso público.info:eu-repo/semantics/openAccesseng2023-04-05T12:59:32Zoai:teses.usp.br:tde-29092021-052421Biblioteca Digital de Teses e Dissertaçõeshttp://www.teses.usp.br/PUBhttp://www.teses.usp.br/cgi-bin/mtd2br.plvirginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.bropendoar:27212023-04-05T12:59:32Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP)false
dc.title.none.fl_str_mv Analyses of the genomes, transcriptomes and phenotypic characterization of Salmonella Typhimurium strains isolated from humans, food and swine in Brazil
Análises dos genomas, transcriptomas e caracterização fenotípica de linhagens de Salmonella Typhimurium isoladas de humanos, alimentos e suínos no Brasil
title Analyses of the genomes, transcriptomes and phenotypic characterization of Salmonella Typhimurium strains isolated from humans, food and swine in Brazil
spellingShingle Analyses of the genomes, transcriptomes and phenotypic characterization of Salmonella Typhimurium strains isolated from humans, food and swine in Brazil
Seribelli, Amanda Aparecida
Phenotypic tests related to virulence
Salmonella Typhimurium
Salmonella Typhimurium
Sequenciamento do genoma completo
Testes fenotípicos relacionados à virulência
Transcriptoma
Transcriptome
Whole genome sequencing
title_short Analyses of the genomes, transcriptomes and phenotypic characterization of Salmonella Typhimurium strains isolated from humans, food and swine in Brazil
title_full Analyses of the genomes, transcriptomes and phenotypic characterization of Salmonella Typhimurium strains isolated from humans, food and swine in Brazil
title_fullStr Analyses of the genomes, transcriptomes and phenotypic characterization of Salmonella Typhimurium strains isolated from humans, food and swine in Brazil
title_full_unstemmed Analyses of the genomes, transcriptomes and phenotypic characterization of Salmonella Typhimurium strains isolated from humans, food and swine in Brazil
title_sort Analyses of the genomes, transcriptomes and phenotypic characterization of Salmonella Typhimurium strains isolated from humans, food and swine in Brazil
author Seribelli, Amanda Aparecida
author_facet Seribelli, Amanda Aparecida
author_role author
dc.contributor.none.fl_str_mv Falcão, Juliana Pfrimer
dc.contributor.author.fl_str_mv Seribelli, Amanda Aparecida
dc.subject.por.fl_str_mv Phenotypic tests related to virulence
Salmonella Typhimurium
Salmonella Typhimurium
Sequenciamento do genoma completo
Testes fenotípicos relacionados à virulência
Transcriptoma
Transcriptome
Whole genome sequencing
topic Phenotypic tests related to virulence
Salmonella Typhimurium
Salmonella Typhimurium
Sequenciamento do genoma completo
Testes fenotípicos relacionados à virulência
Transcriptoma
Transcriptome
Whole genome sequencing
description Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) has been an important cause of gastroenteritis in various countries worldwide. In addition, S. Typhimurium sequence type (ST) 313 has been emerging as a cause of invasive disease mainly in sub-Saharan Africa and its presence was recently described in Brazil. However, in Brazil there are few studies that have elucidated possible differences in the genotypic diversity, gene expression and virulence of S. Typhimurium strains isolated from different sources and belonging to important STs. In the present thesis, six important questions were addressed: (1) What is the diversity of single nucleotide polymorphism (SNP) and resistance genes among S. Typhimurium strains isolated from humans and food? (2) Are genetically distinct the S. Typhimurium ST313 strains isolated from humans and food among each other and in comparison to other STs? (3) How do S. Typhimurium strains isolated from humans and food behave in phenotypic tests related to virulence? (4) What is the genetic diversity of S. Typhimurium strains isolated from swine? (5) What are the genomic differences of S. Typhimurium strains isolated from humans, food and swine? (6) How do the S. Typhimurium ST313 strain behave in a classic animal model and what are their differences in gene expression in comparison to ST19 strains? Phylogenetic results placed the S. Typhimurium strains into two major clades suggesting the existence of a prevalent subtype, likely more adapted, among strains isolated from humans, with some diversity in subtypes in isolates from food. The variety and prevalence of resistant genes found in these Salmonella Typhimurium strains reinforced their potential hazard for humans under treatment and the risk of its presence in foods in Brazil. 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 closed for the ST313 strains. The ability of the studied S. Typhimurium to invade Caco-2 epithelial cells was strain dependent and was not related to the source or the year of isolation. However, S. Typhimurium strains isolated from humans showed greater survival rates in U937 human macrophages and presented higher proportion of isolates with a virulent related profile in G. mellonella larvae in comparison to strains isolated from food suggesting that this difference may be related to the higher frequency of human isolates which contained plasmidial genes, such as spvABCDR operon, pefABCD operon, rck and mig-5. The cgMLST and BLAST Atlas were more efficient at discriminating the swine isolates studied in comparison to wgMLST. The pathogenic potential of the swine strains studied was corroborated by the presence of important Salmonella pathogenicity islands (SPIs) related to the pathogenesis of S. Typhimurium. Phylogenetic analyses grouped the majority of the S. Typhimurium strains of diverse origins into a single cluster suggesting that there was one prevalent subtype that has successful contaminated human, food and animal sources for 30 years in Brazil. The orthologous protein clusters analysis revealed unique genes in the S. Typhimurium studied mainly related to bacterial metabolism and that may be important in their pathogenicity. S. Typhimurium isolates from swine showed greater diversity of STs and prophages in comparison to S. Typhimurium 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 treatment is needed. S. Typhimurium STm30 (ST313) isolated from human feces in Brazil demonstrated greater expression of genes related to pathogenesis at 37°C, besides better colonization and invasion in the murine colon due to higher levels of expression of virulence genes and pro-inflammatory cytokines were also more expressed in this organ, suggesting greater tissue damage in comparison to S. Typhimurium SL1344 (ST19) and S. Typhimurium STm11 (ST19) isolated from human feces in Brazil. Finally, the results obtained contributed for a better characterization of the virulence and genotypic diversity of this important enteropathogen worldwide.
publishDate 2021
dc.date.none.fl_str_mv 2021-04-05
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
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dc.rights.driver.fl_str_mv Liberar o conteúdo para acesso público.
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rights_invalid_str_mv Liberar o conteúdo para acesso público.
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dc.publisher.none.fl_str_mv Biblioteca Digitais de Teses e Dissertações da USP
publisher.none.fl_str_mv Biblioteca Digitais de Teses e Dissertações da USP
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reponame:Biblioteca Digital de Teses e Dissertações da USP
instname:Universidade de São Paulo (USP)
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instname_str Universidade de São Paulo (USP)
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