Disciplina Discipline VPS5746
Epidemiologia Molecular Aplicada ao Estudo de Infecções Bacterianas
Molecular Epidemiology Applied to the Study of Bacterial Infections

Área de Concentração: 10134

Concentration area: 10134

Criação: 26/06/2023

Creation: 26/06/2023

Ativação: 26/06/2023

Activation: 26/06/2023

Nr. de Créditos: 3

Credits: 3

Carga Horária:

Workload:

Docentes Responsáveis:

Professors:

Andrea Micke Moreno

Luisa Zanolli Moreno

Objetivos:

Oferecer ao aluno o conhecimento teórico e prático referente às técnicas empregadas na caracterização molecular de agentes bacterianos envolvidos nas doenças que acometem animais domésticos, silvestres ou sinantrópicos, assim como infecções bacterianas de caráter zoonótico, e respectivas análises com aplicação da epidemiologia molecular ao estudo de infecções bacterianas.

Objectives:

Offer the student theoretical and practical knowledge regarding the techniques used in the molecular characterization of bacterial agents involved in diseases that affect domestic, wild or synanthropic animals, as well as bacterial infections of a zoonotic nature, and respective analyzes with the application of molecular epidemiology to the study of bacterial infections .

Justificativa:

O avanço nos últimos anos na área de biologia molecular levou a utilização de diferentes ferramentas na caracterização de surtos e nos estudos epidemiológicos das doenças de origem bacteriana que afetam os animais e o homem. Esta disciplina visa oferecer aos alunos o entendimento sobre as técnicas direcionadas a genotipagem dos agentes bacterianos e sua aplicação no estudo das doenças infecciosas e do comportamento epidemiológico das mesmas.

Rationale:

The advances in recent years in the area of molecular biology have led to the use of different tools for the characterization of outbreaks and in epidemiological studies of bacterial diseases that affect animals and humans. This course aims to provide students with an understanding of techniques aimed at genotyping bacterial agents and their application in the study of infectious diseases and their epidemiological behavior.

Conteúdo:

1.Introdução à epidemiologia molecular e sua aplicação ao estudo de infecções bacterianas; exemplos da aplicação das técnicas moleculares de tipagem bacteriana. 2.Técnicas de genotipagem dependentes da amplificação de DNA (RAPD, ERIC, etc..). 3.Técnicas que envolvem amplificação de DNA e restrição enzimática (Polimorfismo do comprimento de fragmentos amplificados – AFLP, Polimorfismo no Comprimento de Fragmentos de Restrição – RFLP). 4.Eletroforese em campo pulsado – PFGE. 5.Análise de dados gerados pelas técnicas que geram padrões de bandas (fingerprint) – definição de perfis e genótipos, padrão clonal, análise e interpretação de dendrogramas. 6.Discussão sobre aplicação das metodologias baseadas em fingerprint através do estudo de artigos científicos. 7.Utilização de sequenciamento parcial - 16S rRNA e outros genes. 8.Tipagem por sequenciamento de multilocus (MLST) – definição de alelos, ST, complexo clonal, análise de sequências e aplicação à epidemiologia molecular. 9.Introdução à epidemiologia genômica – plataformas de sequenciamento de nova geração, análise de dados gerados através de mapeamento e montagem de novo, avaliação in silico da MLST (MLST, rMLST, cgMLST) e análise de polimorfismos de base única (SNPs) (wgSNP, cgSNP). 10.Discussão sobre aplicação das metodologias baseadas em sequenciamento através do estudo de artigos científicos. Conteúdo prático: as aulas práticas serão baseadas nos tópicos de análise das técnicas de fingerprint e sequenciamento e interpretação dos dados obtidos.

Content:

1. Introduction to molecular epidemiology and its application to the study of bacterial infections; examples of the application of molecular techniques for bacterial typing. 2. DNA amplification-dependent genotyping techniques (RAPD, ERIC, etc.). 3. Techniques involving DNA amplification and restriction enzymes (Amplified Fragment Length Polymorphism – AFLP, Restriction Fragment Length Polymorphism – RFLP). 4. Pulsed Field Gel Electrophoresis – PFGE. 5. Analysis of data generated by techniques that generate band patterns (fingerprint) – definition of profiles and genotypes, clonal pattern, analysis and interpretation of dendrograms. 6. Discussion on the application of fingerprint-based methodologies through the study of scientific articles. 7. Usagee of partial sequencing - 16S rRNA and other genes. 8. Multilocus sequencing typing (MLST) – definition of alleles, ST, clonal complex, sequence analysis and application to molecular epidemiology. 9. Introduction to genomic epidemiology – next generation sequencing platforms, analysis of data generated through mapping and de novo assembly, in silico evaluation of MLST (MLST, rMLST, cgMLST) and analysis of single base polymorphisms (SNPs) (wgSNP , cgSNP). 10. Discussion on the application of methodologies based on sequencing through the study of scientific articles. Practical content: practical classes will be based on the topics of analysis of fingerprint techniques and sequencing and interpretation of obtained data .

Forma de Avaliação:

A avaliação será baseada na frequência, participação do aluno e na apresentação de seminário. Terá conceito A, o aluno que possuir boa participação, excelente apresentação de seminário e 0-2 faltas. Terá conceito B o aluno assíduo (0-2 faltas) não participativo das discussões ou apresente boa participação com 3-4 faltas e cuja apresentação de seminário apresente a boa qualidade. Terá conceito C o aluno não participativo das discussões com 3-4 faltas ou apresente 5-6 faltas ou cuja apresentação de seminário não apresente a qualidade esperada para um aluno de pós-graduação.

Type of Assessment:

Assessment will be based on attendance, student participation, and seminar presentation. The student who has good participation, excellent seminar presentation and 0-2 absences will have grade A. An assiduous student (0-2 absences) who does not participate in the discussions or presents good participation with 3-4 absences and whose seminar presentation presents good quality will have a B concept. A student who does not participate in the discussions with 3-4 absences or presents 5-6 absences or whose seminar presentation does not present the expected quality for a postgraduate student will ha

Bibliografia:

Deng X, den Bakker HC, Hendriksen RS. Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens. Annu Rev Food Sci Technol. 2016; 7: 353-74. Goering RV. Pulsed field gel electrophoresis: a review of application and interpretation in the molecular epidemiology of infectious disease. Infect Genet Evol. 2010; 10: 866-75. Herschleb J, Ananiev G, Schwartz DC. Pulsed-field gel electrophoresis. Nat Prot. 2007; 2: 677-84. Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems: an application of Simpson´s index of diversity. J Clin Microbiol. 1988; 26: 2465-2466. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MC. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiol. 2012; 158: 1005-15. Kaufmann ME. Pulsed-field gel electrophoresis. Methods Mol Med. 1998; 15: 33-50. Maiden MC, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND. MLST revisited: the gene by-gene approach to bacterial genomics. Nat Rev Microbiol. 2013; 11: 728-36. McLauchlin J, Ripabelli G, Brett MM, Threlfall EJ. Amplified fragment length polymorphism (AFLP) analysis of Clostridium perfringens for epidemiological typing. Int J Food Microbiol. 2000; 56: 21–28. Ruppitsch W, Pietzka A, Prior K, Bletz S, Fernandez HL, Allerberger F, Harmsen D, Mellmann A. Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes. J Clin Microbiol. 2015; 53: 2869–2876. Tang P, Gardy JL. Stopping outbreaks with real-time genomic epidemiology. Genome Med. 2014; 6:104 Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, Persing DH, Swaminathan B. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol. 1995; 33: 2233–9. Van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, Fry NK, Fussing V, Green J, Feil E, Gerner-Smidt P, et al. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Microbiol Infec. 2007; 13: 1–46. Woo PC, Lau SK, Teng JL, Tse H, Yuen KY. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect. 2008; 14: 908-34.

Bibliography:

Deng X, den Bakker HC, Hendriksen RS. Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens. Annu Rev Food Sci Technol. 2016; 7: 353-74. Goering RV. Pulsed field gel electrophoresis: a review of application and interpretation in the molecular epidemiology of infectious disease. Infect Genet Evol. 2010; 10: 866-75. Herschleb J, Ananiev G, Schwartz DC. Pulsed-field gel electrophoresis. Nat Prot. 2007; 2: 677-84. Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems: an application of Simpson´s index of diversity. J Clin Microbiol. 1988; 26: 2465-2466. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MC. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiol. 2012; 158: 1005-15. Kaufmann ME. Pulsed-field gel electrophoresis. Methods Mol Med. 1998; 15: 33-50. Maiden MC, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND. MLST revisited: the gene by-gene approach to bacterial genomics. Nat Rev Microbiol. 2013; 11: 728-36. McLauchlin J, Ripabelli G, Brett MM, Threlfall EJ. Amplified fragment length polymorphism (AFLP) analysis of Clostridium perfringens for epidemiological typing. Int J Food Microbiol. 2000; 56: 21–28. Ruppitsch W, Pietzka A, Prior K, Bletz S, Fernandez HL, Allerberger F, Harmsen D, Mellmann A. Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes. J Clin Microbiol. 2015; 53: 2869–2876. Tang P, Gardy JL. Stopping outbreaks with real-time genomic epidemiology. Genome Med. 2014; 6:104 Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, Persing DH, Swaminathan B. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol. 1995; 33: 2233–9. Van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, Fry NK, Fussing V, Green J, Feil E, Gerner-Smidt P, et al. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Microbiol Infec. 2007; 13: 1–46. Woo PC, Lau SK, Teng JL, Tse H, Yuen KY. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect. 2008; 14: 908-34.

Tipo de oferecimento da disciplina:

Presencial

Class type:

Presencial