Summer Course

Genomics in foodborne pathogen surveillance and outbreak investigation

12.Jul - 13. Jul, 2017 Cod. O12-17

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Description

The Summer Course Genomics in foodborne pathogen surveillance and outbreak investigation is an open teaching action of the European Research Project INNUENDO. The overall objective of the Innuendo international research consortium is to deliver a standardized, cross-sectorial framework for integration of bacterial whole genome sequencing (WGS) in routine surveillance and epidemiological investigations to reduce the burden of disease caused by both epidemic and sporadic food-borne zoonotic infections.

Up to 40 students will attend to the course and will receive theoretical and practical training about application of WGS in surveillance of food pathogens. The workshop will be divided in two parts. The first part will be one day of Scientific Symposium during which invited speakers and speakers within Innuendo consortium will present recent advance in the field. The second part will include a practical hands-on course on bioinformatics solution for public health microbiology. During the hands-on students will learn several bioinformatics tools including those developed within the project.

Program

12-07-2017

08:15 - 00:00

Registration and coffee

08:40 - 09:00

“Opening of the course, wellcome“

Javier Garaizar Candina UPV/EHU - Professor of Microbiology
Gorka Urtaran Ayuntamiento de Vitoria-Gasteiz -
Beatriz Guerra European Food Safety Authority, EFSA - Senior Scientific Officer
Peli Manterola Basque Government - Quality and Food Industries Director
Iván Igartua Ugarte UPV/EHU - Vice-rector of Campus of Álava

09:00 - 09:45

“WGS in surveillance and outbreak detection of foodborne pathogens“

Eduardo N Taboada Public Health Agency of Canada

09:45 - 10:30

“WGS and antibiotic resistance“

Martin Cormican NUI Galway Ireland

10:30 - 11:00

Coffee break

11:00 - 11:10

“EU Capacity-building projects: INNUENDO“

Mirko Rossi University of Helsinki, Finland

11:10 - 11:30

“EU Capacity-building projects: ENGAGE & COMPARE“

Valeria Bortolaia Danish Technical University, Denmark

11:30 - 12:00

“From reads to profiles to trees: challenges and solutions in high throughput sequencing data analysis“

João Carriço Universidade de Lisboa, Portugal

12:00 - 12:30

“Phenotypic prediction using WGS data: virulome and resistome“

Valeria Bortolaia Danish Technical University, Denmark

12:30 - 13:30

Lunch

13:30 - 13:50

“QA/QC and automatization of whole genome sequence analysis: implementation“

Mirko Rossi University of Helsinki, Finland

13:50 - 14:10

“QA/QC and automatization of whole genome sequence analysis: theory“

Miguel Machado Universidade de Lisboa, Portugal

14:10 - 14:40

“GScompare: fast clustering of assembled genomes“

Joseba Bikandi Bikandi University of the Basque Country - Senior Lecturer

14:40 - 15:00

“Whole genome MLST: theory“

João Carriço Universidade de Lisboa, Portugal

15:00 - 15:15

“Whole genome MLST: implementation“

Mickael Silva Universidade de Lisboa, Portugal

15:15 - 15:30

“Whole genome MLST: phylogenetic inference and metadata visualization“

Bruno Gonçalves Universidade de Lisboa, Portugal

15:30 - 16:00

Coffee break

16:00 - 16:30

“A road map to national WGS based surveillance of foodborne bacteria, Finland“

Saara Salmenlinna National Institute for Health and Welfare, Finland

16:30 - 17:00

“Standardized communication during outbreak investigation“

Mirko Rossi University of Helsinki, Finland

17:00 - 00:00

Synthesis

19:00 - 00:00

Venue and Social event

13-07-2017

08:40 - 09:40

“Content of the day, division of groups, setting computer environment“

Joseba Bikandi Bikandi University of the Basque Country - Senior Lecturer

09:00 - 09:20

“Overview of the INNUENDO platform and its modules“

João Carriço Universidade de Lisboa, Portugal

09:20 - 09:45

“The INNUENDO platform: the user interface“

Bruno Gonçalves Universidade de Lisboa, Portugal

09:45 - 10:45

“The INNUENDO platform: QA/QC analysis - INNUca (Part 1)“

Miguel Machado Universidade de Lisboa, Portugal

10:45 - 11:15

Coffee break

11:15 - 12:15

“The INNUENDO platform: QA/QC analysis - INNUca (Part 2)“

Miguel Machado Universidade de Lisboa, Portugal

12:15 - 12:45

“The INNUENDO platform: GScompare for species determination“

Joseba Bikandi Bikandi University of the Basque Country - Senior Lecturer

12:45 - 14:00

Lunch

14:00 - 15:30

“The INNUENDO platform: cg/wgMLST using chewBACCA“

Mickael Silva Universidade de Lisboa, Portugal

Coffee break

15:30 - 16:15

“The INNUENDO platform: from analysis to action, interpreting trees“

Bruno Gonçalves Universidade de Lisboa, Portugal

16:15 - 18:00

“Working in groups, self-learning/testing - Free Coffee break“

Miguel Machado Universidade de Lisboa, Portugal
Mickael Silva Universidade de Lisboa, Portugal -
Bruno Gonçalves Universidade de Lisboa, Portugal -

19:00 - 00:00

Social event

Directors

Javier Garaizar Candina

UPV/EHU

Javier Garaizar Candina es Catedrático de Universidad del área de Microbiología en el Departamento de Inmunología, Microbiología y Parasitología de la Facultad de Farmacia del Campus de Álava de la UPV/EHU. Se doctoró en Medicina y Cirugía en el año 1989. Tiene una amplia experiencia docente, investigadora y de gestión en la UPV/EHU. Ha realizado varias estancias investigadoras postdoctorales, destacando las desarrolladas en el Laboratorio Central de Salud Pública de Londres, Reino Unido, el Centro Médico Erasmus de Roterdam, Holanda, el Centro del Cáncer Sidney Kimmel en San Diego, EEUU, y recientemente la desarrollada en la Universidad de Carolina del Sur, en Columbia, EEUU. Ha sido Vicedecano de Innovación Docente, Relaciones Internacionales y Alumnado y Decano en funciones en la Facultad de Farmacia de la UPV/EHU y Coordinador del Campus de Álava del Servicio de Asesoramiento Educativo y Vicerrector del Campus de Álava.