Workshop at UPV/EHU for project stakeholders


Whole-genome sequencing (WGS) can provide increased discriminatory power over traditional molecular typing approaches for bacterial pathogen populations. For that reason and due to the decreasing sequencing costs, the genomes of several hundreds of thousands of strains of the most important human foodborne pathogens are publicly available and several thousands of genomes a week are currently being sequenced all over the world. This enormous data drove the development of novel sophisticated bioinformatics tools and statistical methods aiming to provide to biologist and epidemiologists the correct framework for inferring population dynamics and reconstructing transmission pathways of foodborne pathogens. Therefore, there is an increasing demand from academic and public health sectors of microbiologist able to analyze large sequence data, but at the same time the is a wide gap of knowledge which limits the successful implementation of these novel technologies. The course “Genomics in foodborne pathogen surveillance and outbreak investigation” aimed in contributing in the professional continuous development of public health stakeholders, providing expert advice on the analysis and interpretation of WGS-based typing data and giving the opportunity to access to the bioinformatic data analysis methodologies currently being developed within the INNUENDO project. With this course we aimed to contribute to structuring research training at the European level and to strengthening European public health capacity in this new genomic era.


The course was been organized by the INNUENDO consortium within the Summer School of the University of Basque Country (UPV/EHU; and sponsored by: EFSA (, Gobierno Vasco/Eusko Jaurlaritza (, master and doctoral school of the University of Basque Country (, Vice-rectorate of Campus of Álava (UPV/EHU), Elika (, Ayuntamiento de Vitoria-Gasteiz/Vitoria-Gasteisko Udala (, ESCMID Food- and Water-borne Infections Study Group – EFWISG (, CSC, the Finnish center of expertise in ICT (

The organization committee have been composed by: Javier Garaizar, University of the Basque Country UPV/EHU, Spain (; Mirko Rossi, University of Helsinki, Finland, (; Joseba Bikandi, University of the Basque Country UPV/EHU, Spain (; João André Carriço, Universidade de Lisboa, Portugal, (

The Summer Course was divided in two parts. The first part was a one day of Scientific Symposium during which invited speakers and speakers within Innuendo consortium presented recent advances in the field. The symposium was broadcast online through a webinar platform.
The second part included a practical hands-on course on bioinformatics solution for public health microbiology. During the hands-on students learned bioinformatics tools developed within INNUENDO project through the INNUENDO platform.
Students were divided in 10 groups of four and they performed a simulation experiment for an outbreak investigation of Shiga-like producing E. coli using the INNUENDO platform and a set of well characterized genomes (Rusconi et al. Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks. Front Microbiol. 2016 Jun 30;7:985). Thanks to the support of CSC, students accessed, through a web browser, a total of 10 virtual machines (VM) with 16 cpus and 80 Gb of RAM each hosted in cPOUTA cluster where the INNUENDO platform was installed. Each group was further divided in two subgroups one playing the role fo human health authority (HHA) and the second the role for food and animal health authority (FAHA). In each group, both HHA and FAHA used the same VM (meaning all have access on the same data) but entering it through different computers, using different user ID and performing analyses on different set of strains. See schema below:

The objective of the day was to identify which of the given strains belonged to the ongoing proposed outbreak investigation using gene-by-gene approach and stimulate the discussion among the students of the same group to identify possible flaws in communication between different authorities. A secondary objective for the day was to identify all possible flaws or limitations of the INNUENDO platform. Student have been ask to “stress test” the platform and report to the developers any errors found. In addition, developers were interviewing the students for asking feedback on the functionality of the platform itself.
Teacher of the course were:
  • Javier Garaizar, University of the Basque Country UPV/EHU, Spain
  • Eduardo N. Taboada, Public Health Agency of Canada, Canada
  • Mark MaGuire, NUI Galway, Ireland
  • Mirko Rossi, University of Helsinki, Finland
  • Valeria Bortolaia, Danish Technical University, Denmark
  • Bruno Gonçalves, Universidade de Lisboa, Portugal,
  • Miguel Machado, Universidade de Lisboa, Portugal,
  • Mickael Silva, Universidade de Lisboa, Portugal,
  • Saara Salmenlinna, National Institute for Health and Welfare, Finland,
  • Joseba Bikandi, University of the Basque Country UPV/EHU, Spain
  • João Carriço, Universidade de Lisboa, Portugal,


12-07-2017 “The theory”

08:15 - 00:00 Registration and coffee
08:40 - 09:00 “Opening of the course, welcome”
  • Javier Garaizar Candina, UPV/EHU - Professor of Microbiology
  • Peio Lopez de Munain, Ayuntamiento de Vitoria-Gasteiz - Deputy Mayor 
  • Beatriz Guerra, European Food Safety Authority, EFSA - Scientific Officer
  • Arantza Madariaga, ELIKA - Director
  • Iván Igartua Ugarte, UPV/EHU - Vice-rector of Campus of Álava 
  • Mirko Rossi, University of Helsinki, Coordinator of INNUENDO

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”: Mark MaGuire, NUI Galway Ireland

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

13:30 - 13:50 “Genome based nomenclature”: Mirko Rossi, University of Helsinki, Finland
13:50 - 14:10 “QA/QC and automatization of whole genome sequence analysis”: Miguel Machado, Universidade de Lisboa, Portugal
14:10 - 14:40 “GScompare: fast clustering of assembled genomes”: Joseba 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

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 and Conclusions

13-07-2017 “The practice”

08:40 - 09:00 “Setting computer environment, division of groups and presentation of the pilot activities”: Mirko Rossi University of Helsinki, Finland
09:00 - 09:20 Lecture “Overview of the INNUENDO platform and its modules”: João Carriço Universidade de Lisboa, Portugal
09:20 - 10:45 Lecture and hands-on “The INNUENDO platform: the user interface”: Bruno Gonçalves Universidade de Lisboa, Portugal

11:15 - 12:00 Lecture and hands-on “The INNUENDO platform: QA/QC analysis - INNUca”: Miguel Machado Universidade de Lisboa, Portugal
12:15 - 12:45 Lecture and hands-on “The INNUENDO platform: cg/wgMLST using chewBACCA”: Mickael Silva Universidade de Lisboa, Portugal

14:00 - 15:30 Lecture and hands-on “The INNUENDO platform: from analysis to action, interpreting trees”: Bruno Gonçalves Universidade de Lisboa, Portugal
15:45 - 16:15 Lecture “GScompare for species determination”: Joseba Bikandi Bikandi University of the Basque Country - Senior Lecturer
16:15 - 18:00 Hands-on “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


A total of 45 Summer Course students from different parts of Europe (mainly from public sector) and 10 Master and Doctorate from UPV/EHU have attended the course. In addition, several stakeholders followed the symposium day from a total of 52 IPs across Europe. The figure below shows the origin of the students:


After the course for collecting feedback, a survey has been submitted to the 45 Summer Course students and 5 persons who participated only to the webinar. The survey was performed using the EUsurvey platform and it is available at this link
A total of 28 persons responded (56%) and details results are presented below. In general the course has been graded really well, especially for those students coming from public sector.

He have asked the student to tell us which of the software presented in the course would you like to use in a near future and if they will be willing to use them in command line. Below the answers. For any information concerning the software please visit this page.

 in a near future in command line
 INNUENDO platform78 %NA 
 chewBBACA (BSR allele calling)68 % 50 %
 INNUca (QA/QC assembly pipeline)64 %50 %
 Dynamic cgMLST implementation in Phyloviz Online64 %NA
 Pathotyping (raw reads fast mapping)57 %25 %
 I don't know18 %0 %
 I do not have the skills for running software in command line NA   39 %

What did you like most about this workshop?

  • Great atmosphere of the group. Vitoria-Gasteiz is very interesting city.
  • The enthusiasm of the organizers/presenters.
  • All the speakers were very clear and knowledgeable, and gave us the possibility to explore and to be updated on the last advances on the Bioinformatics analysis of WGS data for pathogens typing.
  • The thematic presented in a very clear way
  • Excellent tutors and instructors, interactive atmosphere.
  • The dedication and support of the tutors and instructions. Also, the networking possibilities that the course provided.
  • The shown pipelines to analyse WGS data, free available and not only user friendly but also with the option of command line. And apart from the content, of course the city and the social activities :)
  • I really liked the location, the friendly atmosphere, and the group activities and of course the opportunity to learn more about the Innuendo project.
  • hand-on workshop for Innuendo tool
  • personal contact
  • Very good lectures the first day- not only about innuendo, but taking the opportunity to put things into a bigger context
  • Interaction with leading researchers and other participants
  • A combination of theoretical and practical classes, good and kind presenters (and their presentations).
  • I like the effort of the tutors and instructor. They tries to help us as much as they could.
  • Perfect tutors, optimal time divided for lectures and hands on training, very good location, great workshop participants.
  • Everything was very well organized and the workshop contents were very useful.
  • WGS has been largely been used as a research tool, including to guide therapeutic intervention. So this workshop was interesting with easy software presented which i would like to implement in my work

What aspects of the workshop could be improved?

  • The room chosen for the first day (symposium) was not adequate for a screen presentation. Screen was placed too close to the floor. People seated at the back found hard to see the slides.
  • The organization was perfect and the argumentations were a lot and very stimulating but concentrated in only two days. Maybe it could be useful to extend the workshop especially for hands-on training.
  • More time for the hands-on activities.
  • More time for the hands-on training.
  • Division into groups should have accounted for previous experience and skill level. Some additional tasks could have been allocated to those who are already familiar with sequence analysis.
  • It would be very useful to have the presentations, especially for the hands-on activities, to fully understand what the different pipelines do.
  • It would be nice to have a print-out the task for the trainings session next time.
  • Preparation of handouts of the talks and hand-on workshop.
  • More time for discussing in more detail about technical details.
  • It would be good to receive all presentations in pdf.
  • Although some lectures were introducing topics also for non-expert users, some lectures would have needed to start slower introducing the topic rather than digging into details.
  • Hands-on activities was a little hap-hazard. It would have been beneficial if participants could bring their own genome data.
  • More hands-on time, more bioinformatics. I would be happy to learn to run all of the tools we were using at the workshop in a command line mode.
  • I think that the course should include more basic contents to fully understand all the subjects explained during the oral and practical sessions.

What did you take from this workshop and use in your current and/or future profession?

  • How to manage with big data and the different steps that should be done in order to analyse a complete genome sequence. Different techniques to compare ant type genomes.
  • We will use the platform for epidemiological studies.
  • I learnt about current issues on the use of WGS for the detection of food-borne pathogens in food/clinical samples and was a good atmosphere for networking.
  • The addressed topics are essential for my PhD studies. The tools proposed during the workshop show reliability, feasibility and transparency, enough to be adopted to achieve the goals of my projects.
  • I would really like to try and use presented tools.
  • That WGS data analysis can be accessible to anyone; I'll use the platform in a near future in my profession.
  • Use of INNUENDO platform in routine work (hopefully)
  • Bioinformatics tools
  • I would like to use the Innuendo platform when it becomes available to the public.
  • All the pipelines.
  • Especially the QA/QC aspects implemented in the INNUca pipeline are going to be a great help in order to access the quality and to determine thresholds for WGS data.
  • the right knowledge to apply these new investigation methods for my job
  • Innuendo tools will be installed and further tested and possibly used in routine for QC analysis, and outbreak investigation.
  • Being able to download the databank, which (hopefully) will enable us to compare data with other European countries.
  • WGS has been largely used as a research tool, including to therapeutic intervention. So this workshop was interesting with easy software presented which i would like to implemented in my lab.
  • knowledge of Bioinformatics applied to microbiology
  • The most useful was information about core genome WGS approach in WGS data analysis.
  • It is useful to know what innuendo aims for, and I will also bring with me a deeper understanding of the complexity for clustering
  • Everything
  • I learnt quite a lot about technical aspects of Spades, core genome construction and allele calling as well as tree construction.
  • An overview of NGS-based typing and the tools used for it. The major limitations I see in using the platform is the different chemistry (SE Ion Torrent Seq) and a limited number of pathogen species.
  • In my opinion it is necessary to have previous skills to fully understand the contents of the course. I do not think i have the capacity to apply what i was taught in my current profession.
  • the tools are very suitable for my work, and will be helpful for future activities
  • Presentations of the symposium day were very interesting for me. However, the course would be more useful if the software presented during the hands-on activity were already available.
  • I am currently using and I will use all software presented in my current profession.
  • In the future I hope to use INNUENDO for working with bacterial whole genome sequences.
  • I started using the INNUca pipeline in command line environment.


Information concerning the course have been widely disseminated using several media:  El Confidencial, El Correo farmacéuticoEl Diario médicoLa VanguardiaDeia, Madri+dRadio VitoriaOnda Vasca
ECDC and competent EURL have been informed.

The symposium day was recorded and it is fully available online