Profession & Career

ESCMID Panorama

Bioinformatic Tools in Clinical Microbiology, ESCMID Postgraduate Technical Workshop

16 - 19 September 2013, Santander, Spain

Organisers
  • University Hospital Marqués de Valdecilla (HUMV)
  • University of Cantabria (UC)
Course Coordinators
  • Juan María García-Lobo, Santander, Spain
  • Luis Martínez-Martínez, Santander, Spain
Course Objectives

This course provides participants with an introductory/medium level practical approach to the use of bioinformatic tools in microbiology. Theoretical and practical sessions will cover different aspects of applied bioinformatic tools.

Course Venue

University Hospital Marqués de Valdecilla
Continuing Education Facilities
Pabellón 16
Avda. Valdecilla s/n
Santander, Spain

Target Audience

24 – 32 residents, pre-doc students, young post-doc students and staff working in the following fields: clinical microbiology, medical microbiology, biology or any other related scientific area.

Contact Person

Dr Luis Martínez Martínez
Head, Service of Microbiology
Titular Professor, Department
of Molecular Biology
University of Cantabria
Hospital Universitario Marqués de Valdecilla
Pabellón 20, 2ª Pl.
Avda Valdecilla s/n
39008 Santander, Spain

Phone +34 942 202 580
Mobile +34 655 994 678
Fax +34 942 023 462


Administrative Secretariat

Afid Congresos, S. L.
Menéndez Pelayo, 6
Entresuelo A.
39006 Santander (Cantabria)

Phone +34 942 318 180
Fax +34 942 318 653

Course Programme


Presentations are availabe in the ESCMID Online Lecture Library.

Monday, 16 September 2013
  • 09:30 Registration
  • 15:00 Opening
  • 15:30 Introduction: the impact of DNA sequencing in microbiology
  • 16:15 Repeated sequences in bacteria
  • 17:15 Welcome reception
Tuesday, 17 September 2013

  • 09:30 Design of PCR: single and multiplex approaches
  • 10:15 Sequence-based identification of microorganisms
  • 11:00 Break
  • 11:30 Molecular typing of microorgansims: MLST and other approaches
  • 12:15 Principles and methods of massive sequencing
  • 13:00 Lunch
  • 14:30 Practicals: Session I

    • Genes and genomes retrieval from databases
    • The “In Silico Simulation” webpage
    • PC-sized bioinformatics

  • 16:30 Pathogenomics: detection of virulence traits by massive sequencing
  • 20:30 Course dinner
Wednesday, 18 September 2013

  • 09:30 Plasmid genomics
  • 10:15 Resistomics: detection of resistance genes by massive sequencing
  • 11:00 Break
  • 11:30 Epidenomics: application of massive sequencing for outbreak characterisation
  • 12:15 Metagenomics and microbiomes
  • 13:00 Lunch
  • 14:30 Practicals: Session II

    • Comparison of whole genomes
    • Annotation software
    • Artemis

  • 16:30 Bacterial transcriptomics
Thursday, 19 September 2013

  • 09:30 Bioinformatic resources and public health
  • 10:15 Practicals: Session III

    • De novo assembly
    • Aligners
    • SRA: Shot Reads Archives

  • 12:30 Evaluation
  • 12:45 Course picture
  • 13:00 Closing
Confirmed Faculty Members
  • Joseba Bikandi, Bilbao, Spain
  • Isabel Cuesta, Madrid, Spain
  • Giuseppe D’Auria, Valencia, Spain
  • Fernando De la Cruz, Santander, Spain
  • Edward Feil, Bath, United Kingdom
  • Juan María García-Lobo, Santander, Spain
  • Mette V. Larsen, Copenhagen, Denmark
  • Luis Martínez-Martínez, Santander, Spain
  • Jesús Mingorance, Madrid, Spain
  • Alain Ocampo-Sosa, Santander, Spain
  • María Cruz Rodríguez, Santander, Spain
  • Luis Serrano, Barcelona, Spain
  • Ignacio Varela, Santander, Spain
  • Jordi Vila, Barcelona, Spain
Last update: 02 May 2013

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Leaflet