Sequence-Based Typing Methods for Microorganisms

   Deadline for applications: September 10th 2012
   Notification of acceptance dates:
        EARLY: September 3rd 2012
        NORMAL: September 12th 2012
   Course date: September 25th - September 28th 2012


Keith Jolley studied biochemistry at the University of Bath, graduating in 1993. He stayed on to complete his PhD, studying halophilic proteins from Archaea. In 1996, Keith undertook a postdoctoral position at the University of Southampton working on meningococcal surface proteins involved in eliciting immune responses. Continuing this interest in meningococcal biology, he moved to the group of Prof. Martin Maiden at the University of Oxford in 1998, where he has worked on the genetic characterization of bacterial carrier populations. Since then, Keith has gained bioinformatics experience and now works mainly on software development and database design, including development of the software that runs the Neisseria and Campylobacter MLST websites and databases. Recent focus has been on developing the Bacterial Isolate Genome Sequence Database (BIGSdb) platform to flexibly handle large amounts of genome sequence data obtained from multiple isolates in order to address questions of bacterial evolution and the emergence of pathogenicity.

Affiliation: Bacterial population structure and public health/ Martin Maiden Research group, University of Oxford, Oxford, UK

Nick Loman worked as a medical doctor before studying for a PhD in genomics with Prof Mark Pallen at the University of Birmingham. His research interest is the application of high-throughput sequencing to the study of bacterial pathogens, particularly those causing outbreaks in hospitals and in the community including Acinetobacter baumannii, Pseudomonas aeruginosa, Mycobacterium tuberculosis, Escherichia coli and Streptococcus pneumoniae (see these references). Nick is enthusiastic about the use of Internet communication in Science and Medicine, and was instrumental in kick-starting the crowd-sourcing analysis of the German E. coli outbreak strain in June 2011, as published in Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. He writes a popular blog on genomics and sequencing - Pathogens: Genes and Genomes - as well as maintaining a Twitter feed (@pathogenomenick). Nick has 5 years experience of high-throughput sequencing technologies and their associated analytical pipelines.

Affiliation: Bacterial Pathogenomics / Pallen Research group, University of Birmingham ,UK

João Carriço graduated in Applied Chemistry, Biotechnology at Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa. He moved to the field of Bioinformatics during his PhD in the Biomathematics group and the Molecular Genetics unit in Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. After being a researcher for 3 years in the Knowledge Discovery in Bioinformatics he became a Researcher at Instituto de Microbiologia, Faculdade de Medicina, Universidade de Lisboa. His main interest are the development of user-friendly tools for the analysis of typing methods. Examples of these tools can be found at the Comparing Partitions website and the PHYLOViZ software.

Affiliation: Instituto de Microbiologia/Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa

Mário Ramirez did his PhD studies in Molecular Biology at Universidade Nova de Lisboa and at The Rockefeller University, New York, NY, USA. He followed up his studies in a post-doc at the Molecular Genetics Laboratory, Instituto de Tecnologia Química e Biológica, Oeiras. Presently he is an Associate Professor of the Faculty of Medicine, University of Lisbon and the head of Molecular Microbiology and Infection Unit at Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon.
His main interest is to understand the dynamics of populations of bacterial pathogens and how they respond to selective forces. His current work focuses on characterizing the effect of antimicrobial use and human vaccination on the bacterial population. This involves not only a "wet-lab" approach but also a strong theoretical approach in statistics and bioinformatics.

Affiliation: Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa

Nuno Faria graduated in Microbiology and Genetics Biology at Faculdade de Ciências, Universidade de Lisboa in 2002 and obtained his PhD in Molecular Biology at Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa in 2009. Since 2002, Nuno Faria has worked in the characterization of bacterial isolates, initially at the Faculdade de Farmácia, Universidade de Lisboa, still as an undergraduate student. In 2003 he joined the Laboratório de Genética Molecular, ITQB, headed by Prof. Hermínia de Lencastre, as a research student, where he continued to obtain his PhD, and currently as a Pos-tdoctoral fellow. His main research subject is Staphylococcus aureus, where he is interested in the epidemiology, antibiotic resistance, and evolution of this species.

Affiliation: Laboratório de Genética Molecular, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, PT

Teresa Conceição is a Post-doctoral fellow at the Laboratory of Molecular Genetics, ITQB, headed by Prof. Hermínia de Lencastre. She was graduated in Microbiology and Genetics Biology at Faculdade de Ciências, Universidade de Lisboa in 2002 and obtained her PhD in Molecular Biology at Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa in 2010. She has been working on molecular typing of bacterial isolates since 2001, first on Enterobacteriaceae and other Gram-negative rods, and after 2004 when joined the Laboratory Molecular Genetics, she moved to the characterization, epidemiology and evolution of Gram-positive bacteria, namely staphylococci.

Affiliation: Laboratório de Genética Molecular, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, PT

Course Description

Technological advances in DNA sequencing have led to the adoption of sequence-based typing methods as the standard techniques for bacterial identification at strain level, specially due to their portability and reproducibility. The widespread use of remotely accessible databases offering different typing data and the development of diverse data analysis techniques show the impact of Bioinformatics in this field, and the need for understanding how to operate with the databases and algorithms. Recently, the capability of sequencing whole bacterial genomes in a few days using Next Generation Sequencing (NGS) methodologies, opened a new door for the development of more sophisticated strain identification tools.

This training course is directed for the data analysis of sequence based typing methods, from the raw-data to the identification of a strain type by several typing methodologies, and the use of analysis algorithms to create groups of related strains. It will span from Single Locus Sequence Typing methods, such as spa typing or emm typing, to the now established MultiLocus Sequence Typing (MLST) and Multilocus Variable Number of Tandem Repeats Analysis (MLVA) methodologies. The course will also cover methods that apply to whole genome sequence data, and show how NGS data can be analyzed and made sense of, in this context.
The course will be essentially hands-on. Short presentations will be interweaved by tutored assited exercises.
The participants are expected to gradually gain user independence by acquiring new analytical skils in using software and online databases for specific typing methods. Special attention will be given to methods that can use NGS datasets.

Target Audience
This course is aimed to anyone working in molecular epidemiology, that wants to develop or consolidate skills in the use and analysis of sequence-based typing methods. The course will be illustrated with examples from different bacterial species, but the concepts are applicable to any species and to other sequence-based typing methods, not explicitly referred to in the course.

Course Pre-requisites
Basic understanding of molecular biology, namely in microbial typing methodologies and elementary computer interaction skills are expected.
Informative talk
You can watch this video ang extract valuable information about the subject of this course. High-throughput sequencing in clinical microbiology, by Mark Pallen, Uppsala Jun 2012

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:   July 4th 2012