Sequence-Based Typing Methods for Microorganisms
IMPORTANT DATES for SBTM12
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
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 -
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.
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.
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.
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.
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.
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.
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.
Basic understanding of molecular biology, namely in microbial typing methodologies and elementary computer interaction skills are expected.
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
Instituto Gulbenkian de Ciência,
Apartado 14, 2781-901 Oeiras, Portugal
Last updated: July 4th 2012