Genomics and Epidemiological Surveillance of Bacterial Pathogens (San Jose, Costa Rica)

Course aim
This course aims to provide training in the skills required to generate
and interpret next generation sequencing data in a public health setting.

This year’s course will have a strong emphasis on Antimicrobial
Resistance (AMR) and
its spread, whilst also training
participants in the latest laboratory and computational methods for
next
generation sequence analysis and genomic surveillance.

Course background
This is a focused course that was established in 2013 to build strong
links between traditional methods of epidemiological surveillance, modern
molecular typing methods and those based on genomics. Although the course
is built around genomic surveillance the focus of this course is designed
to reflect regional public health priorities, and this year’s course will
have a strong emphasis on AMR.

World-wide over the last few years the surveillance community has been at
a crossroads; deciding whether to continue with traditional methods or to
embrace the unprecedented advances in genomics, sequencing technology and
our ability to interpret high resolution sequence data for surveillance
purposes. This debate has now been resolved and we are now seeing a shift
from the use of molecular typing data for epidemiological surveillance
and public health investigations of infectious disease to using whole
Genome Sequencing (WGS) for this purpose. In some settings WGS is now
being used to define outbreaks and trace infection sources in humans,
animals and the environment. This approach also offers enormous promise
for predicting antimicrobial resistance phenotypes.

Existing studies that have used genomics for mapping the spread of
pathogens have highlighted two things, firstly that genomic datasets are
growing day by day and they offer the context against which to understand
local patterns of disease. Secondly these studies also highlight the
power gained from public health scientists and academic research
scientists working together to better understand infectious disease. This
is the foundation of this course and expert instructors have been
assembled from a wide range of settings in Latin America and Europe,
including national and international public health organisations and
front line high-profile genomic research organisations. We recognise the
synergy between academic research and public health and this is your
opportunity to strengthen this effort by attending the course.

We also have a strong focus on “Train the Trainer” and there will be
opportunities to develop your teaching skills and feedback on how these
courses can be improved to facilitate participants teaching the skills
they have learnt back in their own countries.

Target audience
The course is targeted at clinical molecular biologists
and
microbiologists working in resource-limited countries in Latin
America
and the Caribbean. Please note: The course is free to attend for
non-commercial applicants.

Applicants should have training in standard microbiology lab
techniques
(pipetting, handling of biological samples, etc.). There are
20 places
available and the course will be held in English (with
language support
provided where necessary by Spanish- and
Portuguese-speaking
instructors).

Venue
The 2017 course will be hosted by the Microbiology Faculty and the
Research Center for Molecular and Cell Biology at the main campus of the
University of Costa Rica in San José.

Each course builds upon previous versions, incorporating genomics and
problem solving exercises with modules that demonstrate how traditional
and molecular typing methods -in combination with sequence data – can be
used:
a) for georeferencing (also known as ‘phylogeography’) where the location
of disease causing strains are mapped with detailed genetic and
phenotypic data (for example antibiotic resistance patterns) to look for
regional patterns of disease, and
b) to understand the fine detail of new and emerging infections, the risk
to public health and the management of infectious diseases.

The week-long programme includes:

Laboratory-based practicals: Molecular Sub-typing
techniques:

• Running and interpreting real-time PCR assays (including optimisation and primer design)
• Generating Next Generation Sequencing data

Computational practicals: Informatics and Surveillance

• Practical bioinformatics skills needed to manipulate raw sequence data (some of which will be generated on the course), including: mapping and de novo assemblies, SNP calling, annotation and analysis of genomic information
• Sequence analysis and comparative genomics of next generation sequencing data using Artemis and ACT
• Principles of phylogeny and construction of accurate phylogenies
• Group exercises designed to teach everyday skills required to work in genomic surveillance
• Practical exercises for using GPS to map cases of infectious disease and phenotypes (such as AMR) across the world

Learning outcomes
After attending the course, participants should be able to:

• Recognize the principles of real time PCR and next generation sequencing (including primer design) and how to apply them effectively
• Sequence genomic bacterial DNA
• Use sequence analysis tools effectively
• Explain what a phylogenetic tree is and what it represents
• Formulate projects using the global surveillance platform Microreact
• Perform comparative genomics on multiple genome sequences
• Compare different traditional bacteriological identification methods with modern molecular typing methods and genomics in the context of local and regional resources
• Explain, using examples, how AMR is spread among bacterial pathogens

Course Instructors

Caterina Guzman Verri PIET, Veterinary School, Universidad
Nacional, Costa Rica
Josefina Campos Centro de Referencia Regional PulseNet
AL y C, Argentina
Claire Jenkins Public Health England, UK
Matt Holden University of St Andrews, UK
Nick Thomson Wellcome Trust Sanger Institute, UK
David Aanensen Wellcome Trust Sanger Institute, UK
Silvia Argimon Wellcome Trust Sanger Institute, UK
Leonor Sanchez Buso Wellcome Trust Sanger Institute, UK

Guest Speakers

Enrique Perez-Gutiérrez Pan American Health
Organisation
Foodborne Diseases

Marcelo Galas Pan American Health Organisation
Antimicrobial Resistance

Prerequisites
Applicants should be clinical molecular biologists or microbiologists
working in Latin American or Caribbean countries. Applicants should also
have training in standard microbiology lab techniques (pipetting,
handling of biological samples, etc.). There are 20 places available and
the course will be held in English (with language support provided where
necessary by Spanish- and Portuguese-speaking instructors).

Cost
Overseas courses are free to attend for non-commercial
applicants. Please contact us for the commercial fee.
Limited bursaries to cover travel, accommodation and
sustenance costs
are also available and are awarded on merit. More information on
bursaries can be found under the “Cost / Bursaries” tab

Applications
Applications for this course can be completed online. If you have any
problems with the online application process, please contact us.

Please note: Applications
must be supported by a
recommendation from a scientific or clinical sponsor (e.g. supervisor or
head of department). A request for a supporting
statement will be sent
to your nominated sponsor automatically during
the application process.
Applicants must ensure that their sponsor
provides this supporting
statement by the application deadline. Applications without a supporting
statement cannot be considered.

Deadlines
Deadline for Applications: Closed

Cost
Overseas courses are free to attend for non-commercial
applicants. Please contact us for the commercial fee.

Bursaries
Overseas courses are free to attend for non-commercial applicants.
Limited bursaries to cover travel, accommodation and sustenance costs are
also available and are awarded on merit. If you would like to apply for a
bursary, please complete the bursary section of the online application
form.

Please note that both the applicant
and sponsor are required to provide
a justification for the
bursary as part of the application

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

Bursaries can be applied for as part of the course application form.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.