Genomics and Molecular Epidemiology of Bacterial Pathogens (Ho Chi Minh City, Vietnam)

Bacterial genome sequencing is currently changing the face of
epidemiology and clinical microbiology. Through the emergence of new
technologies and analytical methods, we now have an unprecedented ability
to understand how bacterial populations change, adapt, evolve and spread
internationally. Therefore, the combination of classical microbiology,
epidemiology and bacterial genomics is rapidly becoming a vital set of
tools for how we monitor and tackle the spread of antimicrobial resistant
bacteria across the region.

This course aims to integrate modern laboratory microbiology techniques
with current bacterial genomics methods, thus providing a platform for
the integration of these fields in both clinical and epidemiological
investigations in Asia.

The course is open to microbiologists based in Asian and Australasian
institutes with a specific interest in modern clinical bacteriological
methods. Participants will receive practical laboratory and informatics
training on the latest genomics and molecular techniques for the
identification of organisms and the analysis of bacterial genome
sequencing. The course will specifically focus on bacterial
identification, antimicrobial susceptibility testing, molecular biology,
next generation sequencing, bio-informatics and molecular epidemiology.

There are 20 places available and the course will be held in English.

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

• Identify bacteria using classical and MALI-TOF methods
• Perform antimicrobial susceptibility and ESBL testing
• Prepare and sequence genomic DNA from bacterial isolates
• Perform comparative genomics on multiple genome sequences
• Manipulate illumina sequence data for analyses
• Perform simple phylogenetics and phylogeography

The programme will include lecture, discussion and practical
laboratory/computer-based sessions covering the following topics:

Laboratory-based practicals: Bacteriology

• Bacterial identification using biochemical testing and MALDI-TOF
• Antimicrobial susceptibility testing using VITEK system
• Extended spectrum beta lactamase (ESBL) detection
• Classical antimicrobial susceptibility testing
• DNA Purification
• Sequencing library preparation
• Next Generation Sequencing (MiSeq)

Computational practicals: Informatics and Data Analysis

• Web-based bioinformatics (BLAST, FASTA)
• Sequence analysis and comparative genomics software tools (Artemis, ACT)
• Manipulation of sequence data: mapping and de novo assemblies, SNP calling, annotation and analysis of genomic information
• Phylogenetics
• Georeferencing (phylogeography) practical exercises

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

• Identify bacteria using classical and MALI-TOF methods
• Perform antimicrobial susceptibility and ESBL testing
• Prepare and sequence genomic DNA from bacterial isolates
• Perform comparative genomics on multiple genome sequences
• Manipulate illumina sequence data for analyses
• Perform simple phylogenetics and phylogeography

There are 20 places available and the course will be held in English

Course Instructors
Nicholas
Thomson Wellcome Trust Sanger Institute, UK
Stephen
Baker Oxford University Clinical Research Unit, Ho Chi Minh
City, Vietnam
Matthew
Holden St. Andrews University, UK
Simon
Harris Wellcome Trust Sanger Institute, UK
Claire Ling Shoklo Medical Research Unit, Mae Sot,
Thailand
Christine Boinett Oxford University Clinical Research
Unit, Ho Chi Minh City, Vietnam
Hao Chung Oxford University Clinical Research Unit, Ho
Chi Minh City, Vietnam
Duy Pham Thanh Oxford University Clinical Research Unit,
Ho Chi Minh City, Vietnam

Prerequisites
Applicants should be microbiologists based in Asian or Australasian
institutes with a specific interest in modern clinical bacteriological
methods.

Cost
Overseas courses are free to attend for
non-commercial applicants. Please contact us for the commercial fee.
Additional limited bursaries are available to cover travel and
accommodation costs. Please see the “Bursaries” tab for further details.

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

Bursaries
Overseas courses are free to attend for non-commercial
applicants. Limited bursaries to cover travel, accommodation and
sustenance costs are 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.