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

11 - 16 December 2016Ho Chi Minh City, Vietnam
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    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
  • Programme

    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

  • Instructors / Speakers

    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

  • How to Apply

    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

    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.