Molecular Approaches to Clinical Microbiology in Africa (Cape Town, South Africa)

3–8 September 2017

Cape Town, South Africa


The wind of change is blowing through clinical microbiology, not just in
Africa but across the globe.  Molecular techniques are
revolutionising the routine practice of the identification and
characterisation of pathogens, opening many new opportunities and
challenges in all areas of clinical microbiology from routine diagnosis
to basic research.  This course will examine the impact of molecular
approaches in the African context by a combination of lectures and
tutorials with laboratory and computer practical sessions.

The intensive programme will provide clinical microbiologists and
laboratory scientists working in Africa with a concise yet comprehensive
overview of the latest research and practice in this essential area, with
an emphasis on how these techniques can be applied day-to-day in the
African setting (especially when resources are limited).

There will be an emphasis on approaches that are:
(i) currently applicable in African laboratories
(ii) likely to be applicable in Africa in the foreseeable future ,
(including Whole Genome Sequencing using portable devices)
(iii) of value to participants in interpreting the literature and
assessing the likely utility of new technologies as they are developed.

The course combines an understanding of the latest research techniques
and theoretical approaches, with practical methods to provide a
foundation-level of understanding of the philosophy, methods, and
vocabulary of molecular techniques for those primarily trained in
culture-based microbiology.

PLEASE NOTE: This course is free to attend and bursaries are
available to cover travel and accommodation expenses.

Feedback from the 2016 course (The Gambia)
“I am happy that I attended the course as it helped me understand the
how I can use the basic molecular biology techniques to solve
microbiology problems”
“Well done and continue on the good work.”
“Thank you very much for the good work you are doing and for the
opportunity to be part of this prestigious course.”
“A big thank you for the opportunity given me to attend this advanced
course. You are doing a great demystifying job. Please keep it up. I look
forward to attending more and more of your courses and conferences. Thank
“Attending this course was a true blessing because i am supposed to do
sanger sequencing at my work place and data analysis. so the course came
at the right time and it has sharpened my sequencing skills and
bioinformatic analysisskills, making me more than competent to do m job.
Thank you a lot WGCAC”


The course will be based around three themes, chosen to represent three
of the most pressing clinical imperatives in clinical bacteriology
throughout the continent: Mycobacterium tuberculosis; enteric bacteria
and antimicrobial resistance; and encapsulated bacteria.

For each of these themes the following approaches will be covered:

  • Basic molecular biology techniques including preparing, handling, and storing DNA.
  • PCR, including real-time PCR, methods and applications.
  • Determining sequence variation, its visualisation and interpretation, concentrating on conventional approaches.
  • Bioinformatic analysis of molecular and genomic data, particularly the exploitation of web-based tools.
  • Future technologies, overview and potential for clinical microbiology

These techniques will be explored in the lectures and tutorials and
employed during the course practical sessions in the cross-cutting themes
of pathogen detection and characterisation, including antimicrobial
resistance and the evolution of pathogens, and the application of the
data in the improvement of interventions to reduce disease burden.

Learning Outcomes
After attending this course, participants will have:

  • Gained an appreciation of the advantages and pitfalls of the methods covered and are able to start to apply them in their home institutions
  • Learned that molecular techniques are no more difficult to utilize in the clinical laboratory than bacteriological methods and that many of the skills learned can be applied generically
  • Gained hands-on experience of a range of methods including real-time PCR, conventional sequencing, creating sequence data using next generation single molecule sequencing, and analysing the data with publically available software tools to identify causative organisms in an infection and to track an outbreak using WGS

Instructors and speakers

Course instructors
Martin Antonio Medical Research Council Unit, The Gambia
Cath Arnold Public Health England, UK
Keith Jolley University of Oxford, UK)
Sam Kariuki Kenya Medical Research Institute, Nairobi, Kenya
Martin Maiden University of Oxford, UK
Chisomo Msefula Malawi-Liverpool-Wellcome Trust Research Programme
Mark Nicol University of Cape Town, South Africa

How to apply

Applicants should have demonstrable experience in a relevant field and
be: clinical trainees or specialists in medical microbiology;
postdoctoral scientists; senior technicians; or research assistants with
a Master’s degree.  Clinically qualified applicants are especially
encouraged to apply.

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. If you would like to apply
for a bursary, please complete the bursary section of the online
application form.

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.

Deadline for Applications: Closed


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

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

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,
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

Overseas Courses (held outside of the UK)
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.
will be notified of a bursary award along with their place on
course, usually within one month of the application deadline. The
decision of the selection committee is

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