Microbial Typing and Bioinformatics Workshop Held for African Researchers

Posted on November 10, 2021   by Philippe Sessou

From 16 to 17 September 2021, a two-day training workshop was held for over 100 young French-speaking African researchers on new methods for micro-organism identification and typing and bioinformatics. This scientific event was organised by Dr Philippe Sessou, Microbiology Society Champion, in collaboration with Dr Gildas Hounmanou, University of Abomey-Calavi, Benin. The event brought together a total of 108 participants from 10 African countries. This workshop was held online and in-person.

Opening addresses were given by event organisers Dr Philippe Sessou and Professor Guy Alain Alitonou. After introducing the theme of the workshop which aimed at strengthening the capacities of young African researchers on microbial typing and bioinformatics, the opening speech began by thanking the Microbiology Society for providing funding for this event.

In his address, Professor Guy Alain Alitonou expressed his gratitude to the President of the Organising Committee, Dr Philippe Sessou, for having chosen to place this scientific event under his patronage. On behalf of the Management of the Polytechnic School of Abomey-Calavi, he welcomed all the participants to this workshop on these techniques which today constitutes the key to scientific innovation in all fields, particularly microbiology. For example, he pointed out the importance of these techniques for the identification of the different variants of SARS-CoV-2. He went on to say that this training is essential for the strengthening of scientific capacities of participants on the one hand, and for the development of research in Africa to contribute effectively to the resolution of societal problems in Africa. He acknowledged with gratitude the constant support of the Microbiology Society, which has funded the organisation of this training workshop. While wishing full success to participants, he declared the training workshop open.

Following the Director of EPAC, Dr Philippe Sessou took the floor to welcome all participants. He thanked the Microbiology Society for its support in funding the activities of the champions for the advancement of Microbiology. He also thanked the academic authorities who accompanied the event, as well as Dr Victorien Dougnon, the Society's champion who took part in the event. Then, Dr Philippe Sessou reported on the numerous applications that were received in the framework and which shows the enormous interest that young African researchers have for this training. He ended with a presentation on the Society of Microbiology with emphasis on the reasons for joining, how to join and how to become a champion of the Society. 

At the start of the training itself, the expert trainer Dr Gildas Hounmanou highlighted the different research activities he is carrying out not only in his institution but also in collaboration with several partners around the world. He expressed the wish that the participants take full advantage of this training, to continue the learning on a daily basis at home to deepen the knowledge they will receive during the two days. He then outlined the programme of the training days, and gave resources based on his own research and that of other authors, links giving access to several learning platforms and bioinformatics analyses.

Dr Gildas Hounmanou organised a survey on the different aspects that will be covered during the training to understand the knowledge level of the participants. The training included the following aspects:

1. Brief introduction to Microbial genetics 
2. Molecular typing methods
3. MLST typing exercises
4. Antimicrobial resistance
5. Primer design:
   1. for MLST
   2. for AMR genes
   3. for resistance genes
6. Introduction to NGS
7. Bacterial WGS analysis tools  
8. Assignment for bacterial WGS analysis
9. Downloading bacterial and viral genomes from public repositories
   1. ENA
   2. NCBI
   3. GISAID: SARS-CoV-2
10. Using Enterobase for whole genome analysis
11. Introduction to Ubuntu interface
12. Basic command lines
13. Sequences analysis: SARS-CoV-2
    1. fastqc, assembly
14. Alignment and Phylogeny: SARS-CoV-2

The training for young African researchers was a great success. It helped to strengthen the skills of these young researchers who applied in large numbers.

The speeches can be viewed here