Whole Genome Sequencing for Surveillance of Antimicrobial Resistance in Bacteria

The 10-day theory and hands-on workshop on whole genome sequencing for surveillance of antimicrobial resistance in bacteria was held from 3rd October 2022 to 14th October 2022 at the Noguchi Memorial Institute for Medical Research (NMIMR) with participants from 11 countries: Cameroon, Benin, Zimbabwe, Zambia, Malawi, Eswatini, Sudan, Ghana, Kenya, Nigeria, and Benin.

On the first day of training, participants were warmly welcomed by the Director of NMIMR, the Provost of the College of Health Sciences, the technical lead for SeqAfrica project and the facilitators. The participants were encouraged to make the best use of the training to equipment themselves to help with the fight against the menace of antimicrobial resistance. Group photos were then taken followed by a tour of the NMIMR Advanced Research Laboratories and the lectures for the day.

During the first week (day 1-day 5) of the training, participants had theory and hands-on experience with various lab experiments/procedures for extracting and purifying DNA from bacterial isolates for sequencing. They also quantified the extracted DNA using the fluorometric and spectrophotometric methods. In the subsequent days in the week participants explored the Oxford Nanopore Technology and Illumina sequencing platforms; they prepared libraries; quality checked the libraries using the Bioanalyzer and qPCR machines, pooled the libraries and loaded on the Minion for ONT and Miseq for Illumina. Participants were also introduced to Linux and use of the command lines to analyze the sequenced data.

The second week of the workshop (day 6- day10) was mainly bioinformatics training. Participants were introduced to various platforms (CGE, NCBI among others) and tools for analyzing sequenced data. Participants also worked in groups to discuss the assignment given during the course and made group presentations on the assignment on the last day of the workshop. In the presentations, participants shared individual experiences on knowledge gained and how they intend to apply the knowledge acquired. The workshop came to an end successfully with sharing of certificates, taking of group photos and networking.

In between the days of the week, there was group sightseeing at the University of Ghana campus, National Museum of Ghana, the Independence Square/Arc and its environs. Participants also received souvenirs and support for a cocktail hour from ISN-Medical.

The training was funded by SeqAfrica/Fleming Fund and facilitated by Dr. Beverly Egyir, Dr Marinus van Zwetselaar, Dr. Bright Adu, Dr. Daniel Amoako, Mr. Erkison Ewomazino Odih, Mr. Christian Owusu-Nyantakyi, Mr. Grebstad Amuasi, Miss Felicia Owusu, Mr. William Boateng and Mr. Bright Agbodzi.

There was inspiring feedback from the participants; following are just a few...

‘’I think on the whole course was very timely for me as I will be able to apply the knowledge and skills gained almost immediately to our projects at home’’

‘’Thanks to Seqafrica for giving me the opportunity to learn WGS, this will help me in capacity building in my work station’’


‘’The training was adequate and timely as I prepare to start my PhD studies and taking back the knowledge I have leant to my laboratory. Equipment in the laboratory were plenty and up to date. The facilitators were well vast in the content they taught and very helpful when assistance was needed’’

‘’Training was well organised and facilitators were very resourceful’’

Congratulations to all the participants!!!

The Noguchi Memorial Institute for Medical Research (NMIMR), set up in 1979 as a semi autonomous institute of the University, is the leading biomedical research facility in Ghana.

© 2021 NMIMR

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