From theory to practice: ComBac-Africa holds metagenomic sequencing training in Côte d’Ivoire

As part of ComBac-Africa’s efforts to strengthen the consortium’s capacity to quickly and accurately diagnose severe infections caused by multidrug-resistant pathogen, partners recently organised an intensive metagenomic sequencing workshop.

From 8-10 December, members from across the consortium gathered at Institut Pasteur de Côte d’Ivoire (IPCI) in Abidjan for a three-day training led by Dr Pierre Schneeberger (SwissTPH) and Dr Jacqueline Rehner (USAAR), with additional support from Dr Sonia Renzi (SwissTPH). The workshop brought together 23 participants from Obafemi Awolowo University (OAU), Fondation pour un Centre Suisse de Recherches Scientifique en Côte d’Ivoire (CSRS), Instituto Piaget (IPIAGET), Centre for Malaria and other Tropical Disease Care (CEMTROD) Joseph Sarwuan Tarka University Makurdi (JOSTUM), and Institut Pasteur de Côte d’Ivoire (IPCI).

The event opened with warm remarks from the director of both IPCI, as well as Côte d’Ivoire’s Minister of Health and the Minister of Research. For a period of three days, participants took part in comprehensive theoretical training, structured hands-on practice, and collaborative exchange.

The workshop guided participants through the full workflow of whole-genome and metagenomic sequencing using Oxford Nanopore Technologies (ONT). Sessions began with key theoretical foundations such as microbial nucleic acid extraction, library preparation, and the principles of long-read sequencing. Theoretical sessions were followed by step-by-step practical modules, including DNA extraction from isolates and microbiome samples and hands-on sequencing using the MinION and Flongle platforms, allowing participants to practice each step in the sequencing process themselves.

The training provided an important foundation for harmonising sequencing capacity across the consortium and equipped partner institutions with the skills needed to independently perform whole-genome and metagenomic sequencing using ONT technologies. It also marks a crucial step forward in preparing all partner countries for ComBac-Africa’s upcoming clinical trial, which will evaluate new diagnostic and treatment algorithms designed to combat multidrug-resistant infections in real-world settings – stay tuned for more updates!