ASLM and Africa CDC Collaborate in Ghana to Host Crucial Workshop on Genomics and Bioinformatics of Antimicrobial Resistant Pathogens

In a significant move to bolster public health infrastructure and preparedness, the African Society for Laboratory Medicine (ASLM) and Africa CDC hosted a workshop focused on building capacity for bacterial sequencing and genomic analysis in preparation for the implementation of genomic surveillance for Antimicrobial Resistance (AMR) in Accra, Ghana. This workshop, held from 18-28 June, is a collaborative effort between ASLM, Africa CDC, the Africa Public Health Foundation (APHF), and the Noguchi Memorial Institute of Medical Research (NMIMR), with support from the European Union.

The goal of the training was to equip scientists with the skills required to apply next-generation sequencing to genomic surveillance of AMR. During the first week, participants attended in-class lectures introducing genomics and its role in monitoring and controlling AMR, followed by wet lab practical training. This training covered key quality control aspects to ensure that pure bacterial cultures are isolated and moved onto sequencing processes like DNA extraction, purification, quantification, library preparation, and sequencing using Illumina and Oxford Nanopore workflows. In the second week, participants received hands-on training on bioinformatic analysis.

The training focused on bacterial genomic sequencing and bioinformatics analysis for detecting AMR. Currently, culture, identification, and antibiotic sensitivity testing are the primary methods used for AMR detection. These methods show whether or not the organism is sensitive to the antibiotics being tested (phenotypic tests) but do not provide details about the genetic changes resulting in the organism acquiring resistance to antimicrobials. Genomic sequencing and bioinformatic analysis build on this base by providing additional genetic information about the organisms, thereby improving the monitoring and control of AMR.

Seventeen laboratory scientists from National Public Health Institutes (NPHI) and Reference Laboratories responsible for coordinating AMR surveillance testing activities from nine African member states participated. Five countries (Chad, Ethiopia, Morocco, Zimbabwe, and Nigeria) are piloting Integrated Genomic Surveillance (IGS) for AMR in bloodstream infections, specifically Klebsiella pneumoniae and Escherichia coli, with support from Africa CDC PGI and ASLM. The other four countries (Mozambique, Cameroon, Uganda, and DRC) are participating in the KlebGene project with support from Africa CDC PGI and APHF.

This training is expected to ignite and equip the participants to drive the establishment of robust national integrated genomic sequencing AMR surveillance programmes, in coordination with existing AMR surveillance structures, partnerships, and networks.