Genomic Insights into Antimicrobial Resistance: Unveiling its Impact in Southern and Central Mozambique (IPSN-AMR)
For this project we have defined the following specific objectives:
1. To improve the understanding of the burden and impact of AMR in the dynamics of its emergence and morbi-mortality associated through insights from genomic data in a low resource setting with limited therapeutic options.
2. To investigate the genetic diversity, resistance patterns and virulence profiles of Kp and other ESKAPE-E associated with AMR in Mozambique using whole genome analysis.
3. To strengthen local human resources capacities by conducting genomic surveillance using state-of-the-art technologies (Next Generation Sequencing and Bioinformatics) and to promote leadership and collaborations to respond to local surveillance, research and programmatic needs.
CISM recently acquired and installed an Illumina MiSeq sequencing platform to initiate genomic surveillance of malaria. However, this NGS platform has not been fully utilized for research and surveillance in clinical microbiology due to the absence of trained personnel and specific resources required to establish it as a standard method. Therefore, to achieve the objectives indicated above, we will leverage the collaboration we have with the International Centre for Reference and Research on Escherichia, Shigella and Klebsiella in the Statens Serum Institut, Denmark, which is a reference in the sequencing of Enterobacteriaceae and enteroaggregative Escherichia coli (EAEC) in particular. This collaboration will provide technical support to CISM’s team by assessing the needs at the local laboratory to help establish an implementation plan to proceed with the sequencing of bacterial pathogens locally. We plan to initiate sequencing and training using K. pneumoniae strains, followed by other ESKAPE-E pathogens. These strains have been collected and stored for over 25 years through our IBD surveillance in the Manhiça district. These activities will produce two main outputs: (1) the detailed characterization (genetic diversity, virulence and AMR pattern) at the genomic level of pathogens causing IBD over the past two decades, which have the potential to inform health policy, such as the design and development of interventions (change in the empiric therapy, vaccines, new drugs, etc.); (2) establish the capacity to conduct genomic surveillance, which is invaluable to ensure readiness to respond to any potential health emergency. Additional outputs within this project are to train postgraduate students, who will get mentorship and use the data generated to complete their academic degrees. They will be involved in the data analysis and publication, allowing the project to increase the critical mass of Mozambican researchers.
This project falls within priority #22 of the WHO’s Global Research Agenda for Antimicrobial Resistance in Human Health, under the “Cross-cutting priorities: Antimicrobial resistance epidemiology, burden and drivers” (WHO 2023) which specifies the investigation of the prevalence, incidence, mortality, morbidity and socioeconomic impact of community acquired infections and healthcare-associated infections by resistant WHO bacterial priority pathogens, across socioeconomic settings, especially in low- and middle- income countries, such as Mozambique.