Employing (Home) Organisation: Malawi Liverpool Wellcome Programme
Project title: Training in advanced metagenomic and long-read sequencing methods to explore how antibiotic exposure impacts antibiotic resistance among oral bacteria
I am a clinician and microbiologist with a PhD in pathogen genomics from University College London. Currently, I am an early-career postdoctoral researcher at the Malawi Liverpool Wellcome Programme in the Pneumonia and Meningitis Pathogens Research Group. My research focuses on leveraging community samples and cutting-edge genomic approaches to track antimicrobial-resistant pathogens to inform treatment guidelines and future vaccine policy. Professor Robert Heyderman, and Dr Brenda Kwambana-Adams and Dr Chrispin Chaguza were my motivation for competing for the AREF Award.
Summary of Project Destination
Streptococcus pneumoniae (pneumococcus) is the leading cause of pneumonia, with the highest disease burden in sub-Saharan Africa. While pneumococcal conjugate vaccines have reduced disease, antibiotic-resistant non-vaccine type (NVT) strains are emerging. Some strains acquire antimicrobial resistance (AMR) via mobile genetic elements (MGEs) from other species, however, the full extent of MGE acquisition is unknown. Through the fellowship, I will gain advanced metagenomic and long-read sequencing skills to characterise MGEs. Afterward, I aim to determine if pneumococcal NVTs acquire MGEs from oral Streptococcus species, using long-read sequencing of isolates from Malawi’s pneumococcal carriage and disease surveillance. This project will improve our understanding of AMR gene flow into S. pneumoniae, guiding future vaccine strategies that target disease-causing NVT lineages that acquire MGEs.
Summary of Fellowship Plan
During my fellowship, I will be based at the University of Liverpool’s Centre for Genomics Research, under the mentorship of Professors Steve Paterson and Alistair Darby, experts in metagenomics. I will gain proficiency in DNA extraction techniques, Oxford Nanopore sequencing, and advanced metagenomic analyses. The Malawi Liverpool Wellcome Programme will support me in establishing long-read metagenomic workflows, enabling me to expand my research, support grand funding applications, foster collaborations, and integrate these cutting-edge techniques into local and international research projects.
Quote
“Antimicrobial resistance is a global threat. This fellowship will equip me with advanced sequencing and analytical skills to help tackle this challenge in sub-Saharan Africa. “
Dr. Akuzike Kalizang’oma expects to start his fellowship in November 2025