blantyreESBL

blantyreESBL provides a curated genomic dataset and analytical results for studying antimicrobial resistance and population structure of Klebsiella pneumoniae and Escherichia coli isolates from Blantyre, Malawi.

Key Features:

• Genomic Data Repository: The package includes whole-genome sequencing data for 203 Klebsiella pneumoniae and 473 Escherichia coli isolates.
• Global Contextualization: Isolates are compared to multicountry collections of 484 K. pneumoniae and 10,146 E. coli genomes to place local diversity in a global context.
• Phylogenetic Analysis: The resource supports inference of phylogenetic relationships and exploration of sequence type (ST) diversity and distribution between Malawi and global trends.
• AMR and Virulence Determinants: Analyses include genetic loci linked to antimicrobial resistance and virulence, including siderophore genes and hypermucoidy genes.
• O-Antigen Typing: The package provides O-typing data for K. pneumoniae to assess O-antigen diversity relevant to vaccine considerations.
• Plasmid Characterization: For E. coli, long-read sequencing data are used to characterize plasmids carrying ESBL and carbapenemase genes.

Scientific Applications:

• AMR Surveillance: Use for monitoring antimicrobial resistance trends in sub-Saharan Africa through genomic data.
• Epidemiological Studies: Use to identify locally circulating subclades and globally successful clones of K. pneumoniae and E. coli.
• Vaccine Development: Use to inform analyses of O-antigen diversity relevant to vaccine target selection in Malawi.
• Public Health Interventions: Use to provide genomic insights that can inform antimicrobial stewardship and control strategies for resistant pathogens.

Methodology:

Analyses employ short-read and long-read whole-genome sequencing, phylogenetic inference, O-antigen typing, plasmid characterization from long reads, and contextualization with a curated global collection of bacterial genomes.