Integration of metagenome-assembled genomes with clinical isolates reveals genomic signatures of Klebsiella pneumoniae in carriage and disease

Klebsiella pneumoniae is an opportunistic pathogen causing diseases ranging from gastrointestinal disorders to severe liver abscesses. While clinical isolates of K. pneumoniae have been extensively studied, less is known about asymptomatic variants colonizing the human gut across diverse populations. Genome-resolved metagenomics has offered unprecedented access to metagenome-assembled genomes (MAGs) from diverse host states and geographical locations, opening opportunities to explore health-associated microbial features. Here we analysed 662 human gut-derived K. pneumoniae genomes (319 MAGs, 343 isolates) from 29 countries to investigate the population structure and genomic diversity of K. pneumoniae in carriage and disease. Only 9% of sequence types were found to be shared between healthy and disease states, highlighting distinct diversity across health conditions. Integrating MAGs nearly doubled gut-associated K. pneumoniae phylogenetic diversity, and uncovered 86 lineages without representation among >20,000 Klebsiella isolate genomes from various sources. Genomic signatures linked to pathogenicity and carriage included those involved in antibiotic resistance, iron regulation, restriction modification systems and polysaccharide biosynthesis. Notably, machine learning models integrating MAGs and isolates more accurately classified disease and carriage states compared to isolates alone. These findings showcase the value of metagenomics to understand pathogen evolution with implications for public health surveillance strategies.