# Integration of metagenome-assembled genomes with clinical isolates expands the genomic landscape of gut-associated Klebsiella pneumoniae

## TL;DR

This study shows that metagenomics reveals a much greater diversity of gut-associated Klebsiella pneumoniae than clinical isolates alone, offering new insights into its genomic landscape and health implications.

## Contribution

The integration of metagenome-assembled genomes with clinical isolates nearly doubles the known phylogenetic diversity of gut-associated Klebsiella pneumoniae.

## Key findings

- Over 60% of metagenome-assembled genomes (MAGs) represent new sequence types not found in clinical isolates.
- 214 genes, including 107 putative virulence factors, were exclusively detected in MAGs.
- Combining MAGs and isolates improves classification of disease and carriage states in Klebsiella pneumoniae.

## Abstract

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. Developments in genome-resolved metagenomics have offered unprecedented access to metagenome-assembled genomes (MAGs), expanding the known bacterial diversity within the gut microbiome. Here we analysed 656 human gut-derived K. pneumoniae genomes (317 MAGs, 339 isolates) from 29 countries to investigate the population structure and genomic landscape of gut-associated lineages. Over 60% of MAGs were found to belong to new sequence types, highlighting a large uncharacterized diversity of K. pneumoniae missing among sequenced clinical isolates. In particular, integrating MAGs nearly doubled gut-associated K. pneumoniae phylogenetic diversity, and uncovered 86 MAGs with >0.5% genomic distance compared to 20,792 Klebsiella isolate genomes from various sources. Pan-genome analyses identified 214 genes exclusively detected among MAGs, with 107 predicted to encode putative virulence factors. Notably, combining MAGs and isolates revealed genomic signatures linked to health and disease and more accurately classified disease and carriage states compared to isolates alone. These findings showcase the value of metagenomics to understand pathogen evolution and diversity with implications for public health surveillance strategies.

Klebsiella pneumoniae is a common opportunistic gut pathogen. Here, the authors showcase the value of metagenomics in offering a broader view of the diversity of K. pneumoniae found in the human gut across different regions and health states.