Exploiting intra-species diversity to identify genomic properties that affect the cell biology, proliferation and pathogenicity of Klebsiella pneumoniae

Objective

Klebsiella pneumoniae is an opportunistic pathogen that can cause particularly serious disease and mortality in immune-compromised, elderly, or otherwise vulnerable individuals. A high burden of mortality is attributed to K. pneumoniae: a 2019 study estimated that K. pneumoniae was associated with 790.000 deaths that year. Due to its incidence, mortality, and growing antibiotic resistance, the World Health Organization placed K. pneumoniae at the top of the Bacterial Priority Pathogens List in 2024, highlighting its danger to public health. Despite the high healthcare burden posed by K. pneumoniae, it remains a rather understudied pathogen, particularly regarding non-canonical virulence factors. Antibiotic resistance, for example, is rather well-studied in the pathogen, but our understanding of K. pneumoniae physiology, including the keys to its growth, replication, and survival in diverse environments is limited. K. pneumoniae displays extensive intra-specific diversity, with its pangenome encoding close to 30.000 protein-coding sequences. The general goal of this proposal is to exploit the extensive intra-species diversity of K. pneumoniae to determine how specific genomic properties affect cellular physiology, contribute to growth and proliferation, and underlie pathogenicity. The functional role of selected regions will subsequently be determined in more detail. K. pneumoniae intraspecific diversity will be investigated using a library of 100-200 strains across different growth conditions and antibiotics. A high-throughput cell imaging system will be used to collect various phenotypic measures. Next, genomic studies will uncover genetic differences among the strains, and these differences will be connected to phenotype. Finally, genetic manipulation will be used to confirm the effect of these genetic differences. Such knowledge about the pathogen’s genetic components for success is important in managing K. pneumoniae infections more effectively in the future.