Discovery of pathogen-specific markers for novel antimicrobial targets through multi-omics investigation

Multidrug-resistant strains of Escherichia coli (EC) and Klebsiella pneumoniae (KP) pose a global health threat necessitating alternative treatment approaches. Understanding key pathogenic (PAT) features and their shared regulatory mechanisms, especially when compared to commensal (COM) counterparts, holds the promise of unveiling pathogen-specific markers for anti-virulence strategies.

Employing bioinformatics, we constructed pangenomes encompassing 22,267 EC and 6,740 Klebsiella genomes. Focused on high-risk clonal lineages, we identified genes exclusive to PAT sequence types (ST) while absent in COM ones like EC ST10, Klebsiella variicola (KV), and Klebsiella quasipneumoniae. This set, termed the patho-core genome, was investigated for intriguing markers, subject to detailed analysis and phenotypic exploration. Further investigations involved transcriptomic and proteomic analyses in a urine-like medium for select isolates.

The analysis revealed 273 unique markers for KP and 24 for PAT EC including the L-sorbose phosphotransferase system. Early stationary growth phase induction in nutrient broth supplemented with sorbose prompted diauxic growth in PAT EC STs. Omics investigations revealed co-regulation of metabolic pathways (e.g., purine and tryptophan) and induction of virulence-associated pathways (e.g., flagellar and capsule production). The integrative omics analysis of KP demonstrated similar regulatory profiles for KP, while KV profiles exhibited marked differences. Enhanced growth of KP coincided with the induction of various metabolic pathways, some aligning with the patho-core genome (e.g., cellobiose), and others displaying differential expression (e.g., citrate).

Our study demonstrates that a comprehensive multi-omics approach facilitates the identification of potential targets by comparing PAT with COM bacteria. This highlights the importance of distinct genetic make-ups and regulatory mechanisms that contribute to overall bacterial fitness benefits. The induction of metabolic pathways, expanding nutrient utilization, emerged as a key mechanism. Future studies are warranted to explore the targetability and in vivo relevance of these findings.