Decoding a Phage-Rich Klebsiella pneumoniae Genome Through WGS
End-to-end WGS characterization of a clinically relevant bacterial isolate — uncovering prophage integrations, antimicrobial resistance determinants, and functional diversity.
Challenge
A research team needed to characterize a clinically relevant bacterial isolate suspected of harboring bacteriophage integrations and antimicrobial resistance determinants. The objective was to identify genomic features influencing pathogenicity, antimicrobial resistance, and evolutionary adaptation while generating actionable biological insights from whole-genome sequencing data.
RASA Approach
RASA Life Science Informatics implemented an end-to-end Whole Genome Sequencing (WGS) analysis workflow combining genome assembly, annotation, comparative genomics, phage discovery, and antimicrobial resistance profiling.
Technologies Used
Key Findings
Species Confirmation
Average Nucleotide Identity (ANI) analysis confirmed the isolate as Klebsiella pneumoniae species complex with >98% genomic similarity to reference strains.
Extensive Phage Integration
Multiple complete and near-complete bacteriophage regions revealed a highly phage-rich genome shaped by horizontal gene transfer and recombination events.
Antimicrobial Resistance Discovery
Resistance profiling identified β-lactam, quinolone, fosfomycin, and rifamycin resistance genes — indicating significant multidrug resistance potential.
Functional Diversity
Proteome analysis revealed thousands of protein clusters including phage structural proteins, replication machinery, host adaptation factors, and novel candidates.
Impact
Accelerated Genomic Discovery
Rapid characterization of a complex bacterial genome without extensive laboratory experimentation.
Improved AMR Surveillance
Identified clinically relevant resistance determinants supporting antimicrobial resistance monitoring initiatives.
Host–Phage Dynamics
Revealed extensive phage integration events and their potential role in bacterial evolution and pathogenicity.
Therapeutic Insights
Generated candidate regions for phage therapy development, novel antimicrobial discovery, and host–pathogen interaction research.
Outcome
RASA successfully delivered a comprehensive genomic characterization of a phage-rich Klebsiella pneumoniae isolate, uncovering integrated prophages, multidrug resistance determinants, and extensive functional diversity — providing valuable insights into bacterial evolution, antimicrobial resistance, and potential therapeutic opportunities.
Services Applied
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