iKaptive

iKaptive identifies and types loci responsible for the synthesis of capsular polysaccharides (KL) and lipooligosaccharide outer core (OCL) in Acinetobacter baumannii genome assemblies.

Key Features:

• Curated reference databases: Contains a KL reference database of 92 gene clusters and an OCL reference database of 12 gene clusters with standardized, uniquely numbered KL and OCL annotations.
• BLAST-based locus comparison: Uses BLAST (blastn) to compare input genome assemblies against locus nucleotide sequences and identify best matches by nucleotide coverage.
• In silico typing and variant detection: Assigns KL and OCL types to assemblies and distinguishes known from potentially novel locus variants.
• Validation and performance metrics: Validation on over 630 manually typed A. baumannii draft genomes showed 100% KL/OCL assignment accuracy, and analysis of 3,386 NCBI assemblies detected known KL and OCL in 87% and 90% of cases, respectively.
• Integration with multilocus sequence typing: Output can be combined with multilocus sequence typing (Institut Pasteur scheme) for comparative strain analyses.

Scientific Applications:

• Epidemiological tracking: Enables analysis of capsular polysaccharide (CPS) and outer core (OC) locus variation to track multiply antibiotic-resistant A. baumannii infections.
• Studying locus replacement and diversity: Facilitates detection of multiple KL and OCL types within single sequence type collections to study within-clone locus replacement and diversity.
• Comparative genomics with MLST: Supports integration with Institut Pasteur multilocus sequence typing to provide comprehensive insights into A. baumannii genetic diversity.

Methodology:

Input genome assemblies are compared to the curated KL (92 clusters) and OCL (12 clusters) nucleotide reference databases using BLAST (blastn) to identify best matches by nucleotide coverage, after which KL and OCL types are assigned and known versus potentially novel variants are reported.