Kaptive

Kaptive identifies and types capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) loci in Acinetobacter baumannii genome assemblies to support epidemiological tracking and characterization of surface polysaccharide variation.

Key Features:

• Curated Reference Databases: Contains 92 KL and 12 OCL annotated gene-cluster entries numbered and annotated using a standardized KL/OCL nomenclature.
• In Silico Typing: Compares pre-assembled genomes against the curated reference databases to identify known or novel KL and OCL loci.
• High Accuracy and Coverage: Validated on over 630 manually typed A. baumannii draft genomes with 100% assignment accuracy and detected known KL and OCL in 87% and 90% of 3386 NCBI assemblies, respectively.
• Integration with Epidemiological Data: Outputs can be combined with multi-locus sequence typing (MLST) to reveal within-clone variation of KL and OCL, including variation within global clones such as ST1 (GC1) and ST2 (GC2).

Scientific Applications:

• Epidemiological Surveillance: Provides precise KL and OCL locus typing to support tracking and control of A. baumannii outbreaks.
• Phage Therapy Assessment: Enables evaluation of bacteriophage susceptibility by typing capsular polysaccharides that are common phage targets.

Methodology:

Aligns input genome assemblies against curated KL and OCL reference databases and identifies the best-matching locus for each assembly to classify known and novel variants.