PneumoKITy

PneumoKITy performs serotype determination and relative abundance estimation of Streptococcus pneumoniae from whole genome sequencing (WGS) data using Mash k-mer screening to enable detection of single and mixed serotype samples.

Key Features:

• Mash k-mer screening: Implements Mash k-mer screening for rapid k-mer–based serotype detection from sequence data.
• Performance improvements: Runs up to 29× faster and uses up to 11× less memory than PneumoCaT v1.2.1 on FastQ inputs.
• Serotype coverage: Determines 54 of the 93 serotypes in the SSI Diagnostica phenotypical serotyping scheme at the type level, with remaining serotypes classified to serogroup or subgroup (e.g., 11A/D).
• Mixed serotype detection: Accurately identifies all serotypes present in 92.2% of tested mixed-culture samples.
• Relative abundance estimation: Estimates relative abundance of serotypes with an average deviation of 1.5% from expected values and detects minor serotypes down to 1% concentration.
• Input formats: Accepts both FastQ and assembly file inputs for analysis.

Scientific Applications:

• Nasopharyngeal carriage studies: Detects and quantifies multiple co-occurring pneumococcal serotypes in carriage samples.
• Vaccine effectiveness monitoring: Provides serotype-level data to monitor vaccine impact and serotype replacement.
• Epidemiological surveillance: Supports surveillance of Streptococcus pneumoniae serotype distribution and shifts over time.
• Rapid screening for downstream analysis: Serves as an initial rapid serotype screen that can be complemented with other tools for comprehensive analysis.
• Public health and research: Supplies accurate serotype and abundance data to inform public health decision-making and pneumococcal research.

Methodology:

Uses Mash k-mer screening on FastQ or assembly file inputs.