sonneityping

sonneityping provides a standardized genotyping framework for analysis of Shigella sonnei whole-genome sequencing (WGS) data to assign genotypes and detect antimicrobial resistance determinants.

Key Features:

• Genomic Framework: Implements a robust, S. sonnei-specific genomic framework to assign genotypes and identify resistance determinants from WGS data.
• Integration with Mykrobe Software: Integrated into the Mykrobe software package and rigorously tested on thousands of genomes for genomic analysis.
• Resistance Determinant Identification: Detects antimicrobial resistance determinants including those associated with ciprofloxacin and azithromycin.
• Outbreak Investigation and Surveillance: Applied to over 4,000 S. sonnei isolates from public health laboratories in three countries to identify common genotypes linked with elevated resistance rates.
• Monitoring Resistant Clones: Enables monitoring of resistant clones and their intercontinental spread.

Scientific Applications:

• Epidemiological Studies: Enables tracking of spread and evolution of S. sonnei clones through detailed genotyping.
• Public Health Surveillance: Supports monitoring of antimicrobial resistance trends in S. sonnei to inform public health strategies.
• Outbreak Response: Supports rapid identification of resistant strains during outbreaks to inform interventions.

Methodology:

Application of a standardized genotyping scheme to WGS data; identification of resistance determinants (including ciprofloxacin and azithromycin) from genomic data; implementation within the Mykrobe software; testing on thousands of genomes and application to over 4,000 S. sonnei isolates from public health laboratories in three countries.