ShigEiFinder

ShigEiFinder differentiates and serotypes Shigella and Enteroinvasive Escherichia coli (EIEC) strains using cluster-specific and serotype-specific genomic markers to support clinical and epidemiological genomic analyses.

Key Features:

• Cluster-Specific Gene Markers: Utilizes cluster-specific gene markers identified by comparative genomic analysis to differentiate phylogenetically distinct Shigella and EIEC clusters, with marker accuracy of 99.63% and specificity >97.02%.
• Serotyping Capability: Performs in silico serotyping using serotype-specific O-antigen genes and modification genes to identify over 59 Shigella serotypes and 22 EIEC serotypes with specificity of 99.40% for assembled genomes and 99.38% for mapped reads.
• Data Processing and Accuracy: Processes paired-end Illumina sequencing reads and assembled whole genomes, achieving cluster assignment accuracy of 99.70% for assembled genomes and 99.81% for mapped reads.
• Large-Scale Marker Discovery: Derives markers from comparative genomic analysis of over 17,000 publicly available Shigella/EIEC genomes, including markers for 17 clusters and 53 sporadic EIEC types.

Scientific Applications:

• Clinical Diagnosis: Enables precise differentiation between Shigella and EIEC to inform clinical diagnosis and treatment decisions.
• Epidemiological Investigations: Classifies strains into specific clusters and serotypes to support outbreak investigation and transmission tracking.
• Genomic Research: Facilitates investigation of genetic diversity and evolutionary relationships of Shigella and EIEC using high-resolution marker-based typing.

Methodology:

Examined over 17,000 publicly available Shigella/EIEC genomes to identify distinct clusters and sporadic types, identified cluster-specific gene markers for 17 clusters and 53 sporadic EIEC types, and integrated these markers along with serotype-specific O-antigen and modification genes into a pipeline to perform in silico differentiation and serotyping on paired-end Illumina reads and assembled genomes.