legsta

legsta performs in silico sequence-based typing (SBT) of Legionella pneumophila to assign allelic profiles and improve discrimination for epidemiological investigations, including serogroup 1 strains.

Key Features:

• Extended Genetic Markers: Extends traditional SBT by including additional alleles such as gspA and neuA, with neuA increasing the index of discrimination from 0.932 to 0.963 and enabling finer subdivision of common complexes (e.g., 1,4,3,1,1,1).
• High Discrimination Index: Achieves an index of discrimination (D) >0.94 using six loci (flaA, pilE, asd, mip, mompS, proA) and reaches 0.98 when combined with monoclonal antibody subgrouping.
• Reproducibility and Concordance: Provides high typeability, reproducibility, and epidemiological concordance across clinical and environmental L. pneumophila isolates, including serogroup 1 and other serogroups.
• Database Integration: Supports entry of consensus sequences into an online database to assign individual allele numbers and generate unique allelic profiles for each isolate (e.g., 1,4,3,1,1,1).
• Epidemiological Utility: Produces compact, transportable allelic profiles for rapid comparison of isolates across geographical locations, aiding investigation of travel-associated cases.

Scientific Applications:

• Epidemiological investigation: Typing and comparison of L. pneumophila isolates to support outbreak detection and source attribution.
• Outbreak tracking and control: Enhanced discrimination and concordance to differentiate strains within outbreak settings, including large common complexes.
• Travel-associated case analysis: Rapid comparison of allelic profiles across locations to investigate travel-related infections.
• Public health surveillance and research: Generation of allelic profiles for use by public health officials and researchers studying spread and evolution of Legionella strains.

Methodology:

Consensus sequences are derived from forward and reverse sequencing reads and used to assign allele numbers, producing a multi-locus allelic profile for each isolate.