MLST

MLST assigns multilocus sequence types to bacterial isolates from whole-genome sequencing (WGS) data by identifying MLST alleles and combining allele calls into sequence types.

Key Features:

• Input types: Accepts raw short reads from four sequencing platforms (including Illumina and PacBio) and preassembled genomes.
• Database updates: Uses monthly updates from MLST databases to obtain current allele definitions.
• Allele identification: Employs a BLAST-based ranking method to identify best-matching MLST alleles according to specified schemes.
• Sequence type assignment: Determines sequence types by combining allele calls from the identified MLST alleles.
• Validation: Tested on preassembled genomes from 336 isolates covering 56 MLST schemes, short reads from 387 isolates spanning 10 schemes, and short reads from 29 isolates previously typed by traditional methods.

Scientific Applications:

• Epidemiological studies: Assigns sequence types for surveillance and population comparisons.
• Outbreak investigations: Identifies related strains through sequence type comparisons.
• Microbial ecology research: Enables strain-level typing for studies of microbial diversity and distribution.

Methodology:

Processes short reads and preassembled genomes, uses monthly-updated MLST databases, applies a BLAST-based ranking method to identify best-matching alleles, and assigns sequence types by combining allele calls.