MIRU-profiler

MIRU-profiler performs digital 24-loci Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) typing from whole-genome sequences to provide standardized genotyping of Mycobacterium tuberculosis for epidemiological and research analyses.

Key Features:

• Integration with WGS: Integrates whole-genome sequencing (WGS) data with traditional MIRU-VNTR typing to facilitate interlaboratory comparison.
• In-silico MIRU-VNTR prediction: Predicts MIRU-VNTR profiles from whole-genome sequences using an in-silico workflow that mirrors laboratory genotyping protocols.
• Technical implementation: Implemented in shell scripting and relies on the EMBOSS software suite.
• Allele computation: Computes alleles at the 24 standard loci by determining in-silico PCR amplicon lengths from input genome sequences.
• Output format: Produces a tab-delimited text file detailing the MIRU-VNTR pattern.
• Validation and accuracy: Validated on datasets including complete genomes from NCBI-GenBank, PacBio-sequenced local isolates, BCG vaccine strains, and Illumina-based draft genomes, showing high concordance with experimental genotyping for most complete genomes and accurate inference of 21 out of 24 loci in draft genomes with noted inaccuracies at loci ETRA, QUB11b, and QUB26.
• Batch processing: Supports batch processing of multiple genomes and was tested on 157 complete M. tuberculosis genomes with a total runtime of approximately 14 minutes.

Scientific Applications:

• Epidemiological studies: Supports national TB control programs and outbreak investigations by providing MIRU-VNTR typing from WGS data for transmission tracking.
• Research and development: Facilitates study of genetic diversity and evolutionary patterns within the Mycobacterium tuberculosis complex.
• Clinical diagnostics: Enables integration of WGS-derived MIRU-VNTR profiles with traditional genotyping to improve strain identification and support resistance profiling.

Methodology:

Implemented as shell scripts that use EMBOSS to perform in-silico PCR on whole-genome sequences to determine amplicon lengths at the 24 MIRU-VNTR loci, compute alleles from those lengths, and output tab-delimited MIRU-VNTR patterns with batch-processing support.