DEVELOPMENT AND EVALUATION OF OFFLINE SOFTWARE FOR WORKING WITH THE MLVA MtbC15 9 NOMENCLATURE USING MIRU-VNTR TYPING AND WHOLE-GENOME SEQUENCING DATA OF MYCOBACTERIUM TUBERCULOSIS
Main Article Content
Authors
Y.A.
Skiba
M.A. Aitkhozhin’s Institute of Molecular Biology and Biochemistry, 86 Dosmukhamedov St., Almaty 050012, Kazakhstan
Almaty Branch of the National Center for Biotechnology, 14 Zhahanger St., Almaty 050054, Kazakhstan
D.A.
Naizabayeva
M.A. Aitkhozhin’s Institute of Molecular Biology and Biochemistry, 86 Dosmukhamedov St., Almaty 050012, Kazakhstan
Almaty Branch of the National Center for Biotechnology, 14 Zhahanger St., Almaty 050054, Kazakhstan
Abstract
Molecular epidemiology of tuberculosis is moving from typing by variable-number tandem repeats to whole-genome sequencing (WGS), yet the record of how Mycobacterium tuberculosis genotypes spread over past decades is written in the MLVA MtbC15‑9 nomenclature, and short sequencing reads do not resolve MIRU-VNTR profiles reliably. The codes were assigned by a single web service, MIRU-VNTRplus (https://www.miru-vntrplus.org), whose interactive functions became unavailable in 2026. This work moved the service functions to the laboratory to keep new data linked to that record. Offline software for Windows, MTBC Lab Toolkit, was developed that assigns codes by the exact-match rule of the 15-locus and 9-locus panels, processes sets of profiles, reports the nearest registered types and links MIRU-VNTR profiles with whole-genome sequencing results. Its reference data comprise 3 906 coded profiles from 152 publications and 23 560 MtbC15 types from the service's official table. Of 400 published codes, the software reproduced all 392 agreeing with the official table; the other 8 were publication errors, and no wrong code was returned. A missing locus is not guessed: the software searches known profiles matching the other 23 loci and returns the nearest code only if a single such profile exists. A profile with one locus changed never received its previous code. TB-Profiler and Mykrobe import was verified on their output files; a batch of 3 293 profiles is processed in 7.3 s. The software compares new data, including profiles inferred from long reads, with accumulated and published MIRU-VNTR typing results without an external server.
Keywords
Mycobacterium tuberculosis, MIRU-VNTR, MLVA MtbC15 9, genotype nomenclature, molecular epidemiology, genomic epidemiology, software, whole-genome sequencing, Kazakhstan
Article Details
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